Release/0.8.9 #96

thijssnelleman · 2024-09-27T08:41:53Z

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* Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal (#29) * Release/0.8.2 (#31) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * bugfix feature extractor removal --------- Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Quick fix for documentation generation * Sprk 292 (#33) * Change documentation template * added theme to requirements * Fixed Index page of documentation * Included github action file * Test GitHub Actions * test v2 * test 3 * test 4 * test 5 (?) * test 6 * test7 * test 8 * test 9 * test 10 ? * another one * New approach * check * spelling? * this is getting sad * lesgo * wild test * Polishing * Deleted build files to try something out * Changed the workflow to run on push on main * small fixes --------- Co-authored-by: Noah Peil <[email protected]> * SPRK-275 (#34) * refactoring the random date time stamp getter * Forgot one file * Moving ablation help to its correct location * This file shouldn't exist anymore since last version, weird * Redundant code removal? * Refactoring useless code * Removing dead code * Moving file to correct spot * Refactoring, moving files * Reforming slurm options * refactoring + test fixes * Refactoring solver object usage in Sparkle * test bug fixes * Refactoring solver deterministic parameter * Updating args * Moving compute features help to correct file * code layout * Bug fixes * Getting rid of CSV merge by using file locks instead * Removing dead file * flake8 * Removing unused command enums * Refactoring run configured solver help * Renaming file to be more representative * Moving to more suitable folder * Simplifying run solvers help by making more use of the Solver object * Removing dead code * Refactorign default wrapper out of sparkle * Updating user guide * updating the template * bug fix in results parsing * Setting example to run in parallel by default * bugfix adding solver * Updating printing info from add solver to be more compact and accurate * Factoring settings usage out of performance data frame * Final bug fixes for refactoring global variables out of performance data frame * Updated comments * Pytest fixes * test fix * Removing dead code * flake8 * test fix * Refactoring feature data csv, bug fixes * Bug fixes for Performance dataframe * bugfix performance dataframe * Simplifying Solver imports * Moving missing value into the data structures * Removing dead import * Removing sparkle version from global variables * Removing dead import * Test fix * removing print statement * Refactoring instance set NAME references to PATH for SMAC configurator class * flake8 * Fixing pytests * Removing extra spaces * refactoring instances help * reverting change due to complexity * refactoring global variables out of instances_help * Refactoring global variables out of configurator * pytest fix * Moving CLI related files * Refactoring gv from file help, bug fixes * restoring file * Bugfixes * flake8 + bugfix * Refactoring variables * Setting string variables to Path * Unused import removal * Setting path to performance data csv as path object instead of str * Factoring out double code * Updated comment * dead arguments, flake8 * fixing path variables to actually be paths * Fixing tests, str to path objects * bugfixes * Factoring global variables out of report generation * renaming file * pytest fix * flake8 * Moving check results to generate report command * Removing last run test as its already being resolved by reportingscenario object * Removing get num instances as it can be deduced from the validator data * Removing methods only referenced once * Refactoring configuration report generator with GV, moving class out of GV * flake8 * pytest fixes * flake8 * removing gv references from parallel portfolio report * flake8 * minor fixes for selection reports * Refactoring selection report * selection example fix * refactoring gv from selection * Refactoring performance dataframe usage * Removing global variable references from selection * Flake8 * forgotten print * pytest fix * removing gv from settings help * Bugfix * Removing solver references as str * Fixing bug, giving test a better name * bugfix * Mistake * Bugfix * flake8 * Removing --parallel option from compute features (This should be done using sparkle settings) * Removing unused method * Renaming method to be more clear * Removing dead argument from add solver * Moving add solver argument to argparse custom * Refactoring --parallel argument out of Sparkle * Flake8 * bugfix settings * Bug fix settings * Removing double code and renaming * flake8 fixes * test fix * Removing nearly unused variables from gv * Bugfixes * test fix * Flake8 * Moving slurm settings to settings class * flake8 * Refactoring slurm settings into sparkle settings * Correcting method variable to Path * Bugfix for settings * bugfix config report generation * test fixes * Removing ``in parallel'' from sparkle prints * Parallel portfolio fixes and improvements * Bugfix settings writing * Removing useless write statement * double spaces in print statement * Unnecessary path conversion removal * Removing feature data tmp dir * Bugfolio portfolio selector * Sprk 308 (#35) * Setting up base shared class of extractor and solver * First step towards an OO extractor * flake8 * SPRK-306 (#36) * Update to check_settings_changes to verify if sections in the settings file were added or removed * Changed lists to sets and formatting * More descriptive variable naming --------- Co-authored-by: Noah Peil <[email protected]> * Add entry to CONTRIBUTING.md regarding the custom git clean command * Sprk 271 (#37) * Base setup for new instances object * Preparing configuration to run with instances object instead of paths/str * Fixing up Sparkle with new Instances object * bugfix * Reworking deterministic into flag * Bug fix in pathing * Using instance object for ablation * Minor fixes for ablation report generation * Fixing run configured solver with new object * flake8 * Fixing test of dead code * bug fixes instances * flake8 * Enabling instance set to contain instance * Renaming variable * Test fix * flake8 * Fixing run portfolio selector with more elegant code * Fixing arguments for parallel portfolio * Bugfix * Removing unused code * Prepping to test multi-file instance * Updating extractor * Renaming wrapper * Fixing multi instance extractor * Fixing bugs in adding multi instance extractor * Fixing up add instances * Bugfixes add instances * Fixing up example, enabling solver wrapper to receive lists * Adding sparkle solver wrapper to TCA * Expanding compute features to work with multi-file instances * Forgot to save data structures after modification * Updating compute features to work with multi instance * Bugfixes for compute features multi-file instances * Fixing multi instance examples * Cleaning up compute features core * flake8 * Quickfix for multi-instance run solvers * Removing print statement * Removing old wrappers * Updating remove instances with new object * minor bug fixes * flake8 * Removing unused file * Removing system status file getter * Refactoring file_hlep * Refactoring argument * Fixing run configured solver to use instance sets * Removing dead arguments, unnecessary path conversions * Making sure Sparkle uses solver object * Fixing pytest files * Bugfix solver wrapper * Minor bug fixes * Bugfixes for running solvers * Cleaning up variable types for generate report config * removing print statement * Bugfixes data setting for performance dataframe * bugfix reporting scenario * Bugfix report generation parallel portfolio * Bugfix parallel portfolio report generation * flake8 * bugfix reports * Sprk 202 (#39) * Removing unused configurator files in test * Adding pytests * Fixing up configurator pytests * flake8 * Bugfixes for getting optimal configuration * Removing special string references from sparkle * Add default value for the run-on argument (#38) * Add standard value for the run-on argument which can be overwritten via the command line * Make get_run_on() return enum instead of string * Write run-on argument as a string to the latest.ini file * Last commit was missing one file * Small fix --------- Co-authored-by: Noah Peil <[email protected]> * Starting to refactor how feature data works in sparkle * Restructuring feature data frame * Renaming file and setting up package init * renaming file * Reworking feature extractor workings with feature data frame * Prepping feature extractor wrappers * Preparing feature extractors part 2 * bugfixes for adding/removing instances from fdf * Bugfixes for adding/removing extractors * Updating extractor to handle I/O better * Fixing feature computations to work with new wrapper set up * Fixing featuredataframe imports * Removing dead variables * Correcting settings * Updating manual * Bugfixes for how to compute remaining feature jobs * Added comment * wrapper fix * Bug fixes running selector on single instance * Deleting now unused file * Test fix * Unused code removal * Flake8 * Updating remaining jobs format * pytest fix * Removing unused code * Flake8 * bugfixes * Use extractor object in compute features core * Minor code fixes * Bugfixes regarding runsolver * recompute bugfix * Fixing up extractor wrapper * Fixing comments for featuredataframe * Bugfix for multi file instances * flake8 * Reanming file * bugfix running extractor * Test fix * Removing old configuration example * Replacing old config, deleting old validation test data * New validation example data * Test update * Adding satzilla2024 * Prepping SATZilla2024 example * Prepping Sparkle for new extractor * Moving compute features into the CLI command file * updating extractors * Updating example execution rights * adding description * Updating 2024 wrapper * missing executable * Don't use the last feature * chmod +x * Feature group preparation * Description update * Setting execution permissions * Adding feature mapping * Compilation update SATZilla2024 * Updating example * Execution rights * Fixing wrapper * Bugfixes feature imputation * bugfix get feature groups * Adding new instance set * Updating selection example * renaming instances new set * Bugfix runsolver output parsing * flake8 * minor fix * Update description_SAT-features-competition2024.txt * Adding main to avoid floating code * Fixing settings options without SMAC section * Removing dead code * Settings fix * minor fixes * Fixing last Solver object omission * Status info fix * Sprk 252 (#40) * Change documentation template * added theme to requirements * Fixed Index page of documentation * Included github action file * Test GitHub Actions * test v2 * test 3 * test 4 * test 5 (?) * test 6 * test7 * test 8 * test 9 * test 10 ? * another one * New approach * check * spelling? * this is getting sad * lesgo * wild test * Polishing * Deleted build files to try something out * Changed the workflow to run on push on main * small fixes * Sparkle wait now shows a table * Added output-verbosity to settings * sparkle wait now also shows partition * Restructering. Removed Extensive, rename REDUCED to QUIET, removed partition * Finished new wait command * Flake is killing me * Moved vreebosity from output to general (settings) * Added check interval to settings * Jobs are sorted based on status * Fixed flake8 * Added TEXT class and implemented in sparkle wait * Minor changes --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 283 (#42) * Print update * Refactoring * fixing comments * Bug fixes dataframes * first implementation design of selector OO * refactoring file * Refactoring sparkle to use selector OO solution * flake8 * Removing multiple file creating from perfect selector computation * refactoring copy operations out of marginal contribution * performance dataframe fixes * Changing references to Settings file * Forgot a few * Testing changing reference to gv.settings to settings * Refactoring usage of marginal contribution * flake8 * Updating test * bugfix * Fixing verbosity * Flake8 + pytest fixes * bugfix * pytest mock fixes * more usefull error printing selector * test fix * bugfixes * bugfixes * reordering tests * flake8 * new test files * Removing dead command * Removing dead test * New RunRunner version * Test fixes for new runrunner version * Showing new column based on runrunner update in sparkle wait * fix for pytest * Sprk 160 (#44) * Prepping tests to use all a different scenario file * Fixing tests to always use specific test set * Removing dead variables from global variables * Minor changes ablation * reducing git ignore * Removing logging from Platform (CLI functionality) * Removing non-CLI references to global variables, moving sparkle log * settings mistake * Creating init for CLI packages * Pre release test branch (#45) * Trying to move global variables * init fllake8 * flake8 * Moving tools to be part of Sparkle lib * Updating setup to not include the tests * renaming latex dir * Creating manifest, updating setup.py * flake8 * Moving Components into sparkle dir to prepare workable pip install * Update pull-request.yml (#49) * Update pull-request.yml * Update pull-request.yml * SPRK 151 (#46) * Flake8 pre-commit * Pre commit test * Disable test for pre commit * Updating change log and contributing * Reducing test files bloating * Settings mistake * Removing unused test files * Unused test files * Sprk 320 (#50) * Fixing bugs in Ablation * First class design, bug fixes, flake8 * Refactoring ablation object usage * fixing pytests * Moving ablation * Bug fixes for report generation * Bugfixes ablation, refactoring, fixing timezone on smac target algorithm * Adding example download capability to initialise command * Simplifying + comment for init * Updating changelog * Simplifying wait command * Minor variable name and comments fixes * Removing dead variables from global var * Fixes regarding portfolio selector methods * Renaming symbols * Minor refactoring * Minor refactoring * Refactoring method definitions * Bugfixes for initialise * Bugfix init * Removing excess test files * Moving CLI tests to tests folder * Removing unnecessary methods * Refactoring function definitions * Simplifying sat_help methods * sat verify bug fix * Old code reversal * Refactoring snapshit * snapshot bugfix * Logger typing fixes * Minor fixes * Refactoring file help * Redundant string removal * Fixes * Sprk 295 (#51) * Creating parser for solver wrapper output * Change solver status from string to enum * Completed docstring * Merge dev into SPRK-295 --------- Co-authored-by: ngcp1 <[email protected]> * Remove the exclusive flag when running the portfolio selector (#52) * Moving CLI to a better place * Bug fix seed being none for solver * Bugfix run sparkle portfolio core * Bugfixes portfolio selector * Version 0.8.3 release (#53) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Version change * Small fixes --------- Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Release/0.8.3 (#55) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Version change * Small fixes * Bugfix test files --------- Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-auth…

* Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal (#29) * Release/0.8.2 (#31) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * bugfix feature extractor removal --------- Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Quick fix for documentation generation * Sprk 292 (#33) * Change documentation template * added theme to requirements * Fixed Index page of documentation * Included github action file * Test GitHub Actions * test v2 * test 3 * test 4 * test 5 (?) * test 6 * test7 * test 8 * test 9 * test 10 ? * another one * New approach * check * spelling? * this is getting sad * lesgo * wild test * Polishing * Deleted build files to try something out * Changed the workflow to run on push on main * small fixes --------- Co-authored-by: Noah Peil <[email protected]> * SPRK-275 (#34) * refactoring the random date time stamp getter * Forgot one file * Moving ablation help to its correct location * This file shouldn't exist anymore since last version, weird * Redundant code removal? * Refactoring useless code * Removing dead code * Moving file to correct spot * Refactoring, moving files * Reforming slurm options * refactoring + test fixes * Refactoring solver object usage in Sparkle * test bug fixes * Refactoring solver deterministic parameter * Updating args * Moving compute features help to correct file * code layout * Bug fixes * Getting rid of CSV merge by using file locks instead * Removing dead file * flake8 * Removing unused command enums * Refactoring run configured solver help * Renaming file to be more representative * Moving to more suitable folder * Simplifying run solvers help by making more use of the Solver object * Removing dead code * Refactorign default wrapper out of sparkle * Updating user guide * updating the template * bug fix in results parsing * Setting example to run in parallel by default * bugfix adding solver * Updating printing info from add solver to be more compact and accurate * Factoring settings usage out of performance data frame * Final bug fixes for refactoring global variables out of performance data frame * Updated comments * Pytest fixes * test fix * Removing dead code * flake8 * test fix * Refactoring feature data csv, bug fixes * Bug fixes for Performance dataframe * bugfix performance dataframe * Simplifying Solver imports * Moving missing value into the data structures * Removing dead import * Removing sparkle version from global variables * Removing dead import * Test fix * removing print statement * Refactoring instance set NAME references to PATH for SMAC configurator class * flake8 * Fixing pytests * Removing extra spaces * refactoring instances help * reverting change due to complexity * refactoring global variables out of instances_help * Refactoring global variables out of configurator * pytest fix * Moving CLI related files * Refactoring gv from file help, bug fixes * restoring file * Bugfixes * flake8 + bugfix * Refactoring variables * Setting string variables to Path * Unused import removal * Setting path to performance data csv as path object instead of str * Factoring out double code * Updated comment * dead arguments, flake8 * fixing path variables to actually be paths * Fixing tests, str to path objects * bugfixes * Factoring global variables out of report generation * renaming file * pytest fix * flake8 * Moving check results to generate report command * Removing last run test as its already being resolved by reportingscenario object * Removing get num instances as it can be deduced from the validator data * Removing methods only referenced once * Refactoring configuration report generator with GV, moving class out of GV * flake8 * pytest fixes * flake8 * removing gv references from parallel portfolio report * flake8 * minor fixes for selection reports * Refactoring selection report * selection example fix * refactoring gv from selection * Refactoring performance dataframe usage * Removing global variable references from selection * Flake8 * forgotten print * pytest fix * removing gv from settings help * Bugfix * Removing solver references as str * Fixing bug, giving test a better name * bugfix * Mistake * Bugfix * flake8 * Removing --parallel option from compute features (This should be done using sparkle settings) * Removing unused method * Renaming method to be more clear * Removing dead argument from add solver * Moving add solver argument to argparse custom * Refactoring --parallel argument out of Sparkle * Flake8 * bugfix settings * Bug fix settings * Removing double code and renaming * flake8 fixes * test fix * Removing nearly unused variables from gv * Bugfixes * test fix * Flake8 * Moving slurm settings to settings class * flake8 * Refactoring slurm settings into sparkle settings * Correcting method variable to Path * Bugfix for settings * bugfix config report generation * test fixes * Removing ``in parallel'' from sparkle prints * Parallel portfolio fixes and improvements * Bugfix settings writing * Removing useless write statement * double spaces in print statement * Unnecessary path conversion removal * Removing feature data tmp dir * Bugfolio portfolio selector * Sprk 308 (#35) * Setting up base shared class of extractor and solver * First step towards an OO extractor * flake8 * SPRK-306 (#36) * Update to check_settings_changes to verify if sections in the settings file were added or removed * Changed lists to sets and formatting * More descriptive variable naming --------- Co-authored-by: Noah Peil <[email protected]> * Add entry to CONTRIBUTING.md regarding the custom git clean command * Sprk 271 (#37) * Base setup for new instances object * Preparing configuration to run with instances object instead of paths/str * Fixing up Sparkle with new Instances object * bugfix * Reworking deterministic into flag * Bug fix in pathing * Using instance object for ablation * Minor fixes for ablation report generation * Fixing run configured solver with new object * flake8 * Fixing test of dead code * bug fixes instances * flake8 * Enabling instance set to contain instance * Renaming variable * Test fix * flake8 * Fixing run portfolio selector with more elegant code * Fixing arguments for parallel portfolio * Bugfix * Removing unused code * Prepping to test multi-file instance * Updating extractor * Renaming wrapper * Fixing multi instance extractor * Fixing bugs in adding multi instance extractor * Fixing up add instances * Bugfixes add instances * Fixing up example, enabling solver wrapper to receive lists * Adding sparkle solver wrapper to TCA * Expanding compute features to work with multi-file instances * Forgot to save data structures after modification * Updating compute features to work with multi instance * Bugfixes for compute features multi-file instances * Fixing multi instance examples * Cleaning up compute features core * flake8 * Quickfix for multi-instance run solvers * Removing print statement * Removing old wrappers * Updating remove instances with new object * minor bug fixes * flake8 * Removing unused file * Removing system status file getter * Refactoring file_hlep * Refactoring argument * Fixing run configured solver to use instance sets * Removing dead arguments, unnecessary path conversions * Making sure Sparkle uses solver object * Fixing pytest files * Bugfix solver wrapper * Minor bug fixes * Bugfixes for running solvers * Cleaning up variable types for generate report config * removing print statement * Bugfixes data setting for performance dataframe * bugfix reporting scenario * Bugfix report generation parallel portfolio * Bugfix parallel portfolio report generation * flake8 * bugfix reports * Sprk 202 (#39) * Removing unused configurator files in test * Adding pytests * Fixing up configurator pytests * flake8 * Bugfixes for getting optimal configuration * Removing special string references from sparkle * Add default value for the run-on argument (#38) * Add standard value for the run-on argument which can be overwritten via the command line * Make get_run_on() return enum instead of string * Write run-on argument as a string to the latest.ini file * Last commit was missing one file * Small fix --------- Co-authored-by: Noah Peil <[email protected]> * Starting to refactor how feature data works in sparkle * Restructuring feature data frame * Renaming file and setting up package init * renaming file * Reworking feature extractor workings with feature data frame * Prepping feature extractor wrappers * Preparing feature extractors part 2 * bugfixes for adding/removing instances from fdf * Bugfixes for adding/removing extractors * Updating extractor to handle I/O better * Fixing feature computations to work with new wrapper set up * Fixing featuredataframe imports * Removing dead variables * Correcting settings * Updating manual * Bugfixes for how to compute remaining feature jobs * Added comment * wrapper fix * Bug fixes running selector on single instance * Deleting now unused file * Test fix * Unused code removal * Flake8 * Updating remaining jobs format * pytest fix * Removing unused code * Flake8 * bugfixes * Use extractor object in compute features core * Minor code fixes * Bugfixes regarding runsolver * recompute bugfix * Fixing up extractor wrapper * Fixing comments for featuredataframe * Bugfix for multi file instances * flake8 * Reanming file * bugfix running extractor * Test fix * Removing old configuration example * Replacing old config, deleting old validation test data * New validation example data * Test update * Adding satzilla2024 * Prepping SATZilla2024 example * Prepping Sparkle for new extractor * Moving compute features into the CLI command file * updating extractors * Updating example execution rights * adding description * Updating 2024 wrapper * missing executable * Don't use the last feature * chmod +x * Feature group preparation * Description update * Setting execution permissions * Adding feature mapping * Compilation update SATZilla2024 * Updating example * Execution rights * Fixing wrapper * Bugfixes feature imputation * bugfix get feature groups * Adding new instance set * Updating selection example * renaming instances new set * Bugfix runsolver output parsing * flake8 * minor fix * Update description_SAT-features-competition2024.txt * Adding main to avoid floating code * Fixing settings options without SMAC section * Removing dead code * Settings fix * minor fixes * Fixing last Solver object omission * Status info fix * Sprk 252 (#40) * Change documentation template * added theme to requirements * Fixed Index page of documentation * Included github action file * Test GitHub Actions * test v2 * test 3 * test 4 * test 5 (?) * test 6 * test7 * test 8 * test 9 * test 10 ? * another one * New approach * check * spelling? * this is getting sad * lesgo * wild test * Polishing * Deleted build files to try something out * Changed the workflow to run on push on main * small fixes * Sparkle wait now shows a table * Added output-verbosity to settings * sparkle wait now also shows partition * Restructering. Removed Extensive, rename REDUCED to QUIET, removed partition * Finished new wait command * Flake is killing me * Moved vreebosity from output to general (settings) * Added check interval to settings * Jobs are sorted based on status * Fixed flake8 * Added TEXT class and implemented in sparkle wait * Minor changes --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 283 (#42) * Print update * Refactoring * fixing comments * Bug fixes dataframes * first implementation design of selector OO * refactoring file * Refactoring sparkle to use selector OO solution * flake8 * Removing multiple file creating from perfect selector computation * refactoring copy operations out of marginal contribution * performance dataframe fixes * Changing references to Settings file * Forgot a few * Testing changing reference to gv.settings to settings * Refactoring usage of marginal contribution * flake8 * Updating test * bugfix * Fixing verbosity * Flake8 + pytest fixes * bugfix * pytest mock fixes * more usefull error printing selector * test fix * bugfixes * bugfixes * reordering tests * flake8 * new test files * Removing dead command * Removing dead test * New RunRunner version * Test fixes for new runrunner version * Showing new column based on runrunner update in sparkle wait * fix for pytest * Sprk 160 (#44) * Prepping tests to use all a different scenario file * Fixing tests to always use specific test set * Removing dead variables from global variables * Minor changes ablation * reducing git ignore * Removing logging from Platform (CLI functionality) * Removing non-CLI references to global variables, moving sparkle log * settings mistake * Creating init for CLI packages * Pre release test branch (#45) * Trying to move global variables * init fllake8 * flake8 * Moving tools to be part of Sparkle lib * Updating setup to not include the tests * renaming latex dir * Creating manifest, updating setup.py * flake8 * Moving Components into sparkle dir to prepare workable pip install * Update pull-request.yml (#49) * Update pull-request.yml * Update pull-request.yml * SPRK 151 (#46) * Flake8 pre-commit * Pre commit test * Disable test for pre commit * Updating change log and contributing * Reducing test files bloating * Settings mistake * Removing unused test files * Unused test files * Sprk 320 (#50) * Fixing bugs in Ablation * First class design, bug fixes, flake8 * Refactoring ablation object usage * fixing pytests * Moving ablation * Bug fixes for report generation * Bugfixes ablation, refactoring, fixing timezone on smac target algorithm * Adding example download capability to initialise command * Simplifying + comment for init * Updating changelog * Simplifying wait command * Minor variable name and comments fixes * Removing dead variables from global var * Fixes regarding portfolio selector methods * Renaming symbols * Minor refactoring * Minor refactoring * Refactoring method definitions * Bugfixes for initialise * Bugfix init * Removing excess test files * Moving CLI tests to tests folder * Removing unnecessary methods * Refactoring function definitions * Simplifying sat_help methods * sat verify bug fix * Old code reversal * Refactoring snapshit * snapshot bugfix * Logger typing fixes * Minor fixes * Refactoring file help * Redundant string removal * Fixes * Sprk 295 (#51) * Creating parser for solver wrapper output * Change solver status from string to enum * Completed docstring * Merge dev into SPRK-295 --------- Co-authored-by: ngcp1 <[email protected]> * Remove the exclusive flag when running the portfolio selector (#52) * Moving CLI to a better place * Bug fix seed being none for solver * Bugfix run sparkle portfolio core * Bugfixes portfolio selector * Version 0.8.3 release (#53) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Version change * Small fixes --------- Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Release/0.8.3 (#55) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Version change * Small fixes * Bugfix test files --------- Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Release/0.8.3 (#57) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting f…

* Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal (#29) * Release/0.8.2 (#31) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * bugfix feature extractor removal --------- Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Quick fix for documentation generation * Sprk 292 (#33) * Change documentation template * added theme to requirements * Fixed Index page of documentation * Included github action file * Test GitHub Actions * test v2 * test 3 * test 4 * test 5 (?) * test 6 * test7 * test 8 * test 9 * test 10 ? * another one * New approach * check * spelling? * this is getting sad * lesgo * wild test * Polishing * Deleted build files to try something out * Changed the workflow to run on push on main * small fixes --------- Co-authored-by: Noah Peil <[email protected]> * SPRK-275 (#34) * refactoring the random date time stamp getter * Forgot one file * Moving ablation help to its correct location * This file shouldn't exist anymore since last version, weird * Redundant code removal? * Refactoring useless code * Removing dead code * Moving file to correct spot * Refactoring, moving files * Reforming slurm options * refactoring + test fixes * Refactoring solver object usage in Sparkle * test bug fixes * Refactoring solver deterministic parameter * Updating args * Moving compute features help to correct file * code layout * Bug fixes * Getting rid of CSV merge by using file locks instead * Removing dead file * flake8 * Removing unused command enums * Refactoring run configured solver help * Renaming file to be more representative * Moving to more suitable folder * Simplifying run solvers help by making more use of the Solver object * Removing dead code * Refactorign default wrapper out of sparkle * Updating user guide * updating the template * bug fix in results parsing * Setting example to run in parallel by default * bugfix adding solver * Updating printing info from add solver to be more compact and accurate * Factoring settings usage out of performance data frame * Final bug fixes for refactoring global variables out of performance data frame * Updated comments * Pytest fixes * test fix * Removing dead code * flake8 * test fix * Refactoring feature data csv, bug fixes * Bug fixes for Performance dataframe * bugfix performance dataframe * Simplifying Solver imports * Moving missing value into the data structures * Removing dead import * Removing sparkle version from global variables * Removing dead import * Test fix * removing print statement * Refactoring instance set NAME references to PATH for SMAC configurator class * flake8 * Fixing pytests * Removing extra spaces * refactoring instances help * reverting change due to complexity * refactoring global variables out of instances_help * Refactoring global variables out of configurator * pytest fix * Moving CLI related files * Refactoring gv from file help, bug fixes * restoring file * Bugfixes * flake8 + bugfix * Refactoring variables * Setting string variables to Path * Unused import removal * Setting path to performance data csv as path object instead of str * Factoring out double code * Updated comment * dead arguments, flake8 * fixing path variables to actually be paths * Fixing tests, str to path objects * bugfixes * Factoring global variables out of report generation * renaming file * pytest fix * flake8 * Moving check results to generate report command * Removing last run test as its already being resolved by reportingscenario object * Removing get num instances as it can be deduced from the validator data * Removing methods only referenced once * Refactoring configuration report generator with GV, moving class out of GV * flake8 * pytest fixes * flake8 * removing gv references from parallel portfolio report * flake8 * minor fixes for selection reports * Refactoring selection report * selection example fix * refactoring gv from selection * Refactoring performance dataframe usage * Removing global variable references from selection * Flake8 * forgotten print * pytest fix * removing gv from settings help * Bugfix * Removing solver references as str * Fixing bug, giving test a better name * bugfix * Mistake * Bugfix * flake8 * Removing --parallel option from compute features (This should be done using sparkle settings) * Removing unused method * Renaming method to be more clear * Removing dead argument from add solver * Moving add solver argument to argparse custom * Refactoring --parallel argument out of Sparkle * Flake8 * bugfix settings * Bug fix settings * Removing double code and renaming * flake8 fixes * test fix * Removing nearly unused variables from gv * Bugfixes * test fix * Flake8 * Moving slurm settings to settings class * flake8 * Refactoring slurm settings into sparkle settings * Correcting method variable to Path * Bugfix for settings * bugfix config report generation * test fixes * Removing ``in parallel'' from sparkle prints * Parallel portfolio fixes and improvements * Bugfix settings writing * Removing useless write statement * double spaces in print statement * Unnecessary path conversion removal * Removing feature data tmp dir * Bugfolio portfolio selector * Sprk 308 (#35) * Setting up base shared class of extractor and solver * First step towards an OO extractor * flake8 * SPRK-306 (#36) * Update to check_settings_changes to verify if sections in the settings file were added or removed * Changed lists to sets and formatting * More descriptive variable naming --------- Co-authored-by: Noah Peil <[email protected]> * Add entry to CONTRIBUTING.md regarding the custom git clean command * Sprk 271 (#37) * Base setup for new instances object * Preparing configuration to run with instances object instead of paths/str * Fixing up Sparkle with new Instances object * bugfix * Reworking deterministic into flag * Bug fix in pathing * Using instance object for ablation * Minor fixes for ablation report generation * Fixing run configured solver with new object * flake8 * Fixing test of dead code * bug fixes instances * flake8 * Enabling instance set to contain instance * Renaming variable * Test fix * flake8 * Fixing run portfolio selector with more elegant code * Fixing arguments for parallel portfolio * Bugfix * Removing unused code * Prepping to test multi-file instance * Updating extractor * Renaming wrapper * Fixing multi instance extractor * Fixing bugs in adding multi instance extractor * Fixing up add instances * Bugfixes add instances * Fixing up example, enabling solver wrapper to receive lists * Adding sparkle solver wrapper to TCA * Expanding compute features to work with multi-file instances * Forgot to save data structures after modification * Updating compute features to work with multi instance * Bugfixes for compute features multi-file instances * Fixing multi instance examples * Cleaning up compute features core * flake8 * Quickfix for multi-instance run solvers * Removing print statement * Removing old wrappers * Updating remove instances with new object * minor bug fixes * flake8 * Removing unused file * Removing system status file getter * Refactoring file_hlep * Refactoring argument * Fixing run configured solver to use instance sets * Removing dead arguments, unnecessary path conversions * Making sure Sparkle uses solver object * Fixing pytest files * Bugfix solver wrapper * Minor bug fixes * Bugfixes for running solvers * Cleaning up variable types for generate report config * removing print statement * Bugfixes data setting for performance dataframe * bugfix reporting scenario * Bugfix report generation parallel portfolio * Bugfix parallel portfolio report generation * flake8 * bugfix reports * Sprk 202 (#39) * Removing unused configurator files in test * Adding pytests * Fixing up configurator pytests * flake8 * Bugfixes for getting optimal configuration * Removing special string references from sparkle * Add default value for the run-on argument (#38) * Add standard value for the run-on argument which can be overwritten via the command line * Make get_run_on() return enum instead of string * Write run-on argument as a string to the latest.ini file * Last commit was missing one file * Small fix --------- Co-authored-by: Noah Peil <[email protected]> * Starting to refactor how feature data works in sparkle * Restructuring feature data frame * Renaming file and setting up package init * renaming file * Reworking feature extractor workings with feature data frame * Prepping feature extractor wrappers * Preparing feature extractors part 2 * bugfixes for adding/removing instances from fdf * Bugfixes for adding/removing extractors * Updating extractor to handle I/O better * Fixing feature computations to work with new wrapper set up * Fixing featuredataframe imports * Removing dead variables * Correcting settings * Updating manual * Bugfixes for how to compute remaining feature jobs * Added comment * wrapper fix * Bug fixes running selector on single instance * Deleting now unused file * Test fix * Unused code removal * Flake8 * Updating remaining jobs format * pytest fix * Removing unused code * Flake8 * bugfixes * Use extractor object in compute features core * Minor code fixes * Bugfixes regarding runsolver * recompute bugfix * Fixing up extractor wrapper * Fixing comments for featuredataframe * Bugfix for multi file instances * flake8 * Reanming file * bugfix running extractor * Test fix * Removing old configuration example * Replacing old config, deleting old validation test data * New validation example data * Test update * Adding satzilla2024 * Prepping SATZilla2024 example * Prepping Sparkle for new extractor * Moving compute features into the CLI command file * updating extractors * Updating example execution rights * adding description * Updating 2024 wrapper * missing executable * Don't use the last feature * chmod +x * Feature group preparation * Description update * Setting execution permissions * Adding feature mapping * Compilation update SATZilla2024 * Updating example * Execution rights * Fixing wrapper * Bugfixes feature imputation * bugfix get feature groups * Adding new instance set * Updating selection example * renaming instances new set * Bugfix runsolver output parsing * flake8 * minor fix * Update description_SAT-features-competition2024.txt * Adding main to avoid floating code * Fixing settings options without SMAC section * Removing dead code * Settings fix * minor fixes * Fixing last Solver object omission * Status info fix * Sprk 252 (#40) * Change documentation template * added theme to requirements * Fixed Index page of documentation * Included github action file * Test GitHub Actions * test v2 * test 3 * test 4 * test 5 (?) * test 6 * test7 * test 8 * test 9 * test 10 ? * another one * New approach * check * spelling? * this is getting sad * lesgo * wild test * Polishing * Deleted build files to try something out * Changed the workflow to run on push on main * small fixes * Sparkle wait now shows a table * Added output-verbosity to settings * sparkle wait now also shows partition * Restructering. Removed Extensive, rename REDUCED to QUIET, removed partition * Finished new wait command * Flake is killing me * Moved vreebosity from output to general (settings) * Added check interval to settings * Jobs are sorted based on status * Fixed flake8 * Added TEXT class and implemented in sparkle wait * Minor changes --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 283 (#42) * Print update * Refactoring * fixing comments * Bug fixes dataframes * first implementation design of selector OO * refactoring file * Refactoring sparkle to use selector OO solution * flake8 * Removing multiple file creating from perfect selector computation * refactoring copy operations out of marginal contribution * performance dataframe fixes * Changing references to Settings file * Forgot a few * Testing changing reference to gv.settings to settings * Refactoring usage of marginal contribution * flake8 * Updating test * bugfix * Fixing verbosity * Flake8 + pytest fixes * bugfix * pytest mock fixes * more usefull error printing selector * test fix * bugfixes * bugfixes * reordering tests * flake8 * new test files * Removing dead command * Removing dead test * New RunRunner version * Test fixes for new runrunner version * Showing new column based on runrunner update in sparkle wait * fix for pytest * Sprk 160 (#44) * Prepping tests to use all a different scenario file * Fixing tests to always use specific test set * Removing dead variables from global variables * Minor changes ablation * reducing git ignore * Removing logging from Platform (CLI functionality) * Removing non-CLI references to global variables, moving sparkle log * settings mistake * Creating init for CLI packages * Pre release test branch (#45) * Trying to move global variables * init fllake8 * flake8 * Moving tools to be part of Sparkle lib * Updating setup to not include the tests * renaming latex dir * Creating manifest, updating setup.py * flake8 * Moving Components into sparkle dir to prepare workable pip install * Update pull-request.yml (#49) * Update pull-request.yml * Update pull-request.yml * SPRK 151 (#46) * Flake8 pre-commit * Pre commit test * Disable test for pre commit * Updating change log and contributing * Reducing test files bloating * Settings mistake * Removing unused test files * Unused test files * Sprk 320 (#50) * Fixing bugs in Ablation * First class design, bug fixes, flake8 * Refactoring ablation object usage * fixing pytests * Moving ablation * Bug fixes for report generation * Bugfixes ablation, refactoring, fixing timezone on smac target algorithm * Adding example download capability to initialise command * Simplifying + comment for init * Updating changelog * Simplifying wait command * Minor variable name and comments fixes * Removing dead variables from global var * Fixes regarding portfolio selector methods * Renaming symbols * Minor refactoring * Minor refactoring * Refactoring method definitions * Bugfixes for initialise * Bugfix init * Removing excess test files * Moving CLI tests to tests folder * Removing unnecessary methods * Refactoring function definitions * Simplifying sat_help methods * sat verify bug fix * Old code reversal * Refactoring snapshit * snapshot bugfix * Logger typing fixes * Minor fixes * Refactoring file help * Redundant string removal * Fixes * Sprk 295 (#51) * Creating parser for solver wrapper output * Change solver status from string to enum * Completed docstring * Merge dev into SPRK-295 --------- Co-authored-by: ngcp1 <[email protected]> * Remove the exclusive flag when running the portfolio selector (#52) * Moving CLI to a better place * Bug fix seed being none for solver * Bugfix run sparkle portfolio core * Bugfixes portfolio selector * Version 0.8.3 release (#53) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Version change * Small fixes --------- Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Release/0.8.3 (#55) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Version change * Small fixes * Bugfix test files --------- Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Release/0.8.3 (#57) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rena…

* bugfixes for adding/removing instances from fdf * Bugfixes for adding/removing extractors * Updating extractor to handle I/O better * Fixing feature computations to work with new wrapper set up * Fixing featuredataframe imports * Removing dead variables * Correcting settings * Updating manual * Bugfixes for how to compute remaining feature jobs * Added comment * wrapper fix * Bug fixes running selector on single instance * Deleting now unused file * Test fix * Unused code removal * Flake8 * Updating remaining jobs format * pytest fix * Removing unused code * Flake8 * bugfixes * Use extractor object in compute features core * Minor code fixes * Bugfixes regarding runsolver * recompute bugfix * Fixing up extractor wrapper * Fixing comments for featuredataframe * Bugfix for multi file instances * flake8 * Reanming file * bugfix running extractor * Test fix * Removing old configuration example * Replacing old config, deleting old validation test data * New validation example data * Test update * Adding satzilla2024 * Prepping SATZilla2024 example * Prepping Sparkle for new extractor * Moving compute features into the CLI command file * updating extractors * Updating example execution rights * adding description * Updating 2024 wrapper * missing executable * Don't use the last feature * chmod +x * Feature group preparation * Description update * Setting execution permissions * Adding feature mapping * Compilation update SATZilla2024 * Updating example * Execution rights * Fixing wrapper * Bugfixes feature imputation * bugfix get feature groups * Adding new instance set * Updating selection example * renaming instances new set * Bugfix runsolver output parsing * flake8 * minor fix * Update description_SAT-features-competition2024.txt * Adding main to avoid floating code * Fixing settings options without SMAC section * Removing dead code * Settings fix * minor fixes * Fixing last Solver object omission * Status info fix * Sprk 252 (#40) * Change documentation template * added theme to requirements * Fixed Index page of documentation * Included github action file * Test GitHub Actions * test v2 * test 3 * test 4 * test 5 (?) * test 6 * test7 * test 8 * test 9 * test 10 ? * another one * New approach * check * spelling? * this is getting sad * lesgo * wild test * Polishing * Deleted build files to try something out * Changed the workflow to run on push on main * small fixes * Sparkle wait now shows a table * Added output-verbosity to settings * sparkle wait now also shows partition * Restructering. Removed Extensive, rename REDUCED to QUIET, removed partition * Finished new wait command * Flake is killing me * Moved vreebosity from output to general (settings) * Added check interval to settings * Jobs are sorted based on status * Fixed flake8 * Added TEXT class and implemented in sparkle wait * Minor changes --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 283 (#42) * Print update * Refactoring * fixing comments * Bug fixes dataframes * first implementation design of selector OO * refactoring file * Refactoring sparkle to use selector OO solution * flake8 * Removing multiple file creating from perfect selector computation * refactoring copy operations out of marginal contribution * performance dataframe fixes * Changing references to Settings file * Forgot a few * Testing changing reference to gv.settings to settings * Refactoring usage of marginal contribution * flake8 * Updating test * bugfix * Fixing verbosity * Flake8 + pytest fixes * bugfix * pytest mock fixes * more usefull error printing selector * test fix * bugfixes * bugfixes * reordering tests * flake8 * new test files * Removing dead command * Removing dead test * New RunRunner version * Test fixes for new runrunner version * Showing new column based on runrunner update in sparkle wait * fix for pytest * Sprk 160 (#44) * Prepping tests to use all a different scenario file * Fixing tests to always use specific test set * Removing dead variables from global variables * Minor changes ablation * reducing git ignore * Removing logging from Platform (CLI functionality) * Removing non-CLI references to global variables, moving sparkle log * settings mistake * Creating init for CLI packages * Pre release test branch (#45) * Trying to move global variables * init fllake8 * flake8 * Moving tools to be part of Sparkle lib * Updating setup to not include the tests * renaming latex dir * Creating manifest, updating setup.py * flake8 * Moving Components into sparkle dir to prepare workable pip install * Update pull-request.yml (#49) * Update pull-request.yml * Update pull-request.yml * SPRK 151 (#46) * Flake8 pre-commit * Pre commit test * Disable test for pre commit * Updating change log and contributing * Reducing test files bloating * Settings mistake * Removing unused test files * Unused test files * Sprk 320 (#50) * Fixing bugs in Ablation * First class design, bug fixes, flake8 * Refactoring ablation object usage * fixing pytests * Moving ablation * Bug fixes for report generation * Bugfixes ablation, refactoring, fixing timezone on smac target algorithm * Adding example download capability to initialise command * Simplifying + comment for init * Updating changelog * Simplifying wait command * Minor variable name and comments fixes * Removing dead variables from global var * Fixes regarding portfolio selector methods * Renaming symbols * Minor refactoring * Minor refactoring * Refactoring method definitions * Bugfixes for initialise * Bugfix init * Removing excess test files * Moving CLI tests to tests folder * Removing unnecessary methods * Refactoring function definitions * Simplifying sat_help methods * sat verify bug fix * Old code reversal * Refactoring snapshit * snapshot bugfix * Logger typing fixes * Minor fixes * Refactoring file help * Redundant string removal * Fixes * Sprk 295 (#51) * Creating parser for solver wrapper output * Change solver status from string to enum * Completed docstring * Merge dev into SPRK-295 --------- Co-authored-by: ngcp1 <[email protected]> * Remove the exclusive flag when running the portfolio selector (#52) * Moving CLI to a better place * Bug fix seed being none for solver * Bugfix run sparkle portfolio core * Bugfixes portfolio selector * Version 0.8.3 release (#53) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Version change * Small fixes --------- Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Release/0.8.3 (#55) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Version change * Small fixes * Bugfix test files --------- Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Release/0.8.3 (#57) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Version change * Small fixes * Bugfix test files * Release/0.8.3 (#54) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and run…

* Bugfixes for adding/removing extractors * Updating extractor to handle I/O better * Fixing feature computations to work with new wrapper set up * Fixing featuredataframe imports * Removing dead variables * Correcting settings * Updating manual * Bugfixes for how to compute remaining feature jobs * Added comment * wrapper fix * Bug fixes running selector on single instance * Deleting now unused file * Test fix * Unused code removal * Flake8 * Updating remaining jobs format * pytest fix * Removing unused code * Flake8 * bugfixes * Use extractor object in compute features core * Minor code fixes * Bugfixes regarding runsolver * recompute bugfix * Fixing up extractor wrapper * Fixing comments for featuredataframe * Bugfix for multi file instances * flake8 * Reanming file * bugfix running extractor * Test fix * Removing old configuration example * Replacing old config, deleting old validation test data * New validation example data * Test update * Adding satzilla2024 * Prepping SATZilla2024 example * Prepping Sparkle for new extractor * Moving compute features into the CLI command file * updating extractors * Updating example execution rights * adding description * Updating 2024 wrapper * missing executable * Don't use the last feature * chmod +x * Feature group preparation * Description update * Setting execution permissions * Adding feature mapping * Compilation update SATZilla2024 * Updating example * Execution rights * Fixing wrapper * Bugfixes feature imputation * bugfix get feature groups * Adding new instance set * Updating selection example * renaming instances new set * Bugfix runsolver output parsing * flake8 * minor fix * Update description_SAT-features-competition2024.txt * Adding main to avoid floating code * Fixing settings options without SMAC section * Removing dead code * Settings fix * minor fixes * Fixing last Solver object omission * Status info fix * Sprk 252 (#40) * Change documentation template * added theme to requirements * Fixed Index page of documentation * Included github action file * Test GitHub Actions * test v2 * test 3 * test 4 * test 5 (?) * test 6 * test7 * test 8 * test 9 * test 10 ? * another one * New approach * check * spelling? * this is getting sad * lesgo * wild test * Polishing * Deleted build files to try something out * Changed the workflow to run on push on main * small fixes * Sparkle wait now shows a table * Added output-verbosity to settings * sparkle wait now also shows partition * Restructering. Removed Extensive, rename REDUCED to QUIET, removed partition * Finished new wait command * Flake is killing me * Moved vreebosity from output to general (settings) * Added check interval to settings * Jobs are sorted based on status * Fixed flake8 * Added TEXT class and implemented in sparkle wait * Minor changes --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 283 (#42) * Print update * Refactoring * fixing comments * Bug fixes dataframes * first implementation design of selector OO * refactoring file * Refactoring sparkle to use selector OO solution * flake8 * Removing multiple file creating from perfect selector computation * refactoring copy operations out of marginal contribution * performance dataframe fixes * Changing references to Settings file * Forgot a few * Testing changing reference to gv.settings to settings * Refactoring usage of marginal contribution * flake8 * Updating test * bugfix * Fixing verbosity * Flake8 + pytest fixes * bugfix * pytest mock fixes * more usefull error printing selector * test fix * bugfixes * bugfixes * reordering tests * flake8 * new test files * Removing dead command * Removing dead test * New RunRunner version * Test fixes for new runrunner version * Showing new column based on runrunner update in sparkle wait * fix for pytest * Sprk 160 (#44) * Prepping tests to use all a different scenario file * Fixing tests to always use specific test set * Removing dead variables from global variables * Minor changes ablation * reducing git ignore * Removing logging from Platform (CLI functionality) * Removing non-CLI references to global variables, moving sparkle log * settings mistake * Creating init for CLI packages * Pre release test branch (#45) * Trying to move global variables * init fllake8 * flake8 * Moving tools to be part of Sparkle lib * Updating setup to not include the tests * renaming latex dir * Creating manifest, updating setup.py * flake8 * Moving Components into sparkle dir to prepare workable pip install * Update pull-request.yml (#49) * Update pull-request.yml * Update pull-request.yml * SPRK 151 (#46) * Flake8 pre-commit * Pre commit test * Disable test for pre commit * Updating change log and contributing * Reducing test files bloating * Settings mistake * Removing unused test files * Unused test files * Sprk 320 (#50) * Fixing bugs in Ablation * First class design, bug fixes, flake8 * Refactoring ablation object usage * fixing pytests * Moving ablation * Bug fixes for report generation * Bugfixes ablation, refactoring, fixing timezone on smac target algorithm * Adding example download capability to initialise command * Simplifying + comment for init * Updating changelog * Simplifying wait command * Minor variable name and comments fixes * Removing dead variables from global var * Fixes regarding portfolio selector methods * Renaming symbols * Minor refactoring * Minor refactoring * Refactoring method definitions * Bugfixes for initialise * Bugfix init * Removing excess test files * Moving CLI tests to tests folder * Removing unnecessary methods * Refactoring function definitions * Simplifying sat_help methods * sat verify bug fix * Old code reversal * Refactoring snapshit * snapshot bugfix * Logger typing fixes * Minor fixes * Refactoring file help * Redundant string removal * Fixes * Sprk 295 (#51) * Creating parser for solver wrapper output * Change solver status from string to enum * Completed docstring * Merge dev into SPRK-295 --------- Co-authored-by: ngcp1 <[email protected]> * Remove the exclusive flag when running the portfolio selector (#52) * Moving CLI to a better place * Bug fix seed being none for solver * Bugfix run sparkle portfolio core * Bugfixes portfolio selector * Version 0.8.3 release (#53) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Version change * Small fixes --------- Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Release/0.8.3 (#55) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Version change * Small fixes * Bugfix test files --------- Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Release/0.8.3 (#57) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Version change * Small fixes * Bugfix test files * Release/0.8.3 (#54) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument …

* minor fixes * Fixing last Solver object omission * Status info fix * Sprk 252 (#40) * Change documentation template * added theme to requirements * Fixed Index page of documentation * Included github action file * Test GitHub Actions * test v2 * test 3 * test 4 * test 5 (?) * test 6 * test7 * test 8 * test 9 * test 10 ? * another one * New approach * check * spelling? * this is getting sad * lesgo * wild test * Polishing * Deleted build files to try something out * Changed the workflow to run on push on main * small fixes * Sparkle wait now shows a table * Added output-verbosity to settings * sparkle wait now also shows partition * Restructering. Removed Extensive, rename REDUCED to QUIET, removed partition * Finished new wait command * Flake is killing me * Moved vreebosity from output to general (settings) * Added check interval to settings * Jobs are sorted based on status * Fixed flake8 * Added TEXT class and implemented in sparkle wait * Minor changes --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 283 (#42) * Print update * Refactoring * fixing comments * Bug fixes dataframes * first implementation design of selector OO * refactoring file * Refactoring sparkle to use selector OO solution * flake8 * Removing multiple file creating from perfect selector computation * refactoring copy operations out of marginal contribution * performance dataframe fixes * Changing references to Settings file * Forgot a few * Testing changing reference to gv.settings to settings * Refactoring usage of marginal contribution * flake8 * Updating test * bugfix * Fixing verbosity * Flake8 + pytest fixes * bugfix * pytest mock fixes * more usefull error printing selector * test fix * bugfixes * bugfixes * reordering tests * flake8 * new test files * Removing dead command * Removing dead test * New RunRunner version * Test fixes for new runrunner version * Showing new column based on runrunner update in sparkle wait * fix for pytest * Sprk 160 (#44) * Prepping tests to use all a different scenario file * Fixing tests to always use specific test set * Removing dead variables from global variables * Minor changes ablation * reducing git ignore * Removing logging from Platform (CLI functionality) * Removing non-CLI references to global variables, moving sparkle log * settings mistake * Creating init for CLI packages * Pre release test branch (#45) * Trying to move global variables * init fllake8 * flake8 * Moving tools to be part of Sparkle lib * Updating setup to not include the tests * renaming latex dir * Creating manifest, updating setup.py * flake8 * Moving Components into sparkle dir to prepare workable pip install * Update pull-request.yml (#49) * Update pull-request.yml * Update pull-request.yml * SPRK 151 (#46) * Flake8 pre-commit * Pre commit test * Disable test for pre commit * Updating change log and contributing * Reducing test files bloating * Settings mistake * Removing unused test files * Unused test files * Sprk 320 (#50) * Fixing bugs in Ablation * First class design, bug fixes, flake8 * Refactoring ablation object usage * fixing pytests * Moving ablation * Bug fixes for report generation * Bugfixes ablation, refactoring, fixing timezone on smac target algorithm * Adding example download capability to initialise command * Simplifying + comment for init * Updating changelog * Simplifying wait command * Minor variable name and comments fixes * Removing dead variables from global var * Fixes regarding portfolio selector methods * Renaming symbols * Minor refactoring * Minor refactoring * Refactoring method definitions * Bugfixes for initialise * Bugfix init * Removing excess test files * Moving CLI tests to tests folder * Removing unnecessary methods * Refactoring function definitions * Simplifying sat_help methods * sat verify bug fix * Old code reversal * Refactoring snapshit * snapshot bugfix * Logger typing fixes * Minor fixes * Refactoring file help * Redundant string removal * Fixes * Sprk 295 (#51) * Creating parser for solver wrapper output * Change solver status from string to enum * Completed docstring * Merge dev into SPRK-295 --------- Co-authored-by: ngcp1 <[email protected]> * Remove the exclusive flag when running the portfolio selector (#52) * Moving CLI to a better place * Bug fix seed being none for solver * Bugfix run sparkle portfolio core * Bugfixes portfolio selector * Version 0.8.3 release (#53) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Version change * Small fixes --------- Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Release/0.8.3 (#55) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Version change * Small fixes * Bugfix test files --------- Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Release/0.8.3 (#57) * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fixing execute permission on example * Release/0.8.2 (#30) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct parallel portfolio * flake8 * Adding in solver wrappers for solvers with outdated wrappers * Bugfixes * Big changes * wrapping up report refactoring * flake8 adapt * Clean up * Moving code to more logical place * flake8 * bugfix from refactor * minor refactor * flake8 fixes * Updating parallel portfolio arguments/settings * Renaming the command * bugfix * Moving arguments to argparse custom * Bugfix hadar * Removing dead variables * Refactoring variables pt 2 * Refactoring gv method * Bugfixes * Load snapshot bugfix * remove feature extractor bugfix * Minor bug fixes * flake8 * CLI pass through comments fix * Bug fixes * about test fix * About fix * Bugfix report generation * Forgotten print statement * Reverting refactoring * Updating CLI test * Fixing bug * Final bug fix for test * Removing dead files * Bugfixes remove instances CLI test * remove multi instances bugfix * CLI test fixes * Refactoring SMAC * Refactoring test bugs fix * Updating changelog * Bugfix wrapper, updating changelog, minor refactoring * Minor bug fix solver wrapper * Bug fix validator * Bug fixes in compute features / selection example * Removing useless print statement * flake8 fix * Removing dead variable * Adding file lock for selector writing to performance data csvs * flake8 * Report bugfixing * Bug fixes report * Changelog + bugfix * bugfix feature extractor removal --------- Co-authored-by: Hadar Shavit <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Koen van der Blom <[email protected]> Co-authored-by: Jeroen Rook <[email protected]> * Version change * Small fixes * Bugfix test files * Release/0.8.3 (#54) * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * SPRK-88 (#12) * Creating unified file for CLI arguments * Aggregate all CLI arguments into argparse_custom * Made CLI programs use centralised ArgumentContainers * Fixed SolverPathArgument * Sprk 76 (#7) * Added cpu_time & solver_calls to configuration budget (missing from run_ablation & get_smac_settings) * Fixed some flake8 and pytest errors * Refactor * Updating Runsolver and placing compilation responsibility in platform initialisation (#3) * Updating runsolver * Fixed runsolver make * Updating runsolver and gitignore structure for local compilation * Removing runsolver as part of Sparkle, must now be compiled by user * Fixing sparkle platform intialization with Runsolver compilation * Refactoring, flake8 * Fixes for instant compilation of runsolver (Conda install of required c packages and necessary path modding) --------- Co-authored-by: Thijs Snelleman <[email protected]> * Run workflow on on pull request (#6) * Update SWIG (#5) * Small flake8 fix * Small fixes * Small fixes * Sprk 270 (#8) * temp design check in * Flake8 fixes * Refactoring validator as preparation * Preparing configurator to use validator * Attempting fix for Github * pytest fix for gen rep * Pytest fix for validation scenario * Re-enabling pytest * Prepping for testing * Intermediate check in * Moving configurator implementations in settings * Bugfixes moving configurator * Setting up general configurator CLI * Fixing configurator writing output configurations from each run to a unified CSV * Validator and solver running fix * flake8 fix * Fixing command calls * Fixing settings * Fixing variable name in test * Continuing work on configurators, cleaning up Components directory * Removing unused files * Intermediate check in to check issue with runsolver * Found bug in smac target algorithm, was using the wrong runsolver output file to detect runtime. * Updating solver wrapper to be able to read configurations from file * Bugfixes SMAC wrappers * Reverting sparkle settings to original * Reverting slurm settings to original * Moving direcotries to unified output directory * Correcting file structure * Refactoring, flake8 * Wrapping up file organisation * Refactoring code to work with new implementation * Bug fixes * Fixing code for report generation * flake8 * Fixing solver input for validate after config to match amount of configurations * Attempted bug fix * Bugfix for ablation? * Bugfix ablation * Refactoring configure_solver_help content * Renaming to make a closer match to current contents * description rename * Fixing rename for imports * flake8 * pytest fixes * Fixing variables * pytest fix * Pytest fix * Pytest fix * pytest fixes * Fix * Pytest fix * removing dead code from test * Final fixes * bugfix * pytest fix * Removing smac references from global variables * Removing hard coded smacv2 references from Sparkle all together * PR changes * Minor fixes * flake8 * Minor fixes * Forgot to check in settings file * Bugfixes for ablation * Changed Default CPU value * Added alias to userguide & settings * small fix * corrected method name * Set solver_calls and cpu_time default to None * flake8 hates me --------- Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Split PerformanceMeasureArgument in two and remove current value information for certain CLI arguments * Wrap-up of restructuring argparse arguments * Actual implementation of SPRK-88 * Small fix to generate_report * Removing print statement, correcting my own mistakes for argsv * Formatting string without + operator --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Brian Schiller <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> Co-authored-by: Hadar Shavit <[email protected]> * Fix typo (#10) Minor change * bugfix in dev * SPRK-120 (#15) * Implementation of SPRK-120 * Change requests --------- Co-authored-by: Noah Peil <[email protected]> * Added .kwargs to argparse argument * Replaced * with ** for kwargs * Adding Aaron to contributors list * SPRK-128: Rename clips_per_node (#16) * Rename clis_per_node * Requests * Adding Aaron to contributors list --------- Co-authored-by: Noah Peil <[email protected]> Co-authored-by: Thijs Snelleman <[email protected]> * Fixing permissions * Fixing bug in remove solver, renaming global_variables symbol from sgh (sparkle_global_help) to gv (#14) * SPRK-55 (#13) * Fixes for removing instances from Sparkle through CLI * Intermediate check * ignoring runsolver file from compilation * Fixing all nicknames in commands for configuration * bugfix from different ticket * Refactoring and print improvement * Bugfix feature data frame * Refactoring useless/dead code * bug fix args branch * nickname support run sparkle portfolio selector * Nickname support for generate report * flake8 * Simplified extractor nicknaming code * Simplifying remove instances nickname * Simplifying remove solver * Refactoring * flake8 * Bugfix * sh test fix * Preventing the nickname handler from crashing when args are None * test fix --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 80 - [M] Add pcs validity and running check to wrappers (#17) * Add check argument * Merge duplicate check pcs functions * Add pcsparser * Start with running an instances to check if wrapper runs * Repo change * Do checks before adding. Change executable check return type * Merge and comment on wrong executable check * fixes * flake8 * enviroment fix * Changelog * PR comments fixes * Move messages from reading the pcs files to the cli part * Sprk 285 (#19) * Fixed check_settings_changes KeyError * Finishing SPRK-285 * Revert run_on option strings to lowercase again * Resolved flake8 issues --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 220 (#9) * Add option to set autofolio's timeout * fixup! Add option to set autofolio's timeout * Fix autofolio timeout * Minor fixes selection example * Updating docs for runsolver (#26) * Docs bugfix * Update about usage for docs * typo * trying to fix docs compilation * Bugfixes for docs gen * removing print statement * Updating requirements * Sprk 102 (#25) * Remove redundant code * Added default extractor wrapper * Modified Wrapper * Implemented new wrapper in add_feature_extractor * rewrote extractor wrapper code * Fixed flake8 mistakes * Some fixes (mostly path related) * Requested Changes * Updates * Few more changes * Removing dead imports * Implemented changes to extractor wrapper * Extractor now works * Removed print statements * Minor code layout changes * standardising * Wrapping up wrapper changes for extractors --------- Co-authored-by: Thijs Snelleman <[email protected]> * Improve status monitoring with logfile status (#28) * First implementation of monitoring with logfile status * Formatting and variable renaming * More formatting --------- Co-authored-by: Noah Peil <[email protected]> * Sprk 269 (#18) * refactor * Removing construct parallel portfolio from Sparkle * flake8 * Removing traces of construct…

thijssnelleman and others added 29 commits September 2, 2024 17:00

new distributable 0.8.5

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pypi releasable

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Merge branch 'main' into release/0.8.9

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Merge branch 'main' into release/0.8.9

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thijssnelleman merged commit ccf6a64 into development Sep 27, 2024
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Release/0.8.9 #96

Release/0.8.9 #96

thijssnelleman commented Sep 27, 2024

Release/0.8.9 #96

Release/0.8.9 #96

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thijssnelleman commented Sep 27, 2024