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[REF] Decision Tree Modularization (#756)
* Decision tree refactor with minimal and kundu * Fix commented-out tedana workflow * Appease the style checker * All tremble before the mighty linter * Actually fix incorrect style checker issue * Unfix another style checker error * Attempt to make Black happy, even though it does not actually say what's wrong * ran black * Added elbows to reports * fixing kundu tree and added calc_median * kundu.json added comment * kundu kappa_elbow is GTE not GT * kundu dtm matches main and minimal updated * flake8 style fixes * fixed linting * fixed report elbow warning * removed unneeded second d_table calc function * Links building decision trees to index * Adds ComponentSelector to API docs * Set language to English * Fix dead nilearn link * Add load_config and ComponentSelector to API docs * Fix mixing matrix over-save bug * Separately modularized kappa & rho elbow calcs and created liberal rho elbow (#15) * kundu tree provisionalreject to unclassified * calc_rho_elbow progress * calc_rho_elbow done * Removed calc_varex_upper_p * Removed kappa_rho_elbow tests * both decision trees running * linting fixes * Enable tedana_reclassify as console script * No errors if no xcomp but also no decide_comps (#16) * Update tedana/io.py Co-authored-by: Taylor Salo <[email protected]> * Appease style checker * Appease the style checker? * Force to use up to date setuptools; installation bug otherwise * Remove out of date make entry * Create functional reclassify CLI * Replace blanks with n/a * Maybe appease black * Fix typo Co-authored-by: Eneko Uruñuela <[email protected]> * BIDSify some outputs * Appease black * Heavily revise ComponentSelector module docs * Fixing mid kappa A inconsistency (#17) * Output codes in kundu.json * fixed kappa ratio * Update tedana/selection/selection_nodes.py Co-authored-by: Joshua Teves <[email protected]> * minimal tree keep kappa>2rho Co-authored-by: Joshua Teves <[email protected]> * Drops 3.6 support * Remove 3.6 support from CircleCI tests * Reformat comment * Reduce line length * Update lint in Makefile * Correctly collect API submodule doc * Fix errors * Fix more sphinx * working on selector init documentation * Breaking up outputs.rst * partially updated output_file_descriptions.rst * changed n_bold_comps to n_accepted_comps * n_bold_comps to n_accepted_comps * ComponentSelector.py API docs cleaned up * selection_nodes decision_docs updated * selection_nodes docstrings cleaned up * Fixed a test for selection_nodes * Updated faq for tedana_reclassify and tree options * docstrings in tedica and other small updates * Updated docstrings in selection_utils.py * Update docs/output_file_descriptions.rst * Working on improving selector documentation (#18) * working on selector init documentation * Breaking up outputs.rst * partially updated output_file_descriptions.rst * changed n_bold_comps to n_accepted_comps * n_bold_comps to n_accepted_comps * ComponentSelector.py API docs cleaned up * selection_nodes decision_docs updated * selection_nodes docstrings cleaned up * Fixed a test for selection_nodes * Updated faq for tedana_reclassify and tree options * docstrings in tedica and other small updates * Updated docstrings in selection_utils.py * Update docs/output_file_descriptions.rst Co-authored-by: Joshua Teves <[email protected]> * Remove manual selection * Force user to pick a tree * Fix CLI test * Revert "Force user to pick a tree" This reverts commit 4fc656f. * Revert "Fix CLI test" This reverts commit 4038336. * Make kundu default tree * Attempt to fix error * Adds input data to registry * Revert "Adds input data to registry" This reverts commit c7349bd. * Adds input registration * Appease linter * Add class template start * Add previous workflow registry into new one * Fix failure to update tags and classifications in manual * Fix missing less likely BOOLD tag * Adds more useful reporting for unused metrics * Create generated metrics * Update line terminator * Force black to run before flake8 * Updates percentile call * more doc updates * fixed meica to v2.5 in docstrings * docs building again * more updates to building decision trees * improved docs (#19) * working on selector init documentation * Breaking up outputs.rst * partially updated output_file_descriptions.rst * changed n_bold_comps to n_accepted_comps * n_bold_comps to n_accepted_comps * ComponentSelector.py API docs cleaned up * selection_nodes decision_docs updated * selection_nodes docstrings cleaned up * Fixed a test for selection_nodes * Updated faq for tedana_reclassify and tree options * docstrings in tedica and other small updates * Updated docstrings in selection_utils.py * Update docs/output_file_descriptions.rst * more doc updates * fixed meica to v2.5 in docstrings * docs building again * more updates to building decision trees Co-authored-by: Joshua Teves <[email protected]> * Get rid of optional method keyword * Revert "Get rid of optional method keyword" This reverts commit e5fdec1. * Revert "Updates percentile call" This reverts commit 9d6a487. * Revert "Update line terminator" This reverts commit 8cf697c. * Autodocument ComponentSelector methods/attributes (#20) * Rename ComponentSelector module. * Document the ComponentSelector directly. * fixed rename of component_selector * Fixed remaining transition to component_selector (#21) * working on selector init documentation * Breaking up outputs.rst * partially updated output_file_descriptions.rst * changed n_bold_comps to n_accepted_comps * n_bold_comps to n_accepted_comps * ComponentSelector.py API docs cleaned up * selection_nodes decision_docs updated * selection_nodes docstrings cleaned up * Fixed a test for selection_nodes * Updated faq for tedana_reclassify and tree options * docstrings in tedica and other small updates * Updated docstrings in selection_utils.py * Update docs/output_file_descriptions.rst * more doc updates * fixed meica to v2.5 in docstrings * docs building again * more updates to building decision trees * fixed rename of component_selector Co-authored-by: Joshua Teves <[email protected]> * more doc updates * mostly classification_output_descriptions * Fixed io API and selector API warnings * message message * key parts of docs all updated * output_file_descriptions fully updated * filled testing gaps for component_selector * Updates integration test fnames * Try a numpy fix * Try again * Remove dead code * full selector coverage (#23) * Add tedana_reclassify tests * Actually add test to circle workflow * Maybe actually add it * Change o to outdir * Fix noreports maybe * Fix tedort * CircleCI are you okay? * Circle if you keep this up I will switch to Actions * Revert "Circle if you keep this up I will switch to Actions" This reverts commit ad29c0d. * Maybe silence duecredit and re-trigger Circle * Try something else * Guess that wasn't legal * Switch main to _main * Add to pyproject.toml * Force it to be editable * Add references to resources package * Dispose of sanity check * Add more reclassify tests * Adaptive mask is not a bool * Add label for setup.cfg * Revert "Adaptive mask is not a bool" This reverts commit f7db360. * Add resource files * Clarify variables * Update date and weep * Fixed NoLikelyBOLDBug (#24) * Fixed NoLikelyBOLDBug * Updated docs for Likely BOLD * Added note for when ICA will rerun * updated message * New verbose tag for more detailed logging. * at_least_num_exist to classification_doesnt_exist * Cleaned up selector logging output * fixed debug logging * Temporarily turn on force overwrite for redo ICA * Fixed I007 divergence * calc_varex_thresh now has num_highest_var_comps * fixed linting errors * Update integration test data * Adds csv and text file reading for manual acc/rej * Add tests for CustomEncoder * Adds bibtex warning check test * Appease linter * Fix unused metrics warning * Add reclassify tests and patches to test failures * Make stylistic changes. * Remove trailing whitespace. * Spacing in io. * More minor changes. * Add custom napoleon section "Generated Files" * Replace numTrue/numFalse with n_true/n_false. * Replace ifTrue/ifFalse with if_true/if_false. * Use fill_doc. * Style fixes. * more int32 * more int32 fun * Appease linter * Fixed style issues * Add RICA to Approach section of docs * Fixed CI style check failure * DTM documentation review (#30) * Standardization of usage descriptions * Minor grammar edits * Minor grammar/spelling edits * Update docs/faq.rst --------- * Rename reclassify force (#32) * changed tedana_reclassify and force * Added default messages to CLI workflows * clean up CLI default messages * added t2smap to function from CLI * style fix * Add defaults to --help output (#31) * added ica_reclassify to setup.cfg * Using a more persistent cache for the testing data (#33) * Cleans up how testing datasets are downloaded within test_integration.py. In Main & the current JT_DTM each dataset is downloaded in a slightly different way and the five-echo data are downloaded twice. * Added `data_for_testing_info` which gives the file hash location and local directory name for each of the four files we download. All tests are updated to use this function. * The local copy of testing data will now go into the `.testing_data_cache` subdirectory * The downloaded testing data will be in separate directories from the outputs so the downloaded directories can be completely static * When `download_test_data` is called, it will first download the metadata json to see if the last updated copy on osf.io is newer than the downloaded version and will only download if osf has a newer file. Downloading the metadata will happen frequently, but it will hopefully be fast. * The logger is now used to give a warning if osf.io cannot be accessed, but it will still run using cached data * Change to TestLGR.info * Fixing high variance classification mess (#34) * Added dec_reclassify_high_var_comps plus * clarified diff btwn rho_kundu and _liberal thresh * Clarified docs for minimal tree * Replace versioneer with hatch (#35) * Update gitignore. * Delete _version.py * Adopt new packaging. * Ignore the _version.py file. * Fix CI (#36) * Base the cache on pyproject.toml, not setup.cfg. * Also drop use of setup.py in publishing action. * Add flake8-pyproject as a requirement. (#37) * Try fixing coverage. (#38) * Improving ica_reclassify (#39) * ica_reclassify docs now rendering in usage.html * moves file parsing to ica_reclassify_workflow * added error checks and tests * Ica reclassify registry fixes (#42) * add pandas version check >= 1.5.2 and mod behavior (#938) * add version check and mod behavior if pandas >= 1.5.2 to prevent error in writing csv * formatting * adding P. Molfese --------- Co-authored-by: Molfese <[email protected]> * readded InputHarvester and expanduser * fixed handler base_dir path * mixing matrix file always in registry --------- Co-authored-by: Peter J. Molfese <[email protected]> Co-authored-by: Molfese <[email protected]> * Drop Python 3.6 and 3.7 support (#40) * Drop Python 3.6 and 3.7 support. * line_terminator --> lineterminator * added mixm to 4echo test (#43) * Updating Contributor Information (#41) * Some contributor updates * Added doc to Marco * Added flow charts and some text (#44) * Added flow charts and some text * Finished flow charts and text. Co-authored-by: marco7877 <[email protected]> --------- Co-authored-by: marco7877 <[email protected]> * RTDfix (#45) * Update documentation (#46) * Update docs. * Update docs/building_decision_trees.rst Co-authored-by: Dan Handwerker <[email protected]> --------- Co-authored-by: Dan Handwerker <[email protected]> * Output docs on one page (#47) * Output docs on one page * added new multi-echo lectures --------- Co-authored-by: Joshua Teves <[email protected]> Co-authored-by: handwerkerd <[email protected]> Co-authored-by: Taylor Salo <[email protected]> Co-authored-by: Eneko Uruñuela <[email protected]> Co-authored-by: handwerkerd <[email protected]> Co-authored-by: Taylor Salo <[email protected]> Co-authored-by: Eneko Uruñuela <[email protected]> Co-authored-by: Neha Reddy <[email protected]> Co-authored-by: Peter J. Molfese <[email protected]> Co-authored-by: Molfese <[email protected]> Co-authored-by: marco7877 <[email protected]> Co-authored-by: Taylor Salo <[email protected]>
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