Release/0.8.9

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,38 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: "[BUG]"
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is. What were you trying to accomplish?
+
+**To Reproduce**
+What is the result you get? Explain step wise a minimal reproducible example e.g.:
+*Please include your sparkle_settings.ini file here*
+
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem. If the output is text *please do not make screen shots but paste it instead*
+
+**Computed on**
+ - Specify your Linux setup
+ - Running with Slurm?
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here, such as:
+- The Solver wrapper script for your algorithm
+- An link to your data set, or, if impossible, a description of your data set and preferably a dummy version for reproduction
+- A copy of your `Output/Logs/` directory

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,21 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: "[FEATURE]"
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen. Please give an example of sequence of Sparkle commands you'd hypothetically like to execute to get to your solution.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.
+- If specific software packages / libraries should be used specify it by placing an URL to it in your request. Also specify what kind of requirements the package would have (e.g. "Only runs on the latest version of Java" or "C++ code needs to be compiled on target system")

.github/ISSUE_TEMPLATE/issue-report.md

@@ -0,0 +1,14 @@
+---
+name: Issue report
+about: General issues regarding the Sparke project
+title: "[ISSUE]"
+labels: issue
+assignees: ''
+
+---
+
+**Description**
+Give a general description of your problem. *If you're having issues with running Sparkle's code, consider submitting a BUG report instead*. Don't forget to introduce your context of the situation.
+
+- Please add visuals to your issue description if possible, such as screenshots or drawings
+- Please add a description of what you would consider to be a good solution to the problem, no matter how 'hypothetical' it may be.

.github/workflows/documentation.yml

@@ -1,5 +1,5 @@
 # Simple workflow for deploying static content to GitHub Pages
-name: Deploy static content to Pages
+name: Deploy Documentation
 
 on: # Runs on pushes targeting the default branch
   push:
@@ -39,10 +39,11 @@ jobs:
         run: |
           conda install -y python=3.9 # https://github.com/conda/conda/issues/13560#issuecomment-1992720842
           conda env update --file dev-env.yml --name base
-          pip install sphinx sphinx_rtd_theme myst_parser sphinxcontrib-autoprogram
-      - name: Compile code reports
-        run: pytest --all --cov sparkle/ --cov-report=html:Documentation/source/_static/coverage
-             pytest --all --html=Documentation/source/_static/junit/index.html
+          pip install -r Documentation/requirements.txt
+      - name: Run Code Coverage report
+        run:  pytest --all --cov sparkle/ --cov-report=html:Documentation/source/_static/coverage
+      - name: Run tests report
+        run: pytest --all --html=Documentation/source/_static/junit/index.html
       - name: Build Documentation
         run: |
           cd Documentation
@@ -55,4 +56,4 @@ jobs:
           path: 'Documentation/build/html'
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v4
+        uses: actions/deploy-pages@v4

CHANGELOG.md

@@ -2,7 +2,8 @@
 
 Notable changes to Sparkle will be documented in this file.
 
-## [0.8.9] - 2024/??/??
+## [0.8.9] - 2024/09/27
+- Various updates to Documentation, automated testing and CI pipelines
 
 ### Fixed
 - Bugfix for generating figures in report generation for 'configuration_quality' tutorial

CONTRIBUTING.md

@@ -90,7 +90,7 @@ When releasing a new version (including bugfix versions) of Sparkle to the `main
 2. Update and commit `CHANGELOG.md` by creating a header with the release number and date; move everything from the `[unreleased]` header to the new release header (leaving the `[unreleased]` header empty for the next release).
 3. Update and commit `sparkle/about.py` by changing the version number.
 4. If there were updates to the CLI and/or the examples.md, make sure to re-compile their files for the Documentation. Run `md_to_sh.py` in the Documentation directory to compile the example .mds to executable .sh files, and run `command_descriptions.py` to automatically re-create the documentation for the CLI commands and their arguments. Run `mod_descriptions.py` to update the package descriptions. The documentation itself is after release automatically compiled and deployed to github pages.
-4. Create the compiled zip for PyPi by running `python setup.py sdist bdist_wheel`. Delete build directory and the wheel file, and commit it.
+4. Create the compiled zip for PyPi by running `python setup.py sdist` and commit it.
 5. Merge the new version branch into both `development` and `main`, DO NOT delete the version branch!
 6. Upload the zip to PyPi with `twine upload $ZIPFILE_PATH`
 

Examples/configuration_quality.sh

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
-# Auto-Generated .sh files from the original .md by Sparkle 0.8.8
+# Auto-Generated .sh files from the original .md by Sparkle 0.8.4
 
 ## Algorithm Quality Configuration
-# We can configure an algorithm too based on some quality objective, that can be defined by the user. To see all options for defining {ref}`SparkleObjective <sparkle-objective>`
+# We can configure an algorithm too based on some quality objective, that can be defined by the user. See the {ref}`SparkleObjective <sparkle-objective>` page for all options regarding objective defintions.
 # These steps can also be found as a Bash script in `Examples/configuration_qualty.sh`
 
 ### Initialise the Sparkle platform
@@ -11,20 +11,20 @@ sparkle initialise
 
 ### Add instances
 
-# Add train, and optionally test, instances (in this case for the VRP) in a given directory, without running solvers or feature extractors yet
+# Now we add train, and optionally test, instances for configuring our algorithm (in this case for the VRP). The instance sets are placed in a given directory.
 
 sparkle add_instances Examples/Resources/CVRP/Instances/X-1-10/
 sparkle add_instances Examples/Resources/CVRP/Instances/X-11-20/
 
 ### Add a configurable solver
 
-# Add a configurable solver (here for vehicle routing) with a wrapper containing the executable name of the solver and a string of command line parameters, without running the solver yet
+# Add a configurable solver (In this tutorial its an algorithm for vehicle routing) with a wrapper containing the executable name of the solver and a string of command line parameters.
 
-# The solver directory should contain the solver executable, the `sparkle_solver_wrapper.py` wrapper, and a `.pcs` file describing the configurable parameters
+# The solver directory should contain the `sparkle_solver_wrapper.py` wrapper, and a `.pcs` file describing the configurable parameters.
 
 sparkle add_solver Examples/Resources/CVRP/Solvers/VRP_SISRs/
 
-# If needed solvers can also include additional files or scripts in their directory, but keeping additional files to a minimum speeds up copying.
+# In this case the source directory also contains an executable, as the algorithm has been compiled from another programming language (`C++`). If needed solvers can also include additional files or scripts in their directory, but keeping additional files to a minimum speeds up copying.
 
 ### Configure the solver
 

Examples/configuration_randomforest.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Auto-Generated .sh files from the original .md by Sparkle 0.8.8
+# Auto-Generated .sh files from the original .md by Sparkle 0.8.4
 
 ## Configuring Random Forest on Iris
 

Examples/configuration_runtime.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Auto-Generated .sh files from the original .md by Sparkle 0.8.8
+# Auto-Generated .sh files from the original .md by Sparkle 0.8.4
 
 ## Algorithm Runtime Configuration
 

Examples/parallel_portfolio_runtime.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Auto-Generated .sh files from the original .md by Sparkle 0.8.8
+# Auto-Generated .sh files from the original .md by Sparkle 0.8.4
 
 ## Running a Parallel Portfolio
 # In this tutorial we will measure the runtime performance of several algorithms in parallel. The general idea is that we consider the algorithms as a portfolio that we run in parallel (hence the name) and terminate all running algorithms once a solution is found.

Examples/selection.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Auto-Generated .sh files from the original .md by Sparkle 0.8.8
+# Auto-Generated .sh files from the original .md by Sparkle 0.8.4
 
 ## Algorithm Selection
 

Examples/selection_multi-file_instance.sh

@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-# Auto-Generated .sh files from the original .md by Sparkle 0.8.8
+# Auto-Generated .sh files from the original .md by Sparkle 0.8.4
 
 ## Algorithm selection with multi-file instances
 

README.md

@@ -1,8 +1,8 @@
 # _Sparkle_
 
-[![Tests](.reports/junit/junit-badge.svg)](.reports/junit/junit.html)
+[![Tests](.reports/junit/junit-badge.svg)](https://ada-research.github.io/Sparkle/_static/junit/index.html)
 ![tests status](https://github.com/ada-research/sparkle/actions/workflows/unittest.yml/badge.svg?event=push)
-[![Coverage Status](.reports/coverage/coverage-badge.svg)](.reports/coverage/class_index.html)
+[![Coverage Status](.reports/coverage/coverage-badge.svg)](https://ada-research.github.io/Sparkle/_static/coverage/index.html)
 ![linter](https://github.com/ada-research/sparkle/actions/workflows/linter.yml/badge.svg?event=push)
 ![docs](https://github.com/ada-research/sparkle/actions/workflows/documentation.yml/badge.svg?event=push)
 

sparkle/about.py

@@ -1,7 +1,7 @@
 """Helper module for information about Sparkle."""
 
 name = "Sparkle"
-version = "0.8.8"
+version = "0.8.9"
 description = "Platform for evaluating empirical algorithms/solvers"
 licence = "MIT"
 authors = ["Koen van der Blom",

tests/test_abalation.py

@@ -0,0 +1,45 @@
+"""Test ablation scenario class."""
+
+
+def test_ablation_scenario_constructor() -> None:
+    """Test for ablation scenario constructor."""
+    # TODO: Write test
+    pass
+
+
+def test_create_configuration_file() -> None:
+    """Test for method create_configuration_file."""
+    # TODO: Write test, check that written contents match with expected value
+    pass
+
+
+def test_create_instance_file() -> None:
+    """Test for method create_instance_file."""
+    # TODO: Write test for with training set
+    # TODO: Write test for with test set
+    pass
+
+
+def test_check_for_ablation() -> None:
+    """Test for method check_for_ablation."""
+    # TODO: Write test for when correct file exists
+    # TODO: Write test for when file does not exist
+    # TODO: Write test for when file is corrupted
+    pass
+
+
+def test_read_ablation_table() -> None:
+    """Test for reading an ablation table from file."""
+    # TODO: Write test for correct file
+
+    # TODO: Write test for not existant file
+
+    # TODO: Write test for partially corrupted file
+    pass
+
+
+def test_submit_ablation() -> None:
+    """Test for method submit ablation."""
+    # NOTE: RunRunner calls must be mocked to avoid slurm job submission
+    # TODO: Write test
+    pass

tests/test_extractor.py

@@ -0,0 +1,49 @@
+"""Test files for Extractor class."""
+
+
+def test_extractor_constructor() -> None:
+    """Test for constructor."""
+    # TODO: Write test
+    pass
+
+
+def test_features() -> None:
+    """Test for property features."""
+    # TODO: Write test
+    pass
+
+
+def test_feature_groups() -> None:
+    """Test for property feature_groups."""
+    # TODO: Write test
+    pass
+
+
+def test_output_dimension() -> None:
+    """Test for property output_dimension."""
+    # TODO: Write test
+    pass
+
+
+def test_groupwise_computation() -> None:
+    """Test for property groupwise_computation."""
+    # TODO: Write test
+    pass
+
+
+def test_build_cmd() -> None:
+    """Test for method build_cmd."""
+    # TODO: Write test
+    pass
+
+
+def test_run() -> None:
+    """Test for method run."""
+    # TODO: Write test
+    pass
+
+
+def test_get_feature_vector() -> None:
+    """Test for method get_feature_vector."""
+    # TODO: Write test
+    pass