Merge branch 'main' into remove_extractor_name

.github/actions/install-wine/action.yml

@@ -2,20 +2,29 @@ name: Install packages
 description: This action installs the package and its dependencies for testing
 
 inputs:
-  python-version:
-    description: 'Python version to set up'
-    required: false
   os:
     description: 'Operating system to set up'
-    required: false
+    required: true
 
 runs:
   using: "composite"
   steps:
-    - name: Install wine (needed for Plexon2)
+    - name: Install wine on Linux
+      if: runner.os == 'Linux'
       run: |
         sudo rm -f /etc/apt/sources.list.d/microsoft-prod.list
         sudo dpkg --add-architecture i386
         sudo apt-get update -qq
         sudo apt-get install -yqq --allow-downgrades libc6:i386 libgcc-s1:i386 libstdc++6:i386 wine
       shell: bash
+    - name: Install wine on macOS
+      if: runner.os == 'macOS'
+      run: |
+        brew install --cask xquartz
+        brew install --cask wine-stable
+      shell: bash
+
+    - name: Skip installation on Windows
+      if: ${{ inputs.os == 'Windows' }}
+      run: echo "Skipping Wine installation on Windows. Not necessary."
+      shell: bash

.github/determine_testing_environment.py

@@ -0,0 +1,115 @@
+from pathlib import Path
+import argparse
+import os
+
+
+# We get the list of files change as an input
+parser = argparse.ArgumentParser()
+parser.add_argument("changed_files_in_the_pull_request", nargs="*", help="List of changed files")
+args = parser.parse_args()
+
+changed_files_in_the_pull_request = args.changed_files_in_the_pull_request
+changed_files_in_the_pull_request_paths = [Path(file) for file in changed_files_in_the_pull_request]
+
+# We assume nothing has been changed
+
+core_changed = False
+pyproject_toml_changed = False
+neobaseextractor_changed = False
+extractors_changed = False
+plexon2_changed = False
+preprocessing_changed = False
+postprocessing_changed = False
+qualitymetrics_changed = False
+sorters_changed = False
+sorters_external_changed = False
+sorters_internal_changed = False
+comparison_changed = False
+curation_changed = False
+widgets_changed = False
+exporters_changed = False
+sortingcomponents_changed = False
+generation_changed = False
+
+
+for changed_file in changed_files_in_the_pull_request_paths:
+
+    file_is_in_src = changed_file.parts[0] == "src"
+
+
+    if changed_file.name == "pyproject.toml":
+        pyproject_toml_changed = True
+    elif changed_file.name == "neobaseextractor.py":
+        neobaseextractor_changed = True
+    elif changed_file.name == "plexon2.py":
+        plexon2_changed = True
+    elif "core" in changed_file.parts:
+        core_changed = True
+    elif "extractors" in changed_file.parts:
+        extractors_changed = True
+    elif "preprocessing" in changed_file.parts:
+        preprocessing_changed = True
+    elif "postprocessing" in changed_file.parts:
+        postprocessing_changed = True
+    elif "qualitymetrics" in changed_file.parts:
+        qualitymetrics_changed = True
+    elif "comparison" in changed_file.parts:
+        comparison_changed = True
+    elif "curation" in changed_file.parts:
+        curation_changed = True
+    elif "widgets" in changed_file.parts:
+        widgets_changed = True
+    elif "exporters" in changed_file.parts:
+        exporters_changed = True
+    elif "sortingcomponents" in changed_file.parts:
+        sortingcomponents_changed = True
+    elif "generation" in changed_file.parts:
+        generation_changed = True
+    elif "sorters" in changed_file.parts:
+        if "external" in changed_file.parts:
+            sorters_external_changed = True
+        elif "internal" in changed_file.parts:
+            sorters_internal_changed = True
+        else:
+            sorters_changed = True
+
+
+run_everything = core_changed or pyproject_toml_changed or neobaseextractor_changed
+run_generation_tests = run_everything or generation_changed
+run_extractor_tests = run_everything or extractors_changed or plexon2_changed
+run_preprocessing_tests = run_everything or preprocessing_changed
+run_postprocessing_tests = run_everything or postprocessing_changed
+run_qualitymetrics_tests = run_everything or qualitymetrics_changed
+run_curation_tests = run_everything or curation_changed
+run_sortingcomponents_tests = run_everything or sortingcomponents_changed
+
+run_comparison_test = run_everything or run_generation_tests or comparison_changed
+run_widgets_test = run_everything or run_qualitymetrics_tests or run_preprocessing_tests or widgets_changed
+run_exporters_test = run_everything or run_widgets_test or exporters_changed
+
+run_sorters_test = run_everything or sorters_changed
+run_internal_sorters_test = run_everything or run_sortingcomponents_tests or sorters_internal_changed
+
+install_plexon_dependencies = plexon2_changed
+
+environment_varaiables_to_add = {
+    "RUN_EXTRACTORS_TESTS": run_extractor_tests,
+    "RUN_PREPROCESSING_TESTS": run_preprocessing_tests,
+    "RUN_POSTPROCESSING_TESTS": run_postprocessing_tests,
+    "RUN_QUALITYMETRICS_TESTS": run_qualitymetrics_tests,
+    "RUN_CURATION_TESTS": run_curation_tests,
+    "RUN_SORTINGCOMPONENTS_TESTS": run_sortingcomponents_tests,
+    "RUN_GENERATION_TESTS": run_generation_tests,
+    "RUN_COMPARISON_TESTS": run_comparison_test,
+    "RUN_WIDGETS_TESTS": run_widgets_test,
+    "RUN_EXPORTERS_TESTS": run_exporters_test,
+    "RUN_SORTERS_TESTS": run_sorters_test,
+    "RUN_INTERNAL_SORTERS_TESTS": run_internal_sorters_test,
+    "INSTALL_PLEXON_DEPENDENCIES": install_plexon_dependencies,
+}
+
+# Write the conditions to the GITHUB_ENV file
+env_file = os.getenv("GITHUB_ENV")
+with open(env_file, "a") as f:
+    for key, value in environment_varaiables_to_add.items():
+        f.write(f"{key}={value}\n")

.github/run_tests.sh

@@ -1,8 +1,13 @@
 #!/bin/bash
 
 MARKER=$1
+NOVIRTUALENV=$2
+
+# Check if the second argument is provided and if it is equal to --no-virtual-env
+if [ -z "$NOVIRTUALENV" ] || [ "$NOVIRTUALENV" != "--no-virtual-env" ]; then
+  source $GITHUB_WORKSPACE/test_env/bin/activate
+fi
 
-source $GITHUB_WORKSPACE/test_env/bin/activate
 pytest -m "$MARKER" -vv -ra --durations=0 --durations-min=0.001 | tee report.txt; test ${PIPESTATUS[0]} -eq 0 || exit 1
 echo "# Timing profile of ${MARKER}" >> $GITHUB_STEP_SUMMARY
 python $GITHUB_WORKSPACE/.github/build_job_summary.py report.txt >> $GITHUB_STEP_SUMMARY