Merge branch 'main' into add-tests-for-qm-structure

.github/determine_testing_environment.py

@@ -0,0 +1,118 @@
+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 not file_is_in_src:
+
+        if changed_file.name == "pyproject.toml":
+            pyproject_toml_changed = True
+
+    else:
+        if changed_file.name == "neobaseextractor.py":
+            neobaseextractor_changed = True
+        elif changed_file.name == "plexon2.py":
+            extractors_changed = True
+        elif "core" in changed_file.parts:
+            conditions_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
+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/import_test.py

@@ -18,37 +18,52 @@
 
 n_samples = 10
 # Note that the symbols at the end are for centering the table
-markdown_output = f"## \n\n| Imported Module ({n_samples=}) | Importing Time (seconds) | Standard Deviation (seconds) |\n| :--: | :--------------: | :------------------: |\n"
+markdown_output = f"## \n\n| Imported Module ({n_samples=}) | Importing Time (seconds) | Standard Deviation (seconds) | Times List (seconds) |\n| :--: | :--------------: | :------------------: | :-------------: |\n"
 
 exceptions = []
 
 for import_statement in import_statement_list:
     time_taken_list = []
     for _ in range(n_samples):
         script_to_execute = (
-                f"import timeit \n"
-                f"import_statement = '{import_statement}' \n"
-                f"time_taken = timeit.timeit(import_statement, number=1) \n"
-                f"print(time_taken) \n"
-               )
+            f"import timeit \n"
+            f"import_statement = '{import_statement}' \n"
+            f"time_taken = timeit.timeit(import_statement, number=1) \n"
+            f"print(time_taken) \n"
+        )
 
         result = subprocess.run(["python", "-c", script_to_execute], capture_output=True, text=True)
 
         if result.returncode != 0:
-            error_message  = (
-                f"Error when running {import_statement} \n"
-                f"Error in subprocess: {result.stderr.strip()}\n"
+            error_message = (
+                f"Error when running {import_statement} \n" f"Error in subprocess: {result.stderr.strip()}\n"
             )
             exceptions.append(error_message)
             break
 
         time_taken = float(result.stdout.strip())
         time_taken_list.append(time_taken)
 
+    for time in time_taken_list:
+        import_time_threshold = 2.0  # Most of the times is sub-second but there outliers
+        if time >= import_time_threshold:
+            exceptions.append(
+                f"Importing {import_statement} took: {time:.2f} s. Should be <: {import_time_threshold} s."
+            )
+            break
+
+
     if time_taken_list:
-        avg_time_taken = sum(time_taken_list) / len(time_taken_list)
-        std_dev_time_taken = math.sqrt(sum((x - avg_time_taken) ** 2 for x in time_taken_list) / len(time_taken_list))
-        markdown_output += f"| `{import_statement}` | {avg_time_taken:.2f} | {std_dev_time_taken:.2f} |\n"
+        avg_time = sum(time_taken_list) / len(time_taken_list)
+        std_time = math.sqrt(sum((x - avg_time) ** 2 for x in time_taken_list) / len(time_taken_list))
+        times_list_str = ", ".join(f"{time:.2f}" for time in time_taken_list)
+        markdown_output += f"| `{import_statement}` | {avg_time:.2f} | {std_time:.2f} | {times_list_str} |\n"
+
+        import_time_threshold = 1.0
+        if avg_time > import_time_threshold:
+            exceptions.append(
+                f"Importing {import_statement} took: {avg_time:.2f} s in average. Should be <: {import_time_threshold} s."
+            )
 
 if exceptions:
     raise Exception("\n".join(exceptions))

.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