Merge remote-tracking branch 'origin' into ibl_exporter

.github/actions/build-test-environment/action.yml

@@ -21,12 +21,12 @@ runs:
         python -m pip install -U pip  # Official recommended way
         source ${{ github.workspace }}/test_env/bin/activate
         pip install tabulate  # This produces summaries at the end
-        pip install -e .[test,extractors,streaming_extractors,full]
+        pip install -e .[test,extractors,streaming_extractors,test_extractors,full]
       shell: bash
     - name: Force installation of latest dev from key-packages when running dev (not release)
       run: |
         source ${{ github.workspace }}/test_env/bin/activate
-        spikeinterface_is_dev_version=$(python -c "import importlib.metadata; version = importlib.metadata.version('spikeinterface'); print(version.endswith('dev0'))")
+        spikeinterface_is_dev_version=$(python -c "import spikeinterface; print(spikeinterface.DEV_MODE)")
         if [ $spikeinterface_is_dev_version = "True" ]; then
           echo "Running spikeinterface dev version"
           pip install --no-cache-dir git+https://github.com/NeuralEnsemble/python-neo

.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/run_tests.sh

@@ -1,9 +1,14 @@
 #!/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
+python $GITHUB_WORKSPACE/.github/scripts/build_job_summary.py report.txt >> $GITHUB_STEP_SUMMARY
 rm report.txt

.github/scripts/README.MD

@@ -0,0 +1,2 @@
+This folder contains test scripts for running in the CI, that are not run as part of the usual
+CI because they are too long / heavy. These are run on cron-jobs once per week.

.github/scripts/check_kilosort4_releases.py

@@ -0,0 +1,30 @@
+import os
+import re
+from pathlib import Path
+import requests
+import json
+from packaging.version import parse
+import spikeinterface
+
+def get_pypi_versions(package_name):
+    """
+    Make an API call to pypi to retrieve all
+    available versions of the kilosort package.
+    """
+    url = f"https://pypi.org/pypi/{package_name}/json"
+    response = requests.get(url)
+    response.raise_for_status()
+    data = response.json()
+    versions = list(sorted(data["releases"].keys()))
+    # Filter out versions that are less than 4.0.16
+    versions = [ver for ver in versions if parse(ver) >= parse("4.0.16")]
+    return versions
+
+
+if __name__ == "__main__":
+    # Get all KS4 versions from pipi and write to file.
+    package_name = "kilosort"
+    versions = get_pypi_versions(package_name)
+    with open(Path(os.path.realpath(__file__)).parent / "kilosort4-latest-version.json", "w") as f:
+        print(versions)
+        json.dump(versions, f)

.github/scripts/determine_testing_environment.py

@@ -0,0 +1,129 @@
+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
+stream_extractors_changed = False
+github_actions_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
+        extractors_changed = True
+    elif changed_file.name == "plexon2.py":
+        plexon2_changed = True
+    elif changed_file.name == "nwbextractors.py":
+        extractors_changed = True  # There are NWB tests that are not streaming
+        stream_extractors_changed = True
+    elif changed_file.name == "iblextractors.py":
+        stream_extractors_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
+    elif ".github" in changed_file.parts:
+        if "workflows" in changed_file.parts:
+            github_actions_changed = True
+
+
+run_everything = core_changed or pyproject_toml_changed or neobaseextractor_changed or github_actions_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
+
+run_streaming_extractors_test = stream_extractors_changed or github_actions_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,
+    "RUN_STREAMING_EXTRACTORS_TESTS": run_streaming_extractors_test,
+}
+
+# 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/scripts/import_test.py

@@ -0,0 +1,72 @@
+import subprocess
+import math
+
+import_statement_list = [
+    "import spikeinterface",
+    "import spikeinterface.core",
+    "import spikeinterface.extractors",
+    "import spikeinterface.qualitymetrics",
+    "import spikeinterface.preprocessing",
+    "import spikeinterface.comparison",
+    "import spikeinterface.postprocessing",
+    "import spikeinterface.sortingcomponents",
+    "import spikeinterface.curation",
+    "import spikeinterface.exporters",
+    "import spikeinterface.widgets",
+    "import spikeinterface.full",
+]
+
+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) | 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"
+        )
+
+        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"
+            )
+            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 = 3.0  # 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 = 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 = 2.0
+        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))
+
+# This is displayed to GITHUB_STEP_SUMMARY
+print(markdown_output)

.github/scripts/kilosort4-latest-version.json

@@ -0,0 +1 @@
+["4.0.10", "4.0.11", "4.0.12", "4.0.5", "4.0.6", "4.0.7", "4.0.8", "4.0.9"]