Fix codecov tests #1845
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name: Complete tests | |
on: | |
workflow_dispatch: | |
schedule: | |
- cron: "0 12 * * 0" # Weekly on Sunday at noon UTC | |
pull_request: | |
types: [synchronize, opened, reopened] | |
branches: | |
- main | |
env: | |
KACHERY_CLOUD_CLIENT_ID: ${{ secrets.KACHERY_CLOUD_CLIENT_ID }} | |
KACHERY_CLOUD_PRIVATE_KEY: ${{ secrets.KACHERY_CLOUD_PRIVATE_KEY }} | |
KACHERY_ZONE: ${{ secrets.KACHERY_ZONE }} | |
concurrency: # Cancel previous workflows on the same pull request | |
group: ${{ github.workflow }}-${{ github.ref }} | |
cancel-in-progress: true | |
jobs: | |
run: | |
name: ${{ matrix.os }} Python ${{ matrix.python-version }} | |
runs-on: ${{ matrix.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
python-version: ["3.9", "3.12"] # Lower and higher versions we support | |
os: [macos-latest, windows-latest, ubuntu-latest] | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Setup Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Get changed files | |
id: changed-files | |
uses: tj-actions/changed-files@v41 | |
- name: List all changed files | |
shell: bash | |
env: | |
ALL_CHANGED_FILES: ${{ steps.changed-files.outputs.all_changed_files }} | |
run: | | |
for file in ${ALL_CHANGED_FILES}; do | |
echo "$file was changed" | |
done | |
- name: Set testing environment # This decides which tests are run and whether to install special dependencies | |
shell: bash | |
run: | | |
changed_files="${{ steps.changed-files.outputs.all_changed_files }}" | |
python .github/scripts/determine_testing_environment.py $changed_files | |
- name: Display testing environment | |
shell: bash | |
run: | | |
echo "RUN_EXTRACTORS_TESTS=${RUN_EXTRACTORS_TESTS}" | |
echo "RUN_PREPROCESSING_TESTS=${RUN_PREPROCESSING_TESTS}" | |
echo "RUN_POSTPROCESSING_TESTS=${RUN_POSTPROCESSING_TESTS}" | |
echo "RUN_QUALITYMETRICS_TESTS=${RUN_QUALITYMETRICS_TESTS}" | |
echo "RUN_CURATION_TESTS=${RUN_CURATION_TESTS}" | |
echo "RUN_SORTINGCOMPONENTS_TESTS=${RUN_SORTINGCOMPONENTS_TESTS}" | |
echo "RUN_GENERATION_TESTS=${RUN_GENERATION_TESTS}" | |
echo "RUN_COMPARISON_TESTS=${RUN_COMPARISON_TESTS}" | |
echo "RUN_WIDGETS_TESTS=${RUN_WIDGETS_TESTS}" | |
echo "RUN_EXPORTERS_TESTS=${RUN_EXPORTERS_TESTS}" | |
echo "RUN_SORTERS_TESTS=${RUN_SORTERS_TESTS}" | |
echo "RUN_INTERNAL_SORTERS_TESTS=${RUN_INTERNAL_SORTERS_TESTS}" | |
echo "INSTALL_PLEXON_DEPENDENCIES=${INSTALL_PLEXON_DEPENDENCIES}" | |
echo "RUN_STREAMING_EXTRACTORS_TESTS=${RUN_STREAMING_EXTRACTORS_TESTS}" | |
- name: Install packages | |
run: | | |
pip install -e .[test_core] | |
shell: bash | |
- name: Test core | |
run: pytest -m "core" | |
shell: bash | |
- name: Install Dependencies for Timing Display | |
run: | | |
pip install tabulate | |
pip install pandas | |
shell: bash | |
- name: Get current hash (SHA) of the ephy_testing_data repo | |
shell: bash | |
id: repo_hash | |
run: echo "dataset_hash=$(git ls-remote https://gin.g-node.org/NeuralEnsemble/ephy_testing_data.git HEAD | cut -f1)" >> $GITHUB_OUTPUT | |
- name: Cache datasets | |
if: env.RUN_EXTRACTORS_TESTS == 'true' | |
id: cache-datasets | |
uses: actions/cache/restore@v4 | |
with: | |
path: ~/spikeinterface_datasets | |
key: ${{ runner.os }}-datasets-${{ steps.repo_hash.outputs.dataset_hash }} | |
restore-keys: ${{ runner.os }}-datasets | |
- name: Install git-annex | |
shell: bash | |
if: env.RUN_EXTRACTORS_TESTS == 'true' | |
run: | | |
pip install datalad-installer | |
if [ ${{ runner.os }} = 'Linux' ]; then | |
wget https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz | |
mkdir /home/runner/work/installation | |
mv git-annex-standalone-amd64.tar.gz /home/runner/work/installation/ | |
workdir=$(pwd) | |
cd /home/runner/work/installation | |
tar xvzf git-annex-standalone-amd64.tar.gz | |
echo "$(pwd)/git-annex.linux" >> $GITHUB_PATH | |
cd $workdir | |
elif [ ${{ runner.os }} = 'macOS' ]; then | |
datalad-installer --sudo ok git-annex --method brew | |
elif [ ${{ runner.os }} = 'Windows' ]; then | |
datalad-installer --sudo ok git-annex --method datalad/git-annex:release | |
fi | |
git config --global filter.annex.process "git-annex filter-process" # recommended for efficiency | |
- name : Install Plexon dependencies | |
if: env.INSTALL_PLEXON_DEPENDENCIES == 'true' | |
uses: ./.github/actions/install-wine | |
- name: Set execute permissions on run_tests.sh | |
shell: bash | |
run: chmod +x .github/run_tests.sh | |
- name: Test extractors | |
shell: bash | |
env: | |
HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_plugin_path_maxwell | |
if: env.RUN_EXTRACTORS_TESTS == 'true' | |
run: | | |
pip install -e .[extractors,streaming_extractors,test_extractors] | |
./.github/run_tests.sh "extractors and not streaming_extractors" --no-virtual-env | |
- name: Test streaming extractors | |
shell: bash | |
if: env.RUN_STREAMING_EXTRACTORS_TESTS == 'true' | |
run: | | |
pip install -e .[streaming_extractors,test_extractors] | |
./.github/run_tests.sh "streaming_extractors" --no-virtual-env | |
- name: Test preprocessing | |
shell: bash | |
if: env.RUN_PREPROCESSING_TESTS == 'true' | |
run: | | |
pip install -e .[preprocessing,test_preprocessing] | |
./.github/run_tests.sh "preprocessing and not deepinterpolation" --no-virtual-env | |
- name: Install remaining testing dependencies # TODO: Remove this step once we have better modularization | |
shell: bash | |
run: | | |
pip install -e .[test] | |
- name: Test postprocessing | |
shell: bash | |
if: env.RUN_POSTPROCESSING_TESTS == 'true' | |
run: | | |
pip install -e .[full] | |
./.github/run_tests.sh postprocessing --no-virtual-env | |
- name: Test quality metrics | |
shell: bash | |
if: env.RUN_QUALITYMETRICS_TESTS == 'true' | |
run: | | |
pip install -e .[qualitymetrics] | |
./.github/run_tests.sh qualitymetrics --no-virtual-env | |
- name: Test comparison | |
shell: bash | |
if: env.RUN_COMPARISON_TESTS == 'true' | |
run: | | |
pip install -e .[full] | |
./.github/run_tests.sh comparison --no-virtual-env | |
- name: Test core sorters | |
shell: bash | |
if: env.RUN_SORTERS_TESTS == 'true' | |
run: | | |
pip install -e .[full] | |
./.github/run_tests.sh sorters --no-virtual-env | |
- name: Test internal sorters | |
shell: bash | |
if: env.RUN_INTERNAL_SORTERS_TESTS == 'true' | |
run: | | |
pip install -e .[full] | |
./.github/run_tests.sh sorters_internal --no-virtual-env | |
- name: Test curation | |
shell: bash | |
if: env.RUN_CURATION_TESTS == 'true' | |
run: | | |
pip install -e .[full] | |
./.github/run_tests.sh curation --no-virtual-env | |
- name: Test widgets | |
shell: bash | |
if: env.RUN_WIDGETS_TESTS == 'true' | |
run: | | |
pip install -e .[full,widgets] | |
./.github/run_tests.sh widgets --no-virtual-env | |
- name: Test exporters | |
shell: bash | |
if: env.RUN_EXPORTERS_TESTS == 'true' | |
run: | | |
pip install -e .[full] | |
./.github/run_tests.sh exporters --no-virtual-env | |
- name: Test sortingcomponents | |
shell: bash | |
if: env.RUN_SORTINGCOMPONENTS_TESTS == 'true' | |
run: | | |
pip install -e .[full] | |
./.github/run_tests.sh sortingcomponents --no-virtual-env | |
- name: Test generation | |
shell: bash | |
if: env.RUN_GENERATION_TESTS == 'true' | |
run: | | |
pip install -e .[full] | |
./.github/run_tests.sh generation --no-virtual-env |