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all-tests.yml
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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 }}
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-13, 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 especial dependencies
shell: bash
run: |
changed_files="${{ steps.changed-files.outputs.all_changed_files }}"
python .github/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 extracotors
shell: bash
if: env.RUN_STREAMING_EXTRACTORS_TESTS
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]
./.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