From 09ff624817b53d30d35f1e4f9060edabab45a308 Mon Sep 17 00:00:00 2001 From: Alessio Buccino Date: Wed, 4 Dec 2024 10:33:40 +0100 Subject: [PATCH 1/4] Remove venv in full-tests-with-codecov --- .../actions/build-test-environment/action.yml | 36 +++++++------------ .github/workflows/all-tests.yml | 2 +- 2 files changed, 14 insertions(+), 24 deletions(-) diff --git a/.github/actions/build-test-environment/action.yml b/.github/actions/build-test-environment/action.yml index 723e8a702f..a212bd64d5 100644 --- a/.github/actions/build-test-environment/action.yml +++ b/.github/actions/build-test-environment/action.yml @@ -1,41 +1,20 @@ 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 - runs: using: "composite" steps: - name: Install dependencies run: | - sudo apt install git git config --global user.email "CI@example.com" git config --global user.name "CI Almighty" - python -m venv ${{ github.workspace }}/test_env # Environment used in the caching step - 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,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 spikeinterface; print(spikeinterface.DEV_MODE)") - if [ $spikeinterface_is_dev_version = "True" ]; then - echo "Running spikeinterface dev version" - pip install --no-cache-dir git+https://github.com/NeuralEnsemble/python-neo - pip install --no-cache-dir git+https://github.com/SpikeInterface/probeinterface - fi - echo "Running tests for release, using pyproject.toml versions of neo and probeinterface" + - name: Install git-annex shell: bash - - name: git-annex install run: | + pip install datalad-installer wget https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz mkdir /home/runner/work/installation mv git-annex-standalone-amd64.tar.gz /home/runner/work/installation/ @@ -44,4 +23,15 @@ runs: tar xvzf git-annex-standalone-amd64.tar.gz echo "$(pwd)/git-annex.linux" >> $GITHUB_PATH cd $workdir + git config --global filter.annex.process "git-annex filter-process" # recommended for efficiency + - 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 spikeinterface; print(spikeinterface.DEV_MODE)") + if [ $spikeinterface_is_dev_version = "True" ]; then + echo "Running spikeinterface dev version" + pip install --no-cache-dir git+https://github.com/NeuralEnsemble/python-neo + pip install --no-cache-dir git+https://github.com/SpikeInterface/probeinterface + fi + echo "Running tests for release, using pyproject.toml versions of neo and probeinterface" shell: bash diff --git a/.github/workflows/all-tests.yml b/.github/workflows/all-tests.yml index dcaec8b272..a9c840d5d5 100644 --- a/.github/workflows/all-tests.yml +++ b/.github/workflows/all-tests.yml @@ -47,7 +47,7 @@ jobs: echo "$file was changed" done - - name: Set testing environment # This decides which tests are run and whether to install especial dependencies + - 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 }}" From 8500b9d0f4488794dcc6d6b71afec2ebf4697b1d Mon Sep 17 00:00:00 2001 From: Alessio Buccino Date: Wed, 4 Dec 2024 10:48:11 +0100 Subject: [PATCH 2/4] Oups --- .github/actions/build-test-environment/action.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/actions/build-test-environment/action.yml b/.github/actions/build-test-environment/action.yml index a212bd64d5..c2524d2c16 100644 --- a/.github/actions/build-test-environment/action.yml +++ b/.github/actions/build-test-environment/action.yml @@ -26,7 +26,6 @@ runs: git config --global filter.annex.process "git-annex filter-process" # recommended for efficiency - 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 spikeinterface; print(spikeinterface.DEV_MODE)") if [ $spikeinterface_is_dev_version = "True" ]; then echo "Running spikeinterface dev version" From 922606b6d4d279da103b7e7edde3ecb79a76e3c8 Mon Sep 17 00:00:00 2001 From: Alessio Buccino Date: Wed, 4 Dec 2024 11:16:01 +0100 Subject: [PATCH 3/4] Oups 2 --- .github/workflows/full-test-with-codecov.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/full-test-with-codecov.yml b/.github/workflows/full-test-with-codecov.yml index 407c614ebf..f8ed2aa7a9 100644 --- a/.github/workflows/full-test-with-codecov.yml +++ b/.github/workflows/full-test-with-codecov.yml @@ -45,7 +45,6 @@ jobs: env: HDF5_PLUGIN_PATH: ${{ github.workspace }}/hdf5_plugin_path_maxwell run: | - source ${{ github.workspace }}/test_env/bin/activate pytest -m "not sorters_external" --cov=./ --cov-report xml:./coverage.xml -vv -ra --durations=0 | tee report_full.txt; test ${PIPESTATUS[0]} -eq 0 || exit 1 echo "# Timing profile of full tests" >> $GITHUB_STEP_SUMMARY python ./.github/scripts/build_job_summary.py report_full.txt >> $GITHUB_STEP_SUMMARY From 986a74a30c94a49ed2a2dd6183e8ddc078105b85 Mon Sep 17 00:00:00 2001 From: Alessio Buccino Date: Thu, 5 Dec 2024 09:02:31 +0100 Subject: [PATCH 4/4] Pin ONE-API version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index fc09ad9198..22fbdc7f22 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -73,7 +73,7 @@ extractors = [ ] streaming_extractors = [ - "ONE-api>=2.7.0", # alf sorter and streaming IBL + "ONE-api>=2.7.0,<2.10.0", # alf sorter and streaming IBL "ibllib>=2.36.0", # streaming IBL # Following dependencies are for streaming with nwb files "pynwb>=2.6.0",