WIP changes to paper, plus some bug fixes #88
Workflow file for this run
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| name: CI Tests (Jupyter) | |
| on: | |
| push: | |
| paths-ignore: | |
| - 'paper/**' | |
| - '.gitattributes' | |
| - '.gitmodules' | |
| - 'CITATION.cff' | |
| - 'LICENSE' | |
| - 'README.md' | |
| pull_request: | |
| paths-ignore: | |
| - 'paper/**' | |
| - '.gitattributes' | |
| - '.gitmodules' | |
| - 'CITATION.cff' | |
| - 'LICENSE' | |
| - 'README.md' | |
| workflow_dispatch: | |
| inputs: | |
| debug_enabled: | |
| description: 'Pause before tests for tmate debugging' | |
| required: false | |
| default: 'false' | |
| defaults: | |
| run: | |
| shell: bash -leo pipefail {0} | |
| jobs: | |
| run-tests: | |
| name: "Run Jupyter CI tests (Python ${{ matrix.python-version }}, IPython ${{ matrix.ipython-version }})" | |
| runs-on: ubuntu-latest | |
| # only run on pull requests between forks to avoid duplicate runs with 'push' event | |
| if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| # for each Python version, test with earliest and latest supported IPython version | |
| - python-version: 3.6 | |
| ipython-version: 5.5.0 # earliest version supported by davos | |
| - python-version: 3.6 | |
| ipython-version: 7.16 # latest version to support Python 3.6 | |
| - python-version: 3.7 | |
| ipython-version: 5.5.0 # earliest version supported by davos | |
| - python-version: 3.7 | |
| ipython-version: 7.31 # latest version to support Python 3.7 | |
| - python-version: 3.8 | |
| ipython-version: 7.3.0 # earliest version to support Python 3.8 | |
| - python-version: 3.8 | |
| ipython-version: 8.12.2 # latest version to support Python 3.8 | |
| - python-version: 3.9 | |
| ipython-version: 7.15 # earliest version to support Python 3.9 | |
| - python-version: 3.9 | |
| ipython-version: latest | |
| - python-version: '3.10' | |
| ipython-version: 8.0 # earliest version to support Python 3.10 | |
| - python-version: '3.10' | |
| ipython-version: latest | |
| - python-version: 3.11 | |
| ipython-version: 8.8.0 # earliest version to support Python 3.11 | |
| - python-version: 3.11 | |
| ipython-version: latest | |
| env: | |
| HEAD_FORK: ${{ github.repository_owner }} | |
| HEAD_SHA: ${{ github.event_name == 'pull_request' && github.event.pull_request.head.sha || github.sha }} | |
| IPYTHON_VERSION: ${{ matrix.ipython-version }} | |
| # MAMBA_NO_BANNER: 1 | |
| NOTEBOOK_TYPE: jupyter | |
| PYTHON_VERSION: ${{ matrix.python-version }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| ref: ${{ env.HEAD_SHA }} | |
| - name: install miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| # miniforge-variant: Mambaforge | |
| # miniforge-version: 4.13.0-1 | |
| # use-mamba: true | |
| # channels: conda-forge,defaults | |
| # channel-priority: strict | |
| auto-activate-base: true | |
| activate-environment: "" | |
| - name: setup base environment | |
| run: | | |
| # install Python 3.9 (used to run notebooks via selenium, not the tests themselves) | |
| conda install python=3.9 | |
| # install Firefox browser: | |
| # - remove pre-installed snap package | |
| [[ -x "$(command -v snap)" ]] && sudo snap remove firefox | |
| # - add Mozilla PPA as a repository | |
| sudo add-apt-repository -y ppa:mozillateam/ppa | |
| # - alter Firefox package priority to prefer the deb package from the PPA | |
| echo ' | |
| Package: * | |
| Pin: release o=LP-PPA-mozillateam | |
| Pin-Priority: 1001 | |
| ' | sudo tee /etc/apt/preferences.d/mozilla-firefox | |
| # - install the proper version | |
| sudo apt install -y --allow-downgrades firefox | |
| # install python packages | |
| pip install notebook \ | |
| pytest==6.2 \ | |
| selenium==3.141 \ | |
| geckodriver-autoinstaller \ | |
| ipykernel==5.0.0 \ | |
| "jupyter_client<=7.3.2" \ | |
| "tornado<=6.1" \ | |
| "urllib3<2.0" | |
| # install geckodriver | |
| driver_path=$(python -c ' | |
| from pathlib import Path | |
| import geckodriver_autoinstaller | |
| driver_src = Path(geckodriver_autoinstaller.install(cwd=True)) | |
| driver_dest = driver_src.rename(driver_src.parents[1].joinpath(driver_src.name)) | |
| driver_src.parent.rmdir() | |
| print(driver_dest) | |
| ') | |
| # export path to driver as environment variable | |
| echo "DRIVER_PATH=$driver_path" >> $GITHUB_ENV | |
| - name: setup notebook kernel environment | |
| run: | | |
| # create & activate kernel environment | |
| conda create -n kernel-env python=$PYTHON_VERSION | |
| conda activate kernel-env | |
| # install davos & various test requirements in kernel environment | |
| [[ "$PYTHON_VERSION" =~ ^3.(6|7)$ ]] && pip install typing-extensions | |
| pip install "ipykernel==5.0.0" \ | |
| ipython-genutils \ | |
| requests \ | |
| fastdtw==0.3.4 \ | |
| tqdm==4.41.1 \ | |
| "numpy<=1.23.5" | |
| [[ "$PYTHON_VERSION" =~ ^3.11$ ]] && pip install scipy==1.11.1 || pip install "scipy<=1.7.3" | |
| if [[ "$IPYTHON_VERSION" == "latest" ]]; then | |
| pip install --upgrade IPython | |
| else | |
| pip install IPython==$IPYTHON_VERSION | |
| fi | |
| pip install . | |
| # make environment available as a jupyter kernel | |
| python -m ipykernel install --prefix=/usr/share/miniconda --name=kernel-env | |
| conda deactivate | |
| - name: record environment | |
| run: | | |
| { | |
| # get packages in base environment | |
| printf '=%.0s' {1..20}; printf ' base '; printf '=%.0s' {1..20}; printf '\n' | |
| conda env export -n base | |
| # get packages in kernel environment | |
| printf '=%.0s' {1..20}; printf ' kernel-env '; printf '=%.0s' {1..20}; printf '\n' | |
| conda env export -n kernel-env | |
| # get firefox browser & webdriver version | |
| printf '=%.0s' {1..20}; printf ' firefox '; printf '=%.0s' {1..20}; printf '\n' | |
| firefox --full-version | |
| $DRIVER_PATH --version | |
| # get jupyter kernels available in base environment | |
| printf '=%.0s' {1..20}; printf ' jupyter kernels '; printf '=%.0s' {1..20}; printf '\n' | |
| jupyter kernelspec list | |
| } > ${{ github.workspace }}/environment-info.txt | |
| cat ${{ github.workspace }}/environment-info.txt | |
| - name: launch Jupyter server | |
| run: jupyter notebook --no-browser --port=8888 --NotebookApp.token= & | |
| - name: debug runner | |
| if: | | |
| github.event_name == 'workflow_dispatch' | |
| && github.event.inputs.debug_enabled == 'true' | |
| uses: mxschmitt/action-tmate@v3 | |
| - name: run pytest | |
| id: run-pytest | |
| run: pytest -sv tests/ | |
| - name: upload artifacts on failure | |
| uses: actions/upload-artifact@v3 | |
| if: failure() | |
| with: | |
| name: artifacts-python${{ matrix.python-version }}-ipython${{ matrix.ipython-version }} | |
| path: | | |
| ${{ github.workspace }}/tests/*.ipynb | |
| ${{ github.workspace }}/environment-info.txt |