Update imread/imwrite functionality and tests #2502
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| # Official DOc on GitHub Workflow Syntax: https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions | |
| # Conda based env testing: https://github.com/conda-incubator/setup-miniconda | |
| name: Run tests | |
| on: | |
| # Trigger the workflow on push but only for the master branch | |
| push: | |
| branches: | |
| - master | |
| # Trigger current workflow on PR from ANY branch | |
| pull_request: | |
| branches: | |
| - '**' | |
| # Cron based trigger | |
| schedule: | |
| # https://docs.github.com/en/free-pro-team@latest/actions/reference/workflow-syntax-for-github-actions#onschedule | |
| # i.e. this runs every day at 4:33AM for the master branch. | |
| - cron: '33 4 * * *' | |
| env: | |
| # Even when given -y, apt will still sometimes hang at a prompt if a package | |
| # has clarifications to ask; DEBIAN_FRONTEND=noninteractive prevents that, | |
| # This will be defined for non-debian platforms below too, but there's no harm in that. | |
| # (TravisCI quietly defined this on all their platforms, but we have to give it manually on GithubCI.) | |
| DEBIAN_FRONTEND: 'noninteractive' | |
| jobs: | |
| ultra_matrix_test: | |
| name: Matrix Test of Python ${{ matrix.python-version }} on ${{ matrix.os }} | |
| # Matrix driven OS | |
| runs-on: ${{ matrix.os }} | |
| # Default shell for ALL subsequent steps. | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| # Defining matrix for OS and Python | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ "ubuntu-latest", "macos-latest", "windows-latest"] | |
| python-version: [ ">=3.11" ] | |
| # Main steps for the test to be reproduced across OS x Python | |
| steps: | |
| # Step 0: Checkout code. | |
| - uses: actions/checkout@v2 | |
| # Step 1: List main repo by time modified, and print path | |
| - name: List all current repository files and modification date | |
| # Parameters. | |
| run: | | |
| ls -lasth | |
| pwd | |
| # Step 2: Install environment. | |
| - name: Install ADS from release branch (Unix) | |
| if: runner.os != 'Windows' | |
| run: ./install_ads -y | |
| - name: Install ADS from release branch (Windows) | |
| if: runner.os == 'Windows' | |
| shell: cmd | |
| run: install_ads.bat | |
| # Step 2a: Modify MKL_THREADING_LAYER (Ubuntu only) | |
| # See https://github.com/pytorch/pytorch/issues/37377#issuecomment-629530272 | |
| - name: Set MKL_THREADING_LAYER | |
| if: matrix.os == 'ubuntu-latest' | |
| run: | | |
| echo "MKL_THREADING_LAYER=GNU" >> $GITHUB_ENV | |
| # Step 2b: Add ADS to the PATH | |
| - name: Update environment variables | |
| # NB: I'm not sure what GHA's syntax is for cmd.exe, so we use bash just for this one change | |
| # In a user install, the user would perform this step using the Windows PATH-changing GUI. | |
| run: | | |
| if [ "$RUNNER_OS" == "Windows" ]; then | |
| echo "${GITHUB_WORKSPACE}" >> $ADS_DIR | |
| echo "${GITHUB_WORKSPACE}\bin" >> $GITHUB_PATH | |
| else | |
| # NB: install_ads edits ~/.bashrc, but those environment changes don't get passed to subsequent steps in GH Actions. | |
| # So, we filter through the .bashrc and pass the values to $GITHUB_ENV and $GITHUB_PATH. | |
| # Relevant documentation: https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#environment-files | |
| cat ~/.bashrc | grep "export ADS_DIR" | cut -d " " -f 2 >> $GITHUB_ENV | |
| cat ~/.bashrc | grep "export PATH" | grep -o "/.*" | cut -d ':' -f 1 >> $GITHUB_PATH | |
| fi | |
| # Step 3: Full PyTest | |
| - name: Test with pytest (Unix) | |
| if: runner.os != 'Windows' | |
| run: | | |
| source ads_conda/bin/activate ads_conda/envs/venv_ads | |
| pytest ./test/ -v --cov AxonDeepSeg/ --cov-report=lcov | |
| - name: Test with pytest (Windows) | |
| if: runner.os == 'Windows' | |
| shell: cmd | |
| run: | | |
| CALL ads_conda\Scripts\activate.bat ads_conda\envs\venv_ads | |
| pytest.exe ./test/ -v --cov AxonDeepSeg/ --cov-report=lcov | |
| # Step 4: Submnit to coveralls | |
| - name: Submit to coveralls | |
| uses: coverallsapp/github-action@v2 | |
| with: | |
| flag-name: ${matrix.os} | |
| parallel: true | |
| # This step is MANDATORY and used to indicate matrix completion to coveralls.io | |
| # See here: https://coveralls-python.readthedocs.io/en/latest/usage/configuration.html#github-actions-support | |
| finish: | |
| needs: ultra_matrix_test | |
| if: ${{ always() }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Coveralls Finished | |
| uses: coverallsapp/github-action@v2 | |
| with: | |
| github-token: ${{ secrets.github_token }} | |
| parallel-finished: true | |
| carryforward: "ubuntu-latest,macos-12,windows-latest" |