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Merge pull request #11 from catalystneuro/basic_spec
Initial setup
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| name: Codespell | ||
| on: | ||
| pull_request: | ||
| workflow_dispatch: | ||
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| jobs: | ||
| codespell: | ||
| name: Check for spelling errors | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Checkout | ||
| uses: actions/checkout@v3 | ||
| - name: Codespell | ||
| uses: codespell-project/actions-codespell@v2 |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,183 @@ | ||
| name: Run all tests | ||
| on: | ||
| pull_request: | ||
| schedule: | ||
| - cron: '0 5 * * 0' # once every Sunday at midnight ET | ||
| workflow_dispatch: | ||
|
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| jobs: | ||
| run-all-tests: | ||
| name: ${{ matrix.name }} | ||
| runs-on: ${{ matrix.os }} | ||
| defaults: | ||
| run: | ||
| shell: bash | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| include: | ||
| - { name: linux-python3.8-minimum , requirements: minimum , python-ver: "3.8" , os: ubuntu-latest } | ||
| - { name: linux-python3.8 , requirements: pinned , python-ver: "3.8" , os: ubuntu-latest } | ||
| - { name: linux-python3.9 , requirements: pinned , python-ver: "3.9" , os: ubuntu-latest } | ||
| - { name: linux-python3.10 , requirements: pinned , python-ver: "3.10", os: ubuntu-latest } | ||
| - { name: linux-python3.11 , requirements: pinned , python-ver: "3.11", os: ubuntu-latest } | ||
| - { name: linux-python3.12 , requirements: pinned , python-ver: "3.12", os: ubuntu-latest } | ||
| - { name: linux-python3.12-upgraded , requirements: upgraded , python-ver: "3.12", os: ubuntu-latest } | ||
| - { name: windows-python3.8-minimum , requirements: minimum , python-ver: "3.8" , os: windows-latest } | ||
| - { name: windows-python3.8 , requirements: pinned , python-ver: "3.8" , os: windows-latest } | ||
| - { name: windows-python3.9 , requirements: pinned , python-ver: "3.9" , os: windows-latest } | ||
| - { name: windows-python3.10 , requirements: pinned , python-ver: "3.10", os: windows-latest } | ||
| - { name: windows-python3.11 , requirements: pinned , python-ver: "3.11", os: windows-latest } | ||
| - { name: windows-python3.12 , requirements: pinned , python-ver: "3.12", os: windows-latest } | ||
| - { name: windows-python3.12-upgraded , requirements: upgraded , python-ver: "3.12", os: windows-latest } | ||
| - { name: macos-python3.8-minimum , requirements: minimum , python-ver: "3.8" , os: macos-latest } | ||
| - { name: macos-python3.8 , requirements: pinned , python-ver: "3.8" , os: macos-latest } | ||
| - { name: macos-python3.9 , requirements: pinned , python-ver: "3.9" , os: macos-latest } | ||
| - { name: macos-python3.10 , requirements: pinned , python-ver: "3.10", os: macos-latest } | ||
| - { name: macos-python3.11 , requirements: pinned , python-ver: "3.11", os: macos-latest } | ||
| - { name: macos-python3.12 , requirements: pinned , python-ver: "3.12", os: macos-latest } | ||
| - { name: macos-python3.12-upgraded , requirements: upgraded , python-ver: "3.12", os: macos-latest } | ||
| steps: | ||
| - name: Cancel non-latest runs | ||
| uses: styfle/cancel-workflow-action@0.11.0 | ||
| with: | ||
| all_but_latest: true | ||
| access_token: ${{ github.token }} | ||
|
|
||
| - uses: actions/checkout@v3 | ||
| with: | ||
| submodules: 'recursive' | ||
| fetch-depth: 0 # fetch tags | ||
|
|
||
| - name: Set up Python | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: ${{ matrix.python-ver }} | ||
|
|
||
| - name: Install build dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| python -m pip list | ||
| python -m pip check | ||
| - name: Install run requirements (minimum) | ||
| if: ${{ matrix.requirements == 'minimum' }} | ||
| run: | | ||
| python -m pip install -r requirements-min.txt -r requirements-dev.txt | ||
| python -m pip install -e . | ||
| - name: Install run requirements (pinned) | ||
| if: ${{ matrix.requirements == 'pinned' }} | ||
| run: | | ||
| python -m pip install -r requirements-dev.txt | ||
| python -m pip install -e . | ||
| - name: Install run requirements (upgraded) | ||
| if: ${{ matrix.requirements == 'upgraded' }} | ||
| run: | | ||
| python -m pip install -r requirements-dev.txt | ||
| python -m pip install -U -e . | ||
| - name: Run tests | ||
| run: | | ||
| pytest -v | ||
| - name: Build wheel and source distribution | ||
| run: | | ||
| python -m pip install --upgrade build | ||
| python -m build | ||
| ls -1 dist | ||
| - name: Test installation from a wheel (POSIX) | ||
| if: ${{ matrix.os != 'windows-latest' }} | ||
| run: | | ||
| python -m venv test-wheel-env | ||
| source test-wheel-env/bin/activate | ||
| python -m pip install dist/*-none-any.whl | ||
| python -c "import ndx_microscopy" | ||
| - name: Test installation from a wheel (windows) | ||
| if: ${{ matrix.os == 'windows-latest' }} | ||
| run: | | ||
| python -m venv test-wheel-env | ||
| test-wheel-env/Scripts/activate.bat | ||
| python -m pip install dist/*-none-any.whl | ||
| python -c "import ndx_microscopy" | ||
| run-all-tests-on-conda: | ||
| name: ${{ matrix.name }} | ||
| runs-on: ubuntu-latest | ||
| defaults: | ||
| run: | ||
| shell: bash -l {0} # needed for conda environment to work | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| include: | ||
| - { name: conda-linux-python3.8-minimum , requirements: minimum , python-ver: "3.8" , os: ubuntu-latest } | ||
| - { name: conda-linux-python3.8 , requirements: pinned , python-ver: "3.8" , os: ubuntu-latest } | ||
| - { name: conda-linux-python3.9 , requirements: pinned , python-ver: "3.9" , os: ubuntu-latest } | ||
| - { name: conda-linux-python3.10 , requirements: pinned , python-ver: "3.10", os: ubuntu-latest } | ||
| - { name: conda-linux-python3.11 , requirements: pinned , python-ver: "3.11", os: ubuntu-latest } | ||
| - { name: conda-linux-python3.12 , requirements: pinned , python-ver: "3.12", os: ubuntu-latest } | ||
| - { name: conda-linux-python3.12-upgraded , requirements: upgraded , python-ver: "3.12", os: ubuntu-latest } | ||
| steps: | ||
| - name: Cancel any previous incomplete runs | ||
| uses: styfle/cancel-workflow-action@0.11.0 | ||
| with: | ||
| access_token: ${{ github.token }} | ||
|
|
||
| - uses: actions/checkout@v3 | ||
| with: | ||
| submodules: 'recursive' | ||
| fetch-depth: 0 # fetch tags | ||
|
|
||
| - name: Set up Conda | ||
| uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| auto-update-conda: true | ||
| auto-activate-base: true | ||
| activate-environment: true | ||
| python-version: ${{ matrix.python-ver }} | ||
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| - name: Install build dependencies | ||
| run: | | ||
| conda config --set always_yes yes --set changeps1 no | ||
| conda info | ||
| conda config --show-sources | ||
| conda list --show-channel-urls | ||
| - name: Install run requirements (minimum) | ||
| if: ${{ matrix.requirements == 'minimum' }} | ||
| run: | | ||
| python -m pip install -r requirements-min.txt -r requirements-dev.txt | ||
| python -m pip install -e . | ||
| - name: Install run requirements (pinned) | ||
| if: ${{ matrix.requirements == 'pinned' }} | ||
| run: | | ||
| python -m pip install -r requirements-dev.txt | ||
| python -m pip install -e . | ||
| - name: Install run requirements (upgraded) | ||
| if: ${{ matrix.requirements == 'upgraded' }} | ||
| run: | | ||
| python -m pip install -r requirements-dev.txt | ||
| python -m pip install -U -e . | ||
| - name: Run tests | ||
| run: | | ||
| pytest -v | ||
| - name: Build wheel and source distribution | ||
| run: | | ||
| python -m pip install --upgrade build | ||
| python -m build | ||
| ls -1 dist | ||
| - name: Test installation from a wheel (POSIX) | ||
| run: | | ||
| python -m venv test-wheel-env | ||
| source test-wheel-env/bin/activate | ||
| python -m pip install dist/*-none-any.whl | ||
| python -c "import ndx_microscopy" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| name: Run code coverage | ||
| on: | ||
| pull_request: | ||
| workflow_dispatch: | ||
|
|
||
| jobs: | ||
| run-coverage: | ||
| name: ${{ matrix.os }} | ||
| runs-on: ${{ matrix.os }} | ||
| # TODO handle forks | ||
| # run pipeline on either a push event or a PR event on a fork | ||
| # if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name | ||
| defaults: | ||
| run: | ||
| shell: bash | ||
| strategy: | ||
| matrix: | ||
| os: [ubuntu-latest, windows-latest, macos-latest] | ||
| env: # used by codecov-action | ||
| OS: ${{ matrix.os }} | ||
| PYTHON: '3.11' | ||
| steps: | ||
| - name: Cancel any previous incomplete runs | ||
| uses: styfle/cancel-workflow-action@0.11.0 | ||
| with: | ||
| all_but_latest: true | ||
| access_token: ${{ github.token }} | ||
|
|
||
| - uses: actions/checkout@v3 | ||
| with: | ||
| submodules: 'recursive' | ||
| fetch-depth: 0 # fetch tags | ||
|
|
||
| - name: Set up Python | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: ${{ env.PYTHON }} | ||
|
|
||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip | ||
| python -m pip install -r requirements-dev.txt | ||
| - name: Install package | ||
| run: | | ||
| python -m pip install -e . # must install in editable mode for coverage to find sources | ||
| python -m pip list | ||
| - name: Run tests and generate coverage report | ||
| run: | | ||
| pytest --cov | ||
| python -m coverage xml # codecov uploader requires xml format | ||
| python -m coverage report -m | ||
| # TODO uncomment after setting up repo on codecov.io | ||
| # - name: Upload coverage to Codecov | ||
| # uses: codecov/codecov-action@v3 | ||
| # with: | ||
| # fail_ci_if_error: true |
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@@ -114,3 +114,6 @@ venv.bak/ | |
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| # Mac finder | ||
| .DS_Store | ||
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| # PyCharm | ||
| .idea/ | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,17 @@ | ||
| repos: | ||
| - repo: https://github.com/pre-commit/pre-commit-hooks | ||
| rev: v4.6.0 | ||
| hooks: | ||
| - id: check-yaml | ||
| - id: check-toml | ||
| - id: end-of-file-fixer | ||
| - id: trailing-whitespace | ||
| - id: check-added-large-files | ||
| - repo: https://github.com/psf/black | ||
| rev: 24.4.2 | ||
| hooks: | ||
| - id: black | ||
| - repo: https://github.com/PyCQA/isort | ||
| rev: 5.13.2 | ||
| hooks: | ||
| - id: isort |
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