-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge remote-tracking branch 'origin/basic_spec' into basic_spec
- Loading branch information
Showing
7 changed files
with
303 additions
and
50 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| name: Codespell | ||
| on: | ||
| pull_request: | ||
| workflow_dispatch: | ||
|
|
||
| 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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,183 @@ | ||
| name: Run all tests | ||
| on: | ||
| pull_request: | ||
| schedule: | ||
| - cron: '0 5 * * 0' # once every Sunday at midnight ET | ||
| workflow_dispatch: | ||
|
|
||
| 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/[email protected] | ||
| 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/[email protected] | ||
| 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 }} | ||
|
|
||
| - 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" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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/[email protected] | ||
| 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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.