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- Removed several new and old environment files to lower maintenance
burden.
- environment.yaml
- envs/py3.10-tests.yaml
- envs/py3.11-tests.yaml
- envs/py3.12-tests.yaml
- Removal of the environment files required updating the README.md to
handle creating an environment file for the user.
- We ignore the created environment.yaml file in the .gitignore file
- Removed requirements.txt as all requirements are handled by the
pyproject.toml file.
- Updated docs to fix URL links.
- Also updated comments in untested code to use correct URLs.
- Refactored the test.yaml workflow.
- Refactored the following to remove extraneous line character
- tests/test_basic.py (also renamed the method and module to correlate
with the method being tested in the module.)
- src/holoseq/exceptions.py
- pyproject.toml
- .github/workflows/test.yaml- Loading branch information
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,164 +1,38 @@ | ||
| name: tests | ||
| name: Run tests | ||
| on: | ||
| push: | ||
| tags: | ||
| - 'v[0-9]+.[0-9]+.[0-9]+' | ||
| - 'v[0-9]+.[0-9]+.[0-9]+a[0-9]+' | ||
| - 'v[0-9]+.[0-9]+.[0-9]+b[0-9]+' | ||
| - 'v[0-9]+.[0-9]+.[0-9]+rc[0-9]+' | ||
| pull_request: | ||
| branches: | ||
| - '*' | ||
| workflow_dispatch: | ||
| inputs: | ||
| target: | ||
| description: "How much of the test suite to run" | ||
| type: choice | ||
| default: default | ||
| options: | ||
| - default | ||
| - full | ||
| - downstream | ||
| cache: | ||
| description: "Use cache" | ||
| type: boolean | ||
| default: true | ||
| schedule: | ||
| - cron: '0 15 * * SUN' | ||
|
|
||
| concurrency: | ||
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: true | ||
| push: | ||
| branches: [main] | ||
| paths-ignore: | ||
| - "docs/" | ||
| - "notebooks/" | ||
| - "scripts/" | ||
|
|
||
| jobs: | ||
| pre_commit: | ||
| name: Run pre-commit | ||
| runs-on: 'ubuntu-latest' | ||
| steps: | ||
| - uses: holoviz-dev/holoviz_tasks/[email protected] | ||
| setup: | ||
| name: Setup workflow | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| matrix: ${{ env.MATRIX }} | ||
| matrix_option: ${{ env.MATRIX_OPTION }} | ||
| steps: | ||
| - name: Set matrix option | ||
| run: | | ||
| if [[ '${{ github.event_name }}' == 'workflow_dispatch' ]]; then | ||
| OPTION=${{ github.event.inputs.target }} | ||
| elif [[ '${{ github.event_name }}' == 'schedule' ]]; then | ||
| OPTION="full" | ||
| elif [[ '${{ github.event_name }}' == 'push' && '${{ github.ref_type }}' == 'tag' ]]; then | ||
| OPTION="full" | ||
| else | ||
| OPTION="default" | ||
| fi | ||
| echo "MATRIX_OPTION=$OPTION" >> $GITHUB_ENV | ||
| - name: Set test matrix with 'default' option | ||
| if: env.MATRIX_OPTION == 'default' | ||
| run: | | ||
| MATRIX=$(jq -nsc '{ | ||
| "os": ["ubuntu-latest", "macos-latest", "windows-latest"], | ||
| "python-version": ["3.10", "3.12"], | ||
| "exclude": [ | ||
| { | ||
| "python-version": "3.10", | ||
| "os": "macos-latest" | ||
| } | ||
| ] | ||
| }') | ||
| echo "MATRIX=$MATRIX" >> $GITHUB_ENV | ||
| - name: Set test matrix with 'full' option | ||
| if: env.MATRIX_OPTION == 'full' | ||
| run: | | ||
| MATRIX=$(jq -nsc '{ | ||
| "os": ["ubuntu-latest", "macos-latest", "windows-latest"], | ||
| "python-version": ["3.10", "3.12"], | ||
| "include": [ | ||
| { | ||
| "python-version": "3.10", | ||
| "os": "ubuntu-latest" | ||
| }, | ||
| { | ||
| "python-version": "3.11", | ||
| "os": "ubuntu-latest" | ||
| }, | ||
| , | ||
| { | ||
| "python-version": "3.12", | ||
| "os": "ubuntu-latest" | ||
| } | ||
| ] | ||
| }') | ||
| echo "MATRIX=$MATRIX" >> $GITHUB_ENV | ||
| - name: Set test matrix with 'downstream' option | ||
| if: env.MATRIX_OPTION == 'downstream' | ||
| run: | | ||
| MATRIX=$(jq -nsc '{ | ||
| "os": ["ubuntu-latest"], | ||
| "python-version": ["3.12"] | ||
| }') | ||
| echo "MATRIX=$MATRIX" >> $GITHUB_ENV | ||
| conda_suite: | ||
| name: conda tests:${{ matrix.os }}:${{ matrix.python-version }} | ||
| needs: [pre_commit, setup] | ||
| if: needs.setup.outputs.matrix_option != 'default' | ||
| runs-on: ${{ matrix.os }} | ||
| test: | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: ${{ fromJson(needs.setup.outputs.matrix) }} | ||
| timeout-minutes: 90 | ||
| defaults: | ||
| run: | ||
| shell: bash -el {0} | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
| - uses: conda-incubator/setup-miniconda@v3 | ||
| with: | ||
| auto-update-conda: true | ||
| environment-file: envs/py${{ matrix.python-version }}-tests.yaml | ||
| activate-environment: holoseqtests | ||
| - name: conda info | ||
| run: conda info | ||
| - name: conda list | ||
| run: conda list | ||
| - name: unit tests | ||
| run: pytest -v holoseq --cov=holoseq --cov-append | ||
| pip_test: | ||
| name: pip tests:${{ matrix.os }}:${{ matrix.python-version }} | ||
| needs: [pre_commit, setup] | ||
| timeout-minutes: 90 | ||
| matrix: | ||
| os: [ubuntu-latest] | ||
| version: ["3.10", "3.11", "3.12"] | ||
|
|
||
| runs-on: ${{ matrix.os }} | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: ${{ fromJson(needs.setup.outputs.matrix) }} | ||
| defaults: | ||
| run: | ||
| shell: bash -e {0} | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
| - uses: actions/setup-python@v5 | ||
| - name: Checkout | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Set up Python ${{ matrix.version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| - name: install with geo | ||
| run: python -m pip install -v --prefer-binary -e '.[tests, examples-tests, geo, hvdev, hvdev-geo, dev-extras]' | ||
| - name: python version and pip list | ||
| python-version: ${{ matrix.version }} | ||
|
|
||
| - name: Install dependencies | ||
| run: | | ||
| python --version --version | ||
| python -m pip list | ||
| - name: unit tests | ||
| run: pytest -v hvplot --cov=hvplot --cov-append | ||
| - name: Upload coverage reports to Codecov | ||
| if: github.event_name == 'push' || github.event_name == 'pull_request' | ||
| uses: codecov/codecov-action@v4 | ||
| with: | ||
| fail_ci_if_error: false | ||
| verbose: false | ||
| env: | ||
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | ||
| python -m pip install --upgrade pip | ||
| pip install .[dev,test] | ||
| - name: Run ruff | ||
| uses: astral-sh/ruff-action@v2 | ||
|
|
||
| - name: Run tests | ||
| run: | | ||
| pytest -v tests --cov=src/holoseq --cov-append |
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