Multi anchor crop #140
Workflow file for this run
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# Continuous integration | |
name: CI | |
on: | |
pull_request: | |
types: [opened, reopened, synchronize] | |
paths: | |
- "biogtr/**" | |
- "tests/**" | |
- ".github/workflows/ci.yml" | |
- "environment_cpu.yml" | |
- "pyproject.toml" | |
push: | |
branches: | |
- main | |
paths: | |
- "biogtr/**" | |
- "tests/**" | |
- ".github/workflows/ci.yml" | |
- "environment_cpu.yml" | |
- "pyproject.toml" | |
defaults: | |
# This is needed for running steps within conda environments. | |
run: | |
shell: bash -l {0} | |
jobs: | |
# Lint with black, docstring check with pydocstyle, static type checking with mypy | |
lint: | |
# This job runs: | |
# | |
# 1. Linting with black | |
# | |
# 2. Docstring style checking with pydocstyle | |
# Note: This uses Google-style docstring convention | |
# Ref: https://google.github.io/styleguide/pyguide.html | |
name: Lint | |
runs-on: "ubuntu-22.04" | |
steps: | |
- name: Checkout repo | |
uses: actions/checkout@v3 | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: 3.9 | |
- name: Install dependencies | |
run: | | |
pip install --editable .[dev] | |
- name: Run Black | |
run: | | |
black --check biogtr tests | |
- name: Run pydocstyle | |
run: | | |
pydocstyle --convention=google biogtr/ | |
# Tests with pytest | |
tests: | |
strategy: | |
fail-fast: false | |
matrix: | |
os: ["ubuntu-22.04", "windows-2022"] | |
python: [3.9] | |
name: Tests (${{ matrix.os }}, Python ${{ matrix.python }}) | |
runs-on: ${{ matrix.os }} | |
steps: | |
- name: Checkout repo | |
uses: actions/checkout@v3 | |
- name: Setup Micromamba | |
# https://github.com/mamba-org/setup-micromamba | |
# Note: Set channel-priority in .condarc if needed | |
uses: mamba-org/setup-micromamba@v1 | |
with: | |
environment-file: environment_cpu.yml | |
cache-environment: true | |
cache-environment-key: environment-${{ hashFiles('environment_cpu.yml') }}-${{ hashFiles('pyproject.toml') }} | |
init-shell: >- | |
bash | |
powershell | |
post-cleanup: all | |
- name: Print environment info | |
shell: bash -l {0} | |
run: | | |
which python | |
micromamba info | |
micromamba list | |
pip freeze | |
- name: Test with pytest | |
if: ${{ !(startsWith(matrix.os, 'ubuntu') && matrix.python == 3.9) }} | |
shell: bash -l {0} | |
run: | | |
pytest | |
- name: Test with pytest (with coverage) | |
if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.python == 3.9 }} | |
shell: bash -l {0} | |
run: | | |
pytest --cov=biogtr --cov-report=xml tests/ | |
- name: Upload coverage | |
uses: codecov/codecov-action@v3 | |
if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.python == 3.9 }} | |
with: | |
fail_ci_if_error: false | |
verbose: true |