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docs(py): publish api docs to read the docs using sphinx #642

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docs(py): publish api docs to read the docs using sphinx

docs(py): publish api docs to read the docs using sphinx #642

Workflow file for this run

.github/workflows/python-ci.yml at 228aeae
name: Python CI
permissions:
contents: read
on:
push:
branches:
- main
pull_request:
workflow_dispatch:
env:
RUST_BACKTRACE: full
CARGO_TERM_COLOR: always
FORCE_COLOR: 1
IN_CI: 1
# Only include the debug info necessary for backtraces (file names and line numbers). Any extra
# debug info provided by `debuginfo=1` or `debuginfo=2` require an interactive debugger like
# `lldb` or `gdb`.
RUSTFLAGS: -C debuginfo=line-tables-only
jobs:
test:
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: [windows-latest, macos-latest, ubuntu-latest]
steps:
- name: Checkout repository
uses: actions/checkout@v6
- name: Update Rust
run: rustup update stable && rustup default stable && rustup component add llvm-tools
- name: Setup Python
uses: actions/setup-python@v6
with:
python-version-file: .python-version
- name: Install cargo-llvm-cov
uses: taiki-e/install-action@v2
with:
tool: cargo-llvm-cov@0.8
- name: Create virtual environment
run: python -m venv --upgrade-deps .venv
- name: Activate virtual environment and code coverage (Windows)
if: ${{ matrix.os == 'windows-latest' }}
run: |
# Activate virtual environment.
Add-Content -Value "VIRTUAL_ENV=$PWD\.venv" -Path $Env:GITHUB_ENV
Add-Content -Value "$PWD\.venv\Scripts" -Path $Env:GITHUB_PATH
# Activate code coverage.
cargo llvm-cov show-env >> $Env:GITHUB_ENV
- name: Activate virtual environment and code coverage (non-Windows)
if: ${{ matrix.os != 'windows-latest' }}
run: |
# Activate virtual environment.
echo "VIRTUAL_ENV=$(pwd)/.venv" >> "${GITHUB_ENV}"
echo "$(pwd)/.venv/bin" >> "${GITHUB_PATH}"
# Activate code coverage. We remove single quotes from `llvm-cov`'s output, as Github
# Actions does not understand them.
cargo llvm-cov show-env | tr -d "'" >> "${GITHUB_ENV}"
- name: Build package
uses: PyO3/maturin-action@v1
with:
command: develop
args: --group=cov --locked
- name: Run tests
run: pytest --cov=python/sprocket_bio --cov-report=json:codecov-py.json
- name: Generate llvm-cov report
run: cargo llvm-cov report -p sprocket-py -p wdl-diagnostics -p wdl-grammar -p wdl-ast --codecov --output-path=codecov-rust.json
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v6
with:
token: ${{ secrets.CODECOV_TOKEN }}
files: codecov-py.json,codecov-rust.json
fail_ci_if_error: true
type-check:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v6
- name: Update Rust
run: rustup update stable && rustup default stable
- name: Setup Python
uses: actions/setup-python@v6
with:
python-version-file: .python-version
- name: Create virtual environment
run: python -m venv --upgrade-deps .venv
- name: Activate virtual environment
run: |
echo "VIRTUAL_ENV=$(pwd)/.venv" >> "${GITHUB_ENV}"
echo "$(pwd)/.venv/bin" >> "${GITHUB_PATH}"
- name: Build package
uses: PyO3/maturin-action@v1
with:
command: develop
args: --locked
- name: Check types
run: mypy python
- name: Check stubs
run: python -m mypy.stubtest sprocket_bio
format:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v6
- name: Check formatting
uses: psf/black@stable
with:
use_pyproject: true
sort-imports:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v6
- name: Setup Python
uses: actions/setup-python@v6
with:
python-version-file: .python-version
# `isort` requires third-party dependencies to be installed before running. We skip this
# because `sprocket_bio` doesn't have any dependencies.
- name: Check import sorting
run: |
python -m pip install "isort~=8.0"
isort --check-only --diff python/