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first draft of martinize2 command tutorials #603

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first draft of martinize2 command tutorials

first draft of martinize2 command tutorials #603

Workflow file for this run

.github/workflows/run_tests.yml at 3dc5fd2
# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
name: test package
on:
push:
branches: [ master ]
pull_request:
branches: [ master ]
env:
VERMOUTH_TEST_DSSP: mkdssp
SKIP_GENERATE_AUTHORS: 1
SKIP_WRITE_GIT_CHANGELOG: 1
jobs:
build:
runs-on: ubuntu-20.04
strategy:
matrix:
py_version: ["3.9", "3.10", "3.11", "3.12"]
include:
- py_version: "3.9"
WITH_CODECOV: true
- py_version: "3.10"
WITH_CODECOV: true
- py_version: "3.11"
WITH_CODECOV: true
- py_version: "3.12"
WITH_CODECOV: true
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.py_version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.py_version }}
cache: pip
cache-dependency-path: |
**/setup.cfg
**/requirements-*.txt
**/pyproject.toml
- name: Install dependencies part I
run: |
sudo apt-get install dssp
pip install --upgrade setuptools pip
- name: Install package and requirements
run: |
pip install --upgrade .
pip install -r requirements-tests.txt
- name: Run pytest with codecoverage
run: |
coverage run $(which pytest) -vv --hypothesis-show-statistics
coverage report
coverage xml
- if: ${{ matrix.WITH_CODECOV }}
name: Upload coverage codecov
uses: codecov/codecov-action@v4
with:
token: ${{ secrets.CODECOV_TOKEN }}
files: ./coverage.xml
fail_ci_if_error: true
verbose: true
lint:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python 3
uses: actions/setup-python@v5
with:
python-version: '3.x'
cache: pip
cache-dependency-path: |
**/setup.cfg
**/requirements-*.txt
**/pyproject.toml
- name: Install dependencies
run: |
pip install --upgrade setuptools pip
pip install --upgrade .
pip install -r requirements-tests.txt
- name: Run pylint
run: |
pylint --disable=fixme --fail-under=8.0 vermouth
pylint --disable=fixme --fail-under=9.0 bin/martinize2
docs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python 3
uses: actions/setup-python@v5
with:
python-version: '3.x'
cache: pip
cache-dependency-path: |
**/setup.cfg
**/requirements-*.txt
**/pyproject.toml
- name: Install dependencies
run: |
pip install --upgrade setuptools pip
pip install --upgrade .
pip install -r requirements-docs.txt
- name: Run docs
run: |
mkdir -p doc/source/_static
sphinx-build -EnW -b html doc/source/ doc/build/html
deploy:
needs: [build, lint, docs]
runs-on: ubuntu-latest
environment:
name: testpypi
url: https://test.pypi.org/p/vermouth
permissions:
id-token: write
steps:
- uses: actions/checkout@v4
with:
fetch-tags: true
fetch-depth: 0
- name: Set up Python 3
uses: actions/setup-python@v5
with:
python-version: '3.11'
cache: pip
cache-dependency-path: |
**/setup.cfg
**/requirements-*.txt
**/pyproject.toml
- name: Install dependencies
run: |
pip install --upgrade setuptools pip
pip install --upgrade .
- name: Install pypa/build
run: |
python3 -m pip install build pbr --user
- name: Build a binary wheel and a source tarball
run: python3 -m build --sdist --wheel --outdir dist/
- name: Publish distribution 📦 to PyPI
uses: pypa/gh-action-pypi-publish@release/v1
with:
repository-url: https://test.pypi.org/legacy/