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[CI] switch from Travis CI to GitHub actions
- fix #146 - test MDAnalysis >= 1.0.0, <2 (noted in CHANGELOG)
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‎.github/workflows/docs.yaml

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name: docs deployment
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on:
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push:
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branches:
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- master
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concurrency:
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group: "${{ github.ref }}-${{ github.head_ref }}"
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cancel-in-progress: true
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defaults:
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run:
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shell: bash -l {0}
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jobs:
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docs:
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if: "github.repository == 'MDAnalysis/pmda'"
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: setup_miniconda
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uses: conda-incubator/setup-miniconda@v2
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with:
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python-version: 3.7
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auto-update-conda: true
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channel-priority: flexible
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channels: conda-forge
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add-pip-as-python-dependency: true
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mamba-version: "*"
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- name: install package deps
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run: |
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mamba install 'mdanalysis<2' dask distributed sphinx
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pip install sphinx-sitemap sphinx-rtd-theme
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- name: check install
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run: |
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which python
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which pip
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conda info
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conda list
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- name: install package
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run: |
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pip install -v .
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- name: build docs
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run: |
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python setup.py build_sphinx
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- name: deploy docs
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uses: peaceiris/actions-gh-pages@v3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./build/sphinx/html
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user_name: 'github-actions'
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user_email: 'github-action@users.noreply.github.com'

‎.github/workflows/gh-ci.yaml

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name: GH Actions CI
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on:
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push:
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branches:
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- develop
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- master
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pull_request:
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branches:
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- develop
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- master
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concurrency:
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# Probably overly cautious group naming.
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# Commits to develop/master will cancel each other, but PRs will only cancel
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# commits within the same PR
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group: "${{ github.ref }}-${{ github.head_ref }}"
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cancel-in-progress: true
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defaults:
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run:
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shell: bash -l {0}
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jobs:
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unittests:
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if: "github.repository == 'MDAnalysis/pmda'"
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, ]
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python-version: [2.7, 3.7, 3.8, 3.9]
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include:
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- name: macOS_bigsur_py39
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os: macOS-11
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python-version: 3.9
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- name: macOS_catalina_py37
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os: macOS-10.15
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python-version: 3.7
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env:
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CYTHON_TRACE_NOGIL: 1
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MPLBACKEND: agg
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GH_OS: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v2
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- name: setup_miniconda
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uses: conda-incubator/setup-miniconda@v2
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with:
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python-version: ${{ matrix.python-version }}
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auto-update-conda: true
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channel-priority: flexible
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# The order of these channel matters: both provide "fundamental"
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# software (curl, ssh, ...), but the version in biobuilds are very
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# outdated. This can lead to problem when loading shared libraries,
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# see https://github.com/MDAnalysis/mdanalysis/pull/3126#issuecomment-813112080
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channels: conda-forge, biobuilds
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add-pip-as-python-dependency: true
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mamba-version: "*"
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architecture: x64
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- name: install_deps
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run: |
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mamba install 'mdanalysis>=1,<2' 'mdanalysistests>=1,<2' dask distributed joblib mock codecov
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pip install 'coverage<5' 'pytest-cov==2.10.1' pytest-xdist
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- name: check_setup
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run: |
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# Check OS and python setup
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echo "OS: ${OS_NAME}"
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which python
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which pip
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pip list
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conda info
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conda list
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- name: install PMDA package
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run: python -m pip install -v .
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- name: run tests
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run: |
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pytest -v --cov=pmda --cov-report=xml --color=yes ./pmda/test
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- name: codecov
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uses: codecov/codecov-action@v2
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with:
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file: coverage.xml
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fail_ci_if_error: True
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verbose: True
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pylint_check:
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if: "github.repository == 'MDAnalysis/pmda'"
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: setup_miniconda
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uses: conda-incubator/setup-miniconda@v2
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with:
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python-version: 3.7
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auto-update-conda: true
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channel-priority: flexible
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channels: conda-forge
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add-pip-as-python-dependency: true
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architecture: x64
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- name: install
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run: |
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which pip
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which python
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pip install pylint
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- name: pylint
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env:
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PYLINTRC: .pylintrc
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run: |
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pylint pmda
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pypi_check:
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if: "github.repository == 'MDAnalysis/pmda'"
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: setup_miniconda
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uses: conda-incubator/setup-miniconda@v2
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with:
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python-version: 3.7
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auto-update-conda: true
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channel-priority: flexible
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channels: conda-forge
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add-pip-as-python-dependency: true
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# mamba not enabled as install longer than deps install
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architecture: x64
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- name: install_conda
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run: |
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conda install setuptools twine
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- name: install PMDA
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run: |
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python setup.py sdist
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- name: check package build
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run: |
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DISTRIBUTION=$(ls -t1 dist/pmda-*.tar.gz | head -n 1)
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test -n "${DISTRIBUTION}" || { echo "no distribution dist/pmda-*.tar.gz found"; exit 1; }
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echo "twine check $DISTRIBUTION"
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twine check $DISTRIBUTION

‎.travis.yml

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This file was deleted.

‎CHANGELOG

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* raise ValueError when n_blocks > n_frames (Issue #137, PR #138)
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Changes
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* requires MDAnalysis >= 1.0.0 (#122)
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* requires MDAnalysis >= 1.0.0 and <2.0.0 (#122)
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* dropped official support for Python 3.5 (2.7 and >= 3.6 are supported)
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‎ci/deploy_docs.sh

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This file was deleted.

‎setup.py

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},
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packages=find_packages(),
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install_requires=[
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'MDAnalysis>=1.0.0',
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'MDAnalysis>=1.0.0,<2',
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'dask>=0.18',
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'distributed',
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'six',
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],
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tests_require=[
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'pytest',
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'MDAnalysisTests>=1.0.0', # keep
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'MDAnalysisTests>=1.0.0,<2', # keep
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], )

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