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Merge pull request #52 from MDAnalysis/travis2ghactions
replace Travis CI with GitHub actions
2 parents 4cb391f + 4572c0c commit 779bed1

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‎.github/workflows/docs.yml‎

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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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jobs:
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docs:
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if: github.repository == 'MDAnalysis/MDAnalysisData'
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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 python
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uses: actions/setup-python@v2
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with:
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python-version: 3.9
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Install sphinx, pytest, pytest plugins
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run: |
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python -m pip install wheel
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python -m pip install pytest pytest-cov pytest-pep8 pytest-mock codecov
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python -m pip install sphinx sphinx-sitemap sphinx-rtd-theme
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- name: Install main dependencies
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run: |
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python -m pip install six setuptools tqdm
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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.yml‎

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name: GH Actions CI
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on:
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# run every Sunday at 3:53 UTC
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schedule:
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- cron: "53 3 * * 0"
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push:
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branches:
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- "master"
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pull_request:
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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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jobs:
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unittests:
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name: Test ${{ matrix.os }} with Python ${{ matrix.python-version }}
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if: github.repository == 'MDAnalysis/MDAnalysisData'
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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, 3.6, 3.7, 3.8, 3.9]
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include:
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- os: macOS-latest
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python-version: 2.7
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- os: macOS-latest
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python-version: 3.9
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- os: windows-latest
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python-version: 2.7
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- os: windows-latest
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python-version: 3.9
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steps:
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- uses: actions/checkout@v2
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- name: Setup python
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uses: actions/setup-python@v2
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with:
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python-version: ${{ matrix.python-version }}
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- name: Display Python version
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run: python -c "import sys; print(sys.version)"
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- name: Install testing dependencies (pytest, pytest plugins)
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run: |
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python -m pip install wheel
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python -m pip install pytest pytest-cov pytest-pep8 pytest-mock codecov
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- name: Install package dependencies
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run: |
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python -m pip install six setuptools tqdm
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- name: Install compatibility dependencies for Python 2.7 only
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if: startsWith(matrix.python-version, '2.7')
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run: python -m pip install pathlib2
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- name: Install package
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run: |
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python -m pip install -e .
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- name: Run tests
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run: |
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pytest -v --cov=MDAnalysisData --cov-report=xml --color=yes MDAnalysisData/tests
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- name: Codecov
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uses: codecov/codecov-action@v2
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with:
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name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
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file: ./coverage.xml
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fail_ci_if_error: True
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verbose: True

‎.travis.yml‎

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This file was deleted.

‎CHANGELOG.md‎

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### Changes
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- update online docs theme (#43)
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- tested for Python 2.7, 3.6 - 3.9 on Linux, macOS, Windows (#48)
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## [0.8.0] - 2019-08-13
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‎MDAnalysisData/tests/__init__.py‎

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# tests/__init__.py so that pytest-cov collects data
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# otherwise "CoverageWarning: No data was collected. (no-data-collected)"
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# see https://stackoverflow.com/a/60579142

‎MDAnalysisData/tests/test_base.py‎

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from six.moves.urllib.request import urlretrieve
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try:
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import pathlib
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except ImportError:
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# Python 2.7
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import pathlib2 as pathlib
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import os
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import os.path
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def test_read_description():
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descr = base._read_description("adk_equilibrium.rst")
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assert len(descr) == 1252
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assert descr.startswith(".. -*- coding: utf-8 -*-\n\n.. _`adk-equilibrium-dataset`:")
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assert (descr.startswith( # UNIX
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".. -*- coding: utf-8 -*-\n\n.. _`adk-equilibrium-dataset`:") or
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descr.startswith( # Windows
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".. -*- coding: utf-8 -*-\r\n\r\n.. _`adk-equilibrium-dataset`:"))
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# descr is read with automatic line ending conversion so by splitting into
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# words we don't need to care about that (len(descr) differs between UNIX
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# and Windows)
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n_words = len(descr.split())
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assert n_words == 153
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def test_sha256(tmpdir, some_text):
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filename = "address.txt"
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with tmpdir.as_cwd():
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with open(filename, "w") as txt:
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txt.write(some_text)
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with open(filename, "wb") as txt:
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txt.write(some_text.encode("utf-8"))
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checksum = base._sha256(filename)
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assert checksum == "4446bfb2ec5dedfbd981d059d6005f5144b067b392a00e3bcf98f8302ec8f765"
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@pytest.mark.parametrize('data_home,location', [
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(None, os.path.expanduser("~/MDAnalysis_data")),
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("/tmp/MDAnalysisData", "/tmp/MDAnalysisData"),
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(None,
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pathlib.Path("~/MDAnalysis_data").expanduser()),
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(str(pathlib.Path("/tmp/MDAnalysisData")),
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pathlib.Path("/tmp/MDAnalysisData")),
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])
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def test_get_data_home(data_home, location):
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assert base.get_data_home(data_home=data_home) == location
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assert base.get_data_home(data_home=data_home) == str(location)
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def test_clear_data_home(tmpdir, some_text):
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data_home_path = tmpdir.join("MDAnalysis_data_test")

‎MDAnalysisData/tests/test_package_metadata.py‎

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# -*- coding: utf-8 -*-
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import sys
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import six
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from six.moves import reload_module
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import pytest
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def test_version():
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# very generic because versioneer will provide different strings depending
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# on the repository status
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assert isinstance(MDAnalysisData.__version__, str)
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assert isinstance(MDAnalysisData.__version__, six.string_types)

‎README.md‎

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# MDAnalysisData
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[![Build Status](https://travis-ci.com/MDAnalysis/MDAnalysisData.svg?branch=master)](https://travis-ci.com/MDAnalysis/MDAnalysisData)
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[![Build Status](https://github.com/MDAnalysis/MDAnalysisData/actions/workflows/gh-ci.yaml/badge.svg)](https://github.com/MDAnalysis/GridDataFormats/actions/workflows/ci.yaml)
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[![codecov](https://codecov.io/gh/MDAnalysis/MDAnalysisData/branch/master/graph/badge.svg)](https://codecov.io/gh/MDAnalysis/MDAnalysisData)
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[![docs](https://img.shields.io/badge/docs-latest-brightgreen.svg)](https://www.mdanalysis.org/MDAnalysisData/)
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[![PRs welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square)](http://makeapullrequest.com)
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MDAnalysisData.base.clear_data_home()
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```
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## Contributing new datasets
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Please add new datasets to MDAnalysisData. See [Contributing new
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datasets](https://www.mdanalysis.org/MDAnalysisData/contributing.html)
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for details, but in short:
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1. raise an issue in the [issue
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tracker](https://github.com/MDAnalysis/MDAnalysisData/issues) describing
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what you want to add; this issue will become the focal point for discussions
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where the developers can easily give advice
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2. deposit data in an archive under an [Open
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Data](https://opendatacommons.org/) compatible license (CC0 or
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CC-BY preferred)
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3. write accessor code in MDAnalysisData
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## Credits

‎setup.py‎

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import versioneer
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import os
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import sys
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import warnings
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import codecs
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'Programming Language :: Python :: 2',
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'Programming Language :: Python :: 2.7',
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'Programming Language :: Python :: 3',
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'Programming Language :: Python :: 3.4',
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'Programming Language :: Python :: 3.5',
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'Programming Language :: Python :: 3.6',
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'Programming Language :: Python :: 3.7',
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'Programming Language :: Python :: 3.8',
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'Programming Language :: Python :: 3.9',
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'Topic :: Scientific/Engineering',
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'Topic :: Scientific/Engineering :: Bio-Informatics',
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'Topic :: Scientific/Engineering :: Chemistry',
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'Topic :: Software Development :: Libraries :: Python Modules',
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]
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# Python 2.7 compatibility
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test_requirements = ['pytest', 'pytest-mock']
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if sys.version_info.major < 3:
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test_requirements.append("pathlib2")
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setup(name='MDAnalysisData',
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version=versioneer.get_version(),
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cmdclass=versioneer.get_cmdclass(),
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'setuptools',
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'tqdm',
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],
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tests_require=['pytest', 'pytest-mock'],
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tests_require=test_requirements,
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zip_safe=True,
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)

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