using common workflows

.github/workflows/README.md

@@ -1,30 +1,28 @@
 # Continous Integration Workflows
 
-This package implements different workflows for CI.
+This package implements different workflows for CI, based on our organisation's common workflows.
 They are organised as follows.
 
 ### Documentation
 
 The `documentation` workflow triggers on any push to master, builds the documentation and pushes it to the `gh-pages` branch (if the build is successful).
-It runs on `ubuntu-latest` and `Python 3.7`.
 
 ### Testing Suite
 
 Tests are ensured in the `tests` workflow, which triggers on all pushes.
-It runs on a matrix of all supported operating systems (ubuntu-18.04, ubuntu-20.04, windows-latest and macos-latest) for all supported Python versions (currently `3.7`, `3.8`, `3.9` and `3.10`).
+It runs on a matrix of all supported operating systems for all supported Python versions.
 
 ### Test Coverage
 
 Test coverage is calculated in the `coverage` wokflow, which triggers on pushes to `master` and any push to a `pull request`.
-It runs on `ubuntu-latest` & `Python 3.7`, and reports the coverage results of the test suite to `CodeClimate`,
-
+It reports the coverage results of the test suite to `CodeClimate`.
 
 ### Regular Testing
 
 A `cron` workflow triggers every Monday at 3am (UTC time) and runs the full testing suite, on all available operating systems and supported Python versions.
-It also runs on `Python 3.x` so that newly released Python versions that would break tests are automatically detected.
+It also runs on `Python 3.x` so that newly released Python versions that would break tests are automatically included.
 
 ### Publishing
 
-Publishing to `PyPI` is done through the `publish` workflow, which triggers anytime a `release` is made of the Github repository.
-It builds a `wheel`, checks it, and pushes to `PyPI` if checks are successful.
+Publishing to `PyPI` is done through the `publish` workflow, which triggers anytime a `release` is made of the GitHub repository.
+It builds a `wheel`, checks it, and pushes to `PyPI` if checks are successful.

.github/workflows/coverage.yml

@@ -1,10 +1,6 @@
 # Runs all tests and pushes coverage report to codeclimate
 name: Coverage
 
-defaults:
- run:
- shell: bash
-
 on: # Runs on all push events to master branch and any push related to a pull request
  push:
  branches:
@@ -13,60 +9,7 @@ on: # Runs on all push events to master branch and any push related to a pull r
 
 jobs:
  coverage:
- name: ${{ matrix.os }} / ${{ matrix.python-version }}
- runs-on: ${{ matrix.os }}
- strategy:
- matrix: # only lowest supported Python on latest ubuntu
- os: [ubuntu-latest]
- python-version: [3.7]
-
- steps:
- - uses: actions/checkout@v3
-
- - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
- with:
- python-version: ${{ matrix.python-version }}
- cache: 'pip'
- cache-dependency-path: '**/setup.py'
-
- - name: Get full Python version
- id: full-python-version
- run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
-
- - name: Upgrade pip, setuptools and wheel
- run: python -m pip install --upgrade pip setuptools wheel
-
- - name: Install package
- run: python -m pip install '.[test]'
-
- - name: Set up env for CodeClimate (push)
- run: |
- echo "GIT_BRANCH=${GITHUB_REF/refs\/heads\//}" >> $GITHUB_ENV
- echo "GIT_COMMIT_SHA=$GITHUB_SHA" >> $GITHUB_ENV
- if: github.event_name == 'push'
-
- - name: Set up env for CodeClimate (pull_request)
- env:
- PR_HEAD_SHA: ${{ github.event.pull_request.head.sha }}
- run: |
- echo "GIT_BRANCH=$GITHUB_HEAD_REF" >> $GITHUB_ENV
- echo "GIT_COMMIT_SHA=$PR_HEAD_SHA" >> $GITHUB_ENV
- if: github.event_name == 'pull_request'
-
- - name: Prepare CodeClimate binary
- env:
- CC_TEST_REPORTER_ID: ${{ secrets.CC_TEST_REPORTER_ID }}
- run: |
- curl -LSs 'https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64' >./cc-test-reporter;
- chmod +x ./cc-test-reporter
- ./cc-test-reporter before-build
-
- - name: Run all tests
- run: python -m pytest --cov-report xml --cov=generic_parser
-
- - name: Push Coverage to CodeClimate
- if: ${{ success() }} # only if tests were successful
- env:
- CC_TEST_REPORTER_ID: ${{ secrets.CC_TEST_REPORTER_ID }}
- run: ./cc-test-reporter after-build
+ uses: pylhc/.github/.github/workflows/coverage.yml@master
+ with:
+ src-dir: generic_parser
+ secrets: inherit

.github/workflows/cron.yml

@@ -1,43 +1,13 @@
-# Runs all tests on master everyday at 10 am (UTC time)
+# Runs all tests on master on Mondays at 3 am (UTC time)
 name: Cron Testing
 
-defaults:
- run:
- shell: bash
 
-on:  # Runs on master branch on Mondays at 3am UTC time
+on: 
  schedule:
  - cron: '* 3 * * mon'
 
 jobs:
- tests:
- name: ${{ matrix.os }} / ${{ matrix.python-version }}
- runs-on: ${{ matrix.os }}
- strategy:
- matrix:
- os: [ubuntu-18.04, ubuntu-20.04, macos-latest, windows-latest]
- # Make sure to escape 3.10 with quotes so it doesn't get interpreted as float 3.1 by GA's parser
- python-version: [3.7, 3.8, 3.9, "3.10", 3.x] # crons should always run latest python hence 3.x
-
- steps:
- - uses: actions/checkout@v3
-
- - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
- with:
- python-version: ${{ matrix.python-version }}
- cache: 'pip'
- cache-dependency-path: '**/setup.py'
-
- - name: Get full Python version
- id: full-python-version
- run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
-
- - name: Upgrade pip, setuptools and wheel
- run: python -m pip install --upgrade pip setuptools wheel
-
- - name: Install package
- run: python -m pip install '.[test]'
-
- - name: Run all tests
- run: python -m pytest
+ tests:
+ uses: pylhc/.github/.github/workflows/cron.yml@master
+ with:
+ extra-dependencies: test

.github/workflows/documentation.yml

@@ -1,51 +1,14 @@
 # Build documentation
+# The build is uploaded as artifact if the triggering event is a push for a pull request
+# The build is published to github pages if the triggering event is a push to the master branch (PR merge)
 name: Build and upload documentation
 
-defaults:
- run:
- shell: bash
-
-on: # Runs on any push event to master
+on: # Runs on any push event in a PR or any push event to master
+ pull_request:
  push:
  branches:
  - 'master'
 
 jobs:
  documentation:
- name: ${{ matrix.os }} / ${{ matrix.python-version }}
- runs-on: ${{ matrix.os }}
- strategy:
- matrix: # only lowest supported Python on latest ubuntu
- os: [ubuntu-latest]
- python-version: [3.7]
-
- steps:
- - uses: actions/checkout@v3
-
- - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
- with:
- python-version: ${{ matrix.python-version }}
- cache: 'pip'
- cache-dependency-path: '**/setup.py'
-
- - name: Get full Python version
- id: full-python-version
- run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
-
- - name: Upgrade pip, setuptools and wheel
- run: python -m pip install --upgrade pip setuptools wheel
-
- - name: Install package
- run: python -m pip install '.[doc]'
-
- - name: Build documentation
- run: python -m sphinx -b html doc ./doc_build -d ./doc_build
-
- - name: Upload documentation to gh-pages
- if: ${{ success() }}
- uses: JamesIves/github-pages-deploy-action@3.7.1
- with:
- GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- BRANCH: gh-pages
- FOLDER: doc_build
+ uses: pylhc/.github/.github/workflows/documentation.yml@master

.github/workflows/publish.yml

@@ -1,50 +1,11 @@
 # Publishes to PyPI upon creation of a release
 name: Upload Package to PyPI
 
-defaults:
- run:
- shell: bash
-
 on: # Runs everytime a release is added to the repository
  release:
  types: [created]
 
 jobs:
  deploy:
- name: ${{ matrix.os }} / ${{ matrix.python-version }}
- runs-on: ${{ matrix.os }}
- strategy:
- matrix: # only lowest supported Python on latest ubuntu
- os: [ubuntu-latest]
- python-version: [3.7]
-
-
- steps:
- - uses: actions/checkout@v3
-
- - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
- with:
- python-version: ${{ matrix.python-version }}
- cache: 'pip'
- cache-dependency-path: '**/setup.py'
-
- - name: Get full Python version
- id: full-python-version
- run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
-
- - name: Upgrade pip, setuptools, wheel, build and twine
- run: python -m pip install --upgrade pip setuptools wheel build twine
-
- - name: Build and check build
- run: |
- python -m build
- twine check dist/*
-
- - name: Publish
- if: ${{ success() }}
- env:
- TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
- TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
- run: |
- twine upload dist/*
+ uses: pylhc/.github/.github/workflows/publish.yml@master
+ secrets: inherit

.github/workflows/tests.yml

@@ -1,42 +1,17 @@
 # Runs all tests 
-name: Tests
+name: All Tests
 
 defaults:
  run:
  shell: bash
 
-on: [push] # Runs on all push events to any branch
-
+on: # Runs on any push event to any branch except master (the coverage workflow takes care of that)
+ push:
+ branches-ignore:
+ - 'master'
 
 jobs:
  tests:
- name: ${{ matrix.os }} / ${{ matrix.python-version }}
- runs-on: ${{ matrix.os }}
- strategy:
- matrix:
- os: [ubuntu-18.04, ubuntu-20.04, macos-latest, windows-latest]
- # Make sure to escape 3.10 with quotes so it doesn't get interpreted as float 3.1 by GA's parser
- python-version: [3.7, 3.8, 3.9, "3.10"]
-
- steps:
- - uses: actions/checkout@v3
-
- - name: Set up Python ${{ matrix.python-version }}
- uses: actions/setup-python@v4
- with:
- python-version: ${{ matrix.python-version }}
- cache: 'pip'
- cache-dependency-path: '**/setup.py'
-
- - name: Get full Python version
- id: full-python-version
- run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
-
- - name: Upgrade pip, setuptools and wheel
- run: python -m pip install --upgrade pip setuptools wheel
-
- - name: Install package
- run: python -m pip install '.[test]'
-
- - name: Run basic tests
- run: python -m pytest
+ uses: pylhc/.github/.github/workflows/tests.yml@master
+ with:
+ extra-dependencies: test # test includes hdf5 dependency specifier