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python.yml
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# sync with https://github.com/fphammerle/ical2vdir/blob/master/.github/workflows/python.yml
# https://help.github.com/en/actions/reference/workflow-syntax-for-github-actions
# shown in badge
# https://help.github.com/en/actions/automating-your-workflow-with-github-actions/configuring-a-workflow#adding-a-workflow-status-badge-to-your-repository
name: tests
on:
push:
pull_request:
schedule:
- cron: '0 20 * * 5'
jobs:
code-format:
runs-on: ubuntu-20.04
strategy:
matrix:
python-verison: ['3.9']
steps:
- uses: actions/checkout@v2.3.4
- uses: actions/setup-python@v2.2.2
with:
python-version: ${{ matrix.python-version }}
- run: pip install --upgrade pipenv==2020.8.13
- run: pipenv install --python "$PYTHON_VERSION" --deploy --dev
env:
PYTHON_VERSION: ${{ matrix.python-version }}
- run: pipenv graph
- run: pipenv run black --check .
tests:
runs-on: ubuntu-20.04
strategy:
matrix:
python-version:
- '3.6'
- '3.7'
- '3.8'
- '3.9'
pandas-version:
- '' # locked version
- 0.21.*
- 0.22.*
- 0.23.*
- 0.24.*
- 0.25.*
- 1.1.* # python3.6
- 1.*
exclude:
# https://github.com/pandas-dev/pandas/commit/83807088329b2a7e6422e0d0ba460870a265d3d2#diff-60f61ab7a8d1910d86d9fda2261620314edcae5894d5aaa236b821c7256badd7R768
- python-version: 3.6
pandas-version: 1.*
- python-version: 3.7
pandas-version: 0.21.*
- python-version: 3.7
pandas-version: 0.22.*
# > astroid.exceptions.AttributeInferenceError: '_constructor_expanddim' not found on <ClassDef.Series l.139 at 0x7f314baa6410>.
# https://github.com/fphammerle/freesurfer-volume-reader/runs/1937182916
- python-version: 3.7
pandas-version: 1.1.*
# >/tmp/pip-install-g4jx0np4/numpy/_configtest.c:6: undefined reference to `exp'
# https://travis-ci.org/github/fphammerle/freesurfer-stats/jobs/683704331#L437
- python-version: 3.8
pandas-version: 0.21.*
# https://travis-ci.org/github/fphammerle/freesurfer-stats/jobs/683704330#L437
- python-version: 3.8
pandas-version: 0.22.*
# no python3.8 wheels for pandas v0.24.2 & v0.23.4 available
# https://travis-ci.org/github/fphammerle/freesurfer-stats/builds/701952350
# build takes longer than 10min
# https://travis-ci.org/github/fphammerle/freesurfer-stats/jobs/702077404#L199
- python-version: 3.8
pandas-version: 0.23.*
- python-version: 3.8
pandas-version: 0.24.*
# > astroid.exceptions.AttributeInferenceError: '_constructor_expanddim' not found on <ClassDef.Series l.139 at 0x7f314baa6410>.
# https://github.com/fphammerle/freesurfer-volume-reader/runs/1937182916
- python-version: 3.8
pandas-version: 1.1.*
- python-version: 3.9
pandas-version: 0.21.*
- python-version: 3.9
pandas-version: 0.22.*
- python-version: 3.9
pandas-version: 0.23.*
- python-version: 3.9
pandas-version: 0.24.*
# > Cython-generated file 'pandas/_libs/algos.c' not found.
- python-version: 3.9
pandas-version: 0.25.*
fail-fast: false
steps:
- uses: actions/checkout@v2.3.4
- uses: actions/setup-python@v2.2.2
with:
python-version: ${{ matrix.python-version }}
- run: pip install --upgrade pipenv==2020.8.13
# by default pipenv picks the latest version in PATH
- run: pipenv --python "$(which python)" install --deploy --dev
# `pipenv install --selective-upgrade "pandas==$PANDAS_VERSION"` was not effective
- run: '[ -z "$PANDAS_VERSION" ] || pipenv run pip install "pandas==$PANDAS_VERSION"'
env:
PANDAS_VERSION: ${{ matrix.pandas-version }}
- run: pipenv graph
- run: pipenv run pytest --cov="$(cat *.egg-info/top_level.txt)" --cov-report=term-missing --cov-fail-under=100
- run: pipenv run pylint --load-plugins=pylint_import_requirements "$(cat *.egg-info/top_level.txt)"
# https://github.com/PyCQA/pylint/issues/352
# disable parse-error due to:
# > tests/resources/__init__.py:1:0: F0010: error while code parsing: Unable to load file tests/resources/__init__.py:
# > [Errno 2] No such file or directory: 'tests/resources/__init__.py' (parse-error)
- run: pipenv run pylint --disable=parse-error tests/*
- run: pipenv run mypy "$(cat *.egg-info/top_level.txt)" tests
# >=2.1.0 to support GITHUB_TOKEN
# COVERALLS_REPO_TOKEN required manual configuration of secret
# https://github.com/TheKevJames/coveralls-python/commit/f597109b62fadaf900af79d4f08a7debee5229e2
- run: pip install 'coveralls>=2.1.0,<4'
- run: coveralls
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# https://github.com/TheKevJames/coveralls-python/issues/240#issuecomment-758336355
COVERALLS_SERVICE_NAME: github
test-examples: # sync with https://github.com/fphammerle/freesurfer-surface/blob/dev/.github/workflows/python.yml#L73
runs-on: ubuntu-18.04
strategy:
matrix:
python-version:
- '3.6'
- '3.7'
- '3.8'
- '3.9'
fail-fast: false
defaults:
run:
working-directory: examples/
steps:
- uses: actions/checkout@v2.3.4
- uses: actions/setup-python@v1
with:
python-version: ${{ matrix.python-version }}
- run: pip install --upgrade pipenv==2020.8.13
- run: pipenv --python "$(which python)" install --deploy --dev
# > RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd
- run: python3 -c 'import sys; sys.exit(sys.version_info >= (3, 8))'
|| pipenv run pip install --no-deps numpy==1.20.1
- run: pipenv graph
# > the default behaviour is to abort conversion [...] if one of the cells throws an error
- run: pipenv run jupyter nbconvert --execute --inplace *.ipynb
# revert line specifying version of python interpreter
- run: sudo apt-get update
- run: sudo apt-get install --yes --no-install-recommends patchutils
- run: >-
git diff --unified=0
| grepdiff --output-matching=hunk '^\( "version":\| "execution": {\| "<img src=\\"data:image/png;base64,\)'
| patch --reverse
- run: git diff --exit-code