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tests.yml
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name: Tests
on:
pull_request:
push:
branches: [main, test]
jobs:
pre-commit:
name: Lint
runs-on: ubuntu-18.04
steps:
- name: Cancel Previous Runs
uses: styfle/[email protected]
with:
access_token: ${{ github.token }}
- uses: actions/checkout@v2
- uses: actions/setup-python@v2
- name: install clang-format
if: steps.clang_format.outputs.cache-hit != 'true'
run: |
sudo apt-get remove -y clang-6.0 libclang-common-6.0-dev libclang1-6.0 libllvm6.0
sudo apt-get autoremove
sudo apt-get install clang-format clang-format-6.0
- uses: pre-commit/[email protected]
test:
name: Python
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
python: [ 3.7, 3.9, "3.10" ]
os: [ macos-latest, ubuntu-latest, windows-latest ]
defaults:
run:
shell: bash
steps:
- name: Cancel Previous Runs
uses: styfle/[email protected]
with:
access_token: ${{ github.token }}
- name: Checkout
uses: actions/checkout@v2
- name: Cache conda and dependencies
id: cache
uses: actions/cache@v2
with:
path: |
c:\Miniconda\envs\anaconda-client-env
/usr/share/miniconda/envs/anaconda-client-env
~/osx-conda
~/.profile
key: ${{ runner.os }}-${{ matrix.python}}-conda-v11-${{ hashFiles('python/requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('python/requirements/CI-tests-pip/requirements.txt') }}
- name: Install Conda
uses: conda-incubator/setup-miniconda@v2
if: steps.cache.outputs.cache-hit != 'true'
with:
activate-environment: anaconda-client-env
python-version: ${{ matrix.python }}
channels: conda-forge
channel-priority: strict
auto-update-conda: true
use-only-tar-bz2: true
- name: Fix windows symlinks
working-directory: python
if: matrix.os == 'windows-latest'
run: |
rm -r lib
mkdir lib
cp -r --dereference ../c/subprojects lib/.
cp -r --dereference ../c/tskit lib/.
cp ../c/tskit.h lib/.
- name: Fix windows .profile
if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
run: |
cp ~/.bash_profile ~/.profile
- name: Install conda deps
if: steps.cache.outputs.cache-hit != 'true'
shell: bash -l {0} #We need a login shell to get conda
run: |
conda install --yes --file=python/requirements/CI-tests-conda/requirements.txt
- name: Install pip deps
if: steps.cache.outputs.cache-hit != 'true'
shell: bash -l {0}
run: |
pip install setuptools==57.5.0 #v58 broke some deps https://setuptools.pypa.io/en/latest/history.html#v58-0-0
pip install -r python/requirements/CI-tests-pip/requirements.txt
- name: Fix OSX Cache Write #OSX Won't let the cache restore due to file perms
if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'macos-latest'
run: |
cp -r /usr/local/miniconda/envs/anaconda-client-env ~/osx-conda
- name: Fix OSX Cache Restore
if: steps.cache.outputs.cache-hit == 'true' && matrix.os == 'macos-latest'
run: |
mkdir -p /usr/local/miniconda/envs
sudo cp -r ~/osx-conda /usr/local/miniconda/envs/anaconda-client-env
- name: Build module
working-directory: python
run: |
source ~/.profile
conda activate anaconda-client-env
python setup.py build_ext --inplace
- name: Run tests
working-directory: python
run: |
source ~/.profile
conda activate anaconda-client-env
# pytest -xv -n2
python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 tests
- name: Upload coverage to Codecov
if: matrix.os == 'ubuntu-latest'
uses: codecov/codecov-action@v2
with:
working-directory: python
fail_ci_if_error: true
flags: python-tests
name: codecov-umbrella
verbose: true
msys2:
runs-on: windows-latest
strategy:
matrix:
include:
- { sys: mingw32, env: i686 }
- { sys: mingw64, env: x86_64 }
name: Windows (${{ matrix.sys }}, ${{ matrix.env }})
defaults:
run:
shell: msys2 {0}
steps:
- name: Cancel Previous Runs
uses: styfle/[email protected]
with:
access_token: ${{ github.token }}
- name: 'Checkout'
uses: actions/checkout@v2
- name: Setup MSYS2 ${{matrix.sys}}
uses: msys2/setup-msys2@v2
with:
msystem: ${{matrix.sys}}
update: true
install: >-
git
mingw-w64-${{matrix.env}}-toolchain
mingw-w64-${{matrix.env}}-ninja
mingw-w64-${{matrix.env}}-meson
mingw-w64-${{matrix.env}}-cunit
- name: Build
working-directory: c
run: |
meson build -Dbuild_examples=false
ninja -C build
- name: Run tests
working-directory: c
run: |
ninja -C build test