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tests.yml
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name: Tests
on:
pull_request:
push:
branches:
- main
- idm-ibx-calculations
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:
matrix:
python: [ 3.8, 3.9, "3.10", 3.11 ]
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
with:
submodules: true
- name: Cache conda and dependancies
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
# Install pre-release from non standard label until msprime
# 1.0 is tagged.
conda install -c conda-forge/label/msprime_rc msprime
- name: Install pip deps
if: steps.cache.outputs.cache-hit != 'true'
shell: bash -l {0}
run: 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