Remove shifting of coordinates #2185
Workflow file for this run
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name: tests | |
on: | |
push: | |
branches: [ main ] | |
pull_request: | |
branches: [ main ] | |
jobs: | |
tests: | |
runs-on: ${{ matrix.os }} | |
defaults: | |
run: | |
# Use a login shell, so that ~/.bash_profile is executed and | |
# the conda environment gets initialised. | |
shell: bash -l {0} | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ubuntu-20.04, macos-12, windows-latest] | |
python: ["3.8", "3.10"] | |
env: | |
CONDA_ENV_NAME: stdpopsim | |
OS: ${{ matrix.os }} | |
PYTHON: ${{ matrix.python }} | |
steps: | |
- name: cancel previous runs | |
uses: styfle/cancel-workflow-action@0.6.0 | |
with: | |
access_token: ${{ github.token }} | |
- name: checkout | |
uses: actions/checkout@v2 | |
- name: find conda | |
id: find-conda | |
run: | | |
echo "CONDA=$CONDA" >> $GITHUB_OUTPUT | |
- name: fix conda permissions | |
if: runner.os == 'macOS' | |
run: | | |
# Fix incorrect conda permissions on mac that prevent cache restore. | |
echo "$USER:staff ${{ steps.find-conda.outputs.CONDA }}" | |
sudo chown -R $USER:staff ${{ steps.find-conda.outputs.CONDA }} | |
- name: cache conda | |
id: cache | |
uses: actions/cache@v3 | |
env: | |
# Increase this to reset the cache if the key hasn't changed. | |
CACHE_NUM: 9 | |
with: | |
path: | | |
${{ steps.find-conda.outputs.CONDA }}/envs/${{ env.CONDA_ENV_NAME }} | |
~/.bash_profile | |
key: ${{ runner.os }}-${{ matrix.python }}-conda-${{ hashFiles('requirements/CI/*') }}-${{ env.CACHE_NUM }} | |
- name: install conda | |
uses: conda-incubator/setup-miniconda@v2 | |
if: steps.cache.outputs.cache-hit != 'true' | |
with: | |
activate-environment: ${{ env.CONDA_ENV_NAME }} | |
python-version: ${{ matrix.python }} | |
channels: conda-forge | |
channel-priority: strict | |
auto-update-conda: true | |
use-only-tar-bz2: true | |
- name: move profile | |
if: steps.cache.outputs.cache-hit != 'true' && runner.os != 'Windows' | |
run: | | |
# The setup-miniconda action leaves different shell init files for | |
# different OSes. Bash gives priority to ~/.bash_profile, so here we | |
# ensure that's used for all platforms. | |
mv ~/.profile ~/.bash_profile | |
- name: install dependencies | |
if: steps.cache.outputs.cache-hit != 'true' | |
run: | | |
# We install msprime from conda to avoid GSL-related build issues | |
# when pip installing without binary wheels (on Windows). | |
conda install --yes --file=requirements/CI/conda.txt | |
pip install -r requirements/CI/requirements.txt | |
- name: run test suite | |
run: | | |
python -m pytest \ | |
-n 0 \ | |
-v \ | |
--cov=stdpopsim \ | |
--cov-branch \ | |
--cov-report=term-missing \ | |
--cov-report=xml \ | |
tests | |
- name: upload coverage report to codecov | |
uses: codecov/codecov-action@v3 | |
with: | |
fail_ci_if_error: true | |
env_vars: OS,PYTHON | |
# Use upload token to avoid upload failures. | |
# https://github.com/codecov/codecov-action/issues/837 | |
token: 8ae76ade-9d0e-4a2d-b9ef-1180235be07f |