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adding "generic" human DFE #2056

adding "generic" human DFE

adding "generic" human DFE #2056

Workflow file for this run

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-11, 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: ${{ github.token }}
- name: checkout
uses: actions/checkout@v2
- name: find conda
id: find-conda
run: |
echo "name=CONDA::$CONDA" >> $GITHUB_OUTPUT
- name: fix conda permissions
if: runner.os == 'macOS'
run: |
# Fix incorrect conda permissions on mac that prevent cache restore.
sudo chown -R $USER:staff $CONDA
- name: cache conda
id: cache
uses: actions/cache@v2
env:
# Increase this to reset the cache if the key hasn't changed.
CACHE_NUM: 5
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