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Add lineage tail

Add lineage tail #2077

Workflow file for this run

name: Tests
on:
pull_request:
push:
branches: [main]
jobs:
pre-commit:
name: Lint
runs-on: ubuntu-latest
steps:
- name: Cancel Previous Runs
uses: styfle/[email protected]
with:
access_token: ${{ github.token }}
- uses: actions/checkout@v3
- uses: actions/setup-python@v4
- name: install clang-format
run: |
pip install clang-format==6.0.1
- uses: pre-commit/[email protected]
test:
name: Python
runs-on: ${{ matrix.os }}
strategy:
matrix:
python: [ 3.9, 3.12 ]
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@v4
with:
submodules: true
- name: Cache conda and dependencies
id: cache
uses: actions/cache@v3
with:
path: ${{ env.CONDA }}/envs
key: ${{ runner.os }}-${{ runner.arch }}-${{ matrix.python}}-conda-v2-${{ hashFiles('requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('requirements/CI-tests-pip/requirements.txt') }}
- name: Install Conda
uses: conda-incubator/setup-miniconda@v3
if: steps.cache.outputs.cache-hit != 'true'
with:
activate-environment: anaconda-client-env
python-version: ${{ matrix.python }}
channels: conda-forge, anaconda
channel-priority: strict
auto-update-conda: true
- name: Fix windows symlinks
# This is horrible, but the "git config core.symlinks true" didn't work.
if: matrix.os == 'windows-latest'
run: |
rm lwt_interface
cp -r --dereference git-submodules/tskit/python/lwt_interface ./lwt_interface
- 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=requirements/CI-tests-conda/requirements.txt
- name: Install pip deps
if: steps.cache.outputs.cache-hit != 'true'
shell: bash -l {0}
run: |
pip install -r requirements/CI-tests-pip/requirements.txt
pip uninstall -y msprime
- name: Build module
env:
MSP_CONDA_PREFIX: c:\Miniconda\envs\anaconda-client-env
run: |
source ~/.profile
conda activate anaconda-client-env
python setup.py build_ext --inplace
- name: Run tests
run: |
source ~/.profile
conda activate anaconda-client-env
pytest -xvs -n0