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Concatenate and shift functions #6654

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Concatenate and shift functions

Concatenate and shift functions #6654

Workflow file for this run

.github/workflows/tests.yml at 762dcfb
name: Tests
on:
pull_request:
merge_group:
push:
branches: [main, test]
jobs:
pre-commit:
name: Lint
runs-on: ubuntu-24.04
steps:
- name: Cancel Previous Runs
uses: styfle/[email protected]
with:
access_token: ${{ github.token }}
- uses: actions/[email protected]
- uses: actions/[email protected]
with:
python-version: '3.12'
- name: install clang-format
if: steps.clang_format.outputs.cache-hit != 'true'
run: |
pip install setuptools clang-format==6.0.1
clang-format -version
sudo cp /opt/hostedtoolcache/Python/3.12.10/x64/bin/clang-format /opt/hostedtoolcache/Python/3.12.10/x64/bin/clang-format-6.0
clang-format-6.0 -version
- uses: pre-commit/[email protected]
benchmark:
name: Benchmark
runs-on: ubuntu-24.04
steps:
- name: Cancel Previous Runs
uses: styfle/[email protected]
- uses: actions/[email protected]
- uses: actions/[email protected]
with:
python-version: '3.12'
cache: 'pip'
cache-dependency-path: python/requirements/benchmark.txt
- name: Install deps
run: pip install -r python/requirements/benchmark.txt
- name: Build module
run: |
cd python
python setup.py build_ext --inplace
- name: Run benchmarks
run: |
cd python/benchmark
pip uninstall -y tskit
python run.py
- name: Upload Results
uses: actions/[email protected]
with:
name: benchmark-results
path: python/benchmark
test:
name: Python
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
python: [ 3.9, 3.13 ]
os: [ macos-latest, ubuntu-24.04, windows-latest ]
defaults:
run:
shell: bash
steps:
- name: Cancel Previous Runs
uses: styfle/[email protected]
with:
access_token: ${{ github.token }}
- name: Checkout
uses: actions/[email protected]
- name: Install OSX libs
if: matrix.os == 'macos-latest'
run: |
brew install libxml2 libxslt
- name: Cache conda and dependencies
id: cache
uses: actions/[email protected]
with:
path: ${{ env.CONDA }}/envs
key: ${{ runner.os }}-${{ runner.arch }}-${{ matrix.python}}-conda-v1-${{ hashFiles('python/requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('python/requirements/CI-tests-pip/requirements.txt') }}
- name: Install Conda
uses: conda-incubator/[email protected]
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
- 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 -r python/requirements/CI-tests-pip/requirements.txt
# Remove tskit installed by conda
pip uninstall -y tskit
- name: Build module
working-directory: python
run: |
source ~/.profile
conda activate anaconda-client-env
python setup.py build_ext --inplace
- name: Minidom test
working-directory: python
# Importing either IPython or pytest causes import of xml.dom.minidom
# So to actually test that tskit imports it, we need a minimal test
run: |
source ~/.profile
conda activate anaconda-client-env
python -c "import tskit;tskit.Tree.generate_star(5).tree_sequence.draw_svg(path='test.svg')"
- name: Run tests
working-directory: python
run: |
source ~/.profile
conda activate anaconda-client-env
python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests
- name: Upload coverage to Codecov
uses: codecov/[email protected]
with:
token: ${{ secrets.CODECOV_TOKEN }}
working-directory: python
fail_ci_if_error: false
flags: python-tests
name: codecov-umbrella
verbose: true
msys2:
runs-on: windows-latest
strategy:
matrix:
include:
- { sys: mingw32, env: i686 }
- { sys: mingw64, env: x86_64 }
name: Windows (${{ 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/[email protected]
- name: Setup MSYS2 ${{matrix.sys}}
uses: msys2/[email protected]
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