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Improve IBD documentation and IdentitySegments docs #7427

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Improve IBD documentation and IdentitySegments docs

Improve IBD documentation and IdentitySegments docs #7427

Workflow file for this run

.github/workflows/tests.yml at 35bc2a9
name: Tests
on:
pull_request:
merge_group:
push:
branches: [main, test]
jobs:
pre-commit:
name: Lint
uses: tskit-dev/.github/.github/workflows/lint.yml@v2
test:
name: Python
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
python: [ "3.10", 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: 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: Install uv and set the python version
uses: astral-sh/setup-uv@v6
with:
python-version: ${{ matrix.python }}
version: "0.8.15"
- name: Install dependencies
working-directory: python
run: |
uv venv
uv pip install -r pyproject.toml --extra test
# Remove tskit installed as a dep of msprime
uv pip uninstall tskit
- name: Build module
working-directory: python
run: |
uv run --no-sync 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: |
uv run --no-sync python -c "import tskit;tskit.Tree.generate_star(5).tree_sequence.draw_svg(path='test.svg')"
- name: Run JIT code coverage
working-directory: python
run: |
NUMBA_DISABLE_JIT=1 uv run --no-sync python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 tests/test_jit.py
- name: Upload coverage to Codecov
uses: codecov/[email protected]
with:
token: ${{ secrets.CODECOV_TOKEN }}
working-directory: python
fail_ci_if_error: false
flags: python-tests-no-jit
name: codecov-umbrella
verbose: true
- name: Run tests
working-directory: python
run: |
if [[ "${{ matrix.os }}" == "windows-latest" ]]; then
uv run --no-sync python -m pytest -x --skip-slow --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests
else
uv run --no-sync python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests
fi
- 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
test-numpy1:
name: Numpy 1.x
runs-on: ubuntu-24.04
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: Setup Python
uses: actions/[email protected]
with:
python-version: '3.12'
- name: Install uv
uses: astral-sh/setup-uv@v6
with:
version: "0.8.15"
- name: Install dependencies
working-directory: python
run: |
uv venv
uv pip install -r pyproject.toml --extra test
uv pip uninstall tskit
uv pip install "numpy<2"
- name: Build module
working-directory: python
run: |
uv run --no-sync python setup.py build_ext --inplace
- name: Run tests with numpy 1.x
working-directory: python
run: |
uv run --no-sync python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 tests/test_lowlevel.py tests/test_highlevel.py
- name: Upload coverage to Codecov
uses: codecov/[email protected]
with:
token: ${{ secrets.CODECOV_TOKEN }}
working-directory: python
fail_ci_if_error: false
flags: python-tests-numpy1
name: codecov-numpy1
verbose: true
msys2:
runs-on: windows-latest
strategy:
matrix:
include:
- { sys: mingw32, env: i686 }
- { sys: mingw64, env: x86_64 }
name: Windows (${{ 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