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jeromekelleherbenjeffery
jeromekelleher
authored and
benjeffery
committed
Change build-time dependency to numpy 2, Drop Python 3.8, add 3.12, Add pyproject.toml
1 parent f467db6 commit bb137ff

32 files changed

+210
-296
lines changed

‎.circleci/config.yml

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@@ -183,16 +183,12 @@ jobs:
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command: |
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cd python
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rm -fR build
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python setup.py sdist
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python setup.py check
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python -m twine check dist/*.tar.gz
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python -m pip install build
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python -m venv venv
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source venv/bin/activate
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pip install --upgrade setuptools pip wheel
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python setup.py build_ext
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python setup.py egg_info
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python setup.py bdist_wheel
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pip install dist/*.tar.gz
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python -m build --sdist
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python -m twine check dist/*.tar.gz
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python -m build --wheel
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pip install dist/*.whl
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tskit --help
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build-32:
@@ -218,6 +214,7 @@ workflows:
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test:
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jobs:
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- build
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- build-32
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#Temporarily disabled due avoid compiling numpy on 32bit
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# - build-32
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‎.github/workflows/docker/buildwheel.sh

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@@ -13,15 +13,12 @@ cd python
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for V in "${PYTHON_VERSIONS[@]}"; do
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PYBIN=/opt/python/$V/bin
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rm -rf build/ # Avoid lib build by narrow Python is used by wide python
16-
# Instead of letting setup.py install a newer numpy we install it here
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# using the oldest supported version for ABI compatibility
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$PYBIN/pip install oldest-supported-numpy
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$PYBIN/python setup.py build_ext --inplace
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$PYBIN/python setup.py bdist_wheel
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$PYBIN/python -m pip install build
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$PYBIN/python -m build --wheel
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done
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cd dist
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for whl in *.whl; do
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auditwheel repair "$whl"
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rm "$whl"
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done
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done

‎.github/workflows/docker/shared.env

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@@ -1,6 +1,6 @@
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PYTHON_VERSIONS=(
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cp312-cp312
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cp311-cp311
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cp310-cp310
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cp39-cp39
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cp38-cp38
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)

‎.github/workflows/docs.yml

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@@ -9,17 +9,18 @@ on:
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env:
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COMMIT_EMAIL: [email protected]
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DOXYGEN: true
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MAKE_TARGET: -C python
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OWNER: tskit-dev
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REPO: tskit
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REQUIREMENTS: python/requirements/CI-docs/requirements.txt
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APTGET: doxygen
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jobs:
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build-deploy-docs:
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name: Docs
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Cancel Previous Runs
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uses: styfle/[email protected]
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- uses: actions/checkout@v4
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- name: Install apt deps
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if: env.APTGET
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run: sudo apt-get install -y ${{env.APTGET}}
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- name: Setup Mambaforge
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uses: conda-incubator/setup-miniconda@v3
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with:
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miniforge-variant: Mambaforge
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miniforge-version: latest
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activate-environment: tskit-docs-env
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use-mamba: true
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- uses: actions/setup-python@v5
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- name: Cache Conda env
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uses: actions/cache@v3
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with:
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python-version: "3.10"
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cache: 'pip'
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path: ${{ env.CONDA }}/envs
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key: conda-${{ runner.os }}--${{ runner.arch }}--${{ hashFiles(env.REQUIREMENTS) }}-${{ env.CACHE_NUMBER }}
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env:
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CACHE_NUMBER: 0
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id: cache
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- name: Create venv and install deps
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- name: Update environment
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run: |
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pip install --upgrade pip wheel
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pip install -r ${{env.REQUIREMENTS}}
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mamba install -y python=3.10 doxygen pip
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pip install -r ${{ env.REQUIREMENTS }}
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if: steps.cache.outputs.cache-hit != 'true'
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- name: Build C module
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if: env.MAKE_TARGET
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run: |
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make $MAKE_TARGET
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run: make $MAKE_TARGET
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- name: Build Docs
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run: |
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make -C docs
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run: make -C docs
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- name: Trigger docs site rebuild
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if: github.ref == 'refs/heads/main'
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run: |
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curl -X POST https://github.com/api/repos/tskit-dev/tskit-site/dispatches \
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-H 'Accept: application/vnd.github.everest-preview+json' \
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-u AdminBot-tskit:${{ secrets.ADMINBOT_TOKEN }} \
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--data '{"event_type":"build-docs"}'
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--data '{"event_type":"build-docs"}'

‎.github/workflows/tests.yml

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@@ -60,7 +60,7 @@ jobs:
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strategy:
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fail-fast: false
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matrix:
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python: [ 3.8, 3.9, "3.11" ]
63+
python: [ 3.9, 3.12 ]
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os: [ macos-latest, ubuntu-latest, windows-latest ]
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defaults:
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run:
@@ -121,7 +121,6 @@ jobs:
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if: steps.cache.outputs.cache-hit != 'true'
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shell: bash -l {0}
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run: |
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pip install setuptools==57.5.0 #v58 broke some deps https://setuptools.pypa.io/en/latest/history.html#v58-0-0
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pip install -r python/requirements/CI-tests-pip/requirements.txt
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# Remove tskit installed by conda
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pip uninstall -y tskit
@@ -133,11 +132,6 @@ jobs:
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conda activate anaconda-client-env
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python setup.py build_ext --inplace
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- name: Remove py311 incompatible tests (lack of numba support for 3.11, needed for lshmm)
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if: matrix.python == '3.11'
138-
run: |
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rm python/tests/test_*matching*
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- name: Run tests
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working-directory: python
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run: |

‎.github/workflows/wheels.yml

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@@ -15,7 +15,7 @@ jobs:
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runs-on: macos-latest
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strategy:
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matrix:
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python: [3.8, 3.9, "3.10", 3.11]
18+
python: [3.9, "3.10", 3.11, 3.12]
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steps:
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- name: Checkout
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uses: actions/checkout@v4
@@ -25,21 +25,11 @@ jobs:
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python-version: ${{ matrix.python }}
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- name: Install deps
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run: |
28-
# Upgrade pip to get bdist_wheel
29-
pip install --upgrade pip
30-
pip install setuptools wheel
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# Instead of letting setup.py install a newer numpy we install it here
32-
# using the oldest supported version for ABI compatibility
33-
pip install oldest-supported-numpy
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- name: Build C extension
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run: |
36-
cd python
37-
python -VV
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python setup.py build_ext --inplace
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pip install build
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- name: Build Wheel
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run: |
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cd python
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python setup.py bdist_wheel
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python -m build --wheel
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- name: Delocate to bundle dynamic libs
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run: |
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cd python
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runs-on: windows-latest
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strategy:
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matrix:
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python: [3.8, 3.9, "3.10", 3.11]
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python: [3.9, "3.10", 3.11, 3.12]
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wordsize: [64]
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steps:
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- name: Checkout
@@ -66,12 +56,8 @@ jobs:
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shell: bash
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run: |
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set -ex
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${PYTHON} -m pip install --upgrade pip
70-
${PYTHON} -m pip install setuptools wheel
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# Instead of letting setup.py install a newer numpy we install it here
72-
# using the oldest supported version for ABI compatibility
73-
${PYTHON} -m pip install oldest-supported-numpy
74-
- name: Build C Extension
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${PYTHON} -m pip install build
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- name: Build Wheel
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env:
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PYTHON: "py -${{ matrix.python }}-${{ matrix.wordsize }}"
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shell: bash
@@ -86,15 +72,7 @@ jobs:
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cp -r --dereference ../c/subprojects lib/.
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cp -r --dereference ../c/tskit lib/.
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cp ../c/tskit.h lib/.
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${PYTHON} setup.py build_ext --inplace
90-
- name: Build Wheel
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env:
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PYTHON: "py -${{ matrix.python }}-${{ matrix.wordsize }}"
93-
shell: bash
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run: |
95-
set -ex
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cd python
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${PYTHON} setup.py bdist_wheel
75+
${PYTHON} -m build --wheel
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- name: Upload Wheels
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uses: actions/upload-artifact@v4
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with:
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- name: Checkout
10886
uses: actions/checkout@v4
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110-
- name: Set up Python 3.8
88+
- name: Set up Python 3.9
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uses: actions/setup-python@v5
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with:
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python-version: 3.8
91+
python-version: 3.9
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11593
- name: Build sdist
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shell: bash
11795
run: |
11896
cd python
119-
python setup.py sdist
97+
python -m pip install build
98+
python -m build --sdist
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121100
- name: Upload sdist
122101
uses: actions/upload-artifact@v4
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runs-on: macos-latest
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strategy:
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matrix:
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python: [3.8, 3.9, "3.10", 3.11]
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python: [3.9, "3.10", 3.11, 3.12]
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steps:
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- name: Download wheels
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uses: actions/download-artifact@v4
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runs-on: windows-latest
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strategy:
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matrix:
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python: [3.8, 3.9, "3.10", 3.11]
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python: [3.9, "3.10", 3.11, 3.12]
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wordsize: [64]
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steps:
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- name: Download wheels
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needs: ['manylinux']
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strategy:
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matrix:
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python: [3.8, 3.9, "3.10", 3.11]
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python: [3.9, "3.10", 3.11, 3.12]
190169
include:
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192-
- python: 3.8
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wheel: cp38
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- python: 3.9
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wheel: cp39
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- python: "3.10"
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wheel: cp310
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- python: 3.11
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wheel: cp311
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- python: 3.12
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wheel: cp312
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steps:
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- name: Download wheels
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uses: actions/download-artifact@v4
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repository_url: https://test.pypi.org/legacy/
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- name: Publish distribution to PRODUCTION PyPI
236215
if: github.event_name == 'release' && !startsWith(github.event.release.tag_name, 'C_')
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uses: pypa/gh-action-pypi-publish@release/v1
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uses: pypa/gh-action-pypi-publish@release/v1

‎.mergify.yml

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- "#changes-requested-reviews-by=0"
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- status-success=Docs
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- status-success=Lint
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- status-success=Python (3.8, macos-latest)
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- status-success=Python (3.9, macos-latest)
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- status-success=Python (3.11, macos-latest)
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- status-success=Python (3.8, ubuntu-latest)
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- status-success=Python (3.12, macos-latest)
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- status-success=Python (3.9, ubuntu-latest)
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- status-success=Python (3.11, ubuntu-latest)
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- status-success=Python (3.8, windows-latest)
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- status-success=Python (3.12, ubuntu-latest)
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- status-success=Python (3.9, windows-latest)
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- status-success=Python (3.11, windows-latest)
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- status-success=Python (3.12, windows-latest)
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- "status-success=ci/circleci: build"
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pull_request_rules:
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- name: Automatic rebase, CI and merge
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- label=AUTOMERGE-REQUESTED
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- status-success=Docs
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- status-success=Lint
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- status-success=Python (3.8, macos-latest)
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- status-success=Python (3.9, macos-latest)
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- status-success=Python (3.11, macos-latest)
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- status-success=Python (3.8, ubuntu-latest)
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- status-success=Python (3.12, macos-latest)
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- status-success=Python (3.9, ubuntu-latest)
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- status-success=Python (3.11, ubuntu-latest)
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- status-success=Python (3.8, windows-latest)
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- status-success=Python (3.12, ubuntu-latest)
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- status-success=Python (3.9, windows-latest)
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- status-success=Python (3.11, windows-latest)
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- status-success=Python (3.12, windows-latest)
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- "status-success=ci/circleci: build"
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#- status-success=codecov/patch
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#- status-success=codecov/project/c-tests

‎c/tests/test_minimal_cpp.cpp

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/* * MIT License
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*
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* Copyright (c) 2019-2023 Tskit Developers
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* Copyright (c) 2019-2024 Tskit Developers
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal

‎c/tskit.h

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/*
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* MIT License
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*
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* Copyright (c) 2019 Tskit Developers
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* Copyright (c) 2019-2024 Tskit Developers
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy
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* of this software and associated documentation files (the "Software"), to deal

‎c/tskit/tables.h

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/*
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* MIT License
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*
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* Copyright (c) 2019-2023 Tskit Developers
4+
* Copyright (c) 2019-2024 Tskit Developers
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* Copyright (c) 2017-2018 University of Oxford
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*
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* Permission is hereby granted, free of charge, to any person obtaining a copy

‎python/lwt_interface/dict_encoding_testlib.py

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# MIT License
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#
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# Copyright (c) 2018-2022 Tskit Developers
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# Copyright (c) 2018-2024 Tskit Developers
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#
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# Permission is hereby granted, free of charge, to any person obtaining a copy
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# of this software and associated documentation files (the "Software"), to deal

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