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Upgrade actions, build with numpy2
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‎.circleci/config.yml‎

Lines changed: 41 additions & 29 deletions
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@@ -1,8 +1,12 @@
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version: 2
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version: 2.1
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orbs:
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codecov: codecov/[email protected]
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26
jobs:
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build:
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docker:
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- image: cimg/python:3.7
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- image: cimg/python:3.9
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steps:
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- checkout
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@@ -21,12 +25,12 @@ jobs:
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- run:
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name: Install development dependencies
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command: |
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pyenv global 3.8
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pyenv global 3.9
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pip install -r requirements/CI-tests-complete/requirements.txt --user
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pyenv rehash
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- save_cache:
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key: tsinfer-{{ .Branch }}
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key: tsinfer-{{ .Branch }}-v1
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paths:
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- "/home/circleci/.local"
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@@ -37,6 +41,30 @@ jobs:
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# Write out the status for debugging purposes. Are we checked out at tags?
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git submodule status --recursive
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- run:
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name: Build the distribution tarball.
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command: |
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python -m build --sdist
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python setup.py check
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python -m twine check dist/*.tar.gz --strict
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rm dist/*
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python -m build
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- run:
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name: Install from the distribution tarball
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command: |
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python -m venv venv
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source venv/bin/activate
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pip install dist/*.tar.gz
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python -c 'import tsinfer; print(tsinfer.__version__)'
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#Also check the wheel
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pip uninstall --yes tsinfer
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pip install dist/*.whl
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python -c 'import tsinfer; print(tsinfer.__version__)'
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deactivate
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rm -rf venv
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- run:
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name: Compile Python
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command: |
@@ -45,10 +73,13 @@ jobs:
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- run:
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name: Run Python tests and upload coverage
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command: |
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python3 -m pytest --cov=tsinfer --cov-report=xml --cov-branch -n4 tests
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python3 -m codecov -X gcov -F python
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python3 -m pytest --cov=tsinfer --cov-report=xml --cov-branch -xvs tests
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rm .coverage
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- codecov/upload:
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flags: python
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token: CODECOV_TOKEN
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- run:
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name: Compile C with gcc
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command: |
@@ -79,7 +110,10 @@ jobs:
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gcov -pb ./libtsinfer.a.p/object_heap.c.gcno ../lib/object_heap.c
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gcov -pb ./libtsinfer.a.p/err.c.gcno ../lib/err.c
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cd ..
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codecov -X gcov -F C
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- codecov/upload:
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flags: C
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token: CODECOV_TOKEN
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- run:
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name: Valgrind for C tests.
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command: |
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ninja -C build-clang test
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- run:
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name: Build the distribution tarball.
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command: |
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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 --strict
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rm dist/*
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python -m build
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- run:
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name: Install from the distribution tarball
105-
command: |
106-
python -m venv venv
107-
source venv/bin/activate
108-
pip install dist/*.tar.gz
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python -c 'import tsinfer; print(tsinfer.__version__)'
110-
111-
#Also check the wheel
112-
pip uninstall --yes tsinfer
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pip install dist/*.whl
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python -c 'import tsinfer; print(tsinfer.__version__)'
115-

‎.github/workflows/docker/shared.env‎

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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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cp37-cp37m
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)

‎.github/workflows/docs.yml‎

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runs-on: ubuntu-latest
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steps:
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- name: Cancel Previous Runs
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uses: styfle/cancel-workflow-action@0.11.0
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uses: styfle/cancel-workflow-action@0.12.1
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with:
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access_token: ${{ github.token }}
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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with:
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submodules: true
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- uses: actions/setup-python@v4
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- uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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- uses: actions/cache@v3
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- uses: actions/cache@v4
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id: venv-cache
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with:
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path: venv
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key: docs-venv-v3-${{ hashFiles('requirements/CI-docs/requirements.txt') }}
38+
key: docs-venv-v6-${{ hashFiles('requirements/CI-docs/requirements.txt') }}
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- name: Create venv and install deps (one by one to avoid conflict errors)
4141
if: steps.venv-cache.outputs.cache-hit != 'true'
@@ -63,4 +63,4 @@ jobs:
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curl -X POST https://api.github.com/repos/tskit-dev/tskit-site/dispatches \
6464
-H 'Accept: application/vnd.github.everest-preview+json' \
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-u AdminBot-tskit:${{ 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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pull_request:
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push:
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branches: [main]
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tags:
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jobs:
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pre-commit:
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name: Lint
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runs-on: ubuntu-latest
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steps:
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- name: Cancel Previous Runs
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uses: styfle/cancel-workflow-action@0.11.0
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uses: styfle/cancel-workflow-action@0.12.1
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with:
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access_token: ${{ github.token }}
18-
- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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- uses: actions/checkout@v4
18+
- uses: actions/setup-python@v5
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with:
21-
python-version: "3.10"
20+
python-version: '3.10'
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- name: install clang-format
22+
if: steps.clang_format.outputs.cache-hit != 'true'
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run: |
24-
pip install clang-format==6.0.1
24+
sudo pip install clang-format==6.0.1
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sudo ln -s /usr/local/bin/clang-format /usr/local/bin/clang-format-6.0
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- uses: pre-commit/[email protected]
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test:
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name: Python
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runs-on: ${{ matrix.os }}
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strategy:
32+
fail-fast: false
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matrix:
32-
python: [ 3.7, "3.10" ]
34+
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:
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shell: bash
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steps:
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- name: Cancel Previous Runs
39-
uses: styfle/cancel-workflow-action@0.11.0
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uses: styfle/cancel-workflow-action@0.12.1
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with:
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access_token: ${{ github.token }}
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4345
- name: Checkout
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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with:
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submodules: true
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4850
- name: Cache conda and dependancies
4951
id: cache
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uses: actions/cache@v3
52+
uses: actions/cache@v4
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with:
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path: |
53-
c:\Miniconda\envs\anaconda-client-env
54-
/usr/share/miniconda/envs/anaconda-client-env
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~/osx-conda
56-
~/.profile
57-
key: ${{ runner.os }}-${{ matrix.python}}-conda-v11-${{ hashFiles('requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('requirements/CI-tests-pip/requirements.txt') }}
54+
path: ${{ env.CONDA }}/envs
55+
key: ${{ runner.os }}-${{ runner.arch }}-${{ matrix.python}}-conda-v5-${{ hashFiles('requirements/CI-tests-conda/requirements.txt')}}
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59-
- name: Install Conda
60-
uses: conda-incubator/setup-miniconda@v2
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- name: Install Miniconda with Mamba
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uses: conda-incubator/setup-miniconda@v3
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if: steps.cache.outputs.cache-hit != 'true'
6260
with:
6361
activate-environment: anaconda-client-env
6462
python-version: ${{ matrix.python }}
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channels: conda-forge
66-
channel-priority: strict
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# channel-priority: strict
6765
auto-update-conda: true
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# mamba-version: "*"
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# use-mamba: true
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6969
- name: Fix windows .profile
7070
if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
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shell: bash -l {0} #We need a login shell to get conda
8484
run: conda install --yes --file=requirements/CI-tests-conda/requirements.txt
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86-
- name: Install pip deps
87-
if: steps.cache.outputs.cache-hit != 'true' && matrix.python != 3.7
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shell: bash -l {0}
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run: pip install -r requirements/CI-tests-pip/requirements.txt
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- name: Fix pandas on 3.7
92-
if: steps.cache.outputs.cache-hit != 'true' && matrix.python == 3.7
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shell: bash -l {0}
94-
run: pip install -r requirements/CI-tests-pip/requirements3.7.txt
86+
- name: Install cyvcf2 #Fails if done via conda due to no windows support.
87+
if: steps.cache.outputs.cache-hit != 'true' && matrix.os != 'windows-latest'
88+
run: |
89+
source ~/.profile
90+
conda activate anaconda-client-env
91+
#Install these by pip so we don't pull in cbgen with conda as it isn't available on 3.12
92+
pip install sgkit==0.9.0 cyvcf2==0.31.1 yarl==1.9.4 aiohttp==3.9.5 requests==2.32.3
9593
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- name: Install sgkit only on windows
95+
if: steps.cache.outputs.cache-hit != 'true' && matrix.os == 'windows-latest'
96+
run: |
97+
source ~/.profile
98+
conda activate anaconda-client-env
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#Install these by pip so we don't pull in cbgen with conda as it isn't available on 3.12
100+
pip install sgkit==0.9.0
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97102
- name: Build module
98103
run: |
99104
source ~/.profile
100105
conda activate anaconda-client-env
106+
# Use numpy2 to build the module
107+
pip install "numpy>=2"
101108
python setup.py build_ext --inplace
102109
103110
- name: Run tests
104111
run: |
105112
source ~/.profile
106113
conda activate anaconda-client-env
107-
python -m pytest -xv -n2
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# Test with numpy<2 for numba
115+
pip install "numpy<2"
116+
python -m pytest -xv

‎.mergify.yml‎

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- "#approved-reviews-by>=1"
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- "#changes-requested-reviews-by=0"
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- status-success=Lint
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- status-success=Python (3.7, macos-latest)
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- status-success=Python (3.10, macos-latest)
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- status-success=Python (3.7, ubuntu-latest)
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- status-success=Python (3.10, ubuntu-latest)
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- status-success=Python (3.7, windows-latest)
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- status-success=Python (3.10, windows-latest)
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- status-success=Python (3.9, macos-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 (3.12, ubuntu-latest)
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- status-success=Python (3.9, 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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- base=main
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- label=AUTOMERGE-REQUESTED
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- status-success=Lint
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- status-success=Python (3.7, macos-latest)
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- status-success=Python (3.10, macos-latest)
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- status-success=Python (3.7, ubuntu-latest)
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- status-success=Python (3.10, ubuntu-latest)
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- status-success=Python (3.7, windows-latest)
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- status-success=Python (3.10, windows-latest)
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- status-success=Python (3.9, macos-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 (3.12, ubuntu-latest)
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- status-success=Python (3.9, 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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actions:
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queue:
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name: default
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method: rebase
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rebase_fallback: none
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update_method: rebase
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- name: Remove label after merge
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actions:
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label:
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remove:
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- AUTOMERGE-REQUESTED
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- AUTOMERGE-REQUESTED

‎.pre-commit-config.yaml‎

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rev: v3.2.2
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hooks:
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- id: pyupgrade
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args: [ --py3-plus, --py37-plus ]
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args: [ --py3-plus, --py39-plus ]
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- repo: https://github.com/psf/black
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rev: 22.10.0
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hooks:

‎CHANGELOG.md‎

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# Changelog
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## [0.3.2] - 2024-07-12
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**Breaking Changes**
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7+
- tsinfer now requires Python 3.9 or later
8+
39
## [0.3.1] - 2023-04-19
410

511
Bug fix release for a bad dependency specification.

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