Merge pull request #8 from petrelharp/CI

github CI

.github/workflows/docs.yml

@@ -0,0 +1,54 @@
+name: Build Docs
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+    tags:
+      - '*'
+
+env:
+  COMMIT_EMAIL: [email protected]
+  MAKE_TARGET: -C python
+  OWNER: tskit-dev
+  REPO: tskit
+  REQUIREMENTS: python/requirements/CI-docs/requirements.txt
+
+jobs:
+  build-deploy-docs:
+    name: Docs
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v4
+
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: latest
+          activate-environment: tskit-docs-env
+
+      - name: Cache Conda env
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.CONDA }}/envs
+          key: conda-${{ runner.os }}--${{ runner.arch }}--${{ hashFiles(env.REQUIREMENTS) }}-${{ env.CACHE_NUMBER }}
+        env:
+          CACHE_NUMBER: 0
+        id: cache
+
+      - name: Update environment
+        run: |
+          mamba install -y python=3.12 doxygen pip
+          pip install -r ${{ env.REQUIREMENTS }}
+        if: steps.cache.outputs.cache-hit != 'true'
+
+      - name: Build Docs
+        run: make -C docs

.github/workflows/tests.yml

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+name: Tests
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+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]
+      - 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-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]
+        with:
+          submodules: true
+
+      - name: Cache conda and dependencies
+        id: cache
+        uses: actions/[email protected]
+        with:
+          path: ${{ env.CONDA }}/envs
+          key: ${{ runner.os }}-${{ runner.arch }}-${{ matrix.python}}-conda-${{ hashFiles('requirements/CI-tests-conda/requirements.txt') }}-${{ hashFiles('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, anaconda
+          channel-priority: strict
+          auto-update-conda: true
+
+      - 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 install .
+
+      - name: Run tests
+        run: |
+          source ~/.profile
+          conda activate anaconda-client-env
+          pytest -xvs -n0

requirements/CI-docs-pip/requirements.txt

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+jupyter-book==1.0.0
+breathe==4.35.0
+sphinx-autodoc-typehints==2.2.2
+sphinx-issues==4.1.0
+sphinx-argparse==0.4.0
+svgwrite==1.4.3
+tskit==0.6.0
+scipy==1.14.1
+msprime==1.3.2
+sphinx-book-theme
+

requirements/CI-tests-conda/requirements.txt

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+scipy==1.14.1
+msprime==1.3.2

requirements/CI-tests-pip/requirements.txt

@@ -0,0 +1,5 @@
+tskit==0.6.0
+numpy==2.2.0
+pytest==8.2.2
+pytest-cov==5.0.0
+pytest-xdist==3.6.1

requirements/development.txt

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+tskit
+numpy
+scipy
+pytest
+pytest-cov
+pytest-xdist
+msprime>=1.0.0