Branch stat algo rewrite c

.github/workflows/docs.yml

@@ -17,7 +17,7 @@ env:
 jobs:
   build-deploy-docs:
     name: Docs
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     defaults:
       run:
         shell: bash -l {0}
@@ -27,16 +27,16 @@ jobs:
         with:
           access_token: ${{ github.token }}
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v4.2.2
 
       - name: Setup Conda
-        uses: conda-incubator/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@v3.1.0
         with:
           miniforge-version: latest
           activate-environment: tskit-docs-env
 
       - name: Cache Conda env
-        uses: actions/cache@v4
+        uses: actions/cache@v4.2.0
         with:
           path: ${{ env.CONDA }}/envs
           key: conda-${{ runner.os }}--${{ runner.arch }}--${{ hashFiles(env.REQUIREMENTS) }}-${{ env.CACHE_NUMBER }}
@@ -46,7 +46,7 @@ jobs:
 
       - name: Update environment
         run: |
-          mamba install -y python=3.10 doxygen pip
+          mamba install -y python=3.10 doxygen=1.12.0 pip
           pip install -r ${{ env.REQUIREMENTS }}
         if: steps.cache.outputs.cache-hit != 'true'
 
@@ -55,7 +55,9 @@ jobs:
         run: make $MAKE_TARGET
 
       - name: Build Docs
-        run: make -C docs
+        run: |
+          doxygen -v
+          make -C docs
 
       - name: Trigger docs site rebuild
         if: github.ref == 'refs/heads/main'

.github/workflows/release.yml

@@ -7,12 +7,12 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v4.2.2
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5.3.0
         with:
           python-version: '3.12'
       - name: Install dependencies and set up venv
@@ -39,7 +39,7 @@ jobs:
         run:
           echo ::set-output name=VERSION::$(echo $GITHUB_REF | cut -d / -f 3)
       - name: C Release
-        uses: softprops/action-gh-release@v1
+        uses: softprops/action-gh-release@v2.2.0
         if: startsWith(github.ref, 'refs/tags/') && contains(github.event.ref, 'C_')
         with:
           name: C API ${{ steps.get_version.outputs.VERSION }}
@@ -48,7 +48,7 @@ jobs:
           fail_on_unmatched_files: True
           files: build-gcc/meson-dist/*
       - name: Python Release
-        uses: softprops/action-gh-release@v1
+        uses: softprops/action-gh-release@v2.2.0
         if: startsWith(github.ref, 'refs/tags/') && !contains(github.event.ref, 'C_')
         with:
           name: Python ${{ steps.get_version.outputs.VERSION }}

.github/workflows/tests.yml

@@ -8,14 +8,14 @@ on:
 jobs:
   pre-commit:
     name: Lint
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
       - name: Cancel Previous Runs
         uses: styfle/cancel-workflow-action@0.12.1
         with:
           access_token: ${{ github.token }}
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: actions/checkout@v4.2.2
+      - uses: actions/setup-python@v5.3.0
         with:
           python-version: '3.10'
       - name: install clang-format
@@ -24,16 +24,16 @@ jobs:
           python -m venv env
           source env/bin/activate
           pip install clang-format==6.0.1
-      - uses: pre-commit/action@v3.0.0
+      - uses: pre-commit/action@v3.0.1
 
   benchmark:
     name: Benchmark
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
       - name: Cancel Previous Runs
         uses: styfle/cancel-workflow-action@0.12.1
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: actions/checkout@v4.2.2
+      - uses: actions/setup-python@v5.3.0
         with:
           python-version: '3.11'
           cache: 'pip'
@@ -50,7 +50,7 @@ jobs:
           pip uninstall -y tskit
           python run.py
       - name: Upload Results
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v4.4.3
         with:
           name: benchmark-results
           path: python/benchmark
@@ -62,7 +62,7 @@ jobs:
       fail-fast: false
       matrix:
         python: [ 3.9, 3.12 ]
-        os:  [ macos-latest, ubuntu-latest, windows-latest ]
+        os:  [ macos-latest, ubuntu-24.04, windows-latest ]
     defaults:
       run:
         shell: bash
@@ -73,7 +73,7 @@ jobs:
           access_token: ${{ github.token }}
 
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4.2.2
 
       - name: Install OSX libs
         if: matrix.os == 'macos-latest'
@@ -82,13 +82,13 @@ jobs:
 
       - name: Cache conda and dependencies
         id: cache
-        uses: actions/cache@v4
+        uses: actions/cache@v4.2.0
         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/setup-miniconda@v3
+        uses: conda-incubator/setup-miniconda@v3.1.0
         if: steps.cache.outputs.cache-hit != 'true'
         with:
           activate-environment: anaconda-client-env
@@ -141,7 +141,7 @@ jobs:
           python -m pytest -x --cov=tskit --cov-report=xml --cov-branch -n2 --durations=20 tests
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5.1.1
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
           working-directory: python
@@ -168,10 +168,10 @@ jobs:
         access_token: ${{ github.token }}
 
     - name: 'Checkout'
-      uses: actions/checkout@v4
+      uses: actions/checkout@v4.2.2
 
     - name: Setup MSYS2 ${{matrix.sys}}
-      uses: msys2/setup-msys2@v2
+      uses: msys2/setup-msys2@v2.26.0
       with:
         msystem: ${{matrix.sys}}
         update: true

.github/workflows/wheels.yml

@@ -18,9 +18,9 @@ jobs:
         python: [3.9, "3.10", 3.11, 3.12]
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v4.2.2
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v5.3.0
         with:
           python-version: ${{ matrix.python }}
       - name: Install deps
@@ -36,7 +36,7 @@ jobs:
           pip install delocate
           delocate-wheel -v dist/*.whl
       - name: Upload Wheels
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v4.4.3
         with:
           name: osx-wheel-${{ matrix.python }}
           path: python/dist
@@ -49,7 +49,7 @@ jobs:
         wordsize: [64]
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v4.2.2
       - name: Install deps
         env:
           PYTHON: "py -${{ matrix.python }}-${{ matrix.wordsize }}"
@@ -74,19 +74,19 @@ jobs:
           cp ../c/tskit.h lib/.
           ${PYTHON} -m build --wheel
       - name: Upload Wheels
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v4.4.3
         with:
           name: win-wheel-${{ matrix.python }}-${{ matrix.wordsize }}
           path: python/dist
 
   manylinux:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v4.2.2
 
       - name: Set up Python 3.9
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v5.3.0
         with:
           python-version: 3.9
 
@@ -98,7 +98,7 @@ jobs:
           python -m build --sdist
 
       - name: Upload sdist
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v4.4.3
         with:
           name: sdist
           path: python/dist
@@ -109,7 +109,7 @@ jobs:
           docker run --rm -v `pwd`:/project -w /project quay.io/pypa/manylinux2014_x86_64 bash .github/workflows/docker/buildwheel.sh
 
       - name: Upload Wheels
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v4.4.3
         with:
           name: linux-wheels
           path: python/dist/wheelhouse
@@ -122,11 +122,11 @@ jobs:
         python: [3.9, "3.10", 3.11, 3.12]
     steps:
       - name: Download wheels
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v4.1.8
         with:
           name: osx-wheel-${{ matrix.python }}
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v5.3.0
         with:
           python-version: ${{ matrix.python }}
       - name: Install wheel and test
@@ -145,11 +145,11 @@ jobs:
         wordsize: [64]
     steps:
       - name: Download wheels
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v4.1.8
         with:
           name: win-wheel-${{ matrix.python }}-${{ matrix.wordsize }}
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v5.3.0
         with:
           python-version: ${{ matrix.python }}
       - name: Install wheel and test
@@ -161,7 +161,7 @@ jobs:
           python -c "import tskit"
 
   manylinux-test:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     needs: ['manylinux']
     strategy:
       matrix:
@@ -178,11 +178,11 @@ jobs:
             wheel: cp312
     steps:
       - name: Download wheels
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v4.1.8
         with:
           name: linux-wheels
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5.3.0
         with:
           python-version: ${{ matrix.python }}
       - name: Install wheel and test
@@ -194,23 +194,23 @@ jobs:
 
 
   PyPI_Upload:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     environment: release
     needs: ['windows-test', 'OSX-test', 'manylinux-test']
     permissions:
       id-token: write
     steps:
       - name: Download all
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v4.1.8
       - name: Move to dist
         run: |
           mkdir dist
           cp */*.{whl,gz} dist/.
       - name: Publish distribution to Test PyPI
         if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags') && !contains(github.event.ref, 'C_')
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@v1.12.3
         with:
           repository_url: https://test.pypi.org/legacy/
       - name: Publish distribution to PRODUCTION PyPI
         if: github.event_name == 'release' && !startsWith(github.event.release.tag_name, 'C_')
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@v1.12.3