New layout

.github/workflows/docs.yml

@@ -1,11 +1,13 @@
-name: Build Docs
+name: Docs
+
 on:
   pull_request:
   push:
     branches: [main]
     tags:
       - '*'
   merge_group:
+
 jobs:
   Docs:
-    uses: tskit-dev/.github/.github/workflows/docs-build-template.yml@v1
+    uses: tskit-dev/.github/.github/workflows/docs.yml@v13

.github/workflows/lint.yml

@@ -0,0 +1,8 @@
+name: Lint
+
+on:
+  pull_request:
+
+jobs:
+  Lint:
+    uses: tskit-dev/.github/.github/workflows/lint.yml@v12

.github/workflows/tests.yml

@@ -2,59 +2,26 @@ name: Tests
 
 on:
   pull_request:
-  merge_group:
   push:
     branches: [main, test]
+  merge_group:
 
 jobs:
-  pre-commit:
-    name: Lint
-    uses: tskit-dev/.github/.github/workflows/lint.yml@v2
+  packaging:
+    name: Python packaging
+    uses: tskit-dev/.github/.github/workflows/python-packaging.yml@v12
+    with:
+      cli-test-cmd: tsdate --help
 
   test:
     name: Python
-    runs-on: ${{ matrix.os }}
+    uses: tskit-dev/.github/.github/workflows/python-tests.yml@v12
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python }}
+      coverage-directory: tsdate
+    secrets: inherit
     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/cancel-workflow-action@0.12.1
-        with:
-          access_token: ${{ github.token }}
-
-      - name: Checkout
-        uses: actions/checkout@v4.2.2
-
-      - 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
-        run: |
-          uv venv
-          uv pip install -r pyproject.toml --extra test
-
-      - name: Run tests
-        run: |
-          NUMBA_DISABLE_JIT=1 uv run --no-sync python -m pytest -vv --cov=tsdate --cov-report=xml --cov-branch -n0 tests
-
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v5.4.0
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          fail_ci_if_error: false
-          flags: python-tests
-          name: codecov-umbrella
-          verbose: true
-
-      - name: Build distribution
-        run: |
-          uv run --no-sync python -m build
+        python: ["3.11", "3.13"]
+        os: [macos-latest, ubuntu-24.04, windows-latest]

.github/workflows/wheels.yml

@@ -1,138 +1,52 @@
-name: Build and test wheels
+name: Publish Python release
 
 on:
   push:
-    branches:
-      - main
-      - test
-    tags:
-      - '*'
+    branches: [test-publish]
   release:
     types: [published]
 
 jobs:
-  manylinux:
+  build:
     runs-on: ubuntu-24.04
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4.2.2
+      - uses: actions/checkout@v4.2.2
         with:
-            submodules: true
+          fetch-depth: 0
 
-      - name: Set up Python
-        uses: actions/setup-python@v5.4.0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
         with:
-          python-version: "3.10"
+          python-version: "3.12"
+          version: "0.8.15"
 
-      - name: Build sdist
-        shell: bash
-        run: |
-          python -m pip install --upgrade build
-          python -m build
+      - name: Build
+        run: uv build
 
-      - name: Upload
-        uses: actions/upload-artifact@v4.6.1
+      - uses: actions/upload-artifact@v4
         with:
-          name: sdist-wheel
-          path: dist
-
-
-  OSX-test:
-    needs: ['manylinux']
-    runs-on: macos-15
-    strategy:
-      matrix:
-        python: ["3.10", 3.13]
-    steps:
-      - name: Download wheels
-        uses: actions/download-artifact@v4.2.0
-        with:
-          name: sdist-wheel
-      - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v5.4.0
-        with:
-          python-version: ${{ matrix.python }}
-      - name: Install wheel and test
-        run: |
-          python -VV
-          pip install wheel
-          # Install the local wheel, after getting deps
-          pip install tsdate --only-binary tsdate -f .
-          pip uninstall --yes msprime
-          pip install tsdate --no-index --only-binary tsdate -f .
-          python -c "import tsdate"
+          name: dist
+          path: dist/
 
-  windows-test:
-    needs: ['manylinux']
-    runs-on: windows-latest
-    strategy:
-      matrix:
-        python: ["3.10", 3.13]
-        wordsize: [64]
-    steps:
-      - name: Download wheels
-        uses: actions/download-artifact@v4.2.0
-        with:
-          name: sdist-wheel
-      - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v5.4.0
-        with:
-          python-version: ${{ matrix.python }}
-      - name: Install wheel and test
-        run: |
-          python -VV
-          pip install wheel
-          # Install the local wheel, after getting deps
-          pip install tsdate --only-binary tsdate -f .
-          pip uninstall --yes msprime
-          pip install tsdate --no-index --only-binary tsdate -f .
-          python -c "import tsdate"
-
-  manylinux-test:
+  publish:
     runs-on: ubuntu-24.04
-    needs: ['manylinux']
-    strategy:
-      matrix:
-        python: ["3.10", 3.13]
-    steps:
-      - name: Download wheels
-        uses: actions/download-artifact@v4.2.0
-        with:
-          name: sdist-wheel
-      - name: Set up Python
-        uses: actions/setup-python@v5.4.0
-        with:
-          python-version: ${{ matrix.python }}
-      - name: Install wheel and test
-        run: |
-          python -VV
-          pip install wheel
-          # Install the local wheel, after getting deps
-          pip install tsdate --only-binary tsdate -f .
-          pip uninstall --yes msprime
-          pip install tsdate --no-index --only-binary tsdate -f .
-          python -c "import tsdate"
-
-
-  PyPI_Upload:
-    runs-on: ubuntu-24.04
-    needs: ['windows-test', 'OSX-test', 'manylinux-test']
     environment: release
+    needs: [build]
     permissions:
       id-token: write
     steps:
-      - name: Download all
-        uses: actions/download-artifact@v4.2.0
-      - 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')
+      - uses: actions/download-artifact@v7.0.0
+        with:
+          name: dist
+          path: dist
+
+      - name: Publish to TestPyPI
+        if: github.event_name == 'push' && github.ref_name == 'test-publish'
         uses: pypa/gh-action-pypi-publish@v1.13.0
         with:
-          repository_url: https://test.pypi.org/legacy/
-      - name: Publish distribution to PRODUCTION PyPI
+          repository-url: https://test.pypi.org/legacy/
+          verbose: true
+
+      - name: Publish to PyPI
         if: github.event_name == 'release'
         uses: pypa/gh-action-pypi-publish@v1.13.0
-

docs/Makefile

@@ -1,19 +1,5 @@
-# Need to set PYTHONPATH so that we pick up the local tsdate
-PYPATH=$(shell pwd)/../
-TSDATE_VERSION:=$(shell PYTHONPATH=${PYPATH} \
-   python -c 'import tsdate; print(tsdate.__version__.split("+")[0])')
-
-BUILDDIR      = _build
-
-all: dev
-
-dev:
-	PYTHONPATH=${PYPATH} ./build.sh
-
-dist:
-	@echo Building distribution for tsdate version ${TSDATE_VERSION}
-	sed -i -e s/__TSDATE_VERSION__/${TSDATE_VERSION}/g _config.yml
-	PYTHONPATH=${PYPATH} ./build.sh
+all:
+	./build.sh
 
 clean:
-	rm -fR $(BUILDDIR)
+	rm -fR _build

docs/_config.yml

@@ -48,7 +48,7 @@ sphinx:
         pygments_dark_style: monokai
         navigation_with_keys: false
         logo:
-          text: "Version __TSDATE_VERSION__"
+          text: "Version __PKG_VERSION__"
       pygments_style: monokai
       bibtex_reference_style: author_year
       myst_enable_extensions:

docs/build.sh

@@ -6,7 +6,7 @@
 
 REPORTDIR=_build/html/reports
 
-jupyter-book build -nW --keep-going .
+uv run --project=.. --group docs jupyter-book build . -vnW --keep-going
 RETVAL=$?
 if [ $RETVAL -ne 0 ]; then
     if [ -e $REPORTDIR ]; then

prek.toml

@@ -0,0 +1,40 @@
+# The prek configuration defining linting requirements. This
+# setup is optimised for long-term stability and determinism,
+# and therefore only uses either "builtin" rules or "local"
+# rules implementing lint workflows.  We do not use any remote
+# workflow repos.
+
+[[repos]]
+repo = "builtin"
+hooks = [
+    { id = "check-added-large-files" },
+    { id = "check-merge-conflict" },
+    { id = "mixed-line-ending" },
+    { id = "check-case-conflict" },
+    { id = "check-yaml" },
+    { id = "check-toml" },
+]
+
+[[repos]]
+repo = "local"
+hooks = [
+  {
+    id = "ruff-check",
+    name = "ruff check",
+    language = "system",
+    entry = "ruff check --fix --force-exclude",
+    types = ["python"],
+  },
+]
+
+[[repos]]
+repo = "local"
+hooks = [
+  {
+    id = "ruff-format",
+    name = "ruff format",
+    language = "system",
+    entry = "ruff format --force-exclude",
+    types = ["python"],
+  },
+]