new layout

.github/workflows/docs.yml

@@ -1,11 +1,11 @@
 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@main

.github/workflows/lint.yml

@@ -0,0 +1,11 @@
+name: Lint
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+  merge_group:
+
+jobs:
+  Lint:
+    uses: tskit-dev/.github/.github/workflows/lint.yml@main

.github/workflows/tests.yml

@@ -7,74 +7,19 @@ on:
   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@main
 
   test:
     name: Python
-    runs-on: ${{ matrix.os }}
+    uses: tskit-dev/.github/.github/workflows/python-tests.yml@main
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python }}
+      coverage-directory: tstrait
+    secrets: inherit
     strategy:
       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 }}
-      - 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: Test with pytest
-        run: |
-          uv run --no-sync python -m pytest --cov=tstrait --cov-report=xml --cov-branch -n 0 tests
-      - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v5.1.1
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-      - name: Delete coverage
-        run: |
-            rm .coverage
-
-  dist-tests:
-    name: Distribution
-    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@v4.2.2
-      - uses: actions/setup-python@v5.3.0
-        with:
-          python-version: '3.12'
-      - name: Install dependencies
-        run: |
-          python3 -m pip install --upgrade pip
-          python3 -m pip install twine build
-      - name: Build sdist and wheel
-        run: |
-          python -m build
-      - name: Check distribution artefacts
-        run: |
-          python3 -m twine check dist/*
-      - name: Install wheel
-        run: |
-          python3 -m pip install dist/*.whl
-      - name: Import package
-        # Don't import from current dir
-        run: |
-          cd /
-          python3 -c "import tstrait"
+        python: ["3.11", "3.13"]
+        os: [macos-latest, ubuntu-24.04, windows-latest]

.github/workflows/wheels.yml

@@ -1,126 +1,52 @@
-name: Build and test wheels
+name: Publish Python release
 
 on:
   push:
-    branches:
-      - main
-      - test
-    tags:
-      - '*'
+    branches: [test-publish]
   release:
     types: [published]
 
 jobs:
-  distbuild:
-    name: Build Distribution
+  build:
     runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v4.2.2
-      - uses: actions/setup-python@v5.3.0
         with:
-          python-version: '3.12'
-      - name: Install dependencies
-        run: |
-          python3 -m pip install --upgrade pip
-          python3 -m pip install twine build
-      - name: Build sdist and wheel
-        run: |
-          python -m build
-      - name: Check distribution artefacts
-        run: |
-          python3 -m twine check dist/*
-      - name: Upload wheel and sdist
-        uses: actions/upload-artifact@v4.4.3
-        with:
-          name: wheels
-          path: dist
+          fetch-depth: 0
 
-  OSX-test:
-    needs: ['distbuild']
-    runs-on: macos-latest
-    strategy:
-      matrix:
-        python: ["3.10", "3.11", "3.12", "3.13"]
-    steps:
-      - name: Download wheels
-        uses: actions/download-artifact@v4.1.8
-        with:
-          name: wheels
-      - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v5.3.0
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
         with:
-          python-version: ${{ matrix.python }}
-      - name: Install wheel and test
-        run: |
-          python -VV
-          # Install the local wheel
-          pip install tstrait --only-binary tstrait -f .
-          python -c "import tstrait"
+          python-version: "3.12"
+          version: "0.8.15"
 
-  windows-test:
-    needs: ['distbuild']
-    runs-on: windows-latest
-    strategy:
-      matrix:
-        python: ["3.10", "3.11", "3.12", "3.13"]
-        wordsize: [64]
-    steps:
-      - name: Download wheels
-        uses: actions/download-artifact@v4.1.8
-        with:
-          name: wheels
-      - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v5.3.0
-        with:
-          python-version: ${{ matrix.python }}
-      - name: Install wheel and test
-        run: |
-          python -VV
-          pip install wheel
-          # Install the local wheel
-          pip install tstrait --only-binary tstrait -f .
-          python -c "import tstrait"
+      - name: Build
+        run: uv build
 
-  linux-test:
-    runs-on: ubuntu-24.04
-    needs: ['distbuild']
-    strategy:
-      matrix:
-        python: ["3.10", "3.11", "3.12", "3.13"]
-    steps:
-      - name: Download wheels
-        uses: actions/download-artifact@v4.1.8
+      - uses: actions/upload-artifact@v4
         with:
-          name: wheels
-      - name: Set up Python
-        uses: actions/setup-python@v5.3.0
-        with:
-          python-version: ${{ matrix.python }}
-      - name: Install wheel and test
-        run: |
-          python -VV
-          # Install the local wheel
-          pip install tstrait --only-binary tstrait -f .
-          python -c "import tstrait"
+          name: dist
+          path: dist/
 
-  PyPI_Upload:
+  publish:
     runs-on: ubuntu-24.04
     environment: release
-    needs: ['windows-test', 'OSX-test', 'linux-test']
+    needs: [build]
     permissions:
       id-token: write
     steps:
-      - name: Download all
-        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')
-        uses: pypa/gh-action-pypi-publish@v1.12.3
+      - uses: actions/download-artifact@v7.0.0
         with:
-          repository_url: https://test.pypi.org/legacy/
-      - name: Publish distribution to PRODUCTION PyPI
+          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/
+          verbose: true
+
+      - name: Publish to PyPI
         if: github.event_name == 'release'
-        uses: pypa/gh-action-pypi-publish@v1.12.3
+        uses: pypa/gh-action-pypi-publish@v1.13.0

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.1.2] - 2026-XX-XX
+Unreleased
+
+- Upgrade supported Python versions to 3.11 -> 3.14
+
 ## [0.1.1] - 2025-09-18
 
 ### Update:
@@ -56,7 +61,7 @@
 ### Highlights:
 
 - Initial stable release of tstrait in PyPI https://pypi.org/project/tstrait/
-- Initial stable release of tstrait in conda-forge 
+- Initial stable release of tstrait in conda-forge
 
 ### Documentation:
 

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"],
+  },
+]