New layout

.github/workflows/docs.yml

@@ -1,86 +1,14 @@
-name: Docs
 
+name: Docs
 on:
   pull_request:
   push:
     branches: [main]
+    tags:
+      - '*'
   merge_group:
-
 jobs:
-
-  test:
-    name: Build docs
-    runs-on: ubuntu-24.04
-    defaults:
-      run:
-        shell: bash
-    steps:
-      - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.12.1
-        with:
-          access_token: ${{ github.token }}
-
-      - name: Checkout
-        uses: actions/checkout@v4.2.2
-        with:
-          submodules: true
-
-      - name: Cache conda and dependencies
-        id: cache
-        uses: actions/cache@v4.2.2
-        env:
-          # Increase this to reset the cache if the key hasn't changed.
-          CACHE_NUM: 3
-        with:
-          path: |
-            /usr/share/miniconda/envs/anaconda-client-env
-            ~/osx-conda
-            ~/.profile
-          key: conda-v${{ env.CACHE_NUM }}-${{ hashFiles('pyproject.toml') }}
-
-      - name: Install Conda
-        uses: conda-incubator/setup-miniconda@v3.1.1
-        if: steps.cache.outputs.cache-hit != 'true'
-        with:
-          activate-environment: anaconda-client-env
-          python-version: "3.10"
-          channels: conda-forge
-          channel-priority: strict
-          auto-update-conda: true
-
-      - name: Install slim
-        if: steps.cache.outputs.cache-hit != 'true'
-        shell: bash -l {0} #We need a login shell to get conda
-        run: |
-          conda install --yes slim
-
-      - name: Install uv and pip deps
-        if: steps.cache.outputs.cache-hit != 'true'
-        shell: bash -l {0}
-        run: |
-          pip install uv
-          uv pip install --system -r pyproject.toml --extra docs
-          # Install current pyslim as editable to ensure we get the latest version
-          uv pip install --system -e .
-
-      # # Retaining commented block for next devel cycle
-      # - name: Build SLiM
-      #   run: |
-      #     git clone https://github.com/messerlab/SLiM.git
-      #     cd SLiM
-      #     mkdir -p Release
-      #     cd Release
-      #     cmake -D CMAKE_BUILD_TYPE=Release ..
-      #     make -j 2
-
-      - name: Build docs
-        run: |
-          source ~/.profile
-          conda activate anaconda-client-env
-          export PATH=$PWD/SLiM/Release:$PATH
-          slim -v
-          pip list
-          cd docs && make
-
-
-
+  Docs:
+    uses: tskit-dev/.github/.github/workflows/docs.yml@v14
+    with:
+      install-slim: true

.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@v14

.github/workflows/tests.yml

@@ -7,12 +7,16 @@ on:
   merge_group:
 
 jobs:
+  packaging:
+    name: Python packaging
+    uses: tskit-dev/.github/.github/workflows/python-packaging.yml@v14
+
   test:
     name: Python
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python: ["3.10", 3.13]
+        python: ["3.11", "3.13"]
         os: [macos-latest, ubuntu-24.04, windows-latest]
         sys: [mingw64, ucrt64]
         env: [x86_64, ucrt-x86_64]
@@ -33,7 +37,6 @@ jobs:
           - os: windows-latest
             sys: mingw64
             env: ucrt-x86_64
-
     defaults:
       run:
         shell: bash -l {0}
@@ -78,8 +81,8 @@ jobs:
           path: D:\a\pyslim\pyslim\SLiM
           key: ${{runner.os}}-${{matrix.sys}}-${{matrix.env}}-key
 
-      - name: Build SLiM windows
-        if: ( matrix.os == 'windows-latest'  && steps.cache-slim.outputs.cache-hit != 'true' )
+      - name: Build SLiM (Windows)
+        if: matrix.os == 'windows-latest' && steps.cache-slim.outputs.cache-hit != 'true'
         shell: msys2 {0}
         run: |
           git clone https://github.com/messerlab/SLiM.git
@@ -92,37 +95,29 @@ jobs:
           make -j 2
 
       - name: Install uv and dependencies
-        shell: bash -l {0}
         run: |
           pip install uv
-          uv pip install --system -r pyproject.toml --extra test
+          uv sync --locked --group test --no-default-groups
 
-      - name: Install SLiM macos / linux
-        if: (matrix.os == 'macos-latest' || matrix.os == 'ubuntu-24.04')
-        run: |
-          micromamba install slim -y
+      - name: Install SLiM (macOS / Linux)
+        if: matrix.os == 'macos-latest' || matrix.os == 'ubuntu-24.04'
+        run: micromamba install slim -y
 
       - name: Run tests
-        shell: bash -l {0}
         run: |
-          micromamba info
-          micromamba list
-          export PATH=$PWD/SLiM/Release:$PATH 
-          which slim
-          slim -v
-          python -m pytest \
-            -n 0 \
-            -v \
-            --cov=pyslim \
-            --cov-branch \
-            --cov-report=term-missing \
+          export PATH=$PWD/SLiM/Release:$PATH
+          uv run --no-default-groups --group test pytest \
+            -n 0 -v \
+            --cov=pyslim --cov-branch \
             --cov-report=xml \
             tests
 
-
-      - name: upload coverage report to codecov
+      - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v5.4.0
         with:
-          fail_ci_if_error: true
-          env_vars: OS,PYTHON
           token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true
+          flags: python-tests
+          files: coverage.xml
+          disable_search: true
+          verbose: true

.github/workflows/wheels.yml

@@ -0,0 +1,52 @@
+name: Publish Python release
+
+on:
+  push:
+    branches: [test-publish]
+  release:
+    types: [published]
+
+jobs:
+  build:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4.2.2
+        with:
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          python-version: "3.12"
+          version: "0.8.15"
+
+      - name: Build
+        run: uv build
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    runs-on: ubuntu-24.04
+    environment: release
+    needs: [build]
+    permissions:
+      id-token: write
+    steps:
+      - 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/
+          verbose: true
+
+      - name: Publish to PyPI
+        if: github.event_name == 'release'
+        uses: pypa/gh-action-pypi-publish@v1.13.0

docs/Makefile

@@ -1,18 +1,7 @@
 
-# Need to set PYTHONPATH so that we pick up the local pyslim
-PYPATH=${PWD}/..
-PYSLIM_VERSION:=$(shell PYTHONPATH=${PYPATH} \
-   python3 -c 'import pyslim; print(pyslim.__version__.split("+")[0])')
-
-dev: prereqs
+all: prereqs
 	if (cd _static && md5sum -c pedigrees.ink.svg.md5 | grep -l "FAILED"); then echo "remaking figures with inkscape"; $(MAKE) -C _static; else echo "not remaking figures"; fi
-	PYTHONPATH=${PYPATH} ./build.sh
-
-dist: prereqs
-	@echo Building distribution for pyslim version ${PYSLIM_VERSION}
-	sed -i s/__PYSLIM_VERSION__/${PYSLIM_VERSION}/g _config.yml
-	$(MAKE) -C _static
-	PYTHONPATH=${PYPATH} ./build.sh
+	./build.sh
 
 clean:
 	rm -fR _build

docs/_config.yml

@@ -42,7 +42,7 @@ sphinx:
         logo:
           text: |
             pyslim<br/>
-            version __PYSLIM_VERSION__
+            version __PKG_VERSION__
       issues_github_path: tskit-dev/pyslim
       todo_include_todos: true
       intersphinx_mapping:

docs/build.sh

@@ -6,8 +6,7 @@
 
 REPORTDIR=_build/html/reports
 
-# TODO add -n for nitpick mode.
-jupyter-book build -W --keep-going .
+uv run --project=.. --group docs jupyter-book build . -vnW --keep-going
 RETVAL=$?
 if [ $RETVAL -ne 0 ]; then
     if [ -e $REPORTDIR ]; then