Ecosystem update

.github/workflows/docs.yml

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

.github/workflows/lint.yml

@@ -0,0 +1,9 @@
+name: Lint
+
+on:
+  pull_request:
+  merge_group:
+
+jobs:
+  lint:
+    uses: tskit-dev/.github/.github/workflows/lint.yml@v13

.github/workflows/python-packaging.yml

@@ -0,0 +1,11 @@
+name: Packaging
+
+on:
+  pull_request:
+  merge_group:
+
+jobs:
+  packaging:
+    uses: tskit-dev/.github/.github/workflows/python-packaging.yml@v13
+    with:
+      pyproject-directory: .

.github/workflows/tests.yml

@@ -7,36 +7,16 @@ on:
   merge_group:
 
 jobs:
-  pre-commit:
-    name: Lint
-    uses: tskit-dev/.github/.github/workflows/lint.yml@v2
-
   test:
     name: Python
-    runs-on: ${{ matrix.os }}
+    uses: tskit-dev/.github/.github/workflows/python-tests.yml@v13
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python }}
+      pyproject-directory: .
+      coverage-directory: tscompare
+    secrets: inherit
     strategy:
       matrix:
-        python-version: [ "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 }}
-          version: "0.8.15"
-
-      - name: Install dependencies
-        run: |
-          uv venv
-          uv pip install -e ".[test]"
-      - name: Test with pytest
-        run: |
-          uv run --no-sync python -m pytest --cov=tscompare --cov-report=xml --cov-branch -n 0 tests
+        python: ["3.11", "3.13"]
+        os: [macos-latest, ubuntu-24.04, windows-latest]

.github/workflows/wheels.yml

@@ -0,0 +1,47 @@
+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
+      - uses: astral-sh/setup-uv@v6
+        with:
+          python-version: "3.12"
+          version: "0.8.15"
+      - run: uv build
+      - uses: actions/upload-artifact@v4.6.1
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    runs-on: ubuntu-24.04
+    environment: release
+    needs: [build]
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4.2.0
+        with:
+          name: dist
+          path: dist
+
+      - name: Publish to Test PyPI
+        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

@@ -1,16 +1,6 @@
 
-# Need to set PYTHONPATH so that we pick up the local tscompare
-PYPATH=${PWD}/..
-TSC_VERSION:=$(shell PYTHONPATH=${PYPATH} \
-   python3 -c 'import tscompare; print(tscompare.__version__.split("+")[0])')
-
-dev:
-	PYTHONPATH=${PYPATH} ./build.sh
-
-dist:
-	@echo Building distribution for tscompare version ${TSC_VERSION}
-	sed -i s/__TSCOMPARE__VERSION__/${TSC_VERSION}/g _config.yml
-	PYTHONPATH=${PYPATH} ./build.sh
+all:
+	./build.sh
 
 clean:
 	rm -fR _build

docs/_config.yml

@@ -42,7 +42,7 @@ sphinx:
         navigation_with_keys: false
         pygments_dark_style: monokai
         logo:
-          text: "Version __TSCOMPARE_VERSION__"
+          text: "Version __PKG_VERSION__"
       myst_enable_extensions:
       - colon_fence
       - deflist
@@ -54,7 +54,6 @@ sphinx:
         tskit: ["https://tskit.dev/tskit/docs/stable", null]
         tutorials: ["https://tskit.dev/tutorials/", null]
         stdpopsim: ["https://popsim-consortium.github.io/stdpopsim-docs/stable", null]
-        pyslim: ["https://tskit.dev/pyslim/docs/latest/", null]
         numpy: ["https://numpy.org/doc/stable/", null]
         demes: ["https://popsim-consortium.github.io/demes-docs/main/", null]
         demes-spec: ["https://popsim-consortium.github.io/demes-spec-docs/main/", null]

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"],
+  },
+]

pyproject.toml

@@ -31,7 +31,6 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
@@ -42,10 +41,9 @@ classifiers = [
     "Operating System :: POSIX",
     "Operating System :: MacOS",
 ]
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 dependencies = [
-    "numpy>=1.21.0",
-    "tskit>=0.5.0",
+    "tskit>=1.0.0",
     "scipy>=1.7.0",
 ]
 
@@ -58,39 +56,36 @@ Homepage = "https://tskit.dev/tscompare"
 Documentation = "https://tskit.dev/tscompare/docs/"
 "Source Code" = "https://github.com/tskit-dev/tscompare"
 
-[project.optional-dependencies]
+[dependency-groups]
 test = [
-    "tskit==0.6.0",
-    "numpy==2.2.4",
-    "pytest==8.3.5",
-    "pytest-cov==6.0.0",
-    "pytest-xdist==3.6.1",
-    "scipy==1.15.2",
-    "msprime==1.3.4",
+    "msprime",
+    "pytest",
+    "pytest-cov",
+    "pytest-xdist",
 ]
 docs = [
-    "jupyter-book==1.0.4.post1",
-    "breathe==4.35.0",
-    "sphinx-autodoc-typehints==2.3.0",
-    "sphinx-issues==5.0.0",
-    "sphinx-argparse==0.5.2",
-    "svgwrite==1.4.3",
-    "tskit==0.6.0",
-    "tsinfer==0.4.1",
-    "scipy==1.15.2",
-    "msprime==1.3.4",
+    "jupyter-book<2",
+    "msprime",
+    "sphinx-argparse",
+    "sphinx-autodoc-typehints",
     "sphinx-book-theme",
-    "numcodecs>=0.6,<0.15.1", #Pinned due to https://github.com/zarr-developers/numcodecs/issues/733
-    "setuptools_scm==9.2.0",
+    "sphinx-copybutton",
+    "sphinx-issues",
+    "tsinfer",
+]
+lint = [
+    "ruff==0.15.1",
+    "prek==0.3.3",
+]
+packaging = [
+    "twine",
+    "validate-pyproject[all]",
 ]
 dev = [
-    "tskit",
-    "numpy",
-    "scipy",
-    "pytest",
-    "pytest-cov",
-    "pytest-xdist",
-    "msprime",
+    {include-group = "docs"},
+    {include-group = "lint"},
+    {include-group = "test"},
+    {include-group = "packaging"},
 ]
 
 [tool.setuptools]
@@ -105,3 +100,19 @@ testpaths = [
     "tests",
 ]
 
+[tool.ruff]
+target-version = "py311"
+line-length = 89
+
+[tool.ruff.lint]
+select = ["E", "F", "B", "W", "I", "N", "UP", "A", "PT"]
+fixable = ["ALL"]
+
+ignore = [
+    "A001", "A002", "RUF",
+    "B905", #Don't add strict=False to zips (B905)
+    "E741", # using 'l' as a variable name
+    "N806", "N802", "N803", # Various nags about uppercase vars
+    "PT030", # `pytest.warns(DeprecationWarning)` is too broad.
+]
+