Ecosystem update

.github/workflows/docs.yml

@@ -1,13 +1,11 @@
-name: 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/integration.yml

@@ -0,0 +1,61 @@
+name: Integration tests
+
+on:
+  pull_request:
+  push:
+    branches: [main, test]
+  merge_group:
+
+jobs:
+  end-to-end:
+    name: End to end tests
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4.2.2
+      - uses: astral-sh/setup-uv@v6
+        with:
+          python-version: "3.11"
+          version: "0.8.15"
+      - name: Install dependencies
+        run: uv sync --locked --group test
+
+      - name: Create basedir
+        run: |
+          mkdir -p testrun
+          gunzip -k tests/data/alignments.fasta.gz
+
+      - name: Import alignments
+        run: uv run sc2ts import-alignments -i testrun/dataset.zarr tests/data/alignments.fasta
+
+      - name: Import metadata
+        run: uv run sc2ts import-metadata testrun/dataset.zarr tests/data/metadata.tsv
+
+      - name: Info dataset
+        run: uv run sc2ts info-dataset testrun/dataset.zarr
+
+      - name: Run inference
+        run: |
+          # doing ~10 days here as this is taking a while
+          uv run sc2ts infer tests/data/testrun-conf.toml --stop 2020-02-03
+
+      - name: Validate
+        run: uv run sc2ts validate -v --date-field=date testrun/dataset.zarr testrun/results/test/test_2020-02-02.ts
+
+      - name: MatchDB
+        run: uv run sc2ts info-matches testrun/test.matches.db
+
+  bare-api:
+    name: Bare API tests
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v4.2.2
+      - uses: astral-sh/setup-uv@v6
+        with:
+          python-version: "3.11"
+          version: "0.8.15"
+      - name: Install package only
+        run: uv pip install -e .
+      - name: Run tests
+        run: |
+          # Minimal deps only; avoid picking up conftest and fixtures
+          uv run pytest -v -c /dev/null -p no:sc2ts_fixtures tests/test_api.py

.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 +1,12 @@
+name: Packaging
+
+on:
+  pull_request:
+  merge_group:
+
+jobs:
+  packaging:
+    uses: tskit-dev/.github/.github/workflows/python-packaging.yml@v13
+    with:
+      pyproject-directory: .
+      cli-test-cmd: sc2ts --help

.github/workflows/tests.yml

@@ -0,0 +1,22 @@
+name: Tests
+
+on:
+  pull_request:
+  push:
+    branches: [main, test]
+  merge_group:
+
+jobs:
+  test:
+    name: Python
+    uses: tskit-dev/.github/.github/workflows/python-tests.yml@v13
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python }}
+      pyproject-directory: .
+      coverage-directory: sc2ts
+    secrets: inherit
+    strategy:
+      matrix:
+        python: ["3.10", "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 sc2ts
-PYPATH=${PWD}/..
-SC2TS_VERSION:=$(shell PYTHONPATH=${PYPATH} \
-   python3 -c 'import sc2ts; print(sc2ts.__version__.split("+")[0])')
 
-dev:
-	PYTHONPATH=${PYPATH} ./build.sh
-
-dist:
-	@echo Building distribution for sc2ts version ${SC2TS_VERSION}
-	sed -i s/__SC2TS_VERSION__/${SC2TS_VERSION}/g _config.yml
-	PYTHONPATH=${PYPATH} ./build.sh
+all:
+	./build.sh
 
 clean:
 	rm -fR _build
-

docs/_config.yml

@@ -43,7 +43,7 @@ sphinx:
       navigation_with_keys: false
       pygments_dark_style: monokai
       logo:
-        text: "Version __SC2TS_VERSION__"
+        text: "Version __PKG_VERSION__"
 
     myst_enable_extensions:
       - colon_fence

docs/build.sh

@@ -6,7 +6,7 @@
 
 REPORTDIR=_build/html/reports
 
-jupyter-book build -W . 
+uv run --project=../python --group docs jupyter-book build . -vnW --keep-going
 RETVAL=$?
 if [ $RETVAL -ne 0 ]; then
     if [ -e $REPORTDIR ]; then
@@ -18,4 +18,3 @@ else
     rm -f $REPORTDIR/*
 fi
 exit $RETVAL
-

docs/make_sc2ts_arg_subset.py

@@ -1,5 +1,5 @@
-import tszip
 import numpy as np
+import tszip
 
 ts = tszip.load("sc2ts_viridian_v1.2.trees.tsz")
 

docs/make_viridian_subset.py

@@ -9,4 +9,3 @@
 path = f"viridian_mafft_subset_{k}_v1.vcz"
 ds.copy(path, sample_id=samples)
 sc2ts.Dataset.create_zip(path, path + ".zip")
-

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"],
+  },
+]