Clean up workflows and packaging

.bumpversion.toml

@@ -0,0 +1,27 @@
+[tool.bumpversion]
+current_version = "1.0.1"
+commit = true
+tag = false
+tag_name = "v{new_version}"
+tag_message = "Release version {new_version}"
+message = "bump: version {current_version} → {new_version}"
+
+[[tool.bumpversion.files]]
+filename = "src/cpg_flow/__init__.py"
+search = "__version__ = '{current_version}'"
+replace = "__version__ = '{new_version}'"
+
+[[tool.bumpversion.files]]
+filename = "Dockerfile"
+search = "# VERSION {current_version}"
+replace = "# VERSION {new_version}"
+
+[[tool.bumpversion.files]]
+filename = ".github/workflows/docker.yaml"
+search = "VERSION: {current_version}"
+replace = "VERSION: {new_version}"
+
+[[tool.bumpversion.files]]
+filename = ".github/workflows/test.yaml"
+search = "VERSION: {current_version}"
+replace = "VERSION: {new_version}"

.github/dependabot.yml

@@ -0,0 +1,82 @@
+version: 2
+
+# Multi-ecosystem groups for Python dependencies
+multi-ecosystem-groups:
+  python-minor-patch:
+    applies-to: version-updates
+    update-types:
+      - "minor"
+      - "patch"
+  python-major:
+    applies-to: version-updates
+    update-types:
+      - "major"
+
+updates:
+  # pip ecosystem for pyproject.toml dependencies
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    multi-ecosystem-group: python-minor-patch
+    commit-message:
+      prefix: "chore"
+      include: "scope"
+    ignore:
+      # Don't update hail - pinned at CPG's installed version
+      - dependency-name: "hail"
+      # Don't update Python version
+      - dependency-name: "python"
+    open-pull-requests-limit: 10
+
+  # uv ecosystem for uv.lock file
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    multi-ecosystem-group: python-minor-patch
+    commit-message:
+      prefix: "chore"
+      include: "scope"
+    ignore:
+      # Don't update hail - pinned at CPG's installed version
+      - dependency-name: "hail"
+      # Don't update Python version
+      - dependency-name: "python"
+    open-pull-requests-limit: 10
+
+  # Separate update for major versions (pip)
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    multi-ecosystem-group: python-major
+    commit-message:
+      prefix: "chore"
+      include: "scope"
+    ignore:
+      # Don't update hail - pinned at CPG's installed version
+      - dependency-name: "hail"
+      # Don't update Python version
+      - dependency-name: "python"
+      # Ignore minor and patch updates (handled by the other group)
+      - update-types: ["version-update:semver-minor", "version-update:semver-patch"]
+    open-pull-requests-limit: 10
+
+  # Separate update for major versions (uv)
+  - package-ecosystem: "uv"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    multi-ecosystem-group: python-major
+    commit-message:
+      prefix: "chore"
+      include: "scope"
+    ignore:
+      # Don't update hail - pinned at CPG's installed version
+      - dependency-name: "hail"
+      # Don't update Python version
+      - dependency-name: "python"
+      # Ignore minor and patch updates (handled by the other group)
+      - update-types: ["version-update:semver-minor", "version-update:semver-patch"]
+    open-pull-requests-limit: 10

.github/workflows/package.yaml

@@ -1,9 +1,8 @@
-name: Package
+name: Package and Release
 on:
   push:
     branches:
       - main
-      - alpha
 
   workflow_dispatch:
     inputs:
@@ -16,9 +15,9 @@
 permissions: {}
 
 jobs:
-  package:
-    name: Package
-    if: startsWith(github.event.head_commit.message, 'bump:') != true
+  release:
+    name: Release
+    if: startsWith(github.event.head_commit.message, 'bump:')
     environment: production
     permissions:
       id-token: write
@@ -29,45 +28,29 @@
         shell: bash -l {0}
 
     steps:
-      - name: Setup | Force correct release branch on workflow sha
-        env:
-          REPO: ${{ github.repository }}
-          REF_NAME: ${{ github.ref_name }}
-          SHA: ${{ github.sha }}
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: |
-          set -euo pipefail
-          git clone https://github.com/${REPO} .
-          git checkout -B "${REF_NAME}" "${SHA}"
-          git config user.name "cpg-software-ci-bot"
-          git config user.email "software-team+githubcibot@populationgenomics.org.au"
-          git remote set-url origin "https://x-access-token:${GITHUB_TOKEN}@github.com/${REPO}"
-
-      - name: Action | Semantic Version Release
-        id: release
-        uses: python-semantic-release/python-semantic-release@0dc72ac9058a62054a45f6344c83a423d7f906a8 #v9.21.1
+      - name: Checkout
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 #v4.2.2
         with:
-          root_options: '-v'
-          git_committer_email: 'software-team+githubcibot@populationgenomics.org.au'
-          git_committer_name: 'cpg-software-ci-bot'
-          github_token: ${{ secrets.BOT_ACCESS_TOKEN }}
+          fetch-depth: 0
 
-      - name: Build on no release
-        if: steps.release.outputs.released != 'true'
+      - name: Extract version from commit message
+        id: version
+        env:
+          COMMIT_MESSAGE: ${{ github.event.head_commit.message }}
         run: |
-          echo "No release was made, manual build"
-          make ci-build
+          # Extract version from commit message like "bump: version 1.0.1 → 1.0.2"
+          VERSION=$(echo "$COMMIT_MESSAGE" | grep -oP '→ \K[0-9]+\.[0-9]+\.[0-9]+')
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+          echo "Detected version: $VERSION"
 
-      - name: Publish | Upload package to PyPI
-        uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc #v1.12.4
-        if: steps.release.outputs.released == 'true' || github.event.inputs.force_pypi_release == 'true'
-
-      - name: Publish | Upload to GitHub Release Assets
-        uses: python-semantic-release/publish-action@1aa9f41fac5d531e6764e1991b536783337f3a56 #v9.21.1
-        if: steps.release.outputs.released == 'true'
-        with:
-          github_token: ${{ secrets.BOT_ACCESS_TOKEN }}
-          tag: ${{ steps.release.outputs.tag }}
+      - name: Create and push tag
+        env:
+          VERSION: ${{ steps.version.outputs.version }}
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+          git tag -a "v${VERSION}" -m "Release version ${VERSION}"
+          git push origin "v${VERSION}"
 
       - name: Install uv
         uses: astral-sh/setup-uv@6b9c6063abd6010835644d4c2e1bef4cf5cd0fca #v6.0.1
@@ -78,12 +61,18 @@
         run: |
           uv sync
 
-      - run: uv pip install mike
-
-      - name: Clean stale build metadata
+      - name: Build package
         run: |
-          rm -rf src/*.egg-info || true
+          uv build --sdist --wheel
+
+      - name: Publish | Upload package to PyPI
+        uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e #v1.13.0
+        if: github.event_name == 'push' || github.event.inputs.force_pypi_release == 'true'
 
       - name: Publish | Update docs version
+        env:
+          VERSION: ${{ steps.version.outputs.version }}
+          GIT_COMMITTER_NAME: github-actions[bot]
+          GIT_COMMITTER_EMAIL: github-actions[bot]@users.noreply.github.com
         run: |
-          uv run mike deploy -F docs/mkdocs.yml --push --update-aliases ${{ steps.release.outputs.tag }} latest
+          uv run mike deploy -F docs/mkdocs.yml --push --update-aliases "${VERSION}" latest

.pre-commit-config.yaml

@@ -52,11 +52,3 @@ repos:
   #   rev: v1.1.400
   #   hooks:
   #     - id: pyright
-
-  - repo: https://github.com/alessandrojcm/commitlint-pre-commit-hook
-    rev: v9.22.0
-    hooks:
-      - id: commitlint
-        stages: [commit-msg]
-        args: [--config, .commitlintrc.json]
-        additional_dependencies: ['@commitlint/config-conventional']

Dockerfile

@@ -1,4 +1,5 @@
 FROM australia-southeast1-docker.pkg.dev/analysis-runner/images/driver:latest
+# VERSION 1.0.1
 COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
 
 # Set up working directory for the project