Merge branch 'master' into rule-builder-registry

Author: tvk134

.github/dependabot.yml

@@ -0,0 +1,15 @@
+version: 2
+updates:
+  - package-ecosystem: "uv" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"
+    commit-message:
+      prefix: "chore"
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    commit-message:
+      prefix: "chore"

.github/workflows/ci.yml

@@ -0,0 +1,52 @@
+name: CI Pipeline
+
+on:
+  pull_request:
+    branches: [master]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  validation:
+    if: github.repository == 'sequence-toolbox/SeQUeNCe'
+    name: Run Unit Tests
+    permissions:
+      contents: read
+      code-quality: write
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - ubuntu-latest
+          - macos-latest
+          - windows-latest
+        python-version:
+          - "3.12"
+          - "3.13"
+          - "3.14"
+    runs-on: ${{ matrix.os }}
+    steps:
+    - uses: actions/checkout@v7
+
+    - name: Install uv and set py version
+      uses: astral-sh/setup-uv@v7
+      with:
+        python-version: ${{ matrix.python-version }}
+        enable-cache: true
+
+    - name: Install sequence
+      run: uv sync --locked --all-extras --dev --no-editable
+
+    - name: Run tests
+      run: uv run pytest --cov=. --cov-report=xml
+
+    - name: Upload coverage report
+      if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository
+      uses: actions/upload-code-coverage@v1
+      with:
+        file: coverage.xml
+        language: Python
+        label: code-coverage/pytest

.github/workflows/development.yml

@@ -0,0 +1,33 @@
+name: Mirror to GitLab
+on:
+  push:
+    branches: [ '**' ]
+    tags: [ '**' ]
+  delete:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: mirror-to-gitlab
+  cancel-in-progress: true
+
+jobs:
+  mirror:
+    if: github.repository == 'sequence-toolbox/SeQUeNCe'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout full history
+        uses: actions/checkout@v7
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+      - name: Push to GitLab
+        env:
+          GITLAB_TOKEN: ${{ secrets.GITLAB_KEY }}
+          GITLAB_REPO: ${{ secrets.GITLAB_URL }}
+        run: |
+          git remote add gitlab "https://oauth2:${GITLAB_TOKEN}@${GITLAB_REPO}"
+          git update-ref -d refs/remotes/origin/HEAD || true
+          git push --force --prune gitlab "refs/remotes/origin/*:refs/heads/*" "refs/tags/*:refs/tags/*"

.github/workflows/mirror_gitlab.yml

@@ -0,0 +1,16 @@
+name: Validate PRs
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, edited]
+
+permissions:
+  pull-requests: write
+
+jobs:
+  validate-pr-title:
+    runs-on: ubuntu-latest
+    steps:
+      - name: PR Conventional Commit Validation
+        uses: ytanikin/pr-conventional-commits@1.5.2
+        with:
+          task_types: '["feat","fix","docs","test","ci","refactor","perf","chore","revert"]'

.github/workflows/pr_checks.yml

@@ -1,19 +1,18 @@
-name: CD Pipeline
+name: Publish to PyPi
 
 on:
   push:
     branches: [master]
   release:
     types: [published]
-  workflow_dispatch:
 
 jobs:
   build-release:
     name: Build the release
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.repository == 'sequence-toolbox/SeQUeNCe'
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           persist-credentials: true
       - name: Install uv
@@ -23,7 +22,7 @@ jobs:
       - name: Build wheel and tarball
         run: uv build
       - name: Store dist as an artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: python-release-package-dist
           path: dist/
@@ -33,7 +32,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'push' && github.repository == 'sequence-toolbox/SeQUeNCe'
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           persist-credentials: true
       - name: Install uv
@@ -46,7 +45,7 @@ jobs:
       - name: Build wheel and tarball for test
         run: uv build
       - name: Store test dist as an artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: python-test-package-dist
           path: dist/
@@ -65,12 +64,14 @@ jobs:
 
     steps:
       - name: Download all the dists
-        uses: actions/download-artifact@v5
+        uses: actions/download-artifact@v8
         with:
           name: python-release-package-dist
           path: dist/
       - name: Publish dist to TestPyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@v1.14.0
+        with:
+          attestations: true
 
   publish-to-test-pypi:
     name: Publish dist to TestPyPi
@@ -87,12 +88,12 @@ jobs:
 
     steps:
       - name: Download all the test dists
-        uses: actions/download-artifact@v5
+        uses: actions/download-artifact@v8
         with:
           name: python-test-package-dist
           path: dist/
       - name: Publish dist to TestPyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@v1.14.0
         with:
           attestations: true
           repository-url: https://test.pypi.org/legacy/

.github/workflows/publish.yml

@@ -0,0 +1,39 @@
+name: Generate Release
+on:
+  workflow_dispatch:
+
+permissions: {}
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: false
+
+jobs:
+  release:
+    environment: release
+    runs-on: ubuntu-latest
+    if: github.repository == 'sequence-toolbox/SeQUeNCe'
+    permissions:
+      contents: read
+    steps:
+      - name: Create App Token
+        id: generate-token
+        uses: actions/create-github-app-token@v3
+        with:
+          client-id: ${{ vars.APP_CLIENT_ID }}
+          private-key: ${{ secrets.APP_PRIVATE_KEY }}
+      - name: Checkout Master
+        uses: actions/checkout@v7
+        with:
+          fetch-depth: '0'
+          token: ${{ steps.generate-token.outputs.token }}
+          ref: ${{ github.ref_name }}
+
+      - name: Stamp and release
+        uses: python-semantic-release/python-semantic-release@v10.5.3
+        with:
+          github_token: ${{ steps.generate-token.outputs.token }}
+          git_committer_email: 298530268+sequence-release-bot[bot]@users.noreply.github.com
+          git_committer_name: sequence-release-bot[bot]
+          vcs_release: true
+          changelog: true