Small changes to the workflow test and cov ecosystem

.github/workflows/coverage.yml

@@ -0,0 +1,51 @@
+name: Coverage
+
+on:
+  push:
+    branches:
+      - master
+    paths:
+      - 'web/**'
+      - 'respro/**'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: coverage-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pytest:
+    name: Pytest + Codecov (Python 3.11)
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v7
+        with:
+          fetch-depth: 2
+
+      - name: Set up Python
+        uses: actions/setup-python@v7
+        with:
+          python-version: '3.11'
+          cache: pip
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r web/backend/requirements.txt
+          python -m pip install -e ".[dev]"
+
+      - name: Run test suite with coverage
+        run: |
+          pytest --cov=respro --cov-branch --cov-report=xml --cov-report=term-missing
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v7
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage.xml
+          fail_ci_if_error: false

docs/mkdocs.yml

@@ -76,5 +76,16 @@ markdown_extensions:
 
 plugins:
   - search
+  - glightbox:
+      touchNavigation: true
+      loop: false
+      effect: zoom
+      slide_effect: slide
+      width: 100%
+      height: auto
+      zoomable: true
+      draggable: true
+      skip_classes:
+        - respro-no-lightbox
   - mermaid2:
       version: 11.4.1

pyproject.toml

@@ -37,7 +37,7 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = ['pytest>=7.4', 'pytest-cov>=4.1', 'ruff>=0.1', 'httpx>=0.27', 'fakeredis>=2.0', 'mypy>=1.10']
-docs = ['mkdocs>=1.6', 'mkdocs-material>=9.5', 'mkdocs-mermaid2-plugin>=1.1']
+docs = ['mkdocs>=1.6', 'mkdocs-material>=9.5', 'mkdocs-mermaid2-plugin>=1.1', 'mkdocs-glightbox>=0.4']
 
 [project.scripts]
 respro = 'respro.cli.main:app'

respro/io/genbank.py

@@ -75,7 +75,7 @@ def parse_genbank_sources(genbank_paths: list[Path]) -> list[ParsedGenBankRefere
 
 def parse_genbank_records(genbank_path: Path) -> list[ParsedGenBankReference]:
     """
-    Parse one or more GenBank records from a file.
+    Parse one or more GenBank records from a .gb file.
 
     The project stores one internal reference per GenBank record and one feature per
     CDS feature. Feature identifiers are extracted from the GenBank qualifiers and are