v1.8.2: link colors, favicon encoding, PyPI publish

Author: dial481

.github/workflows/publish.yml

@@ -0,0 +1,18 @@
+name: Publish to PyPI
+on:
+  release:
+    types: [published]
+permissions:
+  id-token: write
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    environment: pypi
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: pip install build
+      - run: python -m build
+      - uses: pypa/gh-action-pypi-publish@release/v1

CHANGELOG.md

@@ -2,12 +2,36 @@
 
 All notable changes are documented here. Format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/); the project follows [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.8.2]
+
+### Fixed
+- **HTML report link colors.** Links in dark mode were browser-default
+  neon blue (#0000EE), unreadable against the dark background. Dark mode
+  now uses #93c5fd; light mode uses #1976d2 (matching the existing accent).
+- **Favicon SVG rendering.** The report's inline SVG favicon used a
+  `linearGradient` with an internal IRI reference (`url(#g)`) that doesn't
+  resolve inside `data:` URIs, rendering the icon invisible. Replaced with
+  a solid fill and URL-encoded angle brackets.
+- **Genotype column header.** Abbreviated "Genotype" to "GT" to prevent
+  column header overlap on narrow/mobile screens.
+
+### Changed
+- **PyPI metadata.** Homepage now points to allelix.io. Added Source and
+  Changelog links.
+- **Automated PyPI publishing.** GitHub Actions workflow publishes to PyPI
+  via Trusted Publishing on every GitHub Release.
+
 ## [1.8.1]
 
 ### Changed
 - **Updated sample reports.** Regenerated `examples/sample_reports/` with
   v1.8.0 report format (5-column table, detail sidebar, dark mode).
 
+### Fixed
+- **Test fixture genotype format.** Corrected the `test_html.py` fixture's
+  `genotype_match` default from `A/G` to the concatenated `AG` form that
+  production emits for SNVs.
+
 ## [1.8.0]
 
 ### Changed
@@ -1622,6 +1646,7 @@ All notable changes are documented here. Format follows [Keep a Changelog](https
 - GitHub Actions CI matrix on Python 3.11 and 3.12.
 
 
+[1.8.2]: https://github.com/dial481/allelix/compare/v1.8.1...v1.8.2
 [1.8.1]: https://github.com/dial481/allelix/compare/v1.8.0...v1.8.1
 [1.8.0]: https://github.com/dial481/allelix/compare/v1.7.0...v1.8.0
 [1.7.0]: https://github.com/dial481/allelix/compare/v1.6.1...v1.7.0
@@ -1630,8 +1655,7 @@ All notable changes are documented here. Format follows [Keep a Changelog](https
 [1.5.3]: https://github.com/dial481/allelix/compare/v1.5.2...v1.5.3
 [1.5.2]: https://github.com/dial481/allelix/compare/v1.5.1...v1.5.2
 [1.5.1]: https://github.com/dial481/allelix/compare/v1.5.0...v1.5.1
-[1.5.0]: https://github.com/dial481/allelix/compare/v1.4.1...v1.5.0
-[1.4.1]: https://github.com/dial481/allelix/compare/v1.4.0...v1.4.1
+[1.5.0]: https://github.com/dial481/allelix/compare/v1.4.0...v1.5.0
 [1.4.0]: https://github.com/dial481/allelix/compare/v1.3.1...v1.4.0
 [1.3.1]: https://github.com/dial481/allelix/compare/v1.3.0...v1.3.1
 [1.3.0]: https://github.com/dial481/allelix/compare/v1.2.0...v1.3.0

README.md

@@ -10,8 +10,9 @@ Open-source command-line toolkit for analyzing raw genotype files from consumer
 > HTML/JSON/terminal reports, methylation + pharmacogenomics focused
 > commands, report diffing, persistent config with commercial-mode
 > safety switch. Build auto-detection from position data (ADR-0021).
-> No regex on prose anywhere in production. **Latest: v1.7.0** — PLINK
-> export, magnitude scoring formalization (ADR-0034). Release notes:
+> No regex on prose anywhere in production. **Latest: v1.8.2** — HTML
+> report redesign with dark mode, PLINK export, and automated PyPI
+> publishing. Release notes:
 > [`CHANGELOG.md`](CHANGELOG.md).
 
 ## Quickstart

SECURITY.md

@@ -2,7 +2,7 @@
 
 ## Supported versions
 
-Only the latest minor release receives security fixes.
+The current and previous minor releases receive security fixes.
 
 | Version | Supported |
 |---------|-----------|

allelix/models.py

@@ -79,7 +79,9 @@ class Annotation:
         magnitude: 0-10 importance score (SNPedia-style).
         description: Human-readable explanation.
         attribution: Display name of the source ("ClinVar", "PharmGKB", ...).
-        genotype_match: Which genotype triggers this annotation (e.g., "T/T").
+        genotype_match: Which genotype triggers this annotation. For SNVs this
+            is a concatenated, sorted allele pair (e.g., "AG", "TT"); the slash
+            form (e.g., "AT/A") appears only for indels.
         references: PubMed IDs or URLs supporting the claim.
         condition: Disease or condition name, if applicable.
         gene: Gene symbol, if known.

allelix/reports/html.py

@@ -101,6 +101,7 @@ def _escape(value: str) -> str:
   --notice-border: #f9a825;
   --notice-warn-bg: #fff3e0;
   --notice-warn-border: #e65100;
+  --link: #1976d2;
 }
 @media (prefers-color-scheme: dark) {
   :root:not([data-theme="light"]) {
@@ -119,6 +120,7 @@ def _escape(value: str) -> str:
     --notice-border: #f9a825;
     --notice-warn-bg: #331a00;
     --notice-warn-border: #e65100;
+    --link: #93c5fd;
   }
 }
 [data-theme="dark"] {
@@ -137,6 +139,7 @@ def _escape(value: str) -> str:
   --notice-border: #f9a825;
   --notice-warn-bg: #331a00;
   --notice-warn-border: #e65100;
+  --link: #93c5fd;
 }
 
 *, *::before, *::after { box-sizing: border-box; }
@@ -152,6 +155,7 @@ def _escape(value: str) -> str:
 }
 h1 { margin-bottom: .25rem; }
 .subtitle { color: var(--text-muted); margin-top: 0; }
+a { color: var(--link); }
 
 .notice {
   background: var(--notice-bg, #fff8e1); border-left: 4px solid var(--notice-border, #f9a825);
@@ -1024,7 +1028,7 @@ def _display_repute(g: list[Annotation]) -> str:
             '<th data-sort="gene" class="sortable">'
             'Gene<span class="sort-arrow"></span></th>'
             '<th data-sort="genotype" class="sortable">'
-            'Genotype<span class="sort-arrow"></span></th>'
+            'GT<span class="sort-arrow"></span></th>'
             '<th data-sort="repute" class="sortable">'
             'Repute<span class="sort-arrow"></span></th>'
             "<th>Summary</th>"
@@ -1090,16 +1094,25 @@ def _display_repute(g: list[Annotation]) -> str:
         "<html lang='en'><head><meta charset='utf-8'>"
         '<meta name="viewport" content="width=device-width, initial-scale=1">'
         '<link rel="icon" type="image/svg+xml" href="data:image/svg+xml,'
-        "<svg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 32 32'>"
-        "<defs><linearGradient id='g' x1='0' y1='0' x2='1' y2='1'>"
-        "<stop offset='0%25' stop-color='%234f46e5'/>"
-        "<stop offset='100%25' stop-color='%2306b6d4'/>"
-        "</linearGradient></defs>"
-        "<path d='M16 2C9 2 8 8 8 8s2-3 8-3 8 3 8 3-1-6-8-6z"
-        "m0 6c-7 0-8 6-8 6s2-3 8-3 8 3 8 3-1-6-8-6z"
-        "m0 6c-7 0-8 6-8 6s2-3 8-3 8 3 8 3-1-6-8-6z"
-        "m0 6c-7 0-8 6-8 6s2-3 8-3 8 3 8 3-1-6-8-6z'"
-        " fill='url(%23g)' opacity='0.9'/></svg>\">"
+        "%3Csvg viewBox='0 0 32 32' fill='none'"
+        " xmlns='http://www.w3.org/2000/svg'%3E"
+        "%3Ccircle cx='16' cy='16' r='14' stroke='%236366f1'"
+        " stroke-width='1.5' opacity='0.3'/%3E"
+        "%3Cpath d='M10 6C10 6 22 12 22 16C22 20 10 26 10 26'"
+        " stroke='%236366f1' stroke-width='2'"
+        " stroke-linecap='round' fill='none'/%3E"
+        "%3Cpath d='M22 6C22 6 10 12 10 16C10 20 22 26 22 26'"
+        " stroke='%236366f1' stroke-width='2'"
+        " stroke-linecap='round' fill='none' opacity='0.4'/%3E"
+        "%3Ccircle cx='10' cy='10' r='2' fill='%236366f1'/%3E"
+        "%3Ccircle cx='22' cy='10' r='2' fill='%236366f1'"
+        " opacity='0.4'/%3E"
+        "%3Ccircle cx='16' cy='16' r='2' fill='%236366f1'"
+        " opacity='0.7'/%3E"
+        "%3Ccircle cx='22' cy='22' r='2' fill='%236366f1'/%3E"
+        "%3Ccircle cx='10' cy='22' r='2' fill='%236366f1'"
+        " opacity='0.4'/%3E"
+        '%3C/svg%3E">'
         f"<title>{_escape(title)}</title>"
         f"<style>{_CSS}</style>"
         "</head><body>"

docs/adr/0028-local-version-tag-convention.md

@@ -74,7 +74,7 @@ never splits on `:`.
 
    In both families, a non-empty tag that doesn't match the current
    version means "stale, rebuild."
-5. Version constants live in `allelix/annotators/_versions.py`. Bump the
+5. Version constants live in `allelix/databases/_versions.py`. Bump the
    constant when local processing logic changes in a way that would
    produce different cache contents from the same input data.
 

docs/adr/0033-schema-version-bump-policy.md

@@ -27,7 +27,7 @@ Going forward, all new fields bump.
 ## Consequences
 
 - Any commit that adds, removes, or renames a field in the JSON report
-  output must increment `_SCHEMA_VERSION` and update
+  output must increment `SCHEMA_VERSION` and update
   `_SUPPORTED_SCHEMA_VERSIONS` in the diff loader.
 - The diff loader's supported-versions set grows monotonically.
 - ADR-0032's body is not edited (ADR immutability). This ADR supersedes