Initial commit

Author: jefferyUstc

.gitignore

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+tools/_preview/
+_shot.html
+_test.html
+_probe.html
+.ipynb_checkpoints/
+.DS_Store

.nojekyll

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+# Bio-Babel.github.io
+
+Source of <https://bio-babel.github.io>. Pages serves `main` from the repo root, so a push
+is a deploy.
+
+`index.html` is the whole page — static markup, nothing rendered at runtime. `assets/js/main.js`
+only adds behaviour: sticky nav, scroll reveals, the stat counters, the stack tier picker, the
+library filter. Changing copy means editing `index.html`.
+
+```bash
+python3 -m http.server 8000
+```
+
+## Constraints
+
+Not preferences — each of these has already caused a bug.
+
+1. **No CDN, no web fonts, no runtime API calls.** Much of the audience is in mainland China,
+   where Google Fonts and `api.github.com` are blocked or slow. Hence the system font stack and
+   the hand-maintained catalog below. To guarantee Inter, self-host the woff2; do not add a
+   `<link>`.
+2. **Paths stay relative**, so the site survives a move to a sub-path or a custom domain.
+3. **`.nojekyll` stays**, or Pages runs Jekyll over the files.
+4. **`og:image` stays a raster at an absolute URL.** Crawlers on X, Facebook, LinkedIn, Slack
+   and Discord reject SVG and ignore relative URLs. Break this and every shared link renders
+   without an image, silently.
+5. **Organization voice.** The libraries and the community lead; the contract layer and its
+   benchmark share one section because they are two of the org's repositories, not the point
+   of it.
+6. **R → Python is the demonstration, not the definition.** Copy may say the problem is
+   particular to no pair of languages — that is a claim about the problem. Do not upgrade it
+   into a claim that the tooling is already language-agnostic: `manifest_api.py` still carries
+   an `r_package` field and the porting skill is still named `r2py-skills`. When that changes,
+   the copy can.
+
+## Hard-coded facts
+
+The catalog is a snapshot (constraint 1), so some numbers are hand-maintained. Find all of them:
+
+```bash
+grep -niE 'seventeen|17 (r )?(librar|classic)|data-(count|filter)=|read-only tools' index.html
+```
+
+That covers the meta and OpenGraph descriptions, the hero pill and paragraph, the stats strip,
+the catalog heading and the five filter counts. The cards themselves are one
+`<article class="lib">` each. Do not trust line numbers in this file — use the grep, and if you
+reword the copy, check the pattern still matches.
+
+| figure | where the truth is |
+|---|---|
+| library and repo counts | `curl -s 'https://api.github.com/orgs/Bio-Babel/repos?per_page=100'` — everything except `.github`, `Bio-Babel.github.io`, `bio-babel-MCP` and `bio-babel-MCPBench` is a library (`bio-babel-toolkit` and `bio-babel-annotator` are private and do not appear) |
+| `1,606` contracted symbols | sum of `symbols/` across each port's `_biobabel/` |
+| `12` read-only MCP tools | asserted by `tests/test_mcp_server.py::tool_count` in `bio-babel-MCP` |
+| per-card versions | PyPI |
+| the argument in the hero and the Why section | `manuscript/Draft_main_text_human.txt` — the copy is drawn from it, so keep the two consistent |
+
+## Logo
+
+```bash
+python3 tools/gen_logo.py     # cairosvg is optional, previews only
+```
+
+Regenerate rather than hand-editing the SVGs: the geometry is transcribed once in the script and
+every file derives from it. Two properties are easy to break —
+
+* **The arches are transparent cut-outs, not white fill.** Whatever sits behind shows through, so
+  the mark must never go on a field near its own violet: the arcade disappears and the tower
+  flattens into a triangle. On the tile the tower is cream for exactly this reason.
+* **The shipped files carry no `<mask>`.** The master artwork (`Bio-Babel/.github`,
+  `profile/imgs/bio-babel-logo.svg`) uses one, and non-browser rasterisers silently drop it and
+  paint a solid square. Everything here is a single nonzero-winding path instead.
+
+`<text>` in the banner is pinned with `textLength`; the viewer's fallback font is unknown and
+without it the tagline overflows the artboard.
+
+| file | use |
+|---|---|
+| `logo-mark.svg` | the mark, flat `#8477C8`. Nav, hero, footer |
+| `logo-mark-mono.svg` | `fill="currentColor"` — inline it to tint from CSS |
+| `logo-mark-ghost.svg` | white, for low-opacity watermarks |
+| `logo-mark-gradient.svg` | violet→gold; point the `logo-mark.svg` references at this for more lift |
+| `logo-tile.svg` | squircle tile — the org avatar and the touch icon |
+| `favicon.svg` | tile with a simplified arcade, so it still reads at 16 px |
+| `logo-wordmark.svg` | mark + `Bio-Babel` + tagline |
+| `logo-banner.svg` | 1080×240 banner, in use in the org profile README |
+| `og-card.png` | 1200×630 link preview, rendered from `tools/og-card.html` — command in its header |