{"id":"readme","title":"Lupine — Project README","subtitle":"The error-geometry program: what is established vs. conjectured, and where to start.","category":"foundations","tags":["overview"],"source":"articles/README.md","lang":"en","words":406,"readMinutes":2,"toc":[{"depth":2,"text":"Boundary","id":"boundary"},{"depth":2,"text":"Sibling Repos","id":"sibling-repos"},{"depth":2,"text":"Quick Checks","id":"quick-checks"},{"depth":2,"text":"Export Contracts","id":"export-contracts"},{"depth":2,"text":"Orientation","id":"orientation"},{"depth":2,"text":"License","id":"license"}],"html":"<h1 id=\"lupine-rhizo\">Lupine Rhizo</h1><p>The Lupine science root system.</p>\n<p>Rhizo is the deep workbench for the Lupine open-science program: Lean proofs,\nRust and Python science engines, MLIP benchmarking loops, evidence generation,\nagents, telemetry, and the export contracts consumed by the public repos.</p>\n<p>If you want the polished molecular viewer, clone <strong>Lupi</strong>. If you want the\npublic research record, read <strong>Lupine Ledger</strong>. If you want the math, LAMMPS\nbridges, MLIP loops, proof obligations, and control-plane machinery, this is\nthe place.</p>\n<h2 id=\"boundary\">Boundary</h2><p>Owns:</p>\n<ul>\n<li><code>glim-think</code>: durable agenda, ledger, routes, feed, evals, and agent loop</li>\n<li><code>cocoindex</code>: evidence indexing experiments for corpus export/query loops</li>\n<li><code>atlas/compute</code>: Cloud Run physics compute lane used by <code>glim-think</code></li>\n<li><code>lean-spec</code>: Lean proof/specification layer</li>\n<li><code>atlas-distill</code>: Rust scoring, policy, benchmark, and fault-line engine</li>\n<li><code>python</code>: Python Distill packages and runtime helpers</li>\n<li><code>mlip_immi</code>: real-data MLIP/IMMI analysis lane</li>\n<li><code>gcp</code>: burst compute, MLIP cells, evidence indexing, and control-plane services</li>\n<li><code>cloudflare</code>: edge/control-plane infrastructure helpers</li>\n<li><code>tools</code>: local science CLIs, telemetry checks, promotion loops</li>\n<li><code>docs</code>, <code>paper</code>, <code>replication</code>: source research corpus and reproducibility</li>\n<li><code>exports</code>: public contracts consumed by Ledger, Lupi, and Science</li>\n</ul>\n<p>Does not own:</p>\n<ul>\n<li>the <code>lupine.science</code> landing site</li>\n<li>the <code>library.lupine.science</code> reader app</li>\n<li>the <code>lupi.live</code> viewer app</li>\n<li>investor or private access surfaces</li>\n<li>generated caches, dependency folders, or large binary artifacts</li>\n</ul>\n<h2 id=\"sibling-repos\">Sibling Repos</h2><ul>\n<li><strong>Lupine Science</strong>: <code>https://github.com/alexwelcing/lupine-science</code><ul>\n<li>Public front door.</li>\n<li>Site: <code>https://lupine.science</code></li>\n</ul>\n</li>\n<li><strong>Lupine Ledger</strong>: <code>https://github.com/alexwelcing/lupine-ledger</code><ul>\n<li>Public evidence record and Library reader.</li>\n<li>Site: <code>https://library.lupine.science</code></li>\n</ul>\n</li>\n<li><strong>Lupi</strong>: <code>https://github.com/alexwelcing/Lupi</code><ul>\n<li>Browser-native molecular viewer.</li>\n<li>Site: <code>https://lupi.live</code></li>\n</ul>\n</li>\n</ul>\n<p>Historical development remains in <code>https://github.com/alexwelcing/lupine</code>\nduring the transition.</p>\n<h2 id=\"quick-checks\">Quick Checks</h2><p>Use Git Bash for Node and build tasks on Windows.</p>\n<pre><code class=\"language-bash\">just think-lint\njust engine-test\njust live-build\n</code></pre>\n<p>Routine validation:</p>\n<pre><code class=\"language-bash\">just verify-light\njust verify\n</code></pre>\n<p>Lean proof gate:</p>\n<pre><code class=\"language-bash\">cd lean-spec\nlake build\n</code></pre>\n<p>Run Lean from inside <code>lean-spec/</code> so elan selects the pinned toolchain.</p>\n<h2 id=\"export-contracts\">Export Contracts</h2><p>Rhizo publishes; public repos consume.</p>\n<p>Current public export:</p>\n<pre><code class=\"language-text\">exports/library-content/latest/\n  manifest.json\n  articles/\n</code></pre>\n<p>Regenerate the Library content bundle from this repo with:</p>\n<pre><code class=\"language-bash\">node scripts/export_library_content.mjs\n</code></pre>\n<p>The Ledger repo verifies <code>library-content.v1</code> before rendering the public\nLibrary.</p>\n<p>Planned contract families:</p>\n<ul>\n<li>Library content bundles</li>\n<li>claim/status manifests</li>\n<li>molecule/evidence manifests</li>\n<li>viewer search and MCP schemas</li>\n<li><code>glim-think</code> route/OpenAPI summaries</li>\n<li>brand and agent-readable text</li>\n</ul>\n<h2 id=\"orientation\">Orientation</h2><ul>\n<li><a href=\"LUPINE.md\" target=\"_blank\" rel=\"noopener\" class=\"ll-raw-source\">LUPINE.md</a>: how Rhizo fits the Lupine constellation</li>\n<li><a href=\"ROOTS.md\" target=\"_blank\" rel=\"noopener\" class=\"ll-raw-source\">ROOTS.md</a>: active root ownership ledger</li>\n<li><a href=\"AGENTS.md\" target=\"_blank\" rel=\"noopener\" class=\"ll-raw-source\">AGENTS.md</a>: operating rules for agents in this repo</li>\n<li><a href=\"docs/ARCHITECTURE.md\" target=\"_blank\" rel=\"noopener\" class=\"ll-raw-source\">docs/ARCHITECTURE.md</a>: system map</li>\n<li><a href=\"docs/working-path.md\" target=\"_blank\" rel=\"noopener\" class=\"ll-raw-source\">docs/working-path.md</a>: practical checkout and checks</li>\n<li><a href=\"docs/repo-split-map.md\" target=\"_blank\" rel=\"noopener\" class=\"ll-raw-source\">docs/repo-split-map.md</a>: extraction map</li>\n<li><a href=\"docs/splits/science-control-plane.md\" target=\"_blank\" rel=\"noopener\" class=\"ll-raw-source\">docs/splits/science-control-plane.md</a>: split packet</li>\n</ul>\n<h2 id=\"license\">License</h2><p>Project-owned code is licensed under AGPL-3.0-or-later. First-party non-code\ncontent is licensed under CC BY-SA 4.0 unless noted. First-party structured\ndata and exported databases are licensed under ODbL 1.0 unless noted.</p>\n<p>Third-party datasets, dependencies, papers, and imported scientific sources\nretain their upstream licenses and notices.</p>\n"}