@iowarp/clio-coder 0.3.1 → 0.3.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (595) hide show
  1. package/CHANGELOG.md +90 -2
  2. package/CONTRIBUTING.md +23 -23
  3. package/README.md +284 -613
  4. package/dist/{acp-FPR54DGL.js → acp-BIYHVZIM.js} +43 -53
  5. package/dist/{agents-OGPIHPJH.js → agents-YT6SSRIT.js} +43 -26
  6. package/dist/assets/codewiki.json +1 -1
  7. package/dist/{auth-IC3K6NIZ.js → auth-5TWEIYDN.js} +20 -12
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  101. package/dist/cli/index.js +62 -54
  102. package/dist/clio-4LY5K2AC.js +25 -0
  103. package/dist/code-nav-7AX6FYE6.js +600 -0
  104. package/dist/codewiki/build-worker.js +66 -0
  105. package/dist/compile-cache-CVJMMODC.js +18 -0
  106. package/dist/{components-DMAOEKFB.js → components-KELWS457.js} +11 -6
  107. package/dist/{config-IRUQ7SE4.js → config-GTLUW2PR.js} +92 -55
  108. package/dist/configure-R6A64DHX.js +42 -0
  109. package/dist/context-5VKGUVJJ.js +866 -0
  110. package/dist/{context-3KWFLHJG.js → context-JFZEJ7W5.js} +15 -13
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  112. package/dist/{context-clear-7TSNPAAI.js → context-clear-6ZHBAZZT.js} +54 -28
  113. package/dist/{context-index-W4RLWOQH.js → context-index-BZ4UYMTC.js} +30 -24
  114. package/dist/dispatch-runner-VKBRCWQC.js +1997 -0
  115. package/dist/{docs-5AWSPS37.js → docs-2C2LTVT2.js} +23 -10
  116. package/dist/{doctor-UC5NAJYQ.js → doctor-KI767GSN.js} +27 -17
  117. package/dist/{eval-U6TJHRLX.js → eval-XSSNATB4.js} +29 -16
  118. package/dist/{evidence-YEGUW4L3.js → evidence-UA6AWDQQ.js} +46 -26
  119. package/dist/{evolve-TXARCTPG.js → evolve-QNTFGV6Z.js} +45 -25
  120. package/dist/{extensions-OZFJ3A3G.js → extensions-QVDOHDGJ.js} +16 -7
  121. package/dist/{fleet-6G3DHNYE.js → fleet-Q7UOMUSG.js} +163 -54
  122. package/dist/{fleet-preflight-DSNT37JK.js → fleet-preflight-DDN536IT.js} +7 -4
  123. package/dist/{init-KZ5QTF6M.js → init-WBB65ZHQ.js} +69 -32
  124. package/dist/{memory-73ESV5YC.js → memory-MD3O64RI.js} +48 -27
  125. package/dist/{models-A4PVNWJK.js → models-BZU34YWD.js} +39 -25
  126. package/dist/monitor-MEQA5C3I.js +661 -0
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  129. package/dist/{preload-6WVMHX3A.js → preload-P6DGH2PZ.js} +2 -2
  130. package/dist/{reset-BGW6OGMV.js → reset-L2FQEE3E.js} +16 -10
  131. package/dist/{run-YTPEYQOH.js → run-IV4Q6RLN.js} +101 -61
  132. package/dist/{share-YIFFV4NQ.js → share-S5BZQC5I.js} +15 -8
  133. package/dist/{skills-2V6RA3OQ.js → skills-LQEKRDTN.js} +34 -14
  134. package/dist/{skills-eval-S2TVJO4F.js → skills-eval-3DC4HEWS.js} +70 -34
  135. package/dist/steer-GGWFUJUD.js +77 -0
  136. package/dist/{targets-TYXLPB23.js → targets-C4SSGQOB.js} +43 -27
  137. package/dist/terminal-lease-IT5JW2NR.js +395 -0
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  140. package/dist/{uninstall-LLLT4F4W.js → uninstall-FZCQCDKC.js} +10 -5
  141. package/dist/{upgrade-33G2LMM5.js → upgrade-7TT7SQ3G.js} +45 -25
  142. package/dist/{usage-ZAFSXKKG.js → usage-GV4PKT3M.js} +62 -31
  143. package/dist/verify-G6V4D2G7.js +716 -0
  144. package/dist/web-fetch-2YHJ3KTG.js +638 -0
  145. package/dist/{wiki-generate-NUQCVOQ3.js → wiki-generate-DQF6Z66B.js} +74 -34
  146. package/dist/worker/entry.js +221 -36
  147. package/dist/workspace-G4ZWUIPR.js +22 -0
  148. package/docs/README.md +22 -17
  149. package/docs/acp.md +168 -16
  150. package/docs/alcf-provider.md +1 -1
  151. package/docs/architecture.md +136 -7
  152. package/docs/artifact-versions.md +1 -1
  153. package/docs/built-in-agents.md +1 -1
  154. package/docs/capacity-and-scheduling.md +1 -1
  155. package/docs/commands-and-modes.md +114 -71
  156. package/docs/config-knobs-audit.md +1 -3
  157. package/docs/configuration-and-targets.md +174 -46
  158. package/docs/context-engine.md +29 -6
  159. package/docs/development-pipeline.md +26 -1
  160. package/docs/dispatch-architecture-rationale.md +1 -1
  161. package/docs/documentation-coverage.md +2 -2
  162. package/docs/documentation-guide.md +1 -1
  163. package/docs/environment-variables.md +13 -5
  164. package/docs/eval-runner.md +1 -1
  165. package/docs/evals-internal.md +1 -1
  166. package/docs/evidence-and-memory.md +6 -2
  167. package/docs/evolution.md +2 -2
  168. package/docs/exit-codes-and-output.md +15 -9
  169. package/docs/extensions-and-sharing.md +9 -9
  170. package/docs/fleet-dispatch.md +7 -5
  171. package/docs/git-commit-provenance.md +120 -0
  172. package/docs/glossary.md +1 -1
  173. package/docs/installation-and-lifecycle.md +34 -27
  174. package/docs/middleware-and-components.md +1 -1
  175. package/docs/model-catalog.md +45 -14
  176. package/docs/observability.md +8 -5
  177. package/docs/performance-methodology.md +491 -0
  178. package/docs/pi-boundary.md +72 -0
  179. package/docs/proactive-memory.md +3 -3
  180. package/docs/prompt-envelope-and-tools.md +24 -3
  181. package/docs/provider-adapter-cookbook.md +57 -4
  182. package/docs/release-cut-checklist.md +129 -115
  183. package/docs/safety-model.md +9 -5
  184. package/docs/scientific-validation.md +3 -3
  185. package/docs/session-lifecycle.md +55 -12
  186. package/docs/skills-marketplace.md +12 -8
  187. package/docs/time-conventions.md +1 -1
  188. package/docs/tool-usage.md +3 -3
  189. package/docs/trace-store.md +1 -1
  190. package/docs/troubleshooting.md +10 -7
  191. package/docs/tui-design.md +47 -10
  192. package/docs/worker-dispatch-mechanics.md +1 -1
  193. package/package.json +19 -22
  194. package/skills/coding/ast-grep/SKILL.md +136 -0
  195. package/skills/coding/ast-grep/evals.md +56 -0
  196. package/skills/coding/ast-grep/references/rule_reference.md +297 -0
  197. package/skills/coding/coding-standards/SKILL.md +113 -0
  198. package/skills/coding/coding-standards/evals.md +34 -0
  199. package/skills/coding/prototype/SKILL.md +86 -0
  200. package/skills/coding/prototype/evals.md +42 -0
  201. package/skills/coding/prototype/references/LOGIC.md +67 -0
  202. package/skills/coding/prototype/references/UI.md +112 -0
  203. package/skills/coding/tdd/SKILL.md +101 -0
  204. package/skills/coding/tdd/evals.md +41 -0
  205. package/skills/coding/tdd/references/mocking.md +59 -0
  206. package/skills/coding/tdd/references/tests.md +77 -0
  207. package/skills/context/context-handoff/SKILL.md +126 -0
  208. package/skills/context/context-handoff/evals.md +57 -0
  209. package/skills/context/context-handoff/scripts/new-handoff.sh +26 -0
  210. package/skills/context/context-prime/SKILL.md +95 -0
  211. package/skills/context/context-prime/evals.md +54 -0
  212. package/skills/meta/clio-dev/SKILL.md +91 -0
  213. package/skills/meta/clio-dev/evals.md +45 -0
  214. package/skills/meta/clio-test/SKILL.md +130 -0
  215. package/skills/meta/clio-test/evals.md +43 -0
  216. package/skills/meta/clio-test/references/harness.md +97 -0
  217. package/skills/meta/clio-test/references/test-map.md +59 -0
  218. package/skills/meta/credentials/SKILL.md +125 -0
  219. package/skills/meta/credentials/evals.md +104 -0
  220. package/skills/meta/find-skills/SKILL.md +72 -0
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  222. package/skills/meta/herdr/SKILL.md +127 -0
  223. package/skills/meta/herdr/evals.md +38 -0
  224. package/skills/meta/skill-craft/SKILL.md +102 -0
  225. package/skills/meta/skill-craft/evals.md +41 -0
  226. package/skills/planning/architecture/SKILL.md +129 -0
  227. package/skills/planning/architecture/evals.md +36 -0
  228. package/skills/planning/backlog/SKILL.md +90 -0
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  230. package/skills/planning/prd/SKILL.md +82 -0
  231. package/skills/planning/prd/evals.md +49 -0
  232. package/skills/planning/product-intent/SKILL.md +112 -0
  233. package/skills/planning/product-intent/evals.md +36 -0
  234. package/skills/planning/tech-spec/SKILL.md +115 -0
  235. package/skills/planning/tech-spec/evals.md +47 -0
  236. package/skills/registry.yaml +136 -0
  237. package/skills/research/arxiv-literature/SKILL.md +104 -0
  238. package/skills/research/arxiv-literature/evals.md +58 -0
  239. package/skills/research/experiment-protocol/SKILL.md +122 -0
  240. package/skills/research/experiment-protocol/evals.md +91 -0
  241. package/skills/research/scientific-debugging/SKILL.md +119 -0
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  243. package/skills/research/scientific-modernization/SKILL.md +138 -0
  244. package/skills/research/scientific-modernization/evals.md +84 -0
  245. package/skills/workflow/design-council/SKILL.md +139 -0
  246. package/skills/workflow/design-council/evals.md +97 -0
  247. package/skills/workflow/grill-me/SKILL.md +186 -0
  248. package/skills/workflow/grill-me/evals.md +78 -0
  249. package/skills/workflow/workflow-distiller/SKILL.md +136 -0
  250. package/skills/workflow/workflow-distiller/evals.md +107 -0
  251. package/src/cli/acp.ts +31 -4
  252. package/src/cli/clio.ts +68 -6
  253. package/src/cli/config-inspect.ts +28 -22
  254. package/src/cli/configure.ts +47 -9
  255. package/src/cli/context-clear.ts +2 -2
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  260. package/src/cli/evidence.ts +4 -1
  261. package/src/cli/extensions.ts +10 -1
  262. package/src/cli/fleet.ts +47 -6
  263. package/src/cli/index.ts +55 -26
  264. package/src/cli/memory.ts +3 -1
  265. package/src/cli/models.ts +1 -1
  266. package/src/cli/modes/json-stream.ts +37 -1
  267. package/src/cli/modes/print.ts +24 -9
  268. package/src/cli/run.ts +2 -2
  269. package/src/cli/skills-eval.ts +23 -8
  270. package/src/cli/skills.ts +19 -4
  271. package/src/cli/targets.ts +4 -0
  272. package/src/cli/text-layout.ts +15 -5
  273. package/src/cli/trace.ts +62 -14
  274. package/src/cli/upgrade.ts +18 -2
  275. package/src/cli/usage.ts +10 -3
  276. package/src/cli/wiki-generate.ts +2 -1
  277. package/src/core/agent-environment.ts +7 -0
  278. package/src/core/bash-exec.ts +72 -1
  279. package/src/core/boot-trace.ts +9 -4
  280. package/src/core/bus-events.ts +20 -4
  281. package/src/core/commit-attribution.ts +157 -0
  282. package/src/core/compile-cache.ts +159 -0
  283. package/src/core/config.ts +131 -2
  284. package/src/core/defaults.ts +39 -5
  285. package/src/core/domain-loader.ts +12 -5
  286. package/src/core/git-commit-attribution.ts +362 -0
  287. package/src/core/incomplete-installation.ts +45 -0
  288. package/src/core/response-schema.ts +1 -1
  289. package/src/core/safe-exec.ts +13 -1
  290. package/src/core/settings-layers.ts +155 -21
  291. package/src/core/skill-activation.ts +1 -1
  292. package/src/core/startup-timer.ts +3 -3
  293. package/src/core/state-file-lock.ts +13 -1
  294. package/src/core/termination.ts +78 -5
  295. package/src/domains/config/classify.ts +15 -3
  296. package/src/domains/config/extension.ts +19 -13
  297. package/src/domains/config/index.ts +10 -0
  298. package/src/domains/config/keybindings.ts +42 -6
  299. package/src/domains/context/bootstrap-prompt.ts +1 -1
  300. package/src/domains/context/bootstrap.ts +111 -18
  301. package/src/domains/context/clear.ts +16 -11
  302. package/src/domains/context/clio-md.ts +111 -9
  303. package/src/domains/context/codewiki/artifact.ts +400 -0
  304. package/src/domains/context/codewiki/build-worker-protocol.ts +24 -0
  305. package/src/domains/context/codewiki/build-worker.ts +54 -0
  306. package/src/domains/context/codewiki/coordinator.ts +182 -0
  307. package/src/domains/context/codewiki/indexer.ts +59 -144
  308. package/src/domains/context/codewiki/paths.ts +67 -0
  309. package/src/domains/context/codewiki/schema.ts +80 -0
  310. package/src/domains/context/codewiki/tree-sitter.ts +1 -1
  311. package/src/domains/context/contract.ts +11 -5
  312. package/src/domains/context/extension.ts +94 -143
  313. package/src/domains/context/fingerprint.ts +3 -1
  314. package/src/domains/context/index.ts +12 -22
  315. package/src/domains/context/project-metadata.ts +19 -0
  316. package/src/domains/context/prompt-context.ts +9 -10
  317. package/src/domains/context/refresh.ts +29 -21
  318. package/src/domains/context/runtime.ts +17 -0
  319. package/src/domains/context/wiki/generate.ts +39 -34
  320. package/src/domains/context/wiki/plan.ts +1 -1
  321. package/src/domains/context/wiki/prompts.ts +21 -8
  322. package/src/domains/dispatch/code-step.ts +20 -1
  323. package/src/domains/dispatch/extension.ts +158 -21
  324. package/src/domains/dispatch/failure-classification.ts +6 -0
  325. package/src/domains/dispatch/fleet-commit-attribution.ts +56 -0
  326. package/src/domains/dispatch/orphan-recovery.ts +50 -8
  327. package/src/domains/dispatch/receipt-integrity.ts +5 -0
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- <h3>Select Gateway Target</h3>
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- <p>Choose an ALCF supercomputing cluster to generate configure commands.</p>
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-
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- <div class="form-group">
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- <label for="clusterSelect">Cluster Gateway</label>
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- <select id="clusterSelect" onchange="updateConfigSim()">
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- <option value="sophia">Sophia Cluster (uses /resource_server/sophia/vllm/v1)</option>
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- <option value="metis">Metis Cluster (uses /resource_server/metis/api/v1)</option>
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- </select>
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- </div>
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-
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- <div class="form-group">
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- <label for="modelSelect">Target Model</label>
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- <select id="modelSelect" onchange="updateConfigSim()">
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- <option value="openai/gpt-oss-120b">openai/gpt-oss-120b (Sophia vLLM id)</option>
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- <option value="gpt-oss-120b">gpt-oss-120b (Metis bare id)</option>
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- <option value="custom">Custom model ID...</option>
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- </select>
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- </div>
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-
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- <div id="customModelGroup" class="form-group" style="display: none;">
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- <label for="customModelText">Custom Model ID</label>
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- <input type="text" id="customModelText" value="openai/gpt-custom-model" oninput="updateConfigSim()">
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- </div>
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-
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- <div class="form-group">
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- <label for="maxTokens">Max Tokens Limit</label>
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- <input type="number" id="maxTokens" value="4096" min="512" max="16384" step="512" oninput="updateConfigSim()">
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- </div>
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- </div>
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- </div>
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-
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- <div class="specs-col">
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- <div class="glass-card">
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- <h3>Generated Configuration Commands</h3>
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- <p>Run these commands inside your Clio Coder session to login and save the target profile:</p>
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-
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- <pre><code id="generatedCommand1">clio-coder auth login alcf</code></pre>
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- <pre><code id="generatedCommand2">clio-coder configure ...</code></pre>
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- <pre><code id="generatedCommand3">clio-coder targets use alcf-sophia</code></pre>
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- </div>
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- </div>
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- </div>
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- </div>
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-
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- <!-- Tab 2: OAuth Flow -->
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- <div class="tab-pane" id="pane-oauth-flow">
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- <div class="glass-card">
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- <h3>Globus OAuth Paste-Code Login</h3>
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- <p>Clio's interactive SSH-friendly OAuth PKCE loop sequence:</p>
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-
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- <div class="flow-diagram">
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- <div class="flow-step active" id="step1">
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- <span class="step-number">1</span>
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- <div class="step-details">
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- <h4>Launch Authentication Command</h4>
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- <p>Operator executes: <code>clio-coder auth login alcf</code></p>
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- </div>
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- </div>
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- <div class="flow-step" id="step2">
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- <span class="step-number">2</span>
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- <div class="step-details">
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- <h4>Authorize via Browser</h4>
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- <p>Clio prints a secure Globus URL. Click to approve and log in through ANL portal.</p>
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- <button type="button" class="oauth-btn" style="margin-top: 0.5rem;" onclick="simulateOAuthStep(2)">Simulate ANL Globus Portal Login</button>
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- </div>
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- </div>
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- <div class="flow-step" id="step3">
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- <span class="step-number">3</span>
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- <div class="step-details">
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- <h4>Paste Authorization Code</h4>
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- <p>Globus displays a code. Paste it back into the Clio prompt: <input type="text" id="pasteCodeSim" placeholder="e.g. abcd1234ef..." style="width:150px; padding:0.25rem 0.5rem; font-size:0.8rem; display:inline-block; vertical-align:middle; margin-left:0.5rem;" oninput="simulateOAuthStep(3)"></p>
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- </div>
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- </div>
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- <div class="flow-step" id="step4">
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- <span class="step-number">4</span>
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- <div class="step-details">
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- <h4>Token Resolved &amp; Saved</h4>
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- <p>Clio exchanges code for OAuth token, verifies it, and stores the encrypted credential locally.</p>
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- </div>
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- </div>
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- </div>
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- </div>
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- </div>
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-
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- <!-- Tab 3: Reference -->
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- <div class="tab-pane" id="pane-reference">
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- <div class="glass-card">
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- <h3>Configure Details</h3>
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- <p>Sophia currently maps to <code>/resource_server/sophia/vllm/v1</code> and Metis maps to <code>/resource_server/metis/api/v1</code>. Wire model IDs must be exact; Metis uses bare names while Sophia uses <code>openai/</code> prefixes.</p>
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-
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- <h3>Implementation files</h3>
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- <ul>
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- <li><code>src/engine/alcf-oauth.ts</code>: PKCE pasting flows</li>
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- <li><code>src/domains/providers/runtimes/cloud/alcf.ts</code>: Sophia/Metis discovery models</li>
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- </ul>
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-
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- <h3 style="margin-top:1.5rem;">Chat Templates Exception</h3>
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- <p>ALCF gateways reject custom client-side <code>chat_template_kwargs</code>. Clio automatically handles this by flagging target profiles with <code>clio.chatTemplateKwargsUnsupported</code>, which strips this field from request bodies before transmitting.</p>
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- </div>
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- </div>
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-
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- <!-- Related Navigation -->
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- <nav class="related-nav" aria-label="Related Pages">
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- <a href="lifecycle_blueprint.html" class="nav-link-card">
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- <span class="nav-label">Previous Blueprint</span>
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- <span class="nav-title">Installation &amp; Lifecycle</span>
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- </a>
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- <a href="environment_blueprint.html" class="nav-link-card next">
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- <span class="nav-label">Next Blueprint</span>
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- <span class="nav-title">Environment Variables</span>
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- </a>
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- </nav>
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- </main>
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- </div>
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-
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- <footer>
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- <p>Clio Coder ALCF Inference Blueprint &bull; Version 0.3.1 &bull; Gnosis Research Center</p>
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- </footer>
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- </div>
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-
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- <script src="shared.js"></script>
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- <script>
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- function updateConfigSim() {
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- const cluster = document.getElementById("clusterSelect").value;
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- const modelMode = document.getElementById("modelSelect").value;
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- const customModelGroup = document.getElementById("customModelGroup");
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-
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- let modelId = modelMode;
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- if (modelMode === "custom") {
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- customModelGroup.style.display = "block";
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- modelId = document.getElementById("customModelText").value;
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- } else {
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- customModelGroup.style.display = "none";
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- // Auto select appropriate model based on cluster
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- if (cluster === "sophia" && modelMode === "gpt-oss-120b") {
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- document.getElementById("modelSelect").value = "openai/gpt-oss-120b";
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- modelId = "openai/gpt-oss-120b";
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- } else if (cluster === "metis" && modelMode === "openai/gpt-oss-120b") {
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- document.getElementById("modelSelect").value = "gpt-oss-120b";
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- modelId = "gpt-oss-120b";
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- }
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- }
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-
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- const tokens = document.getElementById("maxTokens").value;
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- const targetId = `alcf-${cluster}`;
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- const url = cluster === "sophia"
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- ? "https://inference-api.alcf.anl.gov/resource_server/sophia/vllm/v1"
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- : "https://inference-api.alcf.anl.gov/resource_server/metis/api/v1";
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-
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- document.getElementById("generatedCommand2").innerText = `clio-coder configure \\\n --id ${targetId} \\\n --runtime alcf \\\n --url ${url} \\\n --model ${modelId} \\\n --max-tokens ${tokens}`;
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- document.getElementById("generatedCommand3").innerText = `clio-coder targets use ${targetId}`;
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-
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- // Update TOC just in case
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- if (window.initTableOfContents) window.initTableOfContents();
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- }
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-
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- let currentSimStep = 1;
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- function simulateOAuthStep(step) {
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- document.querySelectorAll(".flow-step").forEach(s => s.classList.remove("active"));
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-
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- if (step === 2) {
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- document.getElementById("step2").classList.add("active");
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- } else if (step === 3) {
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- document.getElementById("step3").classList.add("active");
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- const val = document.getElementById("pasteCodeSim").value.trim();
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- if (val.length > 5) {
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- setTimeout(() => {
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- simulateOAuthStep(4);
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- }, 600);
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- }
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- } else if (step === 4) {
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- document.getElementById("step4").classList.add("active");
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- }
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- }
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-
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- // Init
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- window.onload = () => {
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- updateConfigSim();
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- };
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- </script>
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- </body>
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- </html>