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- Add 'Design Documents' section to mkdocs.yml nav (between History and Releases) - Create docs/design_documents/index.md with: - Mission alignment, phase roadmap summary - All 25 DDs organized by phase (Phase 0-4) - Links to GitHub for full specs, roadmap, integration map - How to contribute section - Update docs/index.md: - Add Design Documents to TOC (starred as NEW) - Prominently mention as starting point for technical blueprint Next: Update modeling.md to reference DDs, then open PR. Co-Authored-By: Claude Sonnet 4.5 (1M context) <noreply@anthropic.com>
Major content evolution per DOCS_SITE_EVOLUTION_PROPOSAL.md: - Rewrite modeling.md around Design Documents (5 scales, CyberElegans as history) - Create validation.md explaining DD010 3-tier framework - Create archived_projects.md contextualizing CyberElegans, Geppetto, movement_validation - Update faq.md with 959-cell goal, DD018 egg-laying, Phase 4 completion - Update projects.md with DD-to-project mapping table - Expand c302.md, sibernetic.md, geppetto.md with DD references and roadmaps - Add DD contribution workflow (10 steps) and contributor levels to github.md - Add "Path to 959 Cells" phase table to index.md - Restructure mkdocs.yml nav with "How It Works" and "History" sections - Fix contributor level names to match DD011 (Observer to Senior Contributor) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Copy all DD markdown files (DD001-DD023 + DD014.1/DD014.2 + support docs) from openworm-admin into docs/design_documents/ - Rewrite 93 external GitHub links across 11 files to local relative paths - Add all DDs to mkdocs.yml nav grouped by implementation phase - DDs now render natively on docs.openworm.org with full-text search - Only external DD links remaining: 2 GitHub tree-browsing links in design_documents/index.md (intentional — point to source repo) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Drop the phase label from the infrastructure work — "Phase 0, Phase A, Phase 1..." reads oddly with a letter in the middle of numbers. Now reads as "Infrastructure Bootstrap" without a phase number. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Add "Continue Reading" sections to 18 pages guiding readers to next content - Add DD info boxes and cross-links to all project pages - Hyperlink all bare DD references in FAQ, archived projects, and DD metadata - Fix DD metadata linebreaks (trailing spaces for markdown <br>) - Hyperlink Related DD references in all 24 DD files - Fix broken archived_projects links in FAQ - Add "See today's version" links in archived projects pointing to current pages - Add "Design Document Era" section to full history page - Add DD013 Docker note to releases page Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Converted 393 bare DD### references to clickable [DD###](path) links across 13 files. Only DD016 (archived, no file) remains unlinked. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
The sensorimotor loop diagram was in a code block, making DD links unclickable. Now renders with clickable DD links and arrow formatting. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Converted ~1,800 bare DD### references to clickable [DD###](file.md) links across all 27 DD files. Remaining bare refs are only in code blocks (YAML config examples, PlantUML diagrams) and page titles. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Enables toc permalink in MkDocs Material theme so every heading gets a clickable anchor link for easy sharing. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Inserted blank lines before unordered/ordered list items that immediately followed non-list content. Without the blank line, markdown renders these as inline paragraph text instead of proper <ul><li> elements. Fixed 504 instances across 31 files. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Each DD now shows which implementation phase it belongs to and what layer it covers, with a clickable link back to the relevant section in the Phase Roadmap. DDs with Quick Action Reference tables get two new rows; DDs without get a blockquote after the metadata. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Reordered so readers see the summary first, then the action table. Structure is now: metadata → TL;DR → Quick Action Reference → body. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
… page 229 bare citations (e.g., "Cook et al. 2019") linked to their DOI URLs across 27 files. New references.md page organizes all publications by topic with links to validation tiers. Added to nav and landing page. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…inks DD014 had its own "Phase 1/2/3" that didn't map 1:1 to the Roadmap (DD014 Phase 3 = Roadmap Phase 4). Renamed to "Viewer Stage 1/2/3" with explicit mapping table showing which Roadmap phase each stage belongs to. Fixed 87 mangled DD014.1/DD014.2 links created by the auto-linker wrapping "DD014" inside "DD014.1_..." filenames. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…inst Replace organizational framing (blog posts, paper opportunities, press releases, "shout about it") with concrete user experience: commands to run, behaviors to observe in the viewer, and specific experimental datasets each milestone validates against. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Linked Sarma et al. 2016, Goodman et al. 2002, Yemini et al. 2013, Raizen & Avery 1994, Thomas 1990 throughout DD010 body text and expanded the References section from 3 to 6 entries with DOI links. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
DD010 Tier 1 previously had no specific datasets — just vague "Goodman lab patch-clamp." Now lists 7 neuron classes with named papers: touch neurons (Goodman 2002, O'Hagan 2005, Suzuki 2003), AWC (Chalasani 2007), ASH (Hilliard 2004), AVA (Lindsay 2011), RIM (Liu 2018), pharyngeal (Raizen 1994). Documents the coverage gap (~7 classes with direct data out of 128) and why Tier 1 is non-blocking. Added new "Single-Cell Electrophysiology" section to master references page with all Tier 1 validation sources. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
For the ~121 neuron classes without direct electrophysiology, replaces a single vague sentence with a rigorous validation system: gene-to- electrical-property table (8 major channel genes), 5-step procedure, quantitative acceptance criteria (Spearman rho > 0.5, absence/presence checks), and a concrete testing command. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- DD008 (Data Integration Pipeline) → Phase A (infrastructure, data layer needed before Phase 1 CeNGEN ingestion) - DD014.1 (Visual Rendering Specification) → Phase 1 (companion to DD014 viewer, defines color palette and reference mockups) - DD015 (AI-Native Contributor Model) → Phase A (governance, alongside DD011/DD012) - DD022 (Environmental Modeling) → Phase 2 (substrates and gradients for closed-loop sensory behaviors) - DD023 (Proprioceptive Feedback) → Phase 2 (stretch receptors for stable motor coordination) Updates scope tables, key deliverables, success criteria, datasets, dependency summary, timeline summary (18 → 23 DDs), and blocking dependencies. Fixes DD008 Quick Action Reference from Phase 3 to Phase A. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…plan - Add WormBrowser (2012) history to DD014 Context section with features, technology, and John White's Feb 2026 suggestions (developmental stages, click-to-link, WormAtlas collaboration) - Rename DD014 Stage 3 to "WormSim 2.0" connecting to 2014 Kickstarter promise - Replace all viewer.openworm.org references with wormsim.openworm.org (10 files) - Add deployment timeline table: browser.openworm.org stays live through Phase 3, redirects to wormsim.openworm.org in Phase 4 after feature parity achieved - Add feature parity checklist (WormBrowser features + WormSim 2.0 additions) - Add Phase 1 quick win: click neuron → WormAtlas/WormBase links on existing WormBrowser at browser.openworm.org - Update DD_PHASE_ROADMAP Phase 4 milestone to "WormSim 2.0" Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- Render 6 diagrams via PlantUML web service:
- integration_map.svg: Complete 23-DD dependency graph (was raw PlantUML)
- causal_loop.svg: Sensorimotor loop for modeling.md (replaces broken
Google Drawings link + mangled Unicode arrows)
- chain1-4 SVGs: Core loop, cell differentiation, closed-loop touch,
and visualization pipeline (were ASCII art in INTEGRATION_MAP.md)
- Add DD022 (Environmental Modeling) and DD023 (Proprioception) to
Integration Map PlantUML with dependency edges:
- DD022 -> DD019 (stimulus delivery), DD022 -> DD003 (substrate)
- DD003 -> DD023 (body curvature), DD023 -> DD001 (stretch current)
- DD022/DD023 -> DD014 (visualization exports)
- Update DD count from 21 to 23 in Integration Map header
- Preserve PlantUML source in collapsible details block for re-rendering
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
The old diagram had 30 components and 78 edges — unreadable spaghetti. New approach: group DDs into 10 functional clusters (External Data, Data Access, Core Chain, Neural Extensions, Sensory/Motor, Organs, Whole Organism, Infrastructure, Validation, Visualization) with only major inter-cluster data flows shown. Color-coded arrows: green for core chain, red for closed loop, blue for validation, purple for viz. Detail preserved in the 4 chain diagrams (chain1-4 SVGs) which show per-edge data flow for each pathway. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Re-rendered all 6 PlantUML SVG diagrams with [[url]] links so clicking any DD component navigates to its design document. Switched from markdown image syntax to <object> tags for SVG interactivity support. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
… validation The ConnectomeToolbox already contains neuropeptidergic data as 'extrasynaptic' connections (Bentley 2016, Ripoll-Sánchez 2023) — DD006 was incorrectly proposing to add it. Fixed all references to consume via cect API (DD020) instead. Added Tier 1 functional connectivity validation using Randi 2023 unc-31 mutant data as a natural experiment isolating neuropeptide contribution (unc-31 = no dense-core vesicle release = no neuropeptide signaling). Added references: Pereira 2015, Beets 2022, Wang 2024, Randi 2023, Gleeson et al. ConnectomeToolbox manuscript. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Split Tier 2 into 2a (whole-network FC) and 2b (neuropeptide modulation via wt-vs-unc-31 comparison from Randi 2023). Add ConnectomeToolbox as data source alongside wormneuroatlas. Cross-reference DD006 validation. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Copy mockup PNGs from openworm-admin and embed in each mockup specification section. All 14 views now have visual reference images alongside their property tables. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…view Major changes: - Port MetaWorm (Zhao 2024) analysis into DD001, DD003, DD005, DD006, DD010, DD017, DD020, DD021, DD022 (29 citations across 7 files) - Add "Existing Code Resources" sections to 11 DDs identifying 18 reusable repos from the OpenWorm GitHub org - Create DD024 (Validation Data Acquisition Pipeline) - Create contributing_guide.md (extracted from dd_readme.md) - Consolidate overview: richer index.md with philosophical foundations, MetaWorm related work, cross-references by topic - Remove standalone analysis pages (CODE_REUSE, COMPREHENSIVE_ANALYSIS, dd_readme) — content incorporated into individual DDs - Add DD008 reconciliation note for OWMeta/cect phasing - Add DD001 Boyle & Cohen parameter borrowing clarification - Fix mkdocs.yml: add admonition/details/superfences extensions - Fix 3-space → 4-space list indentation across 12 files Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Comprehensive audit and cleanup of the entire openworm_docs site (35 files): - Fix broken links: dead repositories/ link, 3 Dropbox→DOI replacements, outdated openworm-admin reference, phantom nav entry - Add ~50 DOI hyperlinks to unhyperlinked citations across 10 DD files and references.md (Goodman, Gleeson, Cannon, Kato, Berman, Machamer, Pearl, Schafer, Brown, Pierce-Shimomura, Iino, Zhao, and many more) - Verify Chalfie 1985 DOI across all DDs (8 missing links added) - Upgrade ~115 http:// links to https:// across 18 files - Consolidate duplicated content: FAQ shortened with cross-links to canonical pages (background, DD index, validation) - Add cross-links between non-DD pages and governing Design Documents - Add historical banners to running-nc.md and Live-Video-Protocol.md - Fix image paths in browser.md and docker.md - Clarify DD008 neuropeptide data status (in cect, not yet in OWMeta) - Clean build: zero warnings, zero errors Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…oss-references Add ~30 new references extracted from all 25 Design Documents, create 4 new sections (Chemotaxis, Neural Circuit Variability, Computational Methods, Philosophical Foundations), and hyperlink every DD cross-reference in the Description column so readers can click through to the citing documents. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
DD017's foundation model → ODE parameter pipeline (Component 3) had no infrastructure dependencies and derisks DD005's uncertain expression→ conductance mapping. BioEmu-1's 100,000x MD speedup invalidated the original "computationally expensive" rejection. Extracted into standalone DD025 (Protein Foundation Model Pipeline) scheduled as Phase A parallel track with Phase 1 integration into DD005 calibration. Files changed: - NEW: DD025_Protein_Foundation_Model_Pipeline.md - DD017: Component 3 section replaced with redirect to DD025 - DD005: Alternative #1 promoted, roadmap/issues updated with DD025 refs - DD001: Cross-reference updated from DD017 Component 3 to DD025 - DD_PHASE_ROADMAP: DD025 added to Phase A scope/deliverables/datasets, Phase 1 scope, FAQ, dependency summary, timeline (+7 DDs) - index.md: DD025 added, count updated to 26 - references.md: BioEmu-1 and Boltz-2 entries added, DD025 cross-refs - mkdocs.yml: DD025 nav entry under Infrastructure Bootstrap Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…ntegration map - Replace all Level E neuron references with Level D across 8 files (Level E was erroneous — same as multicompartmental Level D) - Add DevoWorm cross-references to Phase 6, DD004, DD005, and projects.md - Add Karr et al. 2012 whole-cell model precedent to Phase 5 with analysis of how foundation models solve the parameter curation bottleneck for C. elegans - Add bio.rodeo foundation model opportunities table to Phase 5 - Add eukaryotic whole-cell gap note (no Karr-level eukaryotic model exists yet) - Update INTEGRATION_MAP v1.0→v1.1 with DD025, bio.rodeo, 7 new edges - Add Karr 2012 and Karr 2014 dissertation to master references - Restructure DD024 dataset inventory Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Move Phase Placement Rationale, Major Milestones summary, and Success Metrics table from standalone bottom sections into each phase's description. Each phase now opens with a Phase Rationale paragraph, has target dates on its milestone heading, and closes with Cumulative Metrics — eliminating the need to scroll to the bottom for context. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
OpenCL is the only backend producing validated results but is losing platform support. PyTorch/Taichi must achieve result parity before they can replace it. Updates DD003 with stabilization roadmap (graduation criteria, parity tests, Taichi coordinate bug), adds 5 new issues (40-44) to DD013 draft issues, and updates DD004/DD013/Phase Roadmap with cross-backend compatibility notes. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Decomposes DD003 Body Physics Architecture into 22 implementation issues following the DD015 §2.2 Issue Generator methodology: validation scripts, test configs, kernel unit tests, OME-Zarr/WCON export, surface mesh reconstruction, FEM evaluation, Python bindings, and documentation. Cross-references DD013 Issues 40-44 (backend stabilization, also DD003). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
… Computing Validation Replace all responsibility-context references to Padraig Gleeson, Andrey Palyanov, and @slarson with role-based titles (Neural Circuit L4 Maintainer, Body Physics L4 Maintainer, ConnectomeToolbox maintainer, Project Lead) across 8 files. Academic citations, DD author metadata, and historical narrative preserved unchanged. Also adds DD026 (Reservoir Computing Validation), updates DD015 AI Contributor Model (expanded repo table, fork/PR workflow replacing sandbox repo), and adds AI agents community page. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
23 issues covering build integration, CI quality gates, consumer DD integration, multi-dataset validation, documentation, and future evaluation. Also adds DD001 and DD002 draft issues to mkdocs nav. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…ross 33 files The term "differentiation" implies developmental biology (stem cell → neuron), which confused readers. DD005/Phase 1 is about parameterizing neuron classes with distinct ion channel profiles from CeNGEN transcriptomic data — that's specialization, not differentiation. Preserved: filename DD005_Cell_Type_Differentiation_Strategy.md (too many links to rename safely), config key neural.differentiated, code artifacts (C1Differentiated), anchor URLs, and DevoWorm developmental biology refs. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…isting code Add "Existing Code to Reuse" sections to all 18 issues pointing contributors to specific files across c302, muscle_model, sibernetic, and CE_locomotion repos. Reframe 6 issue titles from "create from scratch" to "adapt existing code" and add DD013 Stack Notes for Docker/CI integration where applicable. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…ues (29→25) Comprehensive restructuring of DD001_draft_issues.md driven by deep analysis of existing code across 12+ OpenWorm repos (CE_locomotion, Worm2D, CelegansNeuromechanicalGaitModulation, c302, Sibernetic, NicolettiEtAl2019, NicolettiEtAl2024, BAAIWorm, ChannelWorm2, CElegansNeuroML, OWAT, wormneuroatlas). Key changes: Eliminated 4 issues already implemented in c302 CI: - NeuroML validation CI gate (ci.yml + test.sh already validate) - Connectome dataset switching (7 readers tested in CI) - Level A-D generation verification (test.sh covers all 9×8 combos) - wormneuroatlas integration (test_WNA.py already tests it) Added reuse-first infrastructure: - "Reuse-First Philosophy" preamble with wrap→port→adapt→create hierarchy - "Existing Code to Reuse" field on 20 issues with specific repo paths - "Approach" field on 18 issues making reuse strategy explicit - "DD013 Pipeline Role" field on 4 pipeline-component issues - "Eliminated Issues (Already Implemented)" section documenting progress Major issue rewrites (15 issues): - Issue 1: Port existing C++ body model, don't reimplement - Issue 2: Adapt Sibernetic's existing generate_wcon.py (~300 LOC) - Issue 3: Wrap OWAT StatisticsManager (726 features already computed) - Issue 4: Use OWAT WormFeatures (IS the Schafer toolbox) - Issues 8-12: Survey + adopt existing NeuroML2 channels from Nicoletti (31 channels already in NeuroML2!) instead of converting from NMODL - Issue 14: Consolidate existing neurotransmitter data, not create new - Issue 16: Thin adapter on wormneuroatlas API (data loading is one-liner) - Issue 17: Evaluate existing CElegansNeuroML morphologies (all 302 exist) - Issue 18: Integrate existing channels + morphology + framework for AWC Cross-cutting updates from prior Boyle-Cohen 2D fast path integration: - DD001 main doc: Split Step 3 into 3a/3b, add script table entry - DD003: Add Boyle-Cohen to Alternatives Considered - INTEGRATION_MAP: Add dual trajectory path table, update WCON producer - DD_PHASE_ROADMAP: Add Boyle-Cohen mentions in Phases A, 1, 3 - github-repo-inventory: Update 3 repo annotations Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
… issues to DD015 DD015 §2 (DD Issue Generator) is the right home for issue decomposition methodology. Added: - §2.3 Reuse-First Issue Design: wrap→port→adapt→integrate→extend→create hierarchy, required fields, issue elimination rule - §2.4 DD013 Simulation Stack Integration: pipeline role field, Docker stage placement, openworm.yml configuration requirements Removed from DD001_draft_issues.md: - Reuse-First Philosophy preamble (now in DD015 §2.3) - DD013 Simulation Stack Integration preamble (now in DD015 §2.4) - Eliminated Issues table (internal housekeeping, not relevant to readers) DD001 draft issues file is now clean: just the header and 25 issues. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…003 with code reuse guidance - DD001: Remove 2 validation issues (check_regression.py, Schafer baseline) that belong to DD021 (OWAT owner); renumber 25→23 issues; update all cross-refs - DD021: New draft issues file with those 2 issues retargeted at openworm/open-worm-analysis-toolbox with provenance notes - DD003: Add "Existing Code to Reuse" sections and DD013 Stack Notes - DD002: Fix DD003 cross-reference after renumbering - INTEGRATION_MAP: Correct WCON exporter to reference existing generate_wcon.py - mkdocs.yml: Add DD021 Draft Issues to nav Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
… Roadmap The internal "Phase 1-6" groupings within each DD's draft issues doc were being confused with the larger DD Phase Roadmap phases (Phase 0/A/1/2/3/4). Renamed to "Group 1-6" and added a "Roadmap Context" note to each file explaining how internal groups map to roadmap phases. Files: DD001, DD002, DD003, DD020 draft issues (4 files, 22 headers renamed). DD013/DD021 left unchanged — their Phase A-D labels align with the roadmap. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Deleted 4 duplicate/overlapping issues and merged content: - DD013 Issue 40 (stability scripts) deleted — DD003 Issues 1-2 are canonical - DD001 Issue 5 (sibernetic_c302.py docs) deleted — DD002 Issue 18 is canonical - DD013 Issue 24 (connectome notebook) merged into DD020 Issue 18, deleted - DD001 Issue 20 (c302 notebook) merged into DD013 Issue 24, deleted Renumbered: DD013 44→42, DD001 23→21. Updated all internal dependency chains, cross-references in DD003, and dependency trees. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…ssue 16 DD015 §2.6 establishes three-tier documentation destination policy for the DD Issue Generator: repo-internal (single-repo scope), docs site (cross-repo guides), and BadgeList-aligned (augment existing badges). Includes decision rules so doc issues specify WHERE docs go, not just what they contain. DD002 Issue 16 rewritten to augment existing BadgeList muscle model badge progression (Explorer/Builder/Hacker, 23 earners) rather than creating a guide from scratch. Target changed from c302 repo to docs.openworm.org since the guide spans c302, muscle_model, CE_locomotion, and Sibernetic. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…issues DD020 said Phase 1/Proposed while Roadmap and Integration Map showed Phase 0/Accepted. Fixed the root cause (DD020 header + status), then added systematic phase tracking: - DD020: Status → Accepted, Phase → Phase 0, footer → Complete - Roadmap: Phase 0→A Gap Map table, validation scripts inventory, issue summary - Integration Map: Phase Legend table, chain phase annotations - DD012: Phase field in DD template, Step 6 Phase Synchronization, quality criterion #11 - DD015: Roadmap Phase in issue fields, Phase Consistency Rule, Phase Drift Detection - Draft issues (DD001/002/003/020): structured Roadmap Context tables, per-issue phase tags on all 83 issues, phase-tagged group headers Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…ft issues Links like https://docs.openworm.org/design_documents/DD001_.../ now use relative paths (DD001_Neural_Circuit_Architecture.md#anchor) so they resolve correctly on localhost, staging, or production. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Branch builds are deployed to docs.openworm.org/preview/<branch-name>/ so reviewers can see rendered docs without building locally. Previews are automatically cleaned up when PRs are closed. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…oadmap The Implementation Roadmap section duplicated task breakdowns now covered by DD013_draft_issues.md (42 issues) and DD_PHASE_ROADMAP.md. Replaced with a single paragraph linking to both. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
v2 is deprecated and now hard-fails at job setup. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
pycairo build fails on Ubuntu 24.04 runners without this package. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
The listComments response is already destructured, so comments is the array directly — no need for comments.data. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…al terms - Update DD count from 25 to 27 across 6 files (index, fullhistory, ai_agents, DD015, modeling) to reflect DD024-DD026 and DD014.1/DD014.2 - Add "Getting Started" section to DD001 with repo clone commands, Docker path, and native Python setup so newcomers can actually follow build instructions - Add 30 hyperlinks for domain-specific terms (Hodgkin-Huxley, NeuroML, LEMS, SPH, PCISPH, WCON, OME-Zarr, etc.) on first occurrence across DD001-DD003, DD020, DD_PHASE_ROADMAP, and INTEGRATION_MAP Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add "Getting Started" sections with clone URLs, Docker-vs-native paths, and dependency installation to all Phase 0 DDs so newcomers can follow the build instructions without prior knowledge: - DD002: Same c302 setup as DD001, with cross-reference for existing setup - DD003: Native C++ path with platform-specific OpenCL guidance, Docker recommended to avoid SDK setup complexity - DD020: Distinguish "use cect" (pip install) from "develop cect" (clone + editable install + pytest) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Update the DD012 RFC Process template to require a "Getting Started (Environment Setup)" sub-section in every DD's "How to Build & Test": - Template: expand flat bullet list into structured sub-sections (Prerequisites, Getting Started, Step-by-step, Green light criteria) - Getting Started must include: repo clone URLs, Docker path (recommended), native path with exact install commands, cross-references for shared repos, platform-specific notes where applicable - Quality criterion #10: "Complete Setup Path" — newcomer goes from blank machine to working environment without guessing - Anti-pattern #10: "Missing setup context" — build commands assume repos are already cloned without saying how Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Every non-exempt Design Document now has a "Getting Started (Environment Setup)" sub-section per the DD012 template standard. Includes clone URLs, Docker vs native paths, cross-references for shared repos, and platform-specific notes. DD013 and DD014 received full How to Build & Test sections (were previously missing). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…raft issues DD001 contained ~80 lines of Phase 1-2+ future work (multicompartmental neurons, ion channel library, synaptic optimization, spatial synapses) that made it read like a roadmap instead of a spec. This refactor: - Creates DD027 (Multicompartmental Neuron Models) from DD001's Level D and spatial synapse sections, with full DD012-compliant structure - Redistributes DD001 draft issues to owning DDs: DD005_draft_issues (6 ion channel issues), DD017_draft_issues (3 synaptic optimization issues), DD027_draft_issues (3 multicompartmental issues) - Trims DD001_draft_issues from 21 to 9 retained issues - Replaces extracted DD001 sections with concise forward references - Updates DD count site-wide (27→28), Phase Roadmap, Integration Map, mkdocs.yml nav, and cross-reference indices Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
DD001 should describe what exists now and note known approximations, not how the nervous system model will evolve. Replaced three evolution subsections (synaptic optimization, ion channel expansion, spatial synapses) with a concise "Known Approximations" section. Trimmed forward-looking reference annotations and removed future-only refs. Moved the digested technical details to Phase Roadmap where they belong (Phase 1 ion channel expansion, Phase 2 DD027 staging, Phase 3 synapse weight optimization). Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Summary
docs.openworm.org/preview/<branch>/with a link posted as a PR commentKey files
docs/design_documents/— all 27 DDs plus index, roadmap, integration map, contributing guidedocs/design_documents/*_draft_issues.md— pre-written GitHub issues for 6 DDsmkdocs.yml— expanded nav with full DD hierarchy.github/workflows/mkdocs.yml— PR preview deploy supportdocs/references.md,docs/validation.md,docs/archived_projects.md— new pagesTest plan
docs.openworm.org/preview/integrate-design-documents/!!!/???) render properly (requires pymdownx extensions)🤖 Generated with Claude Code