Repository navigation

Integrate Design Documents into docs site - #114

Open

slarson wants to merge 124 commits into

masterfrom

integrate-design-documents

Open

Integrate Design Documents into docs site#114
slarson wants to merge 124 commits into
masterfrom
integrate-design-documents

Commits on Feb 19, 2026
- Integrate Design Documents into docs.openworm.org
  
  slarson
  and
  claude
  committed
  af351de
- Apply docs site evolution: DD-centric modeling, validation, archives
  
  slarson
  and
  claude
  committed
  d8b2983
- Import all 25 DDs into docs site, convert external links to local
  
  slarson
  and
  claude
  committed
  f3bd782
- Rename Phase A to Infrastructure Bootstrap in reader-facing pages
  
  slarson
  and
  claude
  committed
  1712116
Commits on Feb 20, 2026
- Add navigation footers, DD cross-links, and fix DD metadata rendering
  
  slarson
  and
  claude
  committed
  9c5dab8
- Hyperlink all bare DD references across reader-facing pages
  
  slarson
  and
  claude
  committed
  efa40e0
- Convert causal loop diagram from code fence to rendered markdown
  
  slarson
  and
  claude
  committed
  3007722
- Hyperlink all bare DD cross-references within Design Documents
  
  slarson
  and
  claude
  committed
  d0072a4
- Add permalink buttons to all section headers
  
  slarson
  and
  claude
  committed
  852c64a
- Fix Design Document era date from 2024 to 2026
  
  slarson
  and
  claude
  committed
  283e6cb
- Fix broken list rendering across all docs
  
  slarson
  and
  claude
  committed
  26c2b35
- Add Phase and Layer to every DD with links to Phase Roadmap
  
  slarson
  and
  claude
  committed
  e3b5afe
- Move TL;DR above Quick Action Reference in all DDs
  
  slarson
  and
  claude
  committed
  a58b0df
- Hyperlink all publication citations to DOIs and add master References page
  
  slarson
  and
  claude
  committed
  e635bb7
- Clarify DD014 viewer stages vs. roadmap phases, fix mangled DD014.x links
  
  slarson
  and
  claude
  committed
  a1bc808
- Rewrite roadmap milestones: what you run, what you see, validated against
  
  slarson
  and
  claude
  committed
  1936f35
- Link all bare citations in DD010 to DOIs
  
  slarson
  and
  claude
  committed
  70cd227
- Add concrete Tier 1 electrophysiology datasets to DD010 and references
  
  slarson
  and
  claude
  committed
  f001237
- Add systematic expression-consistency validation for Tier 1 in DD010
  
  slarson
  and
  claude
  committed
  01c7dda
- Add 5 missing DDs to Phase Roadmap: DD008, DD014.1, DD015, DD022, DD023
  
  slarson
  and
  claude
  committed
  0b26c48
- Rename viewer to WormSim 2.0, add WormBrowser history and deployment plan
  
  slarson
  and
  claude
  committed
  ee497dc
- Render PlantUML diagrams to SVG, add DD022/DD023 to Integration Map
  
  slarson
  and
  claude
  committed
  6c527f0
- Simplify Integration Map: cluster DDs, reduce 78 edges to ~20
  
  slarson
  and
  claude
  committed
  cff56d2
- Add clickable DD hyperlinks to all SVG diagrams
  
  slarson
  and
  claude
  committed
  10ab0e5
- DD006: Fix ConnectomeToolbox integration, add functional connectivity validation
  
  slarson
  and
  claude
  committed
  7caa49b
- DD010: Add Tier 2b unc-31 validation, ConnectomeToolbox integration
  
  slarson
  and
  claude
  committed
  72342cf
- DD014.1: Add 14 mockup images for canonical rendering views
  
  slarson
  and
  claude
  committed
  eee323d
Commits on Feb 21, 2026
- Enrich DDs with MetaWorm citations, code reuse, and consolidated overview
  
  slarson
  and
  claude
  committed
  f66f2c0
- Site-wide audit: fix links, add DOIs, upgrade HTTPS, consolidate content
  
  slarson
  and
  claude
  committed
  00f1aa9
Commits on Feb 22, 2026
- Expand master reference list with all DD citations and hyperlinked cross-references
  
  slarson
  and
  claude
  committed
  0bfe558
- Fix line break disease, add repo inventory, rewrite validation page
  
  slarson
  and
  claude
  committed
  9a3fee6
- Bring all 13 non-compliant DDs up to DD012 template spec
  
  slarson
  and
  claude
  committed
  2c97438
- Integrate bio.rodeo foundation models into DDs and fix DD017 DD012 compliance
  
  slarson
  and
  claude
  committed
  e8c7806
- Extract DD017 Component 3 into DD025 and promote to Phase A/Phase 1
  
  slarson
  and
  claude
  committed
  9389eee
- Eliminate Level E, integrate DevoWorm/Karr whole-cell model, update integration map
  
  slarson
  and
  claude
  committed
  f82ba26
- Consolidate rationale, milestones, and metrics into phase descriptions
  
  slarson
  and
  claude
  committed
  d8a6b04
Commits on Feb 23, 2026
- DD003: Add Backend Stabilization Roadmap and cross-cutting docs updates
  
  slarson
  and
  claude
  committed
  f8f390e
- DD003: Generate draft GitHub issues (22 issues across 5 phases)
  
  slarson
  and
  claude
  committed
  0760a14
- Add DD003 and DD013 draft issues to mkdocs nav
  
  slarson
  and
  claude
  committed
  193d344
- Replace named individuals with role-based titles; add DD026 Reservoir Computing Validation
  
  slarson
  and
  claude
  committed
  f5dc7b9
- DD020: Generate draft GitHub issues (23 issues across 6 phases)
  
  slarson
  and
  claude
  committed
  b6a46ec
- Rename "Cell(-Type) Differentiation" to "Cell-Type Specialization" across 33 files
  
  slarson
  and
  claude
  committed
  4a48dfd
- DD002 draft issues: add code reuse guidance and reframe titles for existing code
  
  slarson
  and
  claude
  committed
  7590095
- DD001: Rewrite draft issues for code reuse; eliminate 4 redundant issues (29→25)
  
  slarson
  and
  claude
  committed
  387811a
- Move reuse-first philosophy and DD013 integration guidance from DD001 issues to DD015
  
  slarson
  and
  claude
  committed
  bb69f12
- Move validation infrastructure issues from DD001 to DD021; enhance DD003 with code reuse guidance
  
  slarson
  and
  claude
  committed
  e57ee1a
- Rename Phase → Group in draft issues to avoid confusion with DD Phase Roadmap
  
  slarson
  and
  claude
  committed
  e299a08
- Eliminate duplicate and overlapping issues across DD draft issues files
  
  slarson
  and
  claude
  committed
  5f28ca2
- Add documentation destination policy (DD015 §2.6) and rewrite DD002 Issue 16
  
  slarson
  and
  claude
  committed
  36110c2
Commits on Feb 24, 2026
- Reconcile Phase 0 across docs: fix DD020 drift, add phase tags to 83 issues
  
  slarson
  and
  claude
  committed
  98ddb5a
- Convert 230 hardcoded docs.openworm.org URLs to relative paths in draft issues
  
  slarson
  and
  claude
  committed
  d086e06
- Add PR preview deployments to GitHub Actions workflow
  
  slarson
  and
  claude
  committed
  212425c
- Replace DD013 inline roadmap with pointer to draft issues and phase roadmap
  
  slarson
  and
  claude
  committed
  a89ffbe
- Bump actions/upload-artifact from v2 to v4
  
  slarson
  and
  claude
  committed
  e1c119c
- Add libcairo2-dev to CI apt dependencies
  
  slarson
  and
  claude
  committed
  f53d212
- Fix PR comment script: remove double .data dereference
  
  slarson
  and
  claude
  committed
  c0c49b5
- Fix DD count (25→27), add DD001 setup instructions, hyperlink technical terms
  
  slarson
  and
  claude
  committed
  2c32d12
- Add setup instructions to DD002, DD003, and DD020
  
  slarson
  and
  claude
  committed
  6d981d6
- Require setup instructions in DD template (DD012)
  
  slarson
  and
  claude
  committed
  a0a3f34
- Add Getting Started setup sections to all 19 remaining DDs
  
  slarson
  and
  claude
  committed
  99ffbb8
- Extract forward-looking content from DD001 into DD027; redistribute draft issues
  
  slarson
  and
  claude
  committed
  c858316
- Clean forward-looking content from DD001; move details to Phase Roadmap
  
  slarson
  and
  claude
  committed
  119e1e7
- Fix inverted three-ring diagram in AI agents page
  
  slarson
  and
  claude
  committed
  125fc2f
Commits on Feb 27, 2026
- Add DD028 Project Metrics Dashboard (Phase A)
  
  slarson
  and
  claude
  committed
  66dcc3d
- Complete Phase A inventory: add missing deliverables, fix integration map
  
  slarson
  and
  claude
  committed
  53cb97c
- DD011: Add engagement loop, fast-track assessment, and reactivation campaign
  
  slarson
  and
  claude
  committed
  f5dc2fb
Commits on Feb 28, 2026
- Split Phase A into A1 (Core Infrastructure) and A2 (Governance & Derisking)
  
  slarson
  and
  claude
  committed
  25d1033
- Refine Phase 0 language: "Done" → "Functional, Stabilizing"
  
  slarson
  and
  claude
  committed
  7c74170
Commits on Mar 17, 2026
- Trigger preview rebuild
  slarson
  committed
  795e74c
- Merge master into integrate-design-documents
  
  slarson
  and
  claude
  committed
  8634338
Commits on May 26, 2026
- DD003: reframe Backend Stabilization Roadmap around native ports
  
  slarson
  and
  claude
  committed
  615ae7f
- Migrate DD011/12/15 → /docs/contributing/ section
  
  slarson
  and
  claude
  committed
  12b2251
- Merge contributing-section-migration into integrate-design-documents
  
  slarson
  and
  claude
  committed
  49dbd9a
- DD renumber: contiguous compression (DD013+ → DD011+)
  
  slarson
  and
  claude
  committed
  dfbc5a6
- DD renumber: swap DD001/002/003 so Body Physics leads (DD003→DD001, DD001→DD002, DD002→DD003)
  
  slarson
  and
  claude
  committed
  4037dd7
- DD001: elevate differentiability from byproduct to core property; DD013 narrows accordingly
  
  slarson
  and
  claude
  committed
  eeb9056
- DD001: add prominent Validation Methodology section
  
  slarson
  and
  claude
  committed
  dac96b7
- Spread validation methodology themes across DD002, DD003, DD010, DD011
  
  slarson
  and
  claude
  committed
  fc045d2
- Unlink held-back DD references across the publish set; keep DD001 + /contributing/ live
  
  slarson
  and
  claude
  committed
  a15675b
- DD001 feedback round 1: XPBD discussion, footnote links, MoaW link, README pointer
  
  slarson
  and
  claude
  committed
  0c591cd
- Drop "previous version of new stuff" cruft across publish set
  
  slarson
  and
  claude
  committed
  d3c3294
Commits on May 27, 2026
- Fix publish-set inconsistencies from audit
  
  slarson
  and
  claude
  committed
  518e5a9
- Rewrite DD001 draft issues to match reframed DD001 scope
  
  slarson
  and
  claude
  committed
  a6232f7
- Hyperlink GitHub issue and PR references in DD001 draft issues
  
  slarson
  and
  claude
  committed
  c7eeae1
Commits on May 29, 2026
- Soften publish-set commitments per leadership-risk review
  
  slarson
  and
  claude
  committed
  0b0cebd
- DD001 draft issues: align to sibernetic repo numbering + rescan state
  
  slarson
  and
  claude
  committed
  9cecaea
- DD001 draft issues: map GitHub milestones into the doc
  
  slarson
  and
  claude
  committed
  7ae673e
- DD001 draft issues: stabilize-gold-standard reframe + version milestones
  
  slarson
  and
  claude
  committed
  62e8817
- DD001: separate spec from issue tracking; point at GitHub instead
  
  slarson
  and
  claude
  committed
  5475042
- Codify spec/issue cleavage; promote DD001 as reference DD
  
  slarson
  and
  claude
  committed
  31a779f
- Merge milestone proposal into the issues list
  
  slarson
  and
  claude
  committed
  acec93c
- Codify reference-project pattern; draft public milestone descriptions
  
  slarson
  and
  claude
  committed
  ba1595c
- fix stale anchor after Backend Graduation Criteria section rename
  slarson
  committed
  f16c43f
- Redundancy pass: cut 7 redundant sections / phrasings
  
  slarson
  and
  claude
  committed
  d58a4f0
- Defer-to-milestone reframe; add v0.4.0 + v0.5.0 milestones
  
  slarson
  and
  claude
  committed
  be69537
- fix two more stale #stabilization-sequence anchors after section deletion
  slarson
  committed
  666dbfc
- Rename sibernetic release milestones to use roadmap-phase identifiers
  
  slarson
  and
  claude
  committed
  13b54ae
- Reclassify #163 (chemotaxis): defer to Phase 2 — Environmental Modeling
  
  slarson
  and
  claude
  committed
  9f291aa
- Narrow Issue #250: in-process Simulation handle for closed-loop only
  
  slarson
  and
  claude
  committed
  a66d93d
- Apply all 17 audit recommendations to DD001 draft issues
  
  slarson
  and
  claude
  committed
  96a3a34
- Rename milestones to v0.<phase>.<sub> semver scheme
  
  slarson
  and
  claude
  committed
  a1ae9de
- Renumber project phases strictly numerically; drop duration estimates
  
  slarson
  and
  claude
  committed
  ba8b1fa
- Regroup DD001 draft issues by milestone (no renumbering)
  
  slarson
  and
  claude
  committed
  6273c88
- Move #236 (generalize parity harness) from v0.1.0 to v0.0.9
  
  slarson
  and
  claude
  committed
  7b59e93
- Simplify DD001 draft-issue titles + a few sponsor summaries
  
  slarson
  and
  claude
  committed
  e87188a
- File v0.0.9 issues #233-#240; renumber all draft issues to actual numbers
  
  slarson
  and
  claude
  committed
  377b6d0
- Drop DD001_draft_issues from nav + exclude all unlinked pages from search
  
  slarson
  and
  claude
  committed
  06c57ae
- Unlink all held-back DD references across the publish set
  
  slarson
  and
  claude
  committed
  f9b0d08
- Fix all broken links + missing anchors + add Mind-of-a-Worm links
  
  slarson
  and
  claude
  committed
  159328c
- Hold back contributing/ai-contributors.md from publish set
  
  slarson
  and
  claude
  committed
  2484026
- Reframe 'protect founder time' language for community-facing docs
  
  slarson
  and
  claude
  committed
  a36a6ef
Commits on May 30, 2026
- Reconcile conflicting contribution paths across community/contributing sections
  
  slarson
  and
  claude
  committed
  9f72891
- Fix broken directory-style links from non-root pages
  
  slarson
  and
  claude
  committed
  c590128
- Align Projects page roadmaps with canonical DD_PHASE_ROADMAP
  
  slarson
  and
  claude
  committed
  bfd4bf9
Commits on May 31, 2026
- ai_agents: add BadgeList stewardship to Mind-of-a-Worm's mandate
  
  slarson
  and
  claude
  committed
  bbba4d7
- ai_agents: fix DD numbering in governing-docs callout
  
  slarson
  and
  claude
  committed
  86d0dd0
- docs: sweep DD-number mislabels for de-numbered Contributing pages
  
  slarson
  and
  claude
  committed
  2422f0d
Commits on Jun 5, 2026
- Reconcile Sibernetic milestone numbering with GitHub
  
  slarson
  and
  claude
  committed
  799290c
- Exclude unpublished Design Documents from the docs build
  
  slarson
  and
  claude
  committed
  352d910
- Fix DD reference hygiene on roadmap + integration map
  
  slarson
  and
  claude
  committed
  ccd5ef2
- Surface the contribution on-ramp and AI Contributors in nav
  
  slarson
  and
  claude
  committed
  c0c9318
- Correct open-worm-analysis-toolbox status in repo inventory
  
  slarson
  and
  claude
  committed
  5f5e2ca
Commits on Jul 31, 2026
- Disambiguate OpenWorm Skills from OpenClaw agent skills
  
  slarson
  and
  claude
  committed
  579b2b6
Commits on Oct 28, 2026
- Merge pull request #122 from openworm/master
  pgleeson
  authored
  4dc7ba4

Commits

Commits on Feb 19, 2026

Commits on Feb 20, 2026

Commits on Feb 21, 2026

Commits on Feb 22, 2026

Commits on Feb 23, 2026

Commits on Feb 24, 2026

Commits on Feb 27, 2026

Commits on Feb 28, 2026

Commits on Mar 17, 2026

Commits on May 26, 2026

Commits on May 27, 2026

Commits on May 29, 2026

Commits on May 30, 2026

Commits on May 31, 2026

Commits on Jun 5, 2026

Commits on Jul 31, 2026

Commits on Oct 28, 2026