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af351de
Integrate Design Documents into docs.openworm.org
slarson Feb 19, 2026
d8b2983
Apply docs site evolution: DD-centric modeling, validation, archives
slarson Feb 19, 2026
f3bd782
Import all 25 DDs into docs site, convert external links to local
slarson Feb 19, 2026
1712116
Rename Phase A to Infrastructure Bootstrap in reader-facing pages
slarson Feb 19, 2026
9c5dab8
Add navigation footers, DD cross-links, and fix DD metadata rendering
slarson Feb 20, 2026
efa40e0
Hyperlink all bare DD references across reader-facing pages
slarson Feb 20, 2026
3007722
Convert causal loop diagram from code fence to rendered markdown
slarson Feb 20, 2026
d0072a4
Hyperlink all bare DD cross-references within Design Documents
slarson Feb 20, 2026
852c64a
Add permalink buttons to all section headers
slarson Feb 20, 2026
283e6cb
Fix Design Document era date from 2024 to 2026
slarson Feb 20, 2026
26c2b35
Fix broken list rendering across all docs
slarson Feb 20, 2026
e3b5afe
Add Phase and Layer to every DD with links to Phase Roadmap
slarson Feb 20, 2026
a58b0df
Move TL;DR above Quick Action Reference in all DDs
slarson Feb 20, 2026
e635bb7
Hyperlink all publication citations to DOIs and add master References…
slarson Feb 20, 2026
a1bc808
Clarify DD014 viewer stages vs. roadmap phases, fix mangled DD014.x l…
slarson Feb 20, 2026
1936f35
Rewrite roadmap milestones: what you run, what you see, validated aga…
slarson Feb 20, 2026
70cd227
Link all bare citations in DD010 to DOIs
slarson Feb 20, 2026
f001237
Add concrete Tier 1 electrophysiology datasets to DD010 and references
slarson Feb 20, 2026
01c7dda
Add systematic expression-consistency validation for Tier 1 in DD010
slarson Feb 20, 2026
0b26c48
Add 5 missing DDs to Phase Roadmap: DD008, DD014.1, DD015, DD022, DD023
slarson Feb 20, 2026
ee497dc
Rename viewer to WormSim 2.0, add WormBrowser history and deployment …
slarson Feb 20, 2026
6c527f0
Render PlantUML diagrams to SVG, add DD022/DD023 to Integration Map
slarson Feb 20, 2026
cff56d2
Simplify Integration Map: cluster DDs, reduce 78 edges to ~20
slarson Feb 20, 2026
10ab0e5
Add clickable DD hyperlinks to all SVG diagrams
slarson Feb 20, 2026
7caa49b
DD006: Fix ConnectomeToolbox integration, add functional connectivity…
slarson Feb 20, 2026
72342cf
DD010: Add Tier 2b unc-31 validation, ConnectomeToolbox integration
slarson Feb 20, 2026
eee323d
DD014.1: Add 14 mockup images for canonical rendering views
slarson Feb 20, 2026
f66f2c0
Enrich DDs with MetaWorm citations, code reuse, and consolidated over…
slarson Feb 21, 2026
00f1aa9
Site-wide audit: fix links, add DOIs, upgrade HTTPS, consolidate content
slarson Feb 21, 2026
0bfe558
Expand master reference list with all DD citations and hyperlinked cr…
slarson Feb 22, 2026
9a3fee6
Fix line break disease, add repo inventory, rewrite validation page
slarson Feb 22, 2026
2c97438
Bring all 13 non-compliant DDs up to DD012 template spec
slarson Feb 22, 2026
e8c7806
Integrate bio.rodeo foundation models into DDs and fix DD017 DD012 co…
slarson Feb 22, 2026
9389eee
Extract DD017 Component 3 into DD025 and promote to Phase A/Phase 1
slarson Feb 22, 2026
f82ba26
Eliminate Level E, integrate DevoWorm/Karr whole-cell model, update i…
slarson Feb 22, 2026
d8a6b04
Consolidate rationale, milestones, and metrics into phase descriptions
slarson Feb 22, 2026
f8f390e
DD003: Add Backend Stabilization Roadmap and cross-cutting docs updates
slarson Feb 23, 2026
0760a14
DD003: Generate draft GitHub issues (22 issues across 5 phases)
slarson Feb 23, 2026
193d344
Add DD003 and DD013 draft issues to mkdocs nav
slarson Feb 23, 2026
f5dc7b9
Replace named individuals with role-based titles; add DD026 Reservoir…
slarson Feb 23, 2026
b6a46ec
DD020: Generate draft GitHub issues (23 issues across 6 phases)
slarson Feb 23, 2026
4a48dfd
Rename "Cell(-Type) Differentiation" to "Cell-Type Specialization" ac…
slarson Feb 23, 2026
7590095
DD002 draft issues: add code reuse guidance and reframe titles for ex…
slarson Feb 23, 2026
387811a
DD001: Rewrite draft issues for code reuse; eliminate 4 redundant iss…
slarson Feb 23, 2026
bb69f12
Move reuse-first philosophy and DD013 integration guidance from DD001…
slarson Feb 23, 2026
e57ee1a
Move validation infrastructure issues from DD001 to DD021; enhance DD…
slarson Feb 23, 2026
e299a08
Rename Phase → Group in draft issues to avoid confusion with DD Phase…
slarson Feb 23, 2026
5f28ca2
Eliminate duplicate and overlapping issues across DD draft issues files
slarson Feb 23, 2026
36110c2
Add documentation destination policy (DD015 §2.6) and rewrite DD002 I…
slarson Feb 23, 2026
98ddb5a
Reconcile Phase 0 across docs: fix DD020 drift, add phase tags to 83 …
slarson Feb 24, 2026
d086e06
Convert 230 hardcoded docs.openworm.org URLs to relative paths in dra…
slarson Feb 24, 2026
212425c
Add PR preview deployments to GitHub Actions workflow
slarson Feb 24, 2026
a89ffbe
Replace DD013 inline roadmap with pointer to draft issues and phase r…
slarson Feb 24, 2026
e1c119c
Bump actions/upload-artifact from v2 to v4
slarson Feb 24, 2026
f53d212
Add libcairo2-dev to CI apt dependencies
slarson Feb 24, 2026
c0c49b5
Fix PR comment script: remove double .data dereference
slarson Feb 24, 2026
2c32d12
Fix DD count (25→27), add DD001 setup instructions, hyperlink technic…
slarson Feb 24, 2026
6d981d6
Add setup instructions to DD002, DD003, and DD020
slarson Feb 24, 2026
a0a3f34
Require setup instructions in DD template (DD012)
slarson Feb 24, 2026
99ffbb8
Add Getting Started setup sections to all 19 remaining DDs
slarson Feb 24, 2026
c858316
Extract forward-looking content from DD001 into DD027; redistribute d…
slarson Feb 24, 2026
119e1e7
Clean forward-looking content from DD001; move details to Phase Roadmap
slarson Feb 24, 2026
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95 changes: 93 additions & 2 deletions .github/workflows/mkdocs.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,12 +4,18 @@ on:
branches: [ master, development ]
pull_request:
branches: [ master, development ]
types: [ opened, synchronize, reopened, closed ]

permissions:
contents: write
pull-requests: write

env:
REPO_METADATA_SHAS: repo-metadata-shas.txt

jobs:
build:
if: github.event.action != 'closed'
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
Expand All @@ -21,7 +27,7 @@ jobs:
timeout_minutes: 15
command: |
sudo apt-get update
sudo apt-get install -yqq build-essential libxml2-dev zlib1g-dev bison flex
sudo apt-get install -yqq build-essential libxml2-dev zlib1g-dev bison flex libcairo2-dev pkg-config

- name: Set up Python install env
run: |
Expand Down Expand Up @@ -51,9 +57,71 @@ jobs:
export GITHUB_TOKEN=${{ github.token }}
make build

- name: Deploy branch preview
if: github.event_name == 'pull_request'
run: |
BRANCH_NAME="${{ github.head_ref }}"
SAFE_BRANCH=$(echo "$BRANCH_NAME" | sed 's/[^a-zA-Z0-9-]/-/g')

. venv/bin/activate

# Build with site_url set so navigation works in subdirectory
cat > mkdocs-preview.yml << EOF
INHERIT: mkdocs.yml
site_url: https://docs.openworm.org/preview/$SAFE_BRANCH/
EOF
python -m mkdocs build -f mkdocs-preview.yml --site-dir /tmp/site_preview

# Push to gh-pages under preview/<branch>/
git fetch origin gh-pages:gh-pages
git config user.name github-actions
git config user.email github-actions@github.com
git checkout gh-pages

mkdir -p preview/$SAFE_BRANCH
rm -rf preview/$SAFE_BRANCH/*
cp -r /tmp/site_preview/* preview/$SAFE_BRANCH/

git add preview/$SAFE_BRANCH
git commit -m "Deploy preview: $BRANCH_NAME @ ${GITHUB_SHA::7} [ci skip]" || echo "No changes to commit"
git remote set-url origin https://${{ github.token }}@github.com/${{ github.repository_owner }}/openworm_docs.git
git push origin gh-pages

- name: Comment preview URL on PR
if: github.event_name == 'pull_request'
uses: actions/github-script@v7
with:
script: |
const branch = '${{ github.head_ref }}'.replace(/[^a-zA-Z0-9-]/g, '-');
const url = `https://docs.openworm.org/preview/${branch}/`;
const marker = '<!-- preview-url -->';
const body = `${marker}\n**Preview:** ${url}`;

const { data: comments } = await github.rest.issues.listComments({
owner: context.repo.owner,
repo: context.repo.repo,
issue_number: context.issue.number,
});
const existing = comments.find(c => c.body.includes(marker));
if (existing) {
await github.rest.issues.updateComment({
owner: context.repo.owner,
repo: context.repo.repo,
comment_id: existing.id,
body,
});
} else {
await github.rest.issues.createComment({
owner: context.repo.owner,
repo: context.repo.repo,
issue_number: context.issue.number,
body,
});
}

- name: Archive production artifacts
if: github.ref == 'refs/heads/master'
uses: actions/upload-artifact@v2
uses: actions/upload-artifact@v4
with:
name: built-site
path: site
Expand Down Expand Up @@ -87,3 +155,26 @@ jobs:
git remote set-url origin https://${{ github.token }}@github.com/${{ github.repository_owner }}/openworm_docs.git
git push -f origin gh-pages
fi

cleanup-preview:
if: github.event_name == 'pull_request' && github.event.action == 'closed'
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Remove preview from gh-pages
run: |
BRANCH_NAME="${{ github.head_ref }}"
SAFE_BRANCH=$(echo "$BRANCH_NAME" | sed 's/[^a-zA-Z0-9-]/-/g')

git fetch origin gh-pages:gh-pages
git config user.name github-actions
git config user.email github-actions@github.com
git checkout gh-pages

if [ -d "preview/$SAFE_BRANCH" ]; then
rm -rf preview/$SAFE_BRANCH
git add -A preview/
git commit -m "Remove preview: $BRANCH_NAME [ci skip]"
git remote set-url origin https://${{ github.token }}@github.com/${{ github.repository_owner }}/openworm_docs.git
git push origin gh-pages
fi
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -2,3 +2,4 @@ _build/*
.DS_Store
site
/github.auth
CLAUDE.md
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