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8203128
docs: add ROBIN architecture overview
mattloose Aug 22, 2026
7dc5629
docs: add analysis pipeline overview
mattloose Aug 22, 2026
2e7c369
docs: document methylation classifiers
mattloose Aug 22, 2026
78189ad
docs: document CNV analysis
mattloose Aug 22, 2026
d701f3b
docs: document MGMT analysis
mattloose Aug 22, 2026
19363f9
docs: document target and variant analysis
mattloose Aug 22, 2026
731af08
docs: document fusion and ITD analysis
mattloose Aug 22, 2026
911f6f3
docs: align job reference with release candidate
mattloose Aug 22, 2026
5cee934
docs: add architecture and analysis sections to MkDocs
mattloose Aug 22, 2026
f317c98
docs: add pull request preview deployment
mattloose Aug 22, 2026
8993ed7
ci: add MkDocs PR preview workflow
mattloose Aug 22, 2026
a624f90
Merge pull request #152 from LooseLab/ci/docs-preview-workflow
mattloose Aug 22, 2026
14ce3eb
docs: retrigger preview workflow
mattloose Aug 22, 2026
9d3c64e
ci: fix MkDocs preview workflow YAML
mattloose Aug 22, 2026
8a087a7
ci: fix MkDocs preview workflow YAML
mattloose Aug 22, 2026
b7541a4
chore: remove unused git-lfs dependency
mattloose Aug 22, 2026
bbbbdf0
docs: remove obsolete LFS and private GitHub setup
mattloose Aug 22, 2026
dc00b92
docs: remove obsolete private GitHub token reference
mattloose Aug 22, 2026
7257380
docs: update model download guidance for public repository
mattloose Aug 22, 2026
3558bc6
docs: remove obsolete private asset guidance
mattloose Aug 22, 2026
cadb4a5
Merge 3558bc60ef362fc72e53059615b3a1356bb37c7a into 9d3c64e30401bebbd…
mattloose Aug 22, 2026
a0dfef7
docs: simplify quickstart and first-run flow
mattloose Aug 22, 2026
546925e
docs: clarify home page entry points
mattloose Aug 22, 2026
f1e06e4
docs: make installation self-contained
mattloose Aug 22, 2026
8632f22
docs: reorder navigation for first-time users
mattloose Aug 22, 2026
e04fa5a
docs: make README a concise project entry point
mattloose Aug 22, 2026
75ec183
docs: remove README back-references from CLI overview
mattloose Aug 22, 2026
54416a8
docs: keep sequencing assumptions within MkDocs
mattloose Aug 22, 2026
688ab1d
docs: put installation before quickstart
mattloose Aug 22, 2026
7255aab
build: clean and audit Python package metadata
mattloose Aug 22, 2026
a916f39
chore: standardize licensing as CC BY-NC 4.0
mattloose Aug 22, 2026
e854964
chore: standardize licensing as CC BY-NC 4.0
mattloose Aug 22, 2026
47518b9
chore: standardize licensing as CC BY-NC 4.0
mattloose Aug 22, 2026
8fe4c78
chore: add CC BY-NC 4.0 license
mattloose Aug 22, 2026
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89 changes: 89 additions & 0 deletions .github/workflows/mkdocs-preview.yml
Original file line number Diff line number Diff line change
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# Build MkDocs for pull requests and publish a preview under /preview/pr-<number>/
# on the existing gh-pages branch. Production root and /beta/ are preserved.

name: Publish docs preview

on:
pull_request:
branches:
- release_candidate2
paths:
- "docs/**"
- "mkdocs.yml"
- "requirements-docs.txt"
- ".github/workflows/mkdocs-preview.yml"
workflow_dispatch:

permissions:
contents: write

concurrency:
group: gh-pages-deploy
cancel-in-progress: false

jobs:
build-and-deploy:
if: github.event_name == 'workflow_dispatch' || github.event.pull_request.head.repo.full_name == github.repository
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4

- uses: actions/setup-python@v5
with:
python-version: "3.11"
cache: pip
cache-dependency-path: requirements-docs.txt

- name: Install MkDocs
run: pip install -r requirements-docs.txt

- name: Set preview URL
id: preview
shell: bash
run: |
if [ "${{ github.event_name }}" = "pull_request" ]; then
PR_NUMBER="${{ github.event.pull_request.number }}"
else
PR_NUMBER="manual-${GITHUB_RUN_NUMBER}"
fi
echo "number=${PR_NUMBER}" >> "$GITHUB_OUTPUT"
echo "url=https://looselab.github.io/ROBIN/preview/pr-${PR_NUMBER}/" >> "$GITHUB_OUTPUT"

- name: Build site
env:
PREVIEW_SITE_URL: ${{ steps.preview.outputs.url }}
run: |
cp mkdocs.yml mkdocs.preview.yml
python - <<'PY'
from pathlib import Path
import os
p = Path("mkdocs.preview.yml")
text = p.read_text()
lines = text.splitlines()
preview_url = os.environ["PREVIEW_SITE_URL"]
replaced = False
for i, line in enumerate(lines):
if line.startswith("site_url:"):
lines[i] = f"site_url: {preview_url}"
replaced = True
break
if not replaced:
lines.insert(0, f"site_url: {preview_url}")
p.write_text("\n".join(lines) + "\n")
PY
mkdocs build --strict -f mkdocs.preview.yml

- name: Add .nojekyll
run: touch site/.nojekyll

- name: Deploy preview to GitHub Pages branch
uses: JamesIves/github-pages-deploy-action@v4
with:
folder: site
branch: gh-pages
target-folder: preview/pr-${{ steps.preview.outputs.number }}
clean: true

- name: Preview URL
run: |
echo "Preview: ${{ steps.preview.outputs.url }}"
34 changes: 34 additions & 0 deletions LICENSE
Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
Creative Commons Attribution-NonCommercial 4.0 International

Copyright (c) 2023-present Matt Loose

This work is licensed under the Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0).

You are free to:

Share — copy and redistribute the material in any medium or format.
Adapt — remix, transform, and build upon the material.

Under the following terms:

Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.

NonCommercial — You may not use the material for commercial purposes.

No additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.

The licensor cannot revoke these freedoms as long as you follow the license terms.

Notices:

You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation.

No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material.

The complete legal code for the Creative Commons Attribution-NonCommercial 4.0 International License is available at:
https://creativecommons.org/licenses/by-nc/4.0/legalcode

License summary:
https://creativecommons.org/licenses/by-nc/4.0/

Third-party software, models, data, and other resources included with or used by ROBIN remain subject to their respective licences and terms.
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