[INFRA] Move CI to GitHub Actions, modernize the docs build, and proofread the handbook

[yarikoptic-gitmate]

Travis and CircleCI both pinned toolchains that no longer run, so CI is replaced with GitHub Actions and the docs build is moved onto current MkDocs 1.6 / Material 9. Along the way: a typo and wording pass over the handbook, several broken or moved links fixed, and the Jupyter-on-Discovery page rewritten for Slurm because it still documented PBS.

Locally verified: npm run lint, mkdocs build --clean --strict, and the internal link check all pass. Rendered preview: https://dbic-handbook.readthedocs.io/en/latest/ (per-PR build: https://dbic-handbook--33.org.readthedocs.build/en/33/)

CI and build

• .github/workflows/ci.yml lints Markdown with remark, builds with mkdocs --strict, uploads the site as an artifact, and checks internal links. linkcheck-external.yml checks external links weekly and on demand, so a third-party outage does not block a PR.
• The CircleCI changelog chain (github-changelog-generator → remark → Changelog-bot) is ported to .github/workflows/changelog.yml rather than dropped: a push to master regenerates src/CHANGES.md and commits it back. It never once produced a commit under CircleCI, because the remark --output / remark --frail pair could not converge — remark's writer emits * bullets while the style guide requires -, so the check always rejected the file the format step had just written. The port fixes that with an explicit --setting "bullet: '-'", and runs on the built-in GITHUB_TOKEN instead of a stored token with push access to master. Two smaller things are also corrected: --header-label now carries the # that left the title as a paragraph rather than a heading (cosmetic — it linted clean), and the --base src/pregh-changes.md is not ported, since that file was deleted in October 2019 when this repository was split out of bids-specification and the generator silently ignores a --base path that is not there.
• package.json + lockfile replace npm-requirements.txt; requirements.txt pins mkdocs >=1.6,<2 and mkdocs-material >=9.5,<10. Pipfile (CircleCI-only) is gone. readthedocs.yml becomes .readthedocs.yaml.
• theme_customizations/partials/footer.html was written for Material 4 and its classes (md-footer-nav, md-flex) have no CSS in Material 9, so it rendered unstyled. Replaced with the copyright setting plus navigation.footer. The unused jQuery bundle is removed.
• site_url now reads READTHEDOCS_CANONICAL_URL. master set no site_url at all, so no canonical URL was published before this PR; the point of the environment variable is that Read the Docs serves under /en/<version>/, so a hard-coded root URL would make every page of this PR's preview claim to be the production page.
• Pages that existed but were unreachable (discovery-jupyter.md, kerberos.md, troubleshooting.md, index.md) are wired into the nav, and the eleven placeholder entries get their own stubs — sharing one TODO.md made MkDocs 1.6 render all of them as "PyBIDS".

Content

• Typos and wording throughout; broken links fixed, including a README image path that never existed in the tree, a bids-validator link pointing at a non-existent dbic/ fork, and a CC0 row whose link text and href disagreed.
• rc.dartmouth.edu reorganized from /index.php/... to /hpc/...; the dead links are updated to the pages carrying the same content.
• The mrusers list moved to mrusers@groups.dartmouth.edu, a mail-only domain with no web page, so the old Mailman URL becomes a mailto:.
• discovery-jupyter.md documented #PBS, mksub, myjobs and qdel, none of which exist on the cluster now. Rewritten for sbatch/squeue/scancel, and it now leads with Open OnDemand, which submits the job and proxies the notebook without a password file or ssh tunnel.
• The Kerberos page notes that ssh itself must be built with GSS-API support, and points Debian users at openssh-client-gssapi.
• CODE_OF_CONDUCT.md is removed. DBIC is a Dartmouth facility rather than a standalone open-source community, and the file was inherited verbatim from bids-specification — it still routed harassment reports to a Stanford address. README and CONTRIBUTING now cite Dartmouth's Nondiscrimination and Anti-Harassment Policy and the channels it names (EOATIX, the Title IX reporting form, the anonymous Integrity Helpline).
• Nested lists were rendering flattened on reproin.md, stimuli.md and CONTRIBUTING.md: MkDocs uses Python-Markdown, which needs four-space indentation for nested list content and continuation paragraphs where CommonMark accepts two. The style pass early in this branch regressed kerberos.md and data-paper.md the same way; both are fixed. Written down in CONTRIBUTING.md since no tool in the pipeline catches it.
• Read the Docs has only one active version, latest. Release_Guideline.md linked /en/stable/, which 404s, and Release_Protocol.md told maintainers to trigger stable and tag builds that do not exist; both now say what actually works.

Known gaps

• discovery-jupyter.md's Slurm directives follow Research Computing's documented examples, but nobody has submitted the job on Discovery yet — worth one real run before anyone relies on it. In particular, the page does not name a specific Python module, because neither RC page documents one; it tells the reader to pick via module avail python or a conda environment.
• The Jupyter password flow (jupyter notebook password, hash in jupyter_notebook_config.json) only works with classic Notebook ≤ 6; Notebook 7 dropped that subcommand and reads jupyter_server_config.json. Left as-is because which version Discovery ships is unknown.
• Upstream ReproIn's KNOWN_DATATYPES does not include mrs, so the MRS examples on reproin.md need a heuristic that adds it. The page now says so rather than listing mrs as a type ReproIn knows.
• The 2019 Intro_to_Cluster.pdf has no replacement on the new RC site; that TODO now points at /hpc/intro-to-hpc/.
• The link to .github/workflows/ from CONTRIBUTING.md 404s until this branch merges, which is expected.
• The changelog workflow skips release commits so that the curation Release_Protocol.md asks for survives the release, but the next ordinary merge into master rebuilds the whole file from the pull request titles. Release_Protocol.md now says so. Durable curation would need a --base file, which this repository has not had since 2019.
• If branch protection is ever enabled on master, the changelog workflow's push will be rejected — GITHUB_TOKEN does not bypass protection without an explicit Actions bypass in the ruleset. master is unprotected today.

🤖 Generated with Claude Code

https://claude.ai/code/session_01VRhvoqJnGm6JELocnjyPyB

[yarikoptic-gitmate]

The red check on this PR needs a maintainer action outside the repository, so flagging it rather than working around it.

CircleCI Pipeline — error: "No configuration was found in your project."

That is this PR's doing: it deletes .circleci/config.yml, and CircleCI is still following the repository, so every build now errors with nothing to run. It will stay red until someone with CircleCI access stops the project from building — unfollow / "Stop Building" for dbic/handbook in the CircleCI project settings, or remove the CircleCI GitHub integration. I cannot do that from here.

The alternative, if you would rather not touch CircleCI yet, is to keep a stub .circleci/config.yml with a no-op job so the status goes green. I have not done that, since it leaves dead configuration behind for exactly the thing this PR removes — happy to add it if you prefer.

Everything the PR does control is green on 527a139:

Check	Result
Markdown style	✅
Build handbook	✅
Check internal links	✅
docs/readthedocs.org:dbic-handbook	✅

Also worth noting, since the PR description lists it as a gap: Read the Docs pull-request builds are already enabled, so the rendered preview CircleCI's artifact used to provide is not lost after all — this PR renders at https://dbic-handbook--33.org.readthedocs.build/en/33/ . That build also confirms the site_url change behaves correctly in a real RTD environment: the preview emits <link rel="canonical" href="https://dbic-handbook--33.org.readthedocs.build/en/33/computing/kerberos.html">, i.e. its own URL rather than the production one, because site_url now reads READTHEDOCS_CANONICAL_URL.

---

Generated by Claude Code