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Complete documentation site migration from mkdocs-material to Docusaurus: - Generators for modules, subworkflows, and workflows from parsed metadata - Jinja2 templates with custom override support - Output trees from test snapshots with BACTOPIA_DIR/SAMPLE_NAME/TIMESTAMP - Sidebar separation of Named Workflows and Bactopia Tools - Citations, parameters, audit trail, and Nextflow reports sections - Old mkdocs docs preserved in .old-docs/ Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Pull request overview
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Migrates the documentation site from mkdocs-material to Docusaurus by introducing Docusaurus MDX docs for workflows/subworkflows/modules, plus new sidebars, styling tweaks, and a small CLI/docs/blog scaffold.
Changes:
- Added many generated MDX pages for subworkflows and modules, including input/output/parameters and citations sections.
- Introduced multiple Docusaurus sidebar configs (core docs + workflows/modules/subworkflows/impact separation).
- Added Docusaurus-specific content and tooling (Impact landing page in MDX, CLI stub pages, blog post, generator Makefile).
Reviewed changes
Copilot reviewed 152 out of 438 changed files in this pull request and generated 10 comments.
Show a summary per file
| File | Description |
|---|---|
| subworkflows/hicap.mdx | New Docusaurus MDX page for the hicap subworkflow. |
| subworkflows/gtdb.mdx | New Docusaurus MDX page for the gtdb subworkflow. |
| subworkflows/genotyphi.mdx | New Docusaurus MDX page for the genotyphi subworkflow. |
| subworkflows/gamma.mdx | New Docusaurus MDX page for the gamma subworkflow. |
| subworkflows/fastani.mdx | New Docusaurus MDX page for the fastani subworkflow. |
| subworkflows/emmtyper.mdx | New Docusaurus MDX page for the emmtyper subworkflow. |
| subworkflows/eggnog.mdx | New Docusaurus MDX page for the eggnog subworkflow. |
| subworkflows/ectyper.mdx | New Docusaurus MDX page for the ectyper subworkflow. |
| subworkflows/defensefinder.mdx | New Docusaurus MDX page for the defensefinder subworkflow. |
| subworkflows/clermontyping.mdx | New Docusaurus MDX page for the clermontyping subworkflow. |
| subworkflows/checkm2.mdx | New Docusaurus MDX page for the checkm2 subworkflow. |
| subworkflows/checkm.mdx | New Docusaurus MDX page for the checkm subworkflow. |
| subworkflows/busco.mdx | New Docusaurus MDX page for the busco subworkflow. |
| subworkflows/btyper3.mdx | New Docusaurus MDX page for the btyper3 subworkflow. |
| subworkflows/blastx.mdx | New Docusaurus MDX page for the blastx subworkflow. |
| subworkflows/blastp.mdx | New Docusaurus MDX page for the blastp subworkflow. |
| subworkflows/blastn.mdx | New Docusaurus MDX page for the blastn subworkflow. |
| subworkflows/bactopia_sketcher.mdx | New Docusaurus MDX page for the bactopia_sketcher subworkflow. |
| subworkflows/bactopia_datasets.mdx | New Docusaurus MDX page for the bactopia_datasets subworkflow. |
| subworkflows/ariba.mdx | New Docusaurus MDX page for the ariba subworkflow. |
| subworkflows/amrfinderplus.mdx | New Docusaurus MDX page for the amrfinderplus subworkflow. |
| subworkflows/agrvate.mdx | New Docusaurus MDX page for the agrvate subworkflow. |
| subworkflows/abritamr.mdx | New Docusaurus MDX page for the abritamr subworkflow. |
| subworkflows/abricate.mdx | New Docusaurus MDX page for the abricate subworkflow. |
| src/css/custom.css | Added global table styling in Docusaurus custom CSS. |
| sidebars.ts | Switched main sidebar to autogenerated structure. |
| sidebars-workflows.ts | Added dedicated workflows sidebar with two top-level categories. |
| sidebars-subworkflows.ts | Added dedicated subworkflows sidebar (autogenerated). |
| sidebars-modules.ts | Added dedicated modules sidebar (autogenerated). |
| sidebars-impact.ts | Extended impact sidebar with enhancements/presentations. |
| modules/tbprofiler_collate.mdx | New Docusaurus MDX page for the tbprofiler_collate module. |
| modules/stecfinder.mdx | New Docusaurus MDX page for the stecfinder module. |
| modules/staphopiasccmec.mdx | New Docusaurus MDX page for the staphopiasccmec module. |
| modules/ssuissero.mdx | New Docusaurus MDX page for the ssuissero module. |
| modules/srahumanscrubber_initdb.mdx | New Docusaurus MDX page for the srahumanscrubber_initdb module. |
| modules/snpdists.mdx | New Docusaurus MDX page for the snpdists module. |
| modules/sistr.mdx | New Docusaurus MDX page for the sistr module. |
| modules/shigeifinder.mdx | New Docusaurus MDX page for the shigeifinder module. |
| modules/shigatyper.mdx | New Docusaurus MDX page for the shigatyper module. |
| modules/shigapass.mdx | New Docusaurus MDX page for the shigapass module. |
| modules/seroba_run.mdx | New Docusaurus MDX page for the seroba_run module. |
| modules/seqsero2.mdx | New Docusaurus MDX page for the seqsero2 module. |
| modules/scoary.mdx | New Docusaurus MDX page for the scoary module. |
| modules/roary.mdx | New Docusaurus MDX page for the roary module. |
| modules/rgi_main.mdx | New Docusaurus MDX page for the rgi_main module. |
| modules/rgi_heatmap.mdx | New Docusaurus MDX page for the rgi_heatmap module. |
| modules/quast.mdx | New Docusaurus MDX page for the quast module. |
| modules/pneumocat.mdx | New Docusaurus MDX page for the pneumocat module. |
| modules/plasmidfinder.mdx | New Docusaurus MDX page for the plasmidfinder module. |
| modules/pirate.mdx | New Docusaurus MDX page for the pirate module. |
| modules/phispy.mdx | New Docusaurus MDX page for the phispy module. |
| modules/pbptyper.mdx | New Docusaurus MDX page for the pbptyper module. |
| modules/pasty.mdx | New Docusaurus MDX page for the pasty module. |
| modules/panaroo_run.mdx | New Docusaurus MDX page for the panaroo_run module. |
| modules/nohuman_download.mdx | New Docusaurus MDX page for the nohuman_download module. |
| modules/ngmaster.mdx | New Docusaurus MDX page for the ngmaster module. |
| modules/mobsuite_recon.mdx | New Docusaurus MDX page for the mobsuite_recon module. |
| modules/midas_download.mdx | New Docusaurus MDX page for the midas_download module. |
| modules/meningotype.mdx | New Docusaurus MDX page for the meningotype module. |
| modules/mcroni.mdx | New Docusaurus MDX page for the mcroni module. |
| modules/mash_dist.mdx | New Docusaurus MDX page for the mash_dist module. |
| modules/lissero.mdx | New Docusaurus MDX page for the lissero module. |
| modules/legsta.mdx | New Docusaurus MDX page for the legsta module. |
| modules/ismapper.mdx | New Docusaurus MDX page for the ismapper module. |
| modules/iqtree.mdx | New Docusaurus MDX page for the iqtree module. |
| modules/hpsuissero.mdx | New Docusaurus MDX page for the hpsuissero module. |
| modules/gubbins.mdx | New Docusaurus MDX page for the gubbins module. |
| modules/gtdbtk_download.mdx | New Docusaurus MDX page for the gtdbtk_download module. |
| modules/genotyphi_parse.mdx | New Docusaurus MDX page for the genotyphi_parse module. |
| modules/gamma.mdx | New Docusaurus MDX page for the gamma module. |
| modules/fastani.mdx | New Docusaurus MDX page for the fastani module. |
| modules/emmtyper.mdx | New Docusaurus MDX page for the emmtyper module. |
| modules/eggnog_download.mdx | New Docusaurus MDX page for the eggnog_download module. |
| modules/ectyper.mdx | New Docusaurus MDX page for the ectyper module. |
| modules/defensefinder_update.mdx | New Docusaurus MDX page for the defensefinder_update module. |
| modules/csvtk_join.mdx | New Docusaurus MDX page for the csvtk_join module. |
| modules/clermontyping.mdx | New Docusaurus MDX page for the clermontyping module. |
| modules/checkm2_download.mdx | New Docusaurus MDX page for the checkm2_download module. |
| modules/busco.mdx | New Docusaurus MDX page for the busco module. |
| modules/btyper3.mdx | New Docusaurus MDX page for the btyper3 module. |
| modules/bakta_download.mdx | New Docusaurus MDX page for the bakta_download module. |
| modules/bactopia_teton.mdx | New Docusaurus MDX page for the bactopia_teton module. |
| modules/bactopia_datasets.mdx | New Docusaurus MDX page for the bactopia_datasets module. |
| modules/ariba_getref.mdx | New Docusaurus MDX page for the ariba_getref module. |
| modules/amrfinderplus_update.mdx | New Docusaurus MDX page for the amrfinderplus_update module. |
| modules/agrvate.mdx | New Docusaurus MDX page for the agrvate module. |
| modules/abricate_summary.mdx | New Docusaurus MDX page for the abricate_summary module. |
| modules/abricate_run.mdx | New Docusaurus MDX page for the abricate_run module. |
| impact/index.mdx | Replaced Impact landing page with a Docusaurus MDX CardGrid layout. |
| impact/index.md | Removed legacy markdown Impact landing page. |
| docs/cli/index.md | Added CLI Reference section index page. |
| docs/cli/bactopia.md | Added CLI stub page to validate routing/structure. |
| docs/cli/category.json | Added Docusaurus category metadata for CLI Reference. |
| blog/2026-04-23-bactopia-v4.md | Added blog post announcing v4 and the new docs site. |
| Makefile | Added generator entrypoints for parsing metadata and emitting docs. |
| .old-docs/templates/legacy/citations.j2 | Preserved mkdocs legacy citations template under .old-docs/. |
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Enable Docusaurus versioning for main docs (labeled "dev"), add version dropdown with all 6 legacy mkdocs versions (v2.1.0-v3.1.0) served as static HTML. Legacy pages have asset paths rewritten to absolute, outdated banners replaced with a sticky warning linking to latest, and search/mermaid files stripped to reduce size. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Adds client-side search across all docs instances and blog using @easyops-cn/docusaurus-search-local (lunr.js). Search bar positioned between version dropdown and GitHub icon in navbar. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Two-step pipeline: parse-cli.py introspects Click commands into data/cli.json, generate-cli.py renders Jinja2 templates into developers/cli/*.mdx. Covers all 30 bactopia-py CLI commands with grouped option tables and a categorized index page. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
nf-bactopia converted to plain doc link since it only has an index page. Added sidebarItemsGenerator to filter index docs from autogenerated items in CLI Reference, Subworkflows, and Modules categories. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Add project-level CLAUDE.md with architecture, pipeline, and conventions. Add generate-llms-catalog skill and Python script that produces static/llms.txt (llmstxt.org standard) and static/catalog.json from all doc content (307 pages). Remove unused bin/bactopia-to-md.py and bin/convert-mkdocs-to-mdx.py. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Add <link rel="alternate"> tags to the site <head> so crawlers and LLM-powered tools can discover /llms.txt and /catalog.json. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- Restore full-guide.md from git history with v4 updates (sccmec, image path, sidebar position) - Fix broken Full Guide link in beginners-guide.md - Update tutorial version strings from 3.0.0 to 4.0.0 and replace STAPHOPIASCCMEC process names with SCCMEC - Remove placeholder v4 blog post - Add cli.json to gitignore (generated artifact like bactopia.json) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Show both bactopia CLI and nextflow run alternatives in usage examples
for all workflows, tools, and pipelines. Named pipelines use their
wrapper script names (staphopia, clean-yer-reads, teton) instead of
bactopia --wf. Remove unnecessary --wf bactopia from main workflow.
Add overridable {% block usage %} to base template and use it in
abricate custom template to consolidate examples and usage into one
section.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Add a purple pill-shaped Slack button to the navbar (hidden below 1354px) that links to a static /slack redirect page. When the Slack invite URL expires, only static/slack/index.html needs updating. Also update footer: rename sections, replace Twitter with Bluesky, add Slack to Community. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Add data/tool-categories.yml mapping 67 tools to 9 categories and bin/generate-tools-index.py to produce the grouped index page. The generator fails if any tool MDX file is missing from the mapping, so CI will catch unmapped tools. Added make generate-tools-index target (also included in make generate). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
GitHub Actions workflow builds docs from bactopia source and deploys to Cloudflare Pages. Site URL updated to bactopia.io. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Version snapshots are stored as orphan git branches (snapshot/vX.Y.Z) instead of in the main branch. The deploy workflow assembles active snapshots at build time via git archive. Legacy mkdocs snapshots migrated from static/v*/ to branches. - snapshots.json: registry of all versions with active flag - create-snapshot.yml: builds with announcement banner, pushes orphan branch, and updates snapshots.json on master - deploy.yml: fetches active snapshot branches into build output - docusaurus.config.ts: DOCS_VERSION env var for banner/baseUrl, dynamic version dropdown from snapshots.json - Makefile: snapshot-list, snapshot-add, snapshot-deactivate, snapshot-activate targets Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- CLAUDE.md: add Version Snapshots section with full workflow docs, snapshot Makefile commands, and key files reference - README.md: update Versioning and Deployment sections for branch-based snapshots and Cloudflare Pages - PR template: checklist for content type, version impact, and build verification Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Complete documentation site migration from mkdocs-material to Docusaurus: