implement translation infrastructure - use portuguese as test example by rpetit3 · Pull Request #18 · bactopia/bactopia.github.io

rpetit3 · 2026-05-18T17:52:05Z

Summary

Type of Change

Content update (new or modified documentation)
Correction (typo, broken link, inaccurate information)
Site infrastructure (config, styling, components, CI/CD)
Auto-generation (templates, scripts, data files)

Version Impact

This change affects the current live version only (no snapshot needed)
A version snapshot should be created before merging (new Bactopia release)
A snapshot rebuild is needed after merging (fix to snapshotted content)

Checklist

Site builds without errors (npm run build)
Changes verified in the dev server (npm start)
snapshots.json updated (if adding/removing a version)
LLM catalog regenerated (make llms-catalog) if pages were added/removed/renamed

netlify · 2026-05-18T17:52:10Z

✅ Deploy Preview for bactopia-docs ready!

Name	Link
🔨 Latest commit	`ad601ac`
🔍 Latest deploy log	https://app.netlify.com/projects/bactopia-docs/deploys/6a0b7a44d23b5e0008670f09
😎 Deploy Preview	https://deploy-preview-18--bactopia-docs.netlify.app
📱 Preview on mobile	Toggle QR Code... Use your smartphone camera to open QR code link.

To edit notification comments on pull requests, go to your Netlify project configuration.

Copilot

Pull request overview

This PR adds initial translation infrastructure for the Bactopia documentation site, using Portuguese as the first test locale.

Changes:

Enables Docusaurus i18n for English and Portuguese with a locale dropdown.
Adds Claude-based translation tooling, prompts, glossary post-processing, sync/verify commands, and Makefile targets.
Adds initial Portuguese UI translation JSON files and updates acknowledgements for translation attribution.

Reviewed changes

Copilot reviewed 14 out of 32 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
`docusaurus.config.ts`	Enables Portuguese locale and adds locale dropdown.
`Makefile`	Adds translation sync/full/verify targets.
`bin/translate/__init__.py`	Adds package metadata comments for translation tooling.
`bin/translate/__main__.py`	Enables `python -m bin.translate`.
`bin/translate/api.py`	Adds Claude API integration and retry/continuation logic.
`bin/translate/cli.py`	Adds translation CLI commands for sync, single-file translation, and verification.
`bin/translate/config.py`	Defines translation constants, paths, plugin mappings, and API key validation.
`bin/translate/glossary.py`	Adds glossary-based post-processing and admonition handling.
`bin/translate/sync.py`	Adds source discovery, hash tracking, and orphan detection.
`bin/translate/verify.py`	Adds structural validation checks for translated files.
`bin/translate/prompts/general.md`	Adds general translation rules for Markdown/MDX docs.
`bin/translate/prompts/pt.md`	Adds Brazilian Portuguese-specific translation guidance.
`data/translations/pt/glossary.yml`	Adds Portuguese glossary and protected terms.
`i18n/pt/code.json`	Adds Portuguese theme/UI strings.
`i18n/pt/docusaurus-theme-classic/navbar.json`	Adds Portuguese navbar strings.
`i18n/pt/docusaurus-theme-classic/footer.json`	Adds Portuguese footer strings.
`i18n/pt/docusaurus-plugin-content-blog/options.json`	Adds localized blog metadata.
`i18n/pt/docusaurus-plugin-content-docs/current.json`	Adds localized main docs metadata.
`i18n/pt/docusaurus-plugin-content-docs-impact/current.json`	Adds localized impact docs metadata.
`i18n/pt/docusaurus-plugin-content-docs-developers/current.json`	Adds localized developer docs metadata.
`i18n/pt/docusaurus-plugin-content-docs-bactopia-tools/current.json`	Adds localized tools docs metadata.
`i18n/pt/docusaurus-plugin-content-docs-bactopia-pipelines/current.json`	Adds localized pipelines docs metadata.
`templates/acknowledgements.j2`	Adds translation infrastructure acknowledgement to generated content.
`impact/acknowledgements.md`	Regenerates acknowledgements with translation attribution.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

+ locales: ['en', 'pt'],
+ localeConfigs: {
+ en: { label: 'English', direction: 'ltr' },
+ pt: { label: 'Portugues', direction: 'ltr' },


- Add blog to PLUGIN_MAP with versioned flag for correct i18n path - Fix sync.py to handle non-versioned plugins (blog has no current/ subdir) - Add prompt caching to API calls (system prompt cached across all calls) - Update prompt tone from "professional" to "friendly and approachable" - Remove __pycache__ from tracking and add to .gitignore Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Translated main documentation pages: index, quick-start, installation, beginners-guide, full-guide, tutorial, plus developers/cli/bactopia-docs. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Fix orphan removal bug: only scan plugin dirs present in the filtered file set, preventing --include from deleting other sections' translations. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Fix unclosed code fences: LLM consistently drops trailing ``` at EOF. Added fix_unclosed_fences to post-processing pipeline to prevent recurrence. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

…iles) Completes all content translations: 317 files across 6 sections. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

- Copy blog post images to i18n directory (relative paths need local copies) - Fix broken anchor links in PT full-guide and tutorial where translated headings generate different slug anchors than the English originals Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Changed full-guide.md to ./full-guide.mdx to match actual filename and use proper relative path syntax. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Impact & Outreach -> Impacto e Divulgação Developers -> Desenvolvedores CLI Reference -> Referência CLI Modules -> Módulos Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

rpetit3 · 2026-05-18T20:12:28Z

@Mxrcon howdy here is the PR I mentioned

rpetit3 · 2026-05-18T20:49:31Z

glossary inconsistencies (LLM chose something other than the glossary)

python -m bin.translate verify --locale pt
docs/tutorial.md: glossary term 'sequence type' -> 'tipo de sequência' not found in translation
bactopia-tools/gtdb.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
bactopia-tools/index.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
bactopia-tools/index.mdx: glossary term 'variant calling' -> 'chamada de variantes' not found in translation
bactopia-tools/mashdist.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
bactopia-tools/mashtree.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
bactopia-tools/merlin.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
bactopia-tools/midas.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
bactopia-tools/tbprofiler.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
developers/modules/bactopia_sketcher.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
developers/modules/csvtk_concat.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
developers/modules/deacon_fetch.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
developers/modules/gtdbtk_classifywf.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
developers/modules/gubbins.mdx: glossary term 'variant calling' -> 'chamada de variantes' not found in translation
developers/modules/index.mdx: glossary term 'variant calling' -> 'chamada de variantes' not found in translation
developers/modules/iqtree.mdx: glossary term 'variant calling' -> 'chamada de variantes' not found in translation
developers/modules/mash_dist.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
developers/modules/midas_download.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
developers/modules/ncbigenomedownload.mdx: glossary term 'variant calling' -> 'chamada de variantes' not found in translation
developers/subworkflows/checkm2.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
developers/subworkflows/fastani.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
developers/subworkflows/gubbins.mdx: glossary term 'variant calling' -> 'chamada de variantes' not found in translation
developers/subworkflows/index.mdx: glossary term 'sequence type' -> 'tipo de sequência' not found in translation
developers/subworkflows/iqtree.mdx: glossary term 'variant calling' -> 'chamada de variantes' not found in translation
developers/subworkflows/mashdist.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
developers/subworkflows/ncbigenomedownload.mdx: glossary term 'variant calling' -> 'chamada de variantes' not found in translation
developers/subworkflows/sylph.mdx: glossary term 'reference genome' -> 'genoma de referência' not found in translation
Verified 317 files: 291 ok, 26 with issues

netlify · 2026-08-05T04:43:36Z

✅ Deploy Preview for bactopia-docs ready!

Name	Link
🔨 Latest commit	`0cfe4cd`
🔍 Latest deploy log	https://app.netlify.com/projects/bactopia-docs/deploys/6a72bf75ad4bf90008b6ec86
😎 Deploy Preview	https://deploy-preview-18--bactopia-docs.netlify.app
📱 Preview on mobile	Toggle QR Code... Use your smartphone camera to open QR code link.

To edit notification comments on pull requests, go to your Netlify project configuration.

begin translations
999dd83

CopilotAI review requested due to automatic review settings May 18, 2026 17:52

Copilotstarted reviewing on behalf of rpetit3 May 18, 2026 17:53 View session

CopilotAI reviewed May 18, 2026
View reviewed changes

Comment threaddocusaurus.config.ts Outdated
locales: ['en', 'pt'],
localeConfigs: {
en: { label: 'English', direction: 'ltr' },
pt: { label: 'Portugues', direction: 'ltr' },

rpetit3and others added 9 commits May 18, 2026 13:16

translate docs/ section to Portuguese (7 files)
0a4ff10
Translated main documentation pages: index, quick-start, installation, beginners-guide, full-guide, tutorial, plus developers/cli/bactopia-docs. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

translate bactopia-tools/ section to Portuguese (70 files)
74b793c
Fix orphan removal bug: only scan plugin dirs present in the filtered file set, preventing --include from deleting other sections' translations. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

translate developers/ section to Portuguese (229 files)
9c8ae19
Fix unclosed code fences: LLM consistently drops trailing ``` at EOF. Added fix_unclosed_fences to post-processing pipeline to prevent recurrence. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

translate impact/, bactopia-pipelines/, and blog/ to Portuguese (11 f…
30d349e
…iles) Completes all content translations: 317 files across 6 sections. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

fix broken link to full-guide in beginners-guide (EN and PT)
be6885e
Changed full-guide.md to ./full-guide.mdx to match actual filename and use proper relative path syntax. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

fix typo in config
072cd27

translate sidebar category labels to Portuguese
ebb0fb3
Impact & Outreach -> Impacto e Divulgação Developers -> Desenvolvedores CLI Reference -> Referência CLI Modules -> Módulos Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

tweaks to python code
ad601ac

Merge branch 'master' into i18n-translations
0cfe4cd

Navigation Menu

Uh oh!

implement translation infrastructure - use portuguese as test example - #18

implement translation infrastructure - use portuguese as test example#18
rpetit3 wants to merge 12 commits into
masterfrom
i18n-translations

rpetit3 commented May 18, 2026

Uh oh!

netlifyBot commented May 18, 2026•
edited
Loading

Uh oh!

CopilotAI left a comment

Uh oh!

rpetit3 commented May 18, 2026

Uh oh!

rpetit3 commented May 18, 2026

Uh oh!

netlifyBot commented Aug 5, 2026•
edited
Loading

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Uh oh!

Conversation

rpetit3 commented May 18, 2026

Summary

Type of Change

Version Impact

Checklist

Uh oh!

netlifyBot commented May 18, 2026• edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

✅ Deploy Preview for bactopia-docs ready!

Uh oh!

CopilotAI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

rpetit3 commented May 18, 2026

Uh oh!

rpetit3 commented May 18, 2026

Uh oh!

netlifyBot commented Aug 5, 2026• edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

✅ Deploy Preview for bactopia-docs ready!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

netlifyBot commented May 18, 2026•
edited
Loading

netlifyBot commented Aug 5, 2026•
edited
Loading