From cec75195962b5131f1d0bd6e2927b07d5ed5a47d Mon Sep 17 00:00:00 2001 From: Douglas Ezra Morrison Date: Mon, 28 Sep 2026 16:06:39 -0700 Subject: [PATCH 1/5] Drop the no-new-extensions rule and the stale submodule premise Course sites no longer include mds as a git submodule, so the rule against adding Quarto extensions (justified by every host site having to install them) no longer applies. The project-context sentence now bases the path/anchor interface on URL links instead. Closes #30 Co-Authored-By: Claude Opus 5.5 --- .github/instructions/r-and-config.instructions.md | 6 ++---- CLAUDE.md | 3 +-- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/.github/instructions/r-and-config.instructions.md b/.github/instructions/r-and-config.instructions.md index 3dd00e1cc..36731b59b 100644 --- a/.github/instructions/r-and-config.instructions.md +++ b/.github/instructions/r-and-config.instructions.md @@ -16,10 +16,8 @@ description: "Use when editing R source, Quarto configuration, or GitHub workflo - Run `Rscript -e 'spelling::spell_check_package()'` before finishing changes to `.R` or config files. Fix only errors you introduced, and add legitimate technical terms to `inst/WORDLIST` rather than disabling the check. -- This is a template: every dependency added here lands in every downstream - book, so do not add a new R package or Quarto extension without a clear - reason. Align workflow and render changes with the existing CI patterns - instead of inventing parallel setup. +- Align workflow and render changes with the existing CI patterns instead of + inventing parallel setup. - Do not edit generated files (`README.md` is built from `README.Rmd`; `_site/`, `_freeze/`, and `.quarto/` are build outputs). diff --git a/CLAUDE.md b/CLAUDE.md index 6a1b6b50f..a7b4a3328 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -4,7 +4,7 @@ Project guidance for Claude Code (CLI, IDE, and the GitHub Action). The same con ## Project context -`mds` holds the mathematics that the Morrison-Lab data science courses assume: notation, algebra, calculus, linear algebra and vector calculus, as [Quarto](https://quarto.org/) fragments. It renders on its own as a website, and course sites include it as a git submodule, so a fragment's path and its `#id` anchors are an interface: renaming either breaks every host site. The scaffolding came from the UCD-SERG `qwt` template. +`mds` holds the mathematics that the Morrison-Lab data science courses assume: notation, algebra, calculus, linear algebra and vector calculus, as [Quarto](https://quarto.org/) fragments. It renders on its own as a website, and course sites such as `mlds` link to its pages by URL, so a page's path and its `#id` anchors are an interface: renaming either breaks those links. The scaffolding came from the UCD-SERG `qwt` template. Authoritative style guide: [UCD-SERG Lab Manual](https://ucd-serg.github.io/lab-manual/) (source: ). @@ -80,6 +80,5 @@ rme will drop those appendices and point readers here ## Things to avoid -- Adding new top-level dependencies (R packages, Quarto extensions) without a clear reason; this is a template, so every dependency lands in every downstream book. - Reformatting unrelated files. - Inventing URLs or citations --- only use sources actually present in `references.bib` or explicitly provided. From 7b19ed13544b49378c2126ca9a6073f6816e535b Mon Sep 17 00:00:00 2001 From: Douglas Ezra Morrison Date: Mon, 28 Sep 2026 16:27:40 -0700 Subject: [PATCH 2/5] Drop the extension rule from the review prompt too quarto-review.prompt.md still told reviewers to flag new Quarto extensions, the rule this PR removes elsewhere. Co-Authored-By: Claude Opus 5.5 --- .github/prompts/quarto-review.prompt.md | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/prompts/quarto-review.prompt.md b/.github/prompts/quarto-review.prompt.md index c8069eb14..cd2b7ce25 100644 --- a/.github/prompts/quarto-review.prompt.md +++ b/.github/prompts/quarto-review.prompt.md @@ -24,12 +24,10 @@ Review checklist: chunk and referenced with inline R. 5. Citations and attribution are present where adapted content or factual claims appear, and only sources in `references.bib` are used. -6. No new R package or Quarto extension is added without a clear reason (this is - a template --- every dependency lands in every downstream book). -7. No generated files are edited (`README.md` from `README.Rmd`; `_site/`, +6. No generated files are edited (`README.md` from `README.Rmd`; `_site/`, `_freeze/`, `.quarto/`), and spell/link-check failures are fixed at the source (wordlist or content), not suppressed. -8. The author ran the required local validation: +7. 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"libpng-dev", "libtiff-dev", "libwebp-dev", "libicu-dev", "libfontconfig1-dev", "libfribidi-dev", "libharfbuzz-dev", "libxml2-dev"] + } +} From 75211e6a85c0d526423ba7faeba110616b31b5fd Mon Sep 17 00:00:00 2001 From: Douglas Ezra Morrison Date: Mon, 28 Sep 2026 16:47:35 -0700 Subject: [PATCH 4/5] Remove the pkg.lock the @claude session auto-committed The @claude review run left a generated R dependency lockfile behind and its auto-commit step pushed it to this branch. Nothing references it and it is outside this PR's scope. Co-Authored-By: Claude Opus 5.5 --- .github/pkg.lock | 15268 --------------------------------------------- 1 file changed, 15268 deletions(-) delete mode 100644 .github/pkg.lock diff --git a/.github/pkg.lock b/.github/pkg.lock deleted file mode 100644 index 1a320e7d8..000000000 --- a/.github/pkg.lock +++ /dev/null @@ -1,15268 +0,0 @@ -{ - "lockfile_version": 1, - "os": "Ubuntu 24.04.5 LTS", - "r_version": "R version 4.6.1 (2026-06-24)", - "platform": "x86_64-pc-linux-gnu", - "packages": [ - { - "ref": "deps::.", - "package": "mds-deps", - "version": "0.1.0", - "type": "deps", - "direct": true, - "binary": false, - "dependencies": ["dplyr", "ggplot2", "plotly"], - "deps": [ - { - "ref": "R", - "type": "Depends", - "package": "R", - "op": ">=", - "version": "4.1.0" - }, - { - "ref": "knitr", - "type": "Suggests", - "package": "knitr", - "op": "", - "version": "" - }, - { - "ref": "rmarkdown", - "type": "Suggests", - "package": "rmarkdown", - "op": "", - "version": "" - }, - { - "ref": "spelling", - 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"post_install": {}, - "packages": ["libx11-dev", "git", "libcurl4-openssl-dev", "libssl-dev", "cmake", "make", "libuv1-dev", "libgit2-dev", "zlib1g-dev", "pandoc", "libfreetype6-dev", "libjpeg-dev", "libpng-dev", "libtiff-dev", "libwebp-dev", "libicu-dev", "libfontconfig1-dev", "libfribidi-dev", "libharfbuzz-dev", "libxml2-dev"] - } -} From b5baa01376c1bec28c57f1f08088f3a5954da0c5 Mon Sep 17 00:00:00 2001 From: Douglas Ezra Morrison Date: Mon, 28 Sep 2026 17:02:36 -0700 Subject: [PATCH 5/5] Drop the downstream-books rule from the review workflow The review prompt addendum still told the bot to flag new dependencies because every dependency lands in every downstream book, the premise removed from the instruction files. Course sites no longer include this repo as a submodule. Also drops the same framing from a comment in copilot-setup-steps.yml. Closes #35 Co-Authored-By: Claude Opus 5.5 --- .github/workflows/claude-code-review.yml | 9 +++------ .github/workflows/copilot-setup-steps.yml | 2 +- 2 files changed, 4 insertions(+), 7 deletions(-) diff --git a/.github/workflows/claude-code-review.yml b/.github/workflows/claude-code-review.yml index ecab6cb5e..d7ec9da6f 100644 --- a/.github/workflows/claude-code-review.yml +++ b/.github/workflows/claude-code-review.yml @@ -58,9 +58,8 @@ jobs: # "non-human actor". allowed-bots: 'github-actions[bot],claude' prompt-addendum: | - In addition to the standard checks above, this is the qwt Quarto - website template -- small, prose-heavy, and re-used as a template - for downstream books -- so also prioritize: + In addition to the standard checks above, this is a small, + prose-heavy Quarto website, so also prioritize: 1. **Quarto / prose correctness** - `.qmd` syntax: chunk options use `#|` directives, fenced @@ -72,15 +71,13 @@ jobs: 2. **R code** - Conforms to `.lintr.R` settings (snake_case, line length, etc.). - - No new package dependencies without justification -- every - dependency added here lands in every downstream book. 3. **Build hygiene** - No accidental commits of `_site/`, `_freeze/`, or `.quarto/`. - `README.md` is generated; edits should go to `README.Rmd`. - Bibliography entries in `references.bib` are well-formed BibTeX. - 4. **CI / template impact** + 4. **CI impact** - Workflow changes don't break the `copilot-setup-steps.yml` contract or the publish/preview pipelines. - Spell-check / link-check failures are fixed at the source diff --git a/.github/workflows/copilot-setup-steps.yml b/.github/workflows/copilot-setup-steps.yml index e61915dc0..5761014d9 100644 --- a/.github/workflows/copilot-setup-steps.yml +++ b/.github/workflows/copilot-setup-steps.yml @@ -54,7 +54,7 @@ jobs: id: check_label # Pass the expression result through env (GitHub-recommended) rather # than interpolating it directly into the shell, to avoid the - # expression-injection anti-pattern in code that downstream books copy. + # expression-injection anti-pattern. env: EVENT_NAME: ${{ github.event_name }} LABELS_CONTAIN_SKIP: ${{ contains(github.event.pull_request.labels.*.name, 'skip-cp-setup') }}