NEWS

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BiocBook 1.11.4

New features

• from_bookdown() converts a bookdown book in place, in its own repository and on its current branch, rather than into a new repository. Each step is a commit of its own, numbered [BiocBook 1/10], [BiocBook 2/10]... (the package files, the pages moved to inst/ as they are, the book settings, the removal of the bookdown build, the landing page, cross-references, callouts, figure options, the setup of each page and DESCRIPTION), with a short message, so that the conversion can be reviewed step by step, and squashed or rebased like any other change. The repository needs a first commit to convert on top of. package (by default the book_filename of the book) replaces new_package, commit replaces push, and user defaults to the owner of the origin remote.
• from_bookdown() takes the licence of the book from a Creative Commons licence its pages link to, or from its LICENSE file, and otherwise writes the MIT licence of the template for the authors of the book.

Bug fixes

• from_bookdown() only collapses the blank lines its rewrites create, and keeps the final newline of a page, or its absence: the formatting of the book is left alone.
• MIGRATION.md is no longer committed, nor listed in .Rbuildignore: the commits say what was done, and the file what is left to do, now including the files that are not part of a BiocBook.
• MIGRATION.md no longer claims that the output options it does not translate have no quarto equivalent: for highlight, it gives the highlight-style that keeps the code highlighting of the book.

BiocBook 1.11.3

New features

• from_bookdown() migrates a bookdown book to a BiocBook in one call. It creates the book package from the template, as init() does, and converts the bookdown project into it: pages (with parts and appendices), cross-references, figure layout options and msmbstyle question/solution blocks, bibliographies, CSS and images, DESCRIPTION (title, authors, dependencies), and the setup of the single R session bookdown renders every chapter in. MIGRATION.md lists how often each rule was applied and what still needs to be done by hand.
• The template's biocbook GitHub workflow can be run manually on any branch: it then builds the book against Bioconductor devel without pushing its Docker image or deploying it, so that a branch can be checked before it is merged. Deployments also index the llms.txt of every deployed version of a book in docs/llms.txt.

Bug fixes

• chapters() drops header attributes (e.g. {#sec-intro}) from chapter titles.
• The template's question and answer callouts are styled again: quarto (>= 1.3) drops extra classes from callouts, so they are now wrapped in a .callout-question or .callout-answer div.
• The template's Dockerfile retries the quarto download on transient errors (e.g. HTTP 503 from GitHub), which failed a book's build before anything was installed.
• The template's vignettes/Makefile is portable again: template 1.1.0 switched the llms profile on with GNU make extensions (:= and $(shell ...)), which R CMD check reports as a warning in every book.

Documentation

• ?BiocBook-python and the template's requirements.yml explain why matplotlib >= 3.11 cannot be imported on the Bioconductor images, and how to pin it.

BiocBook 1.11.2

New features

• New books are created from template 1.1.0:
  • python chunks run through reticulate (python.reticulate: true), in the conda environment declared in inst/requirements.yml, which now uses the conda-forge and bioconda channels only and pins python;
  • the book's Docker image provisions that environment when a page runs python, and receives GITHUB_PAT as a BuildKit secret, so that GitHub-only dependencies no longer hit the API rate limit (#6);
  • the biocbook GitHub workflow uses the current major version of every action (actions/upload-artifact@v3, which GitHub has rejected since January 2025, made every new book's workflow fail), and can pin the quarto version a book is built with;
  • books serve an llms.txt file for AI assistants (see below);
  • PDF output is no longer configured.
• enrich_llms_txt(): books built with quarto >= 1.11 serve /llms.txt and a Markdown copy of every page, for AI assistants. Template 1.1.0 switches this on (through an llms quarto profile, only when the installed quarto supports it), and runs enrich_llms_txt() after every render to add the book package, its Docker image, its python environment and its other versions to llms.txt. With an older quarto, enrich_llms_txt() writes a minimal llms.txt listing the chapters.
• python_envs() lists the conda environments setup_python() has cached on a machine, and python_envs(remove = ...) deletes them.
• add_python_chapter() declares BiocBook and reticulate in the book's Suggests, and pins the new page to the knitr engine.

Bug fixes

• setup_python() keys each conda environment on the contents of requirements.yml (envs/<name>-<hash>). Editing the file now gives a new environment, rather than silently re-using the existing one on machines that already had it, and two books only share an environment when they declare exactly the same thing.

BiocBook 1.11.1

New features

• BiocBooks can execute python code: add_python_chapter() adds a page whose python chunks run through reticulate, in a conda environment that setup_python() creates from inst/requirements.yml while the book builds, including on the Bioconductor builders.
• micromamba() finds a micromamba binary, or downloads a pinned and checksummed one, so that books can build their python environment on machines without conda.

Bug fixes

• add_chapter() and add_preamble() insert new pages under the chapters: entry of _book.yml wherever it is, rather than assuming it sits on the third line.