NEWS.md

In Bioconductor/AnVILPublish: Publish Packages and Other Resources to AnVIL Workspaces

AnVILPublish 1.12.0

Bug Fixes

• (v. 1.11.3) Link Rmd (and / or ipynb) vignettes to dashboard

AnVILPublish 1.10.0

• (v. 1.11.1) Remove support for notedown Python module conversion.

AnVILPublish 1.8.0

New Features

• (v. 1.7.1) Support publication output '.Rmd'

• (v. 1.7.2) Support 'Quarto' for Rmd to ipynb conversion

• (v. 1.7.3) Support 'Qmd' files.

User Visible Changes

• (v. 1.7.4) Update workspace publication -- put 'Description' directly under title so it appears in WORKSPACE summary; add current 'Date' to citation if not already defined.

Bug Fixes

• (v. 1.7.4) Workspace dashboard and startup link to notebooks in 'analysis' rather than 'notebook' location; clean up vignette author list.

AnVILPublish 1.4.0

New Features

• (v. 1.3.2) Support _bookdown.yml -- name and order vignettes

AnVILPublish 1.2.0

New Features

• Include README.md on Workspace landing page (thanks Vince Carey).

Bug Fixes

• as_workspace() correctly passes an unboxed 'description' attribute when setting the dashboard.

AnVILPublish 0.0.10

• Add 'best practices' and rationale for Rmarkdown-to-jupyter notebook conversion.

AnVILPublish 0.0.9

• Create a notebook '00-<<workspace name>>' to install package / book dependencies specified in the original source.
• Don't link to vignettes from the DASHBOARD, since the namespace changes in cloned workspaces.
• as_workspace(..., create = FALSE, update=FALSE) now evaluates code, silently.

AnVILPublish 0.0.8

• Support collections of Rmd files that are not packages, e.g., bookdown sites.
• Add R / Bioconductor version to dashboard

AnVILPublish 0.0.7

• Revise Rmd-to-ipynb work flow

• Don't evaluate code chunks (avoids including output in notebook, and side-effects because rmarkdown::render does not start a separate process)

• Insert metadata to use the R kernel. jupytext can do this more elegantly, but does from .md renders code chunks and pre-formatted rather than evaluation cells, and from .Rmd does not process markdown well enough, e.g., not suppporting [foo][]-style links when the definition is elsewhere in the document.

AnVILPublish 0.0.6

• Added a NEWS.md file to track changes to the package.

• Extensive interface renaming

• as_workspace() (formerly package_source_as_workspace())

• as_notebook() (formerly vignettes_to_notebooks())
• add_access() (formerly bioconductor_user_access())

Bioconductor/AnVILPublish documentation built on Nov. 2, 2024, 1:41 p.m.