NEWS

AnVILPublish 1.24.0

New Features

(v. 1.23.1) Add dry.run argument to add_access(), as_notebook(), and as_workspace() to allow local processing and previewing without making remote changes in AnVIL.
(v. 1.23.3) Add AnVILBase to Suggests.

Significant User-Visible Changes

(v. 1.23.1) Remove legacy support for python notedown conversion. A system installation of Quarto is now required to convert .Rmd to .ipynb notebooks, and a clear error is thrown if it is not found.
(v. 1.23.1) Add quarto-cli to SystemRequirements in DESCRIPTION.
(v. 1.23.1) Add URL and BugReports fields to DESCRIPTION.
(v. 1.23.1) Add funding (fnd) role and grant number to package authors.

Bug Fixes

(v. 1.23.1) Handle lowercase .rmd extensions in as_notebook().

AnVILPublish 1.22.0

New Features

(v. 1.21.1) Export create_workspace() for creating a new AnVIL workspace without necessarily populating it from an R package.

AnVILPublish 1.20.0

Significant User-Visible Changes

(v. 1.19.0) Update to use GCPtools for gcloud checks.

AnVILPublish 1.18.0

No significant changes.

AnVILPublish 1.16.0

Significant User-Visible Changes

(v. 1.15.0) Use AnVILGCP for storage and copying functions, replacing AnVIL usage.

Documentation

(v. 1.15.0) Use README.Rmd script for README.md.
(v. 1.15.2) Update AnVILPublishIntro.Rmd and README.md.

AnVILPublish 1.14.0

New Features

(v. 1.13.2) Move BiocManager to Imports as it is used in code.
(v. 1.13.1) Use BiocBaseUtils for internal utility functions.

Documentation

(v. 1.13.0) Add a note to the vignette clarifying that only Google Cloud Platform workspaces are supported.

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())