NEWS

liftr 0.9.2 (2019-06-19)

Switched to absolute URLs for the contributing guidelines and contributor code of conduct in the readme.

Fixed the issue of parsing Bioconductor package names (#45) for R >= 3.5 and the introduction of BiocManager. We thank Tiago Lubiana for contributing the patch.

Added a new argument dry_run in render_docker() for debugging: when set to TRUE, it will only return the Docker commands and not actually run them.
New URL for the documentation website: https://nanx.me/liftr/.

Added a new argument prune in render_docker() to automatically clean up dangling containers and images in case the image build or compilation was not successful (#27). We thank Nicolas Roelandt for suggesting this feature (#25).
Added functions prune_container_auto(), prune_image_auto(), and prune_all_auto() for automatic pruning of dangling containers or images without particular names specified.
Added function install_docker() for guiding the installation of Docker.
Added function check_docker_install()for checking if Docker is properly installed and discoverable.
Added function check_docker_running() for checking if Docker daemon is running.

The argument purge_info was renamed to prune_info in render_docker().
Previous functions for cleaning up specific Docker containers and images purge_container() and purge_image() are now renamed to prune_container() and prune_image().
RStudio addin: the old addin for removing Docker images was refactored into two new addins: one for removing dangling containers and images, one for removing the successfully built image that corresponds to the current document.
Added two new vignettes. Check out vignette("liftr-addins") and vignette("liftr-tidyverse").

Use system font stack instead of Google Fonts in vignettes to avoid pandoc SSL issue.

Supports parsing the liftr metadata from a standalone YAML congfiguration file. This feature makes it possible to run liftr without editing the original R Markdown file [#22].

Added RStudio addins as shortcuts to containerize and render R Markdown documents.
Added new argument cache in render_docker() to improve rendering speed significantly by caching Docker image layers [#18].
Added new argument purge_info to render_docker(). This argument controls whether to output the Docker image and container name into an YAML file for purging purposes later.
Separate the creation and removal of Docker containers and images: removed the old argument reset in render_docker(); added purge_container() and purge_image() for cleaning up.
The ghpkg field is now deprecated. The new remotes field supports devtools remote package name format. Now packages can be installed from GitHub, Bitbucket, Git/SVN servers, URLs, etc.
Added new metadata field include for including any custom Dockerfile snippets into the final Dockerfile. This also fixes #21.

Renamed drender() to render_docker(). drender() is now deprecated.
Better naming scheme for liftr metadata fields.
Tidy up the output Dockerfile by lift().
Added two new examples in inst/examples/: explore tidyverse and Bioconductor RNA-Seq workflow.
New documentation website generated by pkgdown, with a full set of function documentation and vignettes available.
Added Appveyor support for continuous integration under Windows.
Removed Rabix support temporarily to embrace its new version in the future.
Added a new demo video.

Modified examples in documentation to comply with the lastest CRAN Repository Policy.
Installing packages with https.

Added new R Markdown header option pandoc to control Pandoc installation. Automatically set this to false for rocker/rstudio and bioconductor/... images. This solves #12.

Initial version of liftr. This version implemented two functions lift() and drender(). They provide basic support for dockerizing R Markdown documents, with support for running Rabix workflows/tools before rendering R Markdown documents in Docker containers.