Changelog • projecttemplates

projecttemplates 0.6.3

Fixed the path to the Dockerfile in the project build script (misc/docker/build_image.sh).
Added bash headers to template shell scripts.
Set the default values of the arguments github, private and github_actions in template() to FALSE.
Fixed the branch reference for adding a project to GitHub.

Fix for renv when Bioconductor dependencies are included in argument dependencies.

Added the sandbox argument to renvInitialise() to allow the selection of whether sandboxing is used during renv initialisation.

The template run.R script now outputs to misc/run.R. The template README.md has now been updated to reflect this.
The template misc/run.R script now outputs a message to the console upon completion.
The tarchetypes package is now referenced directly in template targets scripts.
The template docker infrastructure now outputs to the directory misc/docker and now includes an image build script (/misc/docker/build_image.sh) and a container run script (/misc/docker/run_container.sh).
jfmisc::writingChecks() now replaces the manuscriptChecks() function in the manuscript template.
The renv::restore() command has now been moved to the template .Rprofile.
The targets package and the magrittr %>% are now loaded via the template .Rprofile.
The bioconductor argument replaces the bioc argument in renvInitialise() to stipulate the Bioconductor version to use.
Added the targetsConfig() function to add a _targets.yaml to a project directory. This file is added automatically by the template() function.
Fixed incorrect outputs in the figures, tables and supplementary output Rmarkdown files in the manuscript template.
knitr is now referenced directly in function calls in output template Rmarkdown files.

The renv directory is now included in the generated .dockerignore file if argument renv = TRUE.
The RStudio project file is now created even if the project template is generated outside of RStudio.
Errors encountered during the retrieval of the git signature are now reported during git initialisation.

Script header added to generated R/utils.R file.
data and exports directories added to the the generated .dockerignore file.
The generated _targets.R file is now formatted using the styler package.

.dockerignore file is now added to output project to ignore the _targets directory if present.
Target build time and object size are now added to the output pipeline graph in run.R.
targets package options set by tar_options_set() now moved to utils.R.

Fixed the use of user renv settings during initialisation to ensure that the user cache is used.
Simplified the renv cache restore term in the generated project Dockerfile.

Fixed warning that is returned when directories in the project path do not exist prior to template generation.

Added pacman as an import to ensure that it is installed in case renv = FALSE is used.
Project templates targets error option now set to "continue" to enable the pipeline to continue if an error is encountered.
The pipeline network graph generation added to the generated run script.

An initial commit is only made in createGit() if a valid git signature is found.
The value of the install argument of pacman loading functions can now be set in utils().
In template(), the pacman install argument in utils() is now dependant on the value of the renv argument.
The installation of project package dependencies is now added to the docker file when the renv argument is FALSE.

Added ignore argument to createGit() to enable the customisation of files and directories ignored by git.
_targets,data and exports folders ignored by git by default.

renvInitialise() now initialises the project library to ensure that Bioconductor and GitHub dependency packages are installed correctly.

Added exports directory to the template skeleton.
Removed the use of BiocManager::install() for installing Bioconductor packages, instead using renv::install().
The rebuild argument has been removed from template() and renvInitialise().
Template project analysis outputs now directed to the exports directory.

CRAN, Bioconductor and GitHub R packages can now be specified in utils().
Bioconductor and GitHub R packages can now be installed upon renv cache initialisation in renvInitialise().

projecttemplates::targetsScript() function now exported.
A run.R script now added to a project directory for executing a targets analysis through projecttemplates::targetsRun().
Project creation can be forced using the force argument of projecttemplate::template().

Removed use of the now defunct usethis::git_credentials() and usethis::github_token().
All git interaction now uses the gert package instead of git2r.

Added a NEWS.md file to track changes to the package.
Added rebuild argument to projecttemplates::template() to force the rebuild of packages on installation into the project renv package cache.
.Rhistory now ignored by git.