NEWS.md

In jasenfinch/projecttemplates: Project Templates for Reproducible Research and Analyses

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.

projecttemplates 0.6.2

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

projecttemplates 0.6.1

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

projecttemplates 0.6.0

• 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.

projecttemplates 0.5.8

• 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.

projecttemplates 0.5.7

• 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.

projecttemplates 0.5.6

• .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.

projecttemplates 0.5.5

• 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.

projecttemplates 0.5.4

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

projecttemplates 0.5.3

• 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.

projecttemplates 0.5.2

• Removed rstudio from the project path in the Dockerfile.

projecttemplates 0.5.1

• 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.

projecttemplates 0.5.0

• renv::restore() moved from utils.R to run.R.

• The generation of renv infrastructure is now optional in template().

• The project Dockerfile is now generated with the in-use R version.

• The project Dockerfile is now specific to the project type.

• The package version and URL now added to all generated files.

projecttemplates 0.4.6

• 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.

projecttemplates 0.4.5

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

projecttemplates 0.4.4

• 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.

projecttemplates 0.4.3

• renv R package cache infrastructure is now initiated using renv::init().

projecttemplates 0.4.2

• 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 0.4.1

• 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().

projecttemplates 0.4.0

• docker argument in projecttemplates::template() now works correctly.

• The project templates now use the targets package for workflow management.

• Intermediate helper functions are now exported.

• Added a pkgdown site available here.

projecttemplates 0.3.5

• Re-added the addition of the remote URL during GitHub repo set-up.

projecttemplates 0.3.4

• Removed use of the now defunct usethis::git_credentials() and usethis::github_token().

• All git interaction now uses the gert package instead of git2r.

projecttemplates 0.3.3

• 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.

jasenfinch/projecttemplates documentation built on July 30, 2023, 5:28 a.m.