Changelog

Source: NEWS.md

umr1283 1.10.4

• chore(DESCRIPTION): update email address.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.10.3...v1.10.4

umr1283 1.10.3

• chore(inst/devcontainer): update devcontainer definition files for VSCode.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.10.2...v1.10.3

umr1283 1.10.2

• fix(R/use_readme.R): backslashes are now escaped.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.10.1...v1.10.2

umr1283 1.10.1

• fix(R/use_targets.R): uses anonymous function with on.exit behaviour for 00-targets.R to make changes even on errors.
• fix(R/create_project.R): allows to create a project without git.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.10.0...v1.10.1

umr1283 1.10.0

• fix(R/use_targets.R): add tar-utils directory, ensure permission after targets is ran.
• feat(R/create_project.R): get function call to use it in README.md file.
• feat(R/use_readme.R): add function call and docker bash command.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.9.2...v1.10.0

umr1283 1.9.2

• fix(R/use_dir_structure.R): mention gittargets earlier.
• fix(R/use_dir_structure.R): remove tarchetypes.
• fix(R/use_targets.R): remove tarchetypes and future.callr.
• chore(inst/devcontainer): update devcontainer definition files for VSCode (https://github.com/mcanouil/vscode-dev-containers/tree/main/umr1283).

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.9.1...v1.9.2

umr1283 1.9.1

Fixes

• In R/use_gitignore.R and R/use_targets.R,
  • fix: no longer ignore _targets and renv directories.

Chores

• chore: update devcontainer definition files for VSCode (https://github.com/mcanouil/vscode-dev-containers/tree/main/umr1283).

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.9.0...v1.9.1

umr1283 1.9.0

Feature

• In R/create_project.R,
  • feat: add devcontainer definition files for VSCode (#3).

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.8.3...v1.9.0

umr1283 1.8.3

Chore

• In inst/fex/fexsend,
  • chore: update fexsend client.

Fixes

• In R/fex.R.
  • fix: parent directory detection.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.8.2...v1.8.3

umr1283 1.8.2

Fixes

• In R/use_gitignore.R.
  • fix: *.Rproj is now excluded from versionning.
• In R/use_targets.R,
  • fix: default targets script no longer rely on *.Rproj.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.8.1...v1.8.2

umr1283 1.8.1

Fixes

• In R/use_rprofile.R,
  • No longer hardcode settings, instead source ~/.Rprofile if it exists and in interactive mode.
• In DESCRIPTION,
  • Bump (minor) version of dependencies.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.8.0...v1.8.1

umr1283 1.8.0

Breaking change

• Remove Python wrapper. (3fedb3a961984d7b165a258e08e11d366794cb78)
  • In R/use_python.R.
  • In R/create_project.R.
  • In R/use_dir_structure.R.
  • In R/migrate_project.R.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.7.0...v1.8.0

umr1283 1.7.0

Features

• In R/create_project.R,
  • Allows to use directory within the project (when working_directory is NULL or "") or symbolic link (058ade53e66482426a8ded231fe2e3553a6dc4a2).
  • Allows to install xaringan template when creating a project (37a417c20c391a1c66b4648fe55b5c7ea4d2bf7f).

Fixes

• In R/use_rprofile.R,
  • Fix duplicated targets lines in .Rprofile (2f8c90b78749a02861fdaf7285364899abc10ec4).
• In R/use_rprofile.R,
  • Fix duplicated .gitignore entry for targets (c2cc1d51ee7b564fe27223a1e838637b8c096869).
  • No longer exclude “outputs” and “logs” (c2cc1d51ee7b564fe27223a1e838637b8c096869).
• In R/use_python.R,
  • Fix unused arguments (fa21f5fbed0638c65da16c8146854b87bb8d73d2).
• In R/use_targets.R,
  • Fix unused arguments (13055f3cc8d3a0b5bee609cb4085329698824d42).
• In R/use_dir_structure.R,
  • Fix unused arguments (ab94c2499b4cb989f09adf0434c04c5b20719f51).
• In R/migrate_project.R,
  • Add a warning message to “discourage” the use of migrate_project (416e79a0d7499433efde68a13809cb8923e5bbe4).
  • Remove default parameter value for working_directory (fc34b29d999ad1e631e5c37e4649b2ac4ff682fb).

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.6.0...v1.7.0

umr1283 1.6.0

• In R/fex.R,
  • Fix URL for pkgdown website.
• In R/create_project.R,

  • No longer create external renv “library” directory.

  • Use a dedicated directory for slides.

    /disks/PROJECT/project
    ├── data
    ├── docs
    ├── scripts
    │   └── _dependencies.R
    ├── reports
    ├── slides
    ├── outputs (symlink to /disks/DATATMP/project/outputs)
    ├── logs
    ├── renv
    ├── README.md
    ├── renv.lock
    └── project.Rproj

• In R/use_targets.R,
  • Add gittargets.
  • No longer use symbolic link for targets store.
• In R/use_python.R,
  • No longer use symbolic link for python library.
• In R/use_xaringan.R,
  • Default directory to slides in the current working directory.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.5.1...v1.6.0

umr1283 1.5.1

• In R/create_project.R,
  • Add check before creating symbolic link.
• In R/migrate_project.R,
  • Add check before creating symbolic link.
• In R/use_dir_structure.R,
  • Add check before creating symbolic link.
  • No longer install R packages, but add a message to install them manually.
• In R/use_git.R,
  • Add check before creating symbolic link.
• In R/use_python.R,
  • Add check before creating symbolic link.
• In R/targets.R,
  • Add check before creating symbolic link.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.5.0...v1.5.1

umr1283 1.5.0

• In R/create_project.R,
  • Remove library symbolic link.
• In R/use_gitignore.R,
  • No longer exclude reports directory by default.
  • Exclude renv directory properly.
• In R/use_rprofile.R,
  • No longer load gert by default (if installed).

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.4.0...v1.5.0

umr1283 1.4.0

• In R/*,
  • Fix lintr warnings.
• In R/use_dir_structure.R,
  • No longer try to install BiocManager or here by default.
  • Install here and tarchetypes by default when targets is required.
• In R/use_dependencies.R,
  • Create empty file, i.e., without # library("BiocManager").

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.3.1...v1.4.0

umr1283 1.3.1

• In inst/fex/fexsend,
  • Updated fexsend (http://fex.belwue.de/download/fexsend).
• In DESCRIPTION,
  • Add SystemRequirements for fexsend.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.3.0...v1.3.1

umr1283 1.3.0

• In DESCRIPTION,
  • Tweak description and title.
  • Tidy dependencies.
  • Update packages.
• In R/use_gitignore.R,
  • Add “core”.
• In R/use_git.R,
  • Do not do anything if .git directory exists.
• In R/use_dir_structure.R,
  • Do not do anything if .Rprofile contains source("renv/activate.R").
• In R/create_project.R,
  • Add “data” directory.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.2.3...v1.3.0

umr1283 1.2.3

• In DESCRIPTION,
  • Remove “RStudio” from title.
• In R/use_xaringan.R,
  • Avoid copying README.Rmd.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.2.2...v1.2.3

umr1283 1.2.2

• In DESCRIPTION,
  • Remove unnecessary LazyData field.
• In R/use_targets.R,
  • Fix typo/bug in _targets.R template script.
  • Edit .Rprofile (if it exists) with shortcut for targets.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.2.1...v1.2.2

umr1283 1.2.1

• In R/fex.R,
  • Fix output when only one file is provided.
  • Improve example.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.2.0...v1.2.1

umr1283 1.2.0

• In R/use_xaringan.R,
  • Download xaringan (https://github.com/umr1283/xaringan-template) template to scripts/slides.
• In R/migrate_project.R,
  • Fix typo.
• In R/use_targets.R,
  • Fix typo.
• In R/use_python.R,
  • Fix typo.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.1.4...v1.2.0

umr1283 1.1.4

• In R/use_targets.R,
  • Improve default targets R script skeleton.
  • Add default targets script launcher.
• In R/use_rprofile.R,
  • Add targets package in .Rprofile, if in interactive session and installed (locally or system-wide depending on the project setup).

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.1.3...v1.1.4

umr1283 1.1.3

• In R/use_affiliation.R,
  • Split in two.
• In R/use_readme.R,
  • Use bullets list for affiliation.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.1.2...v1.1.3

umr1283 1.1.2

• In R/use_targets.R,
  • Improve default targets R script to better work with Docker.
• In inst/fex/fexsend,
  • Fix permission.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.1.1...v1.1.2

umr1283 1.1.1

• In DESCRIPTION,
  • Define markdown format for roxygen2 documentation.
• In R/create_project.R,
  • Improve description.
• In R/migrate_project.R,
  • Improve description.
• In R/use_affiliation.R,
  • Improve description.
• In R/use_targets.R,
  • Improve description.
• In R/use_python.R,
  • Improve description.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.1.0...v1.1.1

umr1283 1.1.0

• In DESCRIPTION,
  • Add prompt in Suggests.
• In R/use_rprofile.R,
  • Add prompt package in .Rprofile, if in interactive session and installed (locally or system-wide depending on the project setup).
  • Add gert package in .Rprofile, if in interactive session and installed (locally or system-wide depending on the project setup).
• In R/use_dir_structure.R,
  • Only load targets, if in interactive session and installed (locally or system-wide depending on the project setup).
• In R/fex.R,
  • New function to upload file(s) using fexsend.
• Add pkgdown.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.0.1...v1.1.0

umr1283 1.0.1

• In R/use_python.R,
  • Remove code related to ensurepip.

Full Changelog: https://github.com/umr1283/umr1283/compare/v1.0.0...v1.0.1

umr1283 1.0.0

• In DESCRIPTION,
  • Remove rmarkdown templates dependencies.
  • Add targets in Suggests.
  • Add withr and callr in Importsto handle project architecture.
• In R/create_project.R (previously R/new_project.R),
  • Set BiocManager to use MRAN with new option as of v1.30.12.
  • Install here using renv by default.
  • Set umask to 0002.
  • Allow to not use MRAN for new project (default).
  • Add support for renv::use_python().
  • Add support for targets.
  • Refactoring using use_- functions.
• In R/migrate_project.R,
  • Set BiocManager to use MRAN with new option as of v1.30.12.
  • Install here using renv by default.
  • Set umask to 0002.
  • Add support for renv::use_python().
  • Refactoring using use_- functions.
• In R/use_targets.R,
  • Create directory structure required for targets.
• In R/use_python.R,
  • Create directory structure required for reticulate and Python within renv.
• In R/use_affiliation.R,
  • Add function to get current affiliation.
• Remove rmarkdown templates.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.8.1...v1.0.0

umr1283 0.8.1

• In R/new_project.R,
  • Add missing documentation.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.8.0...v0.8.1

umr1283 0.8.0

• In DESCRIPTION,
  • Add renv in Suggests.
• In R/new_project.R,
  • Add renv directory structure.
  • Improve project README.
  • Add push to gitlab.
  • Ensure project directory is in 0775.
  • Default BiocManager install.
• In R/migrate_project.R,
  • New function to migrate old project to renv project-like.
  • Default BiocManager install.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.7.9...v0.8.0

umr1283 0.7.9

• In DESCRIPTION,
  • Update dependencies.
• In R/ioslides_presentation.R,
  • Update not exported function from rmarkdown.
• In rmarkdown templates,
  • Update affiliation.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.7.8...v0.7.9

umr1283 0.7.8

• In rmarkdown templates,
  • Add Font-Awesome 5.14.0 icons to ioslides.
• In ioslides_presentation.R,
  • Update to include Font-Awesome 5.14.0 icons.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.7.7...v0.7.8

umr1283 0.7.7

• In rmarkdown templates,
  • Update ggplot2 template code.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.7.6...v0.7.7

umr1283 0.7.6

• In rmarkdown templates,
  • Remove default subdirectory for intermediate Rmarkdown files.
  • Update affiliation.
• In R/new_project.R,
  • Add “reports” to .gitignore.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.7.5...v0.7.6

umr1283 0.7.5

• In rmarkdown templates,
  • Minor code change.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.7.4...v0.7.5

umr1283 0.7.4

• In rmarkdown templates,
  • Remove css style for tables.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.7.3...v0.7.4

umr1283 0.7.3

• In rmarkdown templates,
  • Reorder code in setup chunk.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.7.2...v0.7.3

umr1283 0.7.2

• Fix knitr hook in templates.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.7.1...v0.7.2

umr1283 0.7.1

• Fix outputs directory in templates.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.7.0...v0.7.1

umr1283 0.7.0

• Fix ioslide templates.
• Update setup chunks in all templates.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.6.0...v0.7.0

umr1283 0.6.0

• Rename data to outputs.

  /disks/PROJECT/test
  ├── outputs -> /disks/DATATMP/test
  ├── docs
  ├── logs
  ├── reports
  ├── scripts
  ├── README.md
  ├── .git
  ├── .gitignore
  └── test.Rproj

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.5.0...v0.6.0

umr1283 0.5.0

• Update rmarkdown templates according to project directory tree structure.
• Fix obsolete parameters in chunks of the rmarkdown templates.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.4.1...v0.5.0

umr1283 0.4.1

• Update report template.
• Fix ressources in ioslide template.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.4.0...v0.4.1

umr1283 0.4.0

• Add a logs directory.

  /disks/PROJECT/test
  ├── data -> /disks/DATATMP/test
  ├── docs
  ├── logs
  ├── reports
  ├── scripts
  ├── README.md
  ├── .git
  ├── .gitignore
  └── test.Rproj

• Fix some style in README.md file.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.3.0...v0.4.0

umr1283 0.3.0

• Set 775 permissions for files and directories

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.2.0...v0.3.0

umr1283 0.2.0

• Remove Rmarkdown templates, now in dgapaq:
  • qc_impute - UMR 1283 - QC Imputation (VCF).
  • qc_plink - UMR 1283 - QC PLINK.
• Remove Rmarkdown templates, now in dmapaq:
  • qc_idats - UMR 1283 - QC idats.

Full Changelog: https://github.com/umr1283/umr1283/compare/v0.1.0...v0.2.0

umr1283 0.1.0

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

• Added a RStudio project template UMR 1283 - RStudio Project Templates.

  /disks/PROJECT/test
  ├── data -> /disks/DATATMP/test
  ├── docs
  ├── reports
  ├── scripts
  ├── README.md
  ├── .git
  ├── .gitignore
  └── test.Rproj

• Added Rmarkdown templates for:

  • ioslides - UMR 1283 - ioslides.
  • PowerPoint - UMR 1283 - PowerPoint.
  • HTML report - UMR 1283 - Report.
  • qc_idats - UMR 1283 - QC idats.
  • qc_plink - UMR 1283 - QC PLINK.
  • qc_impute - UMR 1283 - QC Imputation (VCF).