VISCtemplates 2.1.0

Improvements for users

• New infrastructure to support installing and loading datapackages from a designated directory (#331)
  • New function datapackage_path() to access VISCTEMPLATES_DATAPACKAGE_PATH environment variable
  • New argument lib.loc for visc_load_pdata()
• New function install_git_workaround() to avoid remotes::install_git() error on network drive paths (#315)
• Change name of methods folder within each report subfolder to child-docs to be more general-purpose (#309)
• Remove check_pandoc_version() from report templates (#318)
• Line breaks added between multiple contact personnel on title page of PDF report template (#308)
• visc_load_pdata() gives more informative error message when serialized pdata file does not contain an R object of the same name (#303)
• Default behavior of create_visc_project() no longer includes creation of package-specific files DESCRIPTION and NAMESPACE (#306)
• Add option to drop SCHARP logo in PDF output (#312)
• Add visc_load_pdata() examples to report template skeleton (#327)
• Remove install_load_cran_packages() from report template skeleton in favor of using library() calls (#321)
• Reproducibility table formatting changes to coordinate with recent VISCfunctions update that lengthens reproducibility packages table to include packages that are loaded but not attached (#329, #332)

Improvements for package contributors and maintainers

• Repair unit tests to work with testthat 3.3.0 (#317)
• Remove empty "examples" in template study schema to avoid minor issues (#319)
• Run test knits in a callr session to isolate Rmd library calls from main R process (#320)
• Drop dependency on DataPackageR (#324)
• VISCtemplates now depends on R >= 4.1.0 (#334)
• Use base pipe |> in package and templates (#310)

VISCtemplates 2.0.2

Improvements for users

• visc_load_pdata() no longer accepts a dataVersion (e.g. 0.1.2) as its criteria argument. Use a 32-digit data hash, as has long been standard practice. (#297)
• visc_load_pdata() gains a new optional package argument for loading pdata with a non-standard name. (#297)

VISCtemplates 2.0.1

Bug fixes

• visc_load_pdata() now works in datapackage mode for installed datapackages that use LazyData: true in their DESCRIPTION file (#293)
• visc_load_pdata() now also works with standard evaluation, accepting a character string as its first argument (#295)

Improvements for package contributors and maintainers

• Fix Codecov badge and URL (#287)
• CI maintenance (#287, #291, #294)

VISCtemplates 2.0.0

Improvements for users

• Add new helper functions networks_path() and trials_path() (#271)
• Added ADCC template (#109)
• Improvements to Word document formatting (#212, #281)
• Better default colors and shapes for reports, in line with current report practices (#268)
• Added to default gitignore: .aux, .toc, .lof, .lot, .out, .smbdelete, and cache files (#230); .html files in data-raw/ (#255)
• Update PT report naming practice to VDCnnn_assay_PTreport_interim/final_(un)blinded.Rmd (#202)
• Updated README practices
  • Structured README.md files are now created at the assay folder level at the time of calling use_visc_report(),
    and minimally structured README.md files are created at the report folder level at the same time (#233)
  • create_visc_project() now discards README.Rmd after knitting template to README.md (#223, #224)
• Updated names of people in template acknowledgements section (#234)
• Explicitly include reference to data package version in template data package installation code (#257)
• Include pdata object name and data package name in visc_load_pdata() error message (#253)

Bug fixes

• Provide default CRAN mirror if missing in install_load_cran_packages(), e.g., in a child R session during knitting. Fixes 'trying to use CRAN without setting a mirror' error (#218)
• Update template.tex so that flextable package can be used to create tables in PDF documents (#226)
• Fix error when running skeleton.Rmd file interactively (#249)
• Add ggplot2 loading to visc_empty PT report skeleton to avoid rendering error (#256)
• Fix formatting issue in assay folder README template (#266)

Improvements for package contributors and maintainers

• Update and clarify CONTRIBUTING.md (#269)
• Auto-calculate unit test coverage on PRs and view results on Codecov (#250)
• Reorganized and renamed files in inst/ for clarity (#233)
• Update installation of system dependencies and R packages on CI runners (#261, #265, #273, #278, #280)
• Clean up invalid ORCID placeholder generated by usethis 3.0.0 that threw error on R version 4.5.x (#248), then revert once fixed in upstream usethis (#259)

VISCtemplates 1.3.2

Bug Fix

• Fix issue with insert_break() not inserting page breaks at times (#216)

Other improvements

• Reconcile differences between empty report template and other report templates (#204)
• Remove dependency on the full tidyverse, per best practices (#213)

VISCtemplates 1.3.1

Bug Fix

• Re-flip Fred Hutch and SCHARP header logos to fix regression from #196, restoring intended logo positions in #195 (#205)

VISCtemplates 1.3.0

Bug Fixes

• Fix major bug that broke PDF knitting on pandoc >= 3.1.7 (#159)
• Fix bug with latex packages (specifically etex's \reserveinserts command) that broke PDF knitting (#160)
• Fix bug that occurred when a report subdirectory did not already exist, and add unit test (#173)
• Fix insert_break() to actually create a page break (#188)
  • Update documentation to instruct users to use \newpage instead in new code

Improvements to Report Templates

• Update header logo for SCHARP/Fred Hutch branding compliance (#195)
• Update templates and documentation for using correct syntax for multiple citations (#191)
• Add section number to References section in PDF output (#176)
• Clarify expectations for Background section of report (#143)
• Fix BAMA positivity call definition (#144)
• Add Acknowledgments section to report templates (#153)

Testing and Continuous Integration

• Create unit tests to test knit all report templates to PDF and Word (#168, #182, #186, #187, #192)
  • Test locally via devtools::test(); files written to testthat/_snaps
  • On pull requests, test reports are written to file snapshots on GitHub Actions
• Add GitHub Actions runner to test statsrv compatibility by matching its R and pandoc versions (#172)
• Add interactive = FALSE option to interactive functions to facilitate automated unit testing (#168)
• Speed up GitHub Action that renders skeleton.Rmd (#166)
  • But then remove it entirely once superseded by more thorough test knitting (#178)

Documentation and UI Improvements

• Fix bad URL in GitHub setup instructions (#185)
• Add guidance for where to install data packages (#154)
• Add friendly error message to visc_load_pdata() when data package is not installed (#152)
• Specify existence of NAb template in README and vignettes (#189)

Package Maintenance

• Adjust filenames in R/ and tests/ to follow best practices (#175, #179)
• Respect existing getOption('repos') instead of forcing CRAN installations (#163)
• Adjust dependencies in DESCRIPTION (#164)
• Update package authors and maintainer (#190)
• Clean up latex template code, removing commented-out code and reorganizing for better readability (#196)

Release 1.2.0

Summarize changes since 1.1.0 release.

• Update Fred Hutch logo in Word and PDF templates
• Fix continuous integration issues (GitHub actions)
• New GitHub action to auto-generate empty report template in Word and PDF (for verifying format with PRs) and associated template fixes
• Fix double section numbering issue in Word doc template
• Add visc_load_pdata and DataPackageR to Rmd template code

Release 1.1.0

Improvements to use_visc_report():

• A new NAb assay template.
• This function reminds the user to use VISC's report naming convention.

Release 1.0.0

This release implements assay-specific report templates with the create_visc_report() function. See the NEWS for more info.