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Changelog

Source: NEWS.md

whirl 0.3.1

CRAN release: 2025-08-25

  • Improved error handling when the log cannot be created.
  • Added new option environment_secrets to control which secret environment variables not to include in the log.
  • Improved progress bar of run() to show all currently running scripts.
  • Removed verbosity_level argument to run() since it is now completely controlled by zephyr options (see help("whirl-options")).
  • Fixed bug where a script would not execute if using options(warn = 2) (#151)
  • The log now distinguishes between directly and indirectly used packages, and visually highlights their approval status if a list of approved packages is provided.
  • Added check for approved Python packages with the approved_python_packages option similar to for R.
  • Improved how to find used Python packages, so it now only lists the packages actually used in the script.

whirl 0.3.0

CRAN release: 2025-07-08

  • Add write_biocompute() to create BioCompute Objects containing the logs in a standardized JSON format.
  • Calling run() with track_files = TRUE now checks if strace can be attached to the process.
  • Improved json logs and similar returned output from running a script (result column in return from run()).
  • Simplified approved packages check. Now the user supplies a character vector of packages and versions specified as {package}@{version}.
  • Implement use of tag in the returned output. Each script is now tagged with the step name in the summary report.

whirl 0.2.0

CRAN release: 2025-04-15

  • Initial CRAN release.
  • Default input argument of run() set to “_whirl.yml”.
  • Added RStudio addins for running all scripts and the active script.
  • Fix typo in track_files_discards option.
  • Increases unit test coverage and skips run() tests etc. when Quarto is not available.

whirl 0.1.7

  • Enable redirection of logs through the log_dir argument in run().
  • Changed the title on the individual logs to the script name and moved the path to a distinct section within the title-block.
  • Fixed a bug where the hyperlink in the summary files was not rendered correctly.
  • Fixed a bug where the installed python packages were not listed in the log.
  • Enable the use of R expressions in the yaml configuration file.
  • Enables the user to define the working directory for each script with the execute_dir option.

whirl 0.1.6

  • Added support for logging of Python scripts with run().
  • Improved unit tests for run().
  • Fixing a bug where the queue was not returned correctly in some instances.
  • Switched to using Sys.glob() instead of utils::glob2rx().

whirl 0.1.4

whirl 0.1.3

  • Adding additional arguments to run() allowing the user to:
    • control the verbosity level
    • specify whether renv should be checked
    • specify which files to track
    • adjust the output format of the log files.

whirl 0.1.1

  • Fix enabling rendering of md log formats(“gfm”, “commonmark”, “markua”).

whirl 0.1.0

  • First version publicly available on GitHub.

whirl 0.0.5

  • Updated documentation
  • README and vignettes are now ready for users.

whirl 0.0.4

  • Adjusting run() to unify execution of scripts, lists of scripts, and configuration files.
  • Using multiple independent callr::r_session when executing several scripts.
  • Cleanup of namespace and exported functions.

whirl 0.0.3

  • Initial version of run().
  • Substituting spinner with progress bar when executing single scripts.

whirl 0.0.2

  • Update so that the execution (including order of execution) can be controlled through a config file.

whirl 0.0.1

  • First version of package.