NEWS

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whirl 0.3.2.9001

• Added support for named list syntax to specify step names in run() (#201).

whirl 0.3.2 (2026-01-21)

• Fixed bug where warnings were given when scripts are missing a final EOL (#206).
• Fixed bug so no warning is shown when saving options to the temp folder used by whirl (#206).
• Fixed so Quarto is started with the right renv library paths when using renv (#215).
• Added new with_options argument to run(). This is the only options being set in the child sessions now. (#187).

whirl 0.3.1 (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 (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 (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

• Add use_whirl() utility function.

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.