Changes in version 0.3.2.9001                      

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

                 Changes in version 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).

                 Changes in version 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.

                 Changes in version 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.

                 Changes in version 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.

                        Changes in version 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.

                        Changes in version 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().

                        Changes in version 0.1.4                        

  - Add use_whirl() utility function.

                        Changes in version 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.

                        Changes in version 0.1.1                        

  - Fix enabling rendering of md log formats("gfm", "commonmark",
    "markua").

                        Changes in version 0.1.0                        

  - First version publicly available on GitHub.

                        Changes in version 0.0.5                        

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

                        Changes in version 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.

                        Changes in version 0.0.3                        

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

                        Changes in version 0.0.2                        

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

                        Changes in version 0.0.1                        

  - First version of package.