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
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
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
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.