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Add argument for log_write to export log object as Rds #164
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@parmsam-pfizer thanks so much for putting this in, definitely hoping to get this through review this week and into dev branch then we can see what else we might want to look into including in another release. |
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Everything looks good. I did add a few comments for discussion. @thomasp-b @kodesiba @bms63 @parmsam-pfizer Would love to hear your thoughts on:
- Should we export everything into the rds or subset?
- Should we just store the session_info object, rather than capture it's output and store, and let write function capture the output and write it out nicely?
R/log.R
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} | ||
} | ||
) | ||
cleaned_log_list$session_info <- session_info(info = "all") |
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I think you have to do this because we capture the output of session_info and store it, rather than just storing the session info object. I think we can move the capture output to the write function so this will still print pretty, and then you won't need to get the session info again.
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Good idea. Adjusted and updated the unit test.
"unapproved_packages_functions", "errors", "warnings" | ||
) | ||
log_options <- as.list(getOption('log.rx')) | ||
cleaned_log_list <- purrr::map2( |
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I haven't 100% convinced myself, but I'm wondering if we would just return everything to the rds rather than NULL out sections. Those writing the log and those consuming these rds files might be different people with different use cases.
The ability to subset what you want in the rds output sounds interesting. I don't want to clutter up Is J&J interested in this as well or is this just Pfizer folks?
I'm not sure? What are pros and cons? We talked of meeting in June and doing another release in the Summer. Are we trying to get this out before that Summer release? |
NEWS.md
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# logrx 0.2.2 | ||
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- Add `include_rds` argument to `axecute()` to export log as rds file |
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we need to upversion to 0.3.0
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@parmsam-pfizer can you update NEWS to include this under 0.3.0 and resolve the merge conflict
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Done. Thanks!
Thank you for your Pull Request!
We have developed a Pull Request template to aid you and our reviewers. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the logrx codebase remains robust and consistent.
The spirit of logrx
While many packages to facilitate the logging of code already exist in the R ecosystem, it is hard to find a solution that works well for clinical programming applications. Many logging implementations are more implicit and rely on user input to create the log for the execution of a script. While this is useful for logging specific events of an application, in clinical programming a log has a set purpose.
logrx is built around the concept of creating a log for the execution of an R script that provides an overview of what happened as well as the environment that it happened in. We set out to create a flexible logging utility that could provide the necessary information to anyone reviewing the code execution so they can recreate the execution environment and run the code for themselves. Please make sure your Pull Request meets this spirit of logrx.
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.devtools::document()
so all.Rd
files in theman
folder and theNAMESPACE
file in the project root are updated appropriatelypkgdown::build_site()
and check that all affected examples are displayed correctly and that all new functions occur on the "Reference" page.R CMD check
locally and address all errors and warnings -devtools::check()
Adds optional argument (FALSE by default) to export log object into Rds format that users can more easily subset/filter. Addresses the second part of #162.