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Add option for yaml for approved use - #302
nicholas-masel wants to merge 26 commits into
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nicholas-masel
changed the title
…s-in-yaml-file' of https://github.com/pharmaverse/logrx into 199-feature-request-list-approved-packages-and-functions-in-yaml-file
| #' | ||
| #' Default: `"block"` | ||
| #' | ||
| #' @return If `file` is NULL, a tibble with two columns (library, function) and |
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Does the user get a message saying the file was written successfully?
| #' Normalize a yaml approved list to a tibble | ||
| #' | ||
| #' Accepts keys as bare package names (e.g. `base`) or prefixed | ||
| #' (e.g. `package:base`). Values of `"all"`, `"All"`, or `"_all_"` are expanded |
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just wondering on the all option? why is that in here?
| @@ -1,3 +1,35 @@ | |||
| test_that("log_write reads approved list from yaml", { | |||
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should we have a test for a corrupted or poorly filled out yaml file?
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I second this suggestion if possible, definitely something I thought about while looking through the code is what happens if the yaml or other source can't be read
| ## Documentation | ||
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| - Updated `axecute()` documentation to correctly reflect return behavior (#288) | ||
| - Updated `axecute()` documentation to describe behaviour when a log.rx environment already exists |
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| - Updated `axecute()` documentation to describe behaviour when a log.rx environment already exists | |
| - Updated `axecute()` documentation to describe behaviour when a log.rx environment already exists (#276) |
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| - Updated `axecute()` documentation to correctly reflect return behavior (#288) | ||
| - Updated `axecute()` documentation to describe behaviour when a log.rx environment already exists | ||
| - Updated `build_approved()` documentation to reflect YAML support and new arguments |
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| - Updated `build_approved()` documentation to reflect YAML support and new arguments | |
| - Updated `build_approved()` documentation to reflect YAML support and new arguments (#199) |
bms63
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bms63
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I just had some minor questions, but looks great to me. IS this something J&J is using or requested by a user?
…nitr Co-authored-by: bms63 <10111024+bms63@users.noreply.github.com>
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@copilot how to we ignore urls with urlchecker in our link check - https://pharmar.org/white-paper/ is legit link but for some reasons is failing the checker. |
Co-authored-by: bms63 <10111024+bms63@users.noreply.github.com>
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@nicholas-masel copilot fixed the link checker |
| tidylog | ||
| tidyr | ||
| unintrusive | ||
| behaviour |
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any reason for the fun spelling of "behavior"? I don't think we'll need it in our WORDLIST if we spell it the other way
…nd-functions-in-yaml-file
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.
Please check off each taskbox as an acknowledgment that you completed the task. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the
devbranch until you have checked off each task.log_remove().devtools::document()so all.Rdfiles in themanfolder and theNAMESPACEfile 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 checklocally and address all errors and warnings -devtools::check()