first pass at rename from timber to logrx

Author: Nathan Kosiba

.github/ISSUE_TEMPLATE/02_feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature Request
-description: Enchancement to timber functionality
+description: Enchancement to logrx functionality
 title: "Feature Request:  <Insert Issue Title Here>"
 labels: ["enhancement", "programming"]
 assignees:
@@ -8,7 +8,7 @@ body:
   - type: markdown
     attributes:
       value: |
-        Thanks for taking the time to fill out this feature request!  We love keeping timber fresh!
+        Thanks for taking the time to fill out this feature request!  We love keeping logrx fresh!
   - type: textarea
     id: feature
     attributes:

.github/ISSUE_TEMPLATE/03_doc_upates.yml

@@ -8,7 +8,7 @@ body:
   - type: markdown
     attributes:
       value: |
-        The timber team loves documentation!  Help us keep it up to date and fresh!
+        The logrx team loves documentation!  Help us keep it up to date and fresh!
   - type: dropdown
     id: browsers
     attributes:

.github/pull_request_template.md

@@ -1,16 +1,16 @@
 ### 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 timber codebase remains robust and consistent.  
+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 timber
+### 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.
 
-timber 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 timber**.
+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 `dev` branch until you have checked off each task.
 
-- [ ] The spirit of timber is met in your Pull Request
+- [ ] The spirit of logrx is met in your Pull Request
 - [ ] Code is formatted according to the [tidyverse style guide](https://style.tidyverse.org/) 
 - [ ] Updated relevant unit tests or have written new unit tests
 - [ ] Creation/updates to relevant roxygen headers and examples 

.gitignore

@@ -33,9 +33,9 @@ rsconnect/
 .Rproj.user
 inst/doc
 docs
-timber.Rcheck/
-timber*.tar.gz
-timber*.tgz
+logrx.Rcheck/
+logrx*.tar.gz
+logrx*.tgz
 
 scratch.R
 scratch.log

DESCRIPTION

@@ -1,4 +1,4 @@
-Package: timber
+Package: logrx
 Title: A Logging Utility Focus on Clinical Trial Programming Workflows
 Version: 0.1.0
 Authors@R: 
@@ -29,8 +29,8 @@ Authors@R:
     )
 Description: A utility to facilitate the logging and review of R programs in clinical trial programming workflows.
 License: MIT + file LICENSE
-URL: https://github.com/atorus-research/timber
-BugReports: https://github.com/atorus-research/timber/issues
+URL: https://github.com/atorus-research/logrx
+BugReports: https://github.com/atorus-research/logrx/issues
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -5,21 +5,21 @@ export(axecute)
 export(build_approved)
 export(get_file_path)
 export(get_log_element)
+export(get_logrx_metadata)
 export(get_masked_functions)
 export(get_session_info)
-export(get_timber_metadata)
 export(get_unapproved_use)
 export(get_used_functions)
 export(log_cleanup)
 export(log_config)
 export(log_init)
 export(log_remove)
 export(log_write)
+export(logrxAddin)
 export(loudly)
 export(run_safely_loudly)
 export(set_log_element)
 export(set_log_name_path)
-export(timberAddin)
 export(write_errors)
 export(write_file_name_path)
 export(write_log_element)

NEWS.md

@@ -1,15 +1,15 @@
-# timber 0.1.0
+# logrx 0.1.0
 
-Beta release for timber with introduction of numerous new features:
+Beta release for logrx with introduction of numerous new features:
 
 Enhancements
 - Add `to_report` param to `axecute()` to give users ability to filter out which pieces are reported
 - Add return codes when running `axecute()` to determine if there were errors
 - Improve approved packages use with new function `build_approved()` and corresponding vignette
 - Add example articles for adsl and a risk difference table
 
-# timber 0.0.1
+# logrx 0.0.1
 
-Initial alpha release of timber
+Initial alpha release of logrx
 
-See the [GitHub release tracker](https://github.com/atorus-research/timber/releases) for additional release documentation and links to issues. 
+See the [GitHub release tracker](https://github.com/atorus-research/logrx/releases) for additional release documentation and links to issues. 

R/axecute.R

@@ -1,4 +1,4 @@
-### Functions to setup and run code using timber
+### Functions to setup and run code using logrx
 
 #' Create a log and run a file
 #'

R/datasets.R

@@ -4,7 +4,7 @@
 #' A dataset that stores approved packages and functions for use.
 #' Each row contains a `library` and `function_name`.
 #' This dataset is used to illustrate the data format to be stored in
-#' the timber.approved option.
+#' the logrx.approved option.
 #'
 #' @format A tibble with 6 rows and 2 variables:
 #' \describe{
@@ -13,6 +13,6 @@
 #' }
 #'
 #' @examples
-#' timber::approved
+#' logrx::approved
 #'
 "approved"

R/get.R

@@ -1,33 +1,33 @@
 ### Functions to get data for elements of the log
 
 
-#' Returns named list of timber metadata attributes
+#' Returns named list of logrx metadata attributes
 #'
-#' @return Named list of timber package metadata attributes
+#' @return Named list of logrx package metadata attributes
 #' @export
 #'
 #' @importFrom sessioninfo session_info
 #' @importFrom dplyr filter
 #'
 #' @examples
-#' get_timber_metadata()
+#' get_logrx_metadata()
 #'
-get_timber_metadata <- function(){
+get_logrx_metadata <- function(){
 
-   timber_session_info <- session_info()$packages %>%
-      filter(.data$package == "timber")
+   logrx_session_info <- session_info()$packages %>%
+      filter(.data$package == "logrx")
 
-   timber_metadata <- list(
-      info = paste0("This log was generated using timber ",
-                    timber_session_info[['loadedversion']]),
-      version = timber_session_info[['loadedversion']],
-      built = ifelse(!is.na(timber_session_info[['source']]),
-                     timber_session_info[['source']],
+   logrx_metadata <- list(
+      info = paste0("This log was generated using logrx ",
+                    logrx_session_info[['loadedversion']]),
+      version = logrx_session_info[['loadedversion']],
+      built = ifelse(!is.na(logrx_session_info[['source']]),
+                     logrx_session_info[['source']],
                      "Build not able to be determined"),
-      repository_link = "https://github.com/atorus-research/timber"
+      repository_link = "https://github.com/atorus-research/logrx"
    )
 
-   return(timber_metadata)
+   return(logrx_metadata)
 }
 
 #' Gets full path of file being run

R/interact.R

@@ -1,43 +1,43 @@
-### Functions to interact with elements in the timber.log environment
+### Functions to interact with elements in the log.rx environment
 
-#' Adds values to existing named elements in the timber.log environment
+#' Adds values to existing named elements in the log.rx environment
 #'
-#' @param el_key the key of the element in timber.log to be updated
-#' @param el_value the value to be added to the timber.log element
+#' @param el_key the key of the element in log.rx to be updated
+#' @param el_value the value to be added to the log.rx element
 #'
 #' @return Nothing
 #' @export
 #'
 set_log_element <- function(el_key, el_value){
-   # check if key is currently in the timber.log environment
-   if (!(el_key %in% names(getOption('timber.log')))) {
-      stop("element key provided must already exist in timber.log")
+   # check if key is currently in the log.rx environment
+   if (!(el_key %in% names(getOption('log.rx')))) {
+      stop("element key provided must already exist in log.rx")
    }
 
    # check if element is currently not empty
-   if (!is.na(getOption('timber.log')[[el_key]])) {
+   if (!is.na(getOption('log.rx')[[el_key]])) {
       stop("element can not already have a value")
    }
 
    # assign element value to specified element key
-   assign(el_key, el_value, envir = getOption('timber.log'))
+   assign(el_key, el_value, envir = getOption('log.rx'))
 }
 
 
-#' Gets the value of a named element in the timber.log environment
+#' Gets the value of a named element in the log.rx environment
 #'
-#' @param el_key the key of the element in timber.log to be fetched
+#' @param el_key the key of the element in log.rx to be fetched
 #'
-#' @return Value of corresponding element from timber.log environment
+#' @return Value of corresponding element from log.rx environment
 #' @export
 #'
 get_log_element <- function(el_key){
-   if (!(el_key %in% names(getOption('timber.log')))) {
-      stop("element key provided must already exist in timber.log")
+   if (!(el_key %in% names(getOption('log.rx')))) {
+      stop("element key provided must already exist in log.rx")
    }
 
    # assign element value to specified element key
-   el_value <- getOption('timber.log')[[el_key]]
+   el_value <- getOption('log.rx')[[el_key]]
 
    # return value to user
    return(el_value)
@@ -47,7 +47,7 @@ get_log_element <- function(el_key){
 #' Set the log name and path:
 #' 1. As the name and path if specified
 #' 2. As the file name and path if specified
-#' 3. As timber_log.log and . if none of the above are specified
+#' 3. As logrx_log.log and . if none of the above are specified
 #'
 #' @param log_name The log name
 #' @param log_path The log path
@@ -74,7 +74,7 @@ set_log_name_path <- function(log_name = NA, log_path = NA) {
                                 x = file_name,
                                 perl = TRUE))
          } else {
-            set_log_element("log_name", "timber_log.log")
+            set_log_element("log_name", "logrx_log.log")
          }
       }
    }