Merge pull request #216 from pharmaverse/dev

logrx v0.3.0

.github/workflows/check-standard.yaml

@@ -23,9 +23,8 @@ jobs:
       matrix:
         config:
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: '3.5', repos: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: '3.6', repos: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: '4.1', repos: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: '4.2', repos: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 

.github/workflows/spellcheck.yaml

@@ -0,0 +1,33 @@
+---
+name: Spellcheck
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+
+jobs:
+  spell:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          needs: spelling
+
+      - name: Run Spelling Check test
+        uses: insightsengineering/r-spellcheck-action@v3
+        with:
+          exclude: data/*

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: logrx
 Title: A Logging Utility Focus on Clinical Trial Programming Workflows
-Version: 0.2.2
+Version: 0.3.0
 Authors@R: 
     c(
     person(given = "Nathan",
@@ -23,6 +23,10 @@ Authors@R:
            family = "Masel",
            email = "nmasel@its.jnj.com",
            role = "aut"),
+    person(given = "Sam",
+           family = "Parmar",
+           email = "samir.parmar@pfizer.com",
+           role = "aut"),
     person(given = "GSK/Atorus JPT",
            role = c("cph", "fnd"))
     )
@@ -50,7 +54,8 @@ Imports:
     waiter,
     tibble,
     digest,
-    lintr
+    lifecycle,
+    methods
 Suggests: 
     testthat (>= 3.0.0),
     knitr,
@@ -60,8 +65,12 @@ Suggests:
     pkgdown,
     Tplyr,
     haven,
-    here
+    lintr,
+    xml2,
+    here,
+    readr,
+    tidyselect
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 Depends: 
-    R (>= 3.5.0)
+    R (>= 4.0.0)

NAMESPACE

@@ -6,6 +6,7 @@ export(log_config)
 export(log_init)
 export(log_remove)
 export(log_write)
+export(read_log_file)
 export(write_log_header)
 export(write_unapproved_functions)
 export(write_used_functions)
@@ -15,9 +16,9 @@ importFrom(dplyr,distinct)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,mutate)
+importFrom(dplyr,rename_with)
 importFrom(dplyr,select)
 importFrom(dplyr,ungroup)
-importFrom(lintr,lint)
 importFrom(magrittr,"%>%")
 importFrom(miniUI,gadgetTitleBar)
 importFrom(miniUI,miniContentPanel)
@@ -51,14 +52,20 @@ importFrom(shiny,uiOutput)
 importFrom(stats,aggregate)
 importFrom(stringi,stri_wrap)
 importFrom(stringr,str_c)
+importFrom(stringr,str_count)
+importFrom(stringr,str_detect)
+importFrom(stringr,str_extract)
+importFrom(stringr,str_remove)
 importFrom(stringr,str_remove_all)
 importFrom(stringr,str_replace)
 importFrom(stringr,str_replace_all)
 importFrom(stringr,str_starts)
+importFrom(stringr,str_trim)
 importFrom(tibble,tibble)
 importFrom(tidyr,all_of)
 importFrom(tidyr,complete)
 importFrom(tidyr,pivot_wider)
+importFrom(tidyr,separate)
 importFrom(utils,capture.output)
 importFrom(utils,getParseData)
 importFrom(utils,lsf.str)

NEWS.md

@@ -1,3 +1,16 @@
+
+# logrx 0.3.0
+
+- Moved website theme to bootstrap 5, enabled search (#179)
+- Add `show_repo_url` option in `axecute()` to capture repo URL(s) into log file (#167)
+- Moved website theme to Bootstrap 5, enabled search (#179)
+- Add `include_rds` argument to `axecute()` to export log as rds file
+- Add `read_log_file()` to read logrx log file as optional function
+- Add `library_call_linter()` to ensure all library calls are at the top of the script (#163)
+- Remove argument for remove_log_object from `axecute()` still accessible via `log_write()` (#182)
+- Added functionality so `axecute()` works with `.Rmd` files (#140)
+- R Version switched from `>3.5` to `>4.0` in `DESCRIPTION` file (#198)
+
 # logrx 0.2.2
 
  - Hotfix to remove unnecessary `across()` and update `.data$var` top new syntax to match updates in source packages (#172)

R/axecute.R

@@ -8,15 +8,18 @@
 #' @param file String. Path to file to execute
 #' @param log_name String. Name of log file
 #' @param log_path String. Path to log file
-#' @param remove_log_object Boolean. Should the log object be removed after
-#' writing the log file? Defaults to TRUE
+#' @param include_rds Boolean. Option to export log object as Rds file.
+#' Defaults to FALSE
 #' @param quit_on_error Boolean. Should the session quit with status 1 on error?
 #' Defaults to TRUE
 #' @param to_report String vector. Objects to optionally report, may include as
 #' many as necessary:
 #' * messages: any messages generated by program execution
 #' * output: any output generated by program execution
 #' * result: any result generated by program execution
+#' @param show_repo_url Boolean. Should the repository URLs be reported
+#' Defaults to FALSE
+#' @param ... Not used
 #'
 #' @importFrom purrr map_chr
 #'
@@ -31,13 +34,29 @@
 #' close(fileConn)
 #'
 #' axecute(file.path(dir, "hello.R"))
+#'
+#'
+#' fileConn <- file(file.path(dir, "hello.Rmd"))
+#' writeLines(text, fileConn)
+#' close(fileConn)
+#'
+#' axecute(file.path(dir, "hello.Rmd"))
 axecute <- function(file, log_name = NA,
                     log_path = NA,
-                    remove_log_object = TRUE,
+                    include_rds = FALSE,
                     quit_on_error = TRUE,
-                    to_report = c("messages", "output", "result")){
+                    to_report = c("messages", "output", "result"),
+                    show_repo_url = FALSE,
+                    ...){
+   # deprecations
+   if (methods::hasArg(remove_log_object)) {
+      lifecycle::deprecate_stop("0.3.0", "axecute(remove_log_object = )", "axecute(include_rds = )")
+   }
+
+   # remove log object
+   remove_log_object <- TRUE
 
-   # lower everything for consistency and check values
+  # lower everything for consistency and check values
    to_report <- map_chr(to_report, tolower)
    match.arg(to_report, several.ok = TRUE)
 
@@ -51,7 +70,11 @@ axecute <- function(file, log_name = NA,
    any_errors <- get_log_element("errors")
 
    # write log
-   log_write(file = file, remove_log_object = remove_log_object, to_report = to_report)
+   log_write(file = file,
+             remove_log_object = remove_log_object,
+             show_repo_url = show_repo_url,
+             include_rds = include_rds,
+             to_report = to_report)
 
    # if error, quit with status = 1 if not interactive
    if(!interactive() & !is.null(any_errors) & quit_on_error) {

R/get.R

@@ -96,7 +96,7 @@ get_file_path <- function(file = NA, normalize = TRUE){
 #' @noRd
 #'
 get_session_info <- function(){
-   return(capture.output(session_info(info = "all")))
+   return(session_info(info = "all"))
 }
 
 
@@ -155,6 +155,16 @@ get_masked_functions <- function(){
 #'
 get_used_functions <- function(file){
 
+   # if markdown, write R code, including inline, to a script
+   # use this script to find functions used
+   if (grepl("*.Rmd$", file, ignore.case = TRUE)){
+      tmpfile <- tempfile(fileext = ".R")
+      on.exit(unlink(tmpfile))
+      withr::local_options(list(knitr.purl.inline = TRUE))
+      knitr::purl(file, tmpfile)
+      file <- tmpfile
+   }
+
    # catch error
    retfun <- safely(parse,
                     quiet = FALSE,
@@ -191,14 +201,24 @@ get_used_functions <- function(file){
                               names_from = "token") %>%
       ungroup()
 
-   combine_tokens <- wide_tokens %>%
+   # if package is present, but symbol or special is not, a function did not follow the ::
+   # ex. knitr::opts_chunk$set()
+   # for this case, remove row that contains the package
+   # set will still be captured but we will be able to link it to a package in this current version
+   wide_tokens_wo_orphans <- wide_tokens[!(!is.na(wide_tokens$SYMBOL_PACKAGE) & is.na(wide_tokens$SYMBOL_FUNCTION_CALL) & is.na(wide_tokens$SPECIAL)),]
+
+   combine_tokens <- wide_tokens_wo_orphans %>%
       mutate(function_name = coalesce(.data[["SYMBOL_FUNCTION_CALL"]],
                                       .data[["SPECIAL"]]))
 
-   get_library(combine_tokens) %>%
+   distinct_use <- get_library(combine_tokens) %>%
       select(all_of(c("function_name", "library"))) %>%
       distinct()
 
+   distinct_use[is.na(distinct_use)] <- "!!! NOT FOUND !!!"
+
+   distinct_use
+
 }
 
 
@@ -278,15 +298,33 @@ get_unapproved_use <- function(approved_packages, used_packages) {
 #'
 #' @param file File path of file being run
 #'
-#' @importFrom lintr lint
-#'
 #' @return results from `lintr::lint()`
 #'
 #' @noRd
 #'
 get_lint_results <- function(file) {
+
+   if (!requireNamespace("lintr", quietly = TRUE)) {
+      message(strwrap("Linting will not be included in the log. Install the
+         lintr package to use the log.rx.lint feature.",
+         prefix = " ", initial = ""))
+      return()
+   }
+
    # lint file if option is turned on
    if (!is.logical(getOption('log.rx.lint'))) {
-      lint(file, getOption('log.rx.lint'))
+      lintr::lint(file, getOption('log.rx.lint'))
    }
 }
+
+#' Get repository URLs
+#'
+#' Obtain repository URLs possibly used to install packages in session
+#'
+#' @return results from `getOption("repos")` as list
+#'
+#' @noRd
+#'
+get_repo_urls <- function() {
+   as.list(getOption("repos"))
+}

R/globals.R

@@ -0,0 +1,5 @@
+globalVariables(c(
+   "lang",
+   "r_version",
+   "."
+))

R/interact.R

@@ -110,6 +110,13 @@ set_log_name_path <- function(log_name = NA, log_path = NA) {
 #' @noRd
 run_safely <- function(file) "dummy"
 
+#' Is this a R Markdown file
+#' @param file String. Path to file to execute
+#' @noRd
+is_rmarkdown <- function(file) {
+   grepl("*.Rmd$", file, ignore.case = TRUE)
+}
+
 #' Dummy function for running a file
 #' @noRd
 run_file <- function(file){
@@ -118,7 +125,13 @@ run_file <- function(file){
    } else{
       exec_env <- getOption("log.rx.exec.env")
    }
-   source(file, local = exec_env)
+
+   if(is_rmarkdown(file)){
+      rmarkdown::render(file, envir = exec_env)
+   } else{
+      source(file, local = exec_env)
+   }
+
 }
 
 #' Safely run an R script and record results, outputs, messages, errors, warnings
@@ -139,7 +152,7 @@ run_safely_loudly <- function(file) {
    set_log_element("result", ret$result$result)
    set_log_element("warnings", ret$warnings)
    set_log_element("errors", ret$result$error)
-   set_log_element("hash_sum", digest::sha1(readLines(file)))
+   set_log_element("hash_sum", digest::sha1(readLines(file, warn = FALSE)))
 
    # Session Info
    set_log_element("session_info", get_session_info())