simplify qc summary

NEWS.md

@@ -2,7 +2,7 @@
 
 ## New features and changes
 
-- `renderQCReport` Render a QC Report Document. (#135)
+- `renderQCReport` render a QC report document. (#135)
 
 - `logRemove` added to package to assist with removing files from the QC log. (#105)
 

R/findAuthorsQcers.R

@@ -3,14 +3,14 @@ findAuthorsQcers <- function(.repoHistory, .qcLog) {
 
   qclog <- 
     .qcLog %>% 
-    dplyr::transmute(file, rev = as.character(revf), reviewer) %>% 
+    dplyr::transmute(file, rev = as.integer(revf), reviewer) %>% 
     dplyr::filter(rev != "0") %>% 
     dplyr::distinct()
 
   rH_qclog <-
     .repoHistory %>%
     dplyr::left_join(qclog, by = c("file", "rev")) %>%
-    dplyr::arrange(file, -as.numeric(rev)) %>% 
+    dplyr::arrange(file, -rev) %>% 
     dplyr::group_by(file) %>% 
     tidyr::fill(reviewer, .direction = "down") %>%
     dplyr::ungroup()

R/renderQCReport.R

@@ -20,12 +20,6 @@
 #' @export
 renderQCReport <- function(.output_dir = NULL) {
 
-  reportRes <- list()
-
-  reportRes$project <- basename(logRoot())
-
-  reportRes$logSum <- logSummary()
-
   if (is.null(.output_dir)) {
     .output_dir <- tempdir()
   } else {
@@ -37,10 +31,15 @@ renderQCReport <- function(.output_dir = NULL) {
   output_file <- paste0("qc-report-", Sys.Date(), ".pdf")
   output_path <- file.path(.output_dir, output_file)
 
+  params_in <- list(
+    project = basename(logRoot()),
+    logSum = logSummary()
+  )
+
   rmarkdown::render(
     input = system.file("templates", "QCReport.Rmd", package = "review"),
     output_file = output_path,
-    params = list(reportRes = reportRes),
+    params = params_in,
     envir = new.env(),
     quiet = TRUE
   )

R/renderQCSummary.R

@@ -5,8 +5,6 @@
 #' 
 #' The QC status of all scripts checked into SVN by each author will be displayed, 
 #' along with a high level summary of all scripts that need to be QCed.
-#' 
-#' @param .dirs_exclude Character string (optional). Vector of directories to exclude in the summary (relative to log root).
 #'
 #' @param .output_dir Character string (optional). Path to the directory where the output PDF 
 #'   should be saved. If not provided, the document will not be saved locally.
@@ -23,9 +21,7 @@
 #' }
 #'
 #' @export
-renderQCSummary <- function(.dirs_exclude = NULL, .output_dir = NULL) {
-
-  dirSummaryRes <- dirSummary(.dirs_exclude = .dirs_exclude)
+renderQCSummary <- function(.output_dir = NULL) {
 
   if (is.null(.output_dir)) {
     .output_dir <- tempdir()
@@ -38,10 +34,17 @@ renderQCSummary <- function(.dirs_exclude = NULL, .output_dir = NULL) {
   output_file <- paste0("qc-summary-", Sys.Date(), ".pdf")
   output_path <- file.path(.output_dir, output_file)
 
+  params_in <- list(
+    project = basename(logRoot()),
+    repoHistory = repoHistory(),
+    qcLog = logRead(),
+    logPending = logPending()
+  )
+
   rmarkdown::render(
     input = system.file("templates", "QCSummary.Rmd", package = "review"),
     output_file = output_path,
-    params = list(dirSummaryRes = dirSummaryRes),
+    params = params_in,
     envir = new.env(),
     quiet = TRUE
   )

R/repoHistory.R

@@ -27,7 +27,8 @@ repoHistory <- function() {
     ) %>% 
     dplyr::mutate(
       date = as.Date(date),
-      file = sub('.', '', file) # Remove first character
+      file = sub('.', '', file),
+      rev = as.integer(rev)
     )
 
 }

inst/templates/QCReport.Rmd

@@ -1,9 +1,10 @@
 ---
-params: 
-  reportRes: "`r list()`"
 title: "QC Report"
-subtitle: "`r params$reportRes$project`"
+subtitle: "`r params$project`"
 date: "`r format(Sys.time(), '%d %B, %Y %H:%M %Z')`"
+params:
+  project: ""
+  logSum: NULL
 output: pdf_document
 header-includes:
     - \usepackage{caption}
@@ -15,9 +16,7 @@ knitr::opts_chunk$set(echo = FALSE)
 
 ```{r message=FALSE, warning=FALSE}
 
-log_summary_data <- params$reportRes$logSum
-
-log_summary_data %>% 
+params$logSum %>% 
   dplyr::select(file, revf, headf, time) %>% 
   dplyr::mutate(
     Status = dplyr::case_when(
@@ -31,10 +30,11 @@ log_summary_data %>%
   dplyr::rename(
     File = file,
     `QCed...revision` = revf,
-    `Last modified...revision` = headf,
+    `Last...revision` = headf,
   ) %>% 
+  dplyr::arrange(Status, as.numeric(`QCed...revision`)) %>% 
   pmtables::st_new() %>% 
-  pmtables::st_left(File = pmtables::col_ragged(5)) %>% 
+  pmtables::st_left(File = pmtables::col_ragged(8)) %>% 
   pmtables::stable_long() %>%
   pmtables::st_asis()
 ```

inst/templates/QCSummary.Rmd

@@ -1,15 +1,18 @@
 ---
-params: 
-  dirSummaryRes: "`r list()`"
 title: "QC Summary"
-subtitle: "`r params$dirSummaryRes$project`"
+subtitle: "`r params$project`"
 date: "`r format(Sys.time(), '%d %B, %Y %H:%M %Z')`"
+params:
+  project: ""
+  repoHistory: NULL
+  qcLog: NULL
+  logPending: NULL
 output:
   pdf_document:
-    toc: true
-    toc_depth: 3
+  toc: true
+toc_depth: 3
 header-includes:
-    - \usepackage{caption}
+  - \usepackage{caption}
 ---
 
 \captionsetup[table]{labelformat=empty}
@@ -18,116 +21,120 @@ header-includes:
 knitr::opts_chunk$set(echo = FALSE)
 ```
 
-```{r, include=FALSE}
-dir_summary_data <- params$dirSummaryRes$data
-
-qc_status <- params$dirSummaryRes$status
-
-```
-
-\newpage
-
-# Summaries
-
-\newpage
-
-## QC Pending
+# QC Pending
 
 ```{r, results='asis'}
 
-needs_qc <-
-  qc_status %>% 
-  dplyr::filter(Status == "In QC log, needs QC") %>% 
-  dplyr::select(-Status)
-
-if (nrow(needs_qc) == 0) {
-  needs_qc <- dplyr::tibble(Author = "None", File = "None")
-}
+latest_authors <-
+  params$repoHistory %>% 
+  dplyr::group_by(file) %>%
+  dplyr::filter(rev == max(rev)) %>% 
+  dplyr::ungroup() %>% 
+  dplyr::select(file, author)
+
+needs_qc <- params$qcLog %>% dplyr::filter(file %in% params$logPending$file)
+
+needs_qc <- 
+  if (nrow(needs_qc) == 0) {
+    dplyr::tibble(File = "No outstanding QC")
+  } else {
+    needs_qc %>% 
+      dplyr::group_by(file) %>%
+      dplyr::summarize(
+        `Previous QCers` = paste(unique(reviewer), collapse = ", ")
+      ) %>% 
+      dplyr::ungroup() %>% 
+      dplyr::mutate(
+        `Previous QCers` = gsub("anyone, ", "", `Previous QCers`, fixed = TRUE),
+        `Previous QCers` = ifelse(`Previous QCers` == "anyone", "none", `Previous QCers`)
+      ) %>% 
+      dplyr::left_join(latest_authors, by = "file") %>% 
+      dplyr::select(
+        File = file,
+        `Last author` = author,
+        `Previous QCers`
+      )
+  }
 
 needs_qc %>%   
   pmtables::st_new() %>% 
-  pmtables::st_clear_reps("Author") %>%
-  pmtables::st_bold(cols = "Author") %>% 
+  pmtables::st_left(`Previous QCers` = pmtables::col_ragged(4)) %>%
+  pmtables::st_left(File = pmtables::col_ragged(10)) %>%
   pmtables::stable_long() %>%
   pmtables::st_asis()
 
 ```
 
 \newpage
 
-## QC Up to Date
+# Files Not in QC Log
 
 ```{r, results='asis'}
 
-qc_up_to_date <-
-  qc_status %>% 
-  dplyr::filter(Status == "QC up to date") %>% 
-  dplyr::select(-Status)
-
-if (nrow(qc_up_to_date) == 0) {
-  qc_up_to_date <- dplyr::tibble(Author = "None", File = "None")
+at_risk_days <- 20
+
+relevant_dirs <-
+  c(
+    "script"
+  )
+
+relevant_file_types <-
+  c(
+    "R",
+    "Rmd",
+    "yaml",
+    "yml",
+    "ctl",
+    "cpp",
+    "cp",
+    "mod",
+    "stan",
+    "jl",
+    "qmd"
+  )
+
+not_in_log <-
+  params$repoHistory %>% 
+  dplyr::group_by(file) %>% 
+  dplyr::filter(rev == max(rev)) %>% 
+  dplyr::ungroup() %>% 
+  dplyr::mutate(
+    top_dir = sapply(fs::path_split(file), function(x) x[1]),
+    `Last edit` = date,
+    `Days Since...Last Edit` = as.numeric(Sys.Date() - `Last edit`)
+  ) %>% 
+  dplyr::filter(
+    tools::file_ext(file) %in% relevant_file_types,
+    top_dir %in% relevant_dirs,
+    !(file %in% params$qcLog$file)
+  ) %>%
+  dplyr::filter(`Days Since...Last Edit` <= at_risk_days) %>%
+  dplyr::select(
+    File = file, 
+    `Last Author` = author, 
+    `Days Since...Last Edit`
+  ) %>%
+  dplyr::arrange(`Days Since...Last Edit`) %>% 
+  dplyr::distinct()
+
+if (nrow(not_in_log) == 0) {
+  not_in_log <- 
+    dplyr::tibble(
+      File = paste0(
+        "No files that are not in the QC log were modified within the last ",
+        at_risk_days, 
+        " days"
+      )
+    )
 }
 
-qc_up_to_date %>%   
+
+not_in_log %>%   
   pmtables::st_new() %>% 
-  pmtables::st_clear_reps("Author") %>%
-  pmtables::st_bold(cols = "Author") %>% 
-  pmtables::stable_long() %>%
+  pmtables::st_left(File = pmtables::col_ragged(10)) %>%
+  pmtables::stable_long(
+    lt_cap_text = "*Files in this table have been edited within the last (20) days"
+  ) %>%
   pmtables::st_asis()
 
 ```
-
-\newpage
-
-# Contributors
-
-
-\newpage
-
-```{r, results='asis'}
-authors <- 
-  dir_summary_data %>%
-  dplyr::filter(Directory != ".") %>%
-  dplyr::distinct(Author) %>%
-  dplyr::pull(Author)
-
-for (author.i in authors) {
-
-  writeLines(paste0("## ", author.i))
-
-  directories.i <-
-    dir_summary_data %>% 
-    dplyr::filter(Directory != ".") %>%
-    dplyr::filter(Author == author.i) %>% 
-    dplyr::distinct(Directory) %>%
-    dplyr::pull(Directory)
-
-  if (length(directories.i) == 0) {
-    next
-  }
-
-  for (directory.i in directories.i) {
-
-    writeLines(paste0("### ", directory.i))
-
-    tab.i <-
-      dir_summary_data %>%
-      dplyr::filter(Author == author.i) %>%
-      dplyr::filter(Directory == directory.i) %>%
-      dplyr::select(File, `Latest edit`, QCer, Status) %>%
-      dplyr::arrange(Status) %>%
-      pmtables::st_new() %>%
-      pmtables::st_panel("Status") %>%
-      pmtables::stable_long()
-
-    pmtables::st_wrap(tab.i)
-
-    rm(tab.i)
-
-    writeLines("\n")
-    writeLines("\\newpage")
-  }
-
-}
-
-```