Merge pull request #89 from dfe-analytical-services/renv-update

Renv update

.Rprofile

@@ -1,26 +1,40 @@
-source("renv/activate.R")
+# ---------------------------------------------------------
+# This is the .Rprofile file
+#
+# Use it to include any functions you want to run before any other code is run.
+# For example, using renv automatically sources its activate script to the .RProfile file
+# This ensures that all renv checks on package versions happens before any code is run.
+#
+#
+# ---------------------------------------------------------
 
-shhh <- suppressPackageStartupMessages # It's a library, so shhh!
+cat("Sourcing .Rprofile.", fill = TRUE)
 
+source("renv/activate.R")
 
-tidy_code <- function() {
-  shhh(source("global.r"))
-  shhh(tidy_code_function())
+if (system.file(package = "dfeshiny") != "") {
+  library(dfeshiny)
+} else {
+  warning("dfeshiny package is not installed, please run renv::restore() to set up the necessary package environment")
 }
 
+# Function to run tests
 run_tests_locally <- function() {
   Sys.unsetenv("http_proxy")
   Sys.unsetenv("https_proxy")
-  shhh(source("global.R"))
+  source("global.r")
   # message("================================================================================")
   # message("== testthat ====================================================================")
   # message("")
-  # shhh(testthat::test_dir("tests/testthat"))
+  # testthat::test_dir("tests/testthat")
   # message("")
   message("================================================================================")
-  message("== shinytest ===================================================================")
+  message("== shinytest2 ==================================================================")
   message("")
-  shhh(shinytest::testApp())
+  shinytest2::test_app()
   message("")
   message("================================================================================")
 }
+
+# Install commit-hooks locally
+statusWriteCommit <- file.copy(".hooks/pre-commit.R", ".git/hooks/pre-commit", overwrite = TRUE)

.github/workflows/shiny-tests.yaml

@@ -10,7 +10,7 @@ jobs:
   automatedTests:
     runs-on: ${{ matrix.config.os }}
 
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    name: shiny-tests
 
     strategy:
       fail-fast: false
@@ -29,7 +29,6 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: ${{matrix.config.r}}
           use-public-rspm: true
 
       - name: Cache R packages
@@ -53,21 +52,6 @@ jobs:
         run: |
           if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
           renv::restore()
-      - name: Find PhantomJS path
-        id: phantomjs
-        run: |
-          echo "::set-output name=path::$(Rscript -e 'cat(shinytest:::phantom_paths()[[1]])')"
-      - name: Cache PhantomJS
-        uses: actions/cache@v1
-        with:
-          path: ${{ steps.phantomjs.outputs.path }}
-          key: ${{ runner.os }}-phantomjs
-          restore-keys: ${{ runner.os }}-phantomjs
-      - name: Install PhantomJS
-        shell: Rscript {0}
-        run: |
-          options(install.packages.check.source = "no")
-          if (!shinytest::dependenciesInstalled()) shinytest::installDependencies()
       - name: Run tests
         shell: Rscript {0}
         run: |

.hooks/pre-commit.R

@@ -0,0 +1,82 @@
+#!/usr/bin/env Rscript
+cat("Running commit hooks...",fill=TRUE)
+shhh <- suppressPackageStartupMessages # It's a library, so shhh!
+shhh(library(dplyr))
+shhh(library(xfun))
+shhh(library(dfeshiny))
+
+error_flag <- FALSE
+
+datalog <- "datafiles_log.csv"
+log_files <- read.csv(datalog, stringsAsFactors = FALSE)
+ign_files <- read.csv(".gitignore", header = FALSE, stringsAsFactors = FALSE)
+colnames(ign_files)[1] <- "filename"
+
+cat("Contents of the .gitignore file:")
+print(ign_files)
+
+# Run a pass through the .gitignore files and look for any issues
+if(ncol(ign_files)>1){
+  cat("ERROR: It looks like you've got commas in the .gitignore. Please correct the .gitignore file and try again.")
+  error_flag <- TRUE
+} else {
+  for(i in 1:nrow(ign_files)){
+    if(grepl(' ',ign_files$filename[i])){
+      cat("ERROR: It looks like you've got spaces in filenames in the .gitignore. Please rename your files if they contain spaces and update the .gitignore file accordingly.")
+      error_flag <- TRUE
+    }
+  }
+}
+
+suffixes <- "xlsx$|dat$|csv$|tex$|pdf$"
+
+current_files <- data.frame(files = list.files("./", recursive = TRUE)) %>%
+  filter(grepl(suffixes, files), !grepl("renv|datafiles_log.csv", files))
+
+for (file in current_files$files) {
+  if (!file %in% log_files$filename) {
+    cat("Error:", file, "is not recorded in datafiles_log.csv.\n\n")
+    cat("Please add an entry to datafiles_log.csv for this file and mark it as unpublished, published or reference.\n\n")
+    error_flag <- TRUE
+  } else {
+    file_status <- (log_files %>% filter(filename == file))$status
+    if (!file_status %in% c("published", "Published", "reference", "Reference", "dummy", "Dummy")) {
+      if (!file %in% ign_files$filename & !grepl("unpublished",file)) {
+        cat("Error:", file, "is not logged as published or reference data in datafiles_log.csv and is not found in .gitignore.\n\n")
+        cat("If the file contains published or reference data then update its entry in datafiles_log.csv.\n\n")
+        cat("If the file contains unpublished data then add it to the .gitignore file.\n\n")
+        error_flag <- TRUE
+      }
+      else {
+        cat(file,"is recorded in the logfile as unpublished data and in .gitignore and so will not be included as part of the commit.\n\n")
+      }
+    }
+  }
+}
+
+if(grepl('G-Z967JJVQQX', htmltools::includeHTML(("google-analytics.html"))) & 
+   !(toupper(Sys.getenv("USERNAME")) %in% c("CFOSTER4", "CRACE", "LSELBY","RBIELBY", "JMACHIN"))){
+  cat("Cleaning out the template's Google Analytics tag.",fill=TRUE)
+  gsub_file("google-analytics.html", pattern = "G-Z967JJVQQX", replacement = "G-XXXXXXXXXX")
+  gsub_file("ui.R", pattern = "Z967JJVQQX", replacement = "XXXXXXXXXX")
+  system2(command = "git", args=c("add","google-analytics.html"))
+}
+
+if (error_flag) {
+  cat("Warning, aborting commit. Unrecognised data files found, please update .gitignore or datafiles_log.csv.\n")
+  quit(save = "no", status = 1, runLast = FALSE)
+}
+
+tidy_output <- tidy_code()
+if(any(tidy_output)){
+  error_flag <- TRUE
+}
+
+if (error_flag) {
+  cat("Warning: Code did not appear to have been tidied.\nI've run tidy code for you,
+      please check your files and the dashboard still works and then re-stage and try committing again.")
+  quit(save = "no", status = 1, runLast = FALSE)
+}
+
+
+# End of hooks

datafiles_log.csv

@@ -0,0 +1,12 @@
+filename,status
+data/regional_data_FD_PG.csv,published
+data/regional_movement_FD_PG.csv,published
+data/sankey data 1-3YAG_FD_PG.csv,published
+data/sankey data 1-5YAG_FD_PG.csv,published
+data/sankey data 3-5YAG_FD_PG.csv,published
+data/tables_data_3digit_FD_PG.csv,published
+data/boundaries/Regions__December_2019__Boundaries_EN_BFE.cpg,published
+data/boundaries/Regions__December_2019__Boundaries_EN_BFE.dbf,published
+data/boundaries/Regions__December_2019__Boundaries_EN_BFE.prj,published
+data/boundaries/Regions__December_2019__Boundaries_EN_BFE.shp,published
+data/boundaries/Regions__December_2019__Boundaries_EN_BFE.shx,published

global.R

@@ -32,6 +32,7 @@ shhh(library(networkD3))
 shhh(library(styler))
 shhh(library(shinyGovstyle))
 shhh(library(shinyjs))
+shhh(library(dfeshiny))
 # shhh(library(shinya11y))
 
 # update years for text