Merge pull request #21 from TanguyBarthelemy/master

Update readme and styler package

.github/workflows/R-CMD-check.yaml

@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ 'ubuntu-latest', 'windows-latest', 'macOS-latest' ]
-        r: [ 'devel', 'release', 'oldrel-1', '4.2.1', '4.1.1', '4.1.3', '3.6.1' ]
+        r: [ 'devel', 'release', 'oldrel-1', '4.2.3', '4.2.1', '4.1.1', '4.1.3', '4.0.5', '3.6.1' ]
         java: [ '8', '13', '17', '19' ]
         # java: [ '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19' ]
         include:
@@ -33,7 +33,7 @@ jobs:
           # - {os: ubuntu-latest,   r: '3.6.1'}
           # - {os: ubuntu-latest,   r: '4.1.3'}
           # - {os: ubuntu-latest,   r: '4.1.1'}
-          # - {os: ubuntu-latest,   r: '4.2.1'}      
+          # - {os: ubuntu-latest,   r: '4.2.1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -43,7 +43,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
-            
+
       - name: Setup java (x64)
         uses: actions/setup-java@v3
         if: matrix.java != '19'
@@ -52,7 +52,7 @@ jobs:
           java-package: jdk
           distribution: 'zulu'
           architecture: x64
-          
+
       - name: Setup java (x64)
         uses: actions/setup-java@v3
         if: matrix.java == '19'
@@ -61,7 +61,7 @@ jobs:
           java-package: jdk
           distribution: 'temurin'
           architecture: x64
-        
+
       - name: Setup java (x86)
         uses: actions/setup-java@v3
         if: runner.os == 'windows' && matrix.java != '19'
@@ -70,7 +70,7 @@ jobs:
           java-package: jdk
           distribution: 'zulu'
           architecture: x86
-          
+
       - name: Setup java (x86)
         uses: actions/setup-java@v3
         if: runner.os == 'windows' && matrix.java == '19'
@@ -79,14 +79,14 @@ jobs:
           java-package: jdk
           distribution: 'temurin'
           architecture: x86
-      
+
       - name: Set up R
         uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.r }}
           http-user-agent: ${{ matrix.http-user-agent }}
           use-public-rspm: true
-      
+
       # Pour macos, qqs installation supplémentaires
       - name: "[Stage] [macOS] Install libgit2"
         if: runner.os == 'macOS'
@@ -95,7 +95,7 @@ jobs:
       - name: "[Stage] [macOS] Install system libs for pkgdown"
         if: runner.os == 'macOS'
         run: brew install harfbuzz fribidi
-        
+
       - name: Configure java pour macos
         if: runner.os == 'macOS'
         run: R CMD javareconf
@@ -105,27 +105,26 @@ jobs:
         if: ${{ runner.os != 'macOS' }}
         with:
           extra-packages: any::rcmdcheck, XML
-      
+
       # Pour macos, qqs installation supplémentaires
       - name: Install dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
         if: ${{ runner.os == 'macOS' }}
         with:
           packages: knitr, kableExtra, rmarkdown
           extra-packages: any::rcmdcheck, XML, XLConnect
-        
+
       # Pour macos, qqs installation supplémentaires
       - name: Build site
         run: install.packages('textshaping')
         shell: Rscript {0}
         if: ${{ runner.os == 'macOS' && matrix.r == 'devel' }}
-
-      # Pour macos, qqs installation supplémentaires
+
       - name: Build site
         run: install.packages('systemfonts')
         shell: Rscript {0}
         if: ${{ runner.os == 'macOS' && matrix.r == '3.6.1' }}
-        
+
       - uses: r-lib/actions/setup-tinytex@v2
-        
+
       - uses: r-lib/actions/check-r-package@v2

.github/workflows/lint.yaml

@@ -0,0 +1,32 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: lint
+
+jobs:
+  lint:
+    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:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.lintr

@@ -0,0 +1,8 @@
+linters: linters_with_defaults( 
+        object_name_linter = NULL, 
+        cyclocomp_linter = NULL, 
+        line_length_linter = NULL,
+        commented_code_linter = NULL, 
+        indentation_linter(indent = 4L)
+    )
+encoding: "UTF-8"

JDCruncheR.Rproj

@@ -2,7 +2,7 @@ Version: 1.0
 
 RestoreWorkspace: No
 SaveWorkspace: No
-AlwaysSaveHistory: Default
+AlwaysSaveHistory: No
 
 EnableCodeIndexing: Yes
 UseSpacesForTab: Yes
@@ -19,3 +19,5 @@ BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
 PackageRoxygenize: rd,collate,namespace
+
+UseNativePipeOperator: Yes

NEWS.md

@@ -1,5 +1,12 @@
 % Latest JDCruncheR news
 
+# JDCruncheR development
+
+ * Update readme
+ * resolve a bug
+
+---
+
 # JDCruncheR 0.2.4
 
  * The functions' help pages as well as the package vignettes are now available both in French and English.

R/Cruncher.R

@@ -32,50 +32,60 @@ NULL
 cruncher <- function(workspace = workspace,
                      cruncher_bin_directory = getOption("cruncher_bin_directory"),
                      param_file_path, log_file) {
-    if (missing(workspace) || is.null(workspace))
+    if (missing(workspace) || is.null(workspace)) {
         stop("Please call the cruncher() on a valid workspace")
+    }
 
-    if (length(workspace) == 0)
+    if (length(workspace) == 0) {
         stop("The first argument must be a non-null workspace path")
+    }
 
-    if (length(workspace) > 1)
+    if (length(workspace) > 1) {
         stop("Please specify only one workspace path")
+    }
 
     # The path to the workspace must be "whole", not relative/from the setwd.
     workspace <- normalizePath(workspace, mustWork = FALSE)
     workspace <- sub("\\.xml$", "", workspace) # To remove the .xml from the workspace name, if needed
 
     if (missing(param_file_path) || is.null(param_file_path)) {
-        param_file_path <- list.files(path = workspace,
-                                      recursive = TRUE,
-                                      pattern = "\\.params$",
-                                      full.names = TRUE)
-        if (length(param_file_path) != 0)
+        param_file_path <- list.files(
+            path = workspace,
+            recursive = TRUE,
+            pattern = "\\.params$",
+            full.names = TRUE
+        )
+        if (length(param_file_path) != 0) {
             stop("No or more than one .param file was found")
+        }
     }
     workspace <- paste0(workspace, ".xml")
 
-    if (!file.exists(paste0(cruncher_bin_directory, "/jwsacruncher")))
+    if (!file.exists(paste0(cruncher_bin_directory, "/jwsacruncher"))) {
         stop("There is an error in the path to the cruncher bin folder")
-    if (!file.exists(workspace))
+    }
+    if (!file.exists(workspace)) {
         stop("There is an error in the path to the workspace")
-    if (!file.exists(param_file_path))
+    }
+    if (!file.exists(param_file_path)) {
         stop("There is an error in the path to the .params file")
+    }
 
     wd <- getwd()
     setwd(cruncher_bin_directory)
 
     log <- shell(paste0(
-        "jwsacruncher \""
-        , workspace
-        , "\" -x \""
-        , param_file_path, "\""
+        "jwsacruncher \"",
+        workspace,
+        "\" -x \"",
+        param_file_path, "\""
     ), intern = TRUE)
 
     setwd(wd)
 
-    if (!missing(log_file) && !is.null(log_file))
+    if (!missing(log_file) && !is.null(log_file)) {
         writeLines(text = log, con = log_file)
+    }
 
     return(invisible(workspace))
 }
@@ -131,45 +141,47 @@ cruncher_and_param <- function(workspace = workspace,
                                delete_existing_file = NULL,
                                log_file = NULL,
                                ...) {
-
     dossier_temp <- tempdir()
     fichier_param <- create_param_file(dossier_temp, output = output, ...)
-    workspace <- cruncher(workspace = workspace, cruncher_bin_directory = cruncher_bin_directory,
-                          param_file_path = fichier_param, log_file = log_file)
+    workspace <- cruncher(
+        workspace = workspace, cruncher_bin_directory = cruncher_bin_directory,
+        param_file_path = fichier_param, log_file = log_file
+    )
 
     if (rename_multi_documents) {
-        if (is.null(output))
+        if (is.null(output)) {
             output <- paste0(sub("\\.xml", "", workspace), "\\Output")
+        }
 
         noms_multi_documents <- multiprocessing_names(workspace)
-        if (nrow(noms_multi_documents) == 0)
+        if (nrow(noms_multi_documents) == 0) {
             stop("There is no multiprocessing in the workspace!")
+        }
         noms_multi_documents$name <- paste0(output, "\\", noms_multi_documents$name)
         noms_multi_documents$file <- paste0(output, "\\", noms_multi_documents$file)
         noms_multi_documents <- noms_multi_documents[noms_multi_documents$name != noms_multi_documents$file, ]
 
         if (any(file.exists(noms_multi_documents$name))) {
-
             if (is.null(delete_existing_file)) {
                 message <- paste("There is already at least one file in ", output, ".\nDo you want to clear the output folder?")
-                delete_existing_file <- utils::winDialog(type = c("yesnocancel"),
-                                                         message)
+                delete_existing_file <- utils::winDialog(
+                    type = c("yesnocancel"),
+                    message
+                )
 
                 delete_existing_file <- isTRUE(delete_existing_file == "YES")
-
             }
             if (delete_existing_file) {
                 unlink(noms_multi_documents$name[file.exists(noms_multi_documents$name)],
-                       recursive = TRUE)
+                    recursive = TRUE
+                )
                 file.rename(from = noms_multi_documents$file, to = noms_multi_documents$name)
             } else {
                 warning("There were pre-existing files in the output folder: none were removed or renamed.")
             }
-
         } else {
             file.rename(from = noms_multi_documents$file, to = noms_multi_documents$name)
         }
-
     }
 
     return(invisible(workspace))
@@ -205,22 +217,26 @@ multiprocessing_names <- function(workspace) {
         stop("Please call multiprocessing_names() on a valid workspace")
     }
 
-    if (length(workspace) == 0)
+    if (length(workspace) == 0) {
         stop("The first argument must be a non-null workspace path")
+    }
 
-    if (length(workspace) > 1)
+    if (length(workspace) > 1) {
         stop("Please specify only one workspace path")
+    }
 
     workspace <- normalizePath(workspace, mustWork = FALSE)
     workspace <- paste0(sub("\\.xml$", "", workspace), ".xml")
 
-    if (!file.exists(workspace))
+    if (!file.exists(workspace)) {
         stop("The workspace doesn't exist")
+    }
 
     xml_workspace <- suppressWarnings(XML::xmlParse(workspace, error = function(...) {}))
     noms_objets <- XML::xmlToDataFrame(nodes = XML::getNodeSet(
         doc = xml_workspace,
-        path = "//ns2:demetraGenericWorkspace/ns2:items/ns2:item"))
+        path = "//ns2:demetraGenericWorkspace/ns2:items/ns2:item"
+    ))
     noms_multi_documents <- noms_objets[grep("multi-documents", noms_objets$family), ]
     noms_multi_documents <- noms_multi_documents[, c("name", "file")]
 
@@ -288,12 +304,15 @@ NULL
 update_workspace <- function(workspace = workspace,
                              policy = "parameters",
                              cruncher_bin_directory = getOption("cruncher_bin_directory")) {
-
     dossier_temp <- tempdir()
-    fichier_param <- create_param_file(dossier_temp, output = dossier_temp, policy = policy,
-                                       matrix_item = NULL, tsmatrix_series = NULL)
-    workspace <- cruncher(workspace = workspace, cruncher_bin_directory = cruncher_bin_directory,
-                          param_file_path = fichier_param)
+    fichier_param <- create_param_file(dossier_temp,
+        output = dossier_temp, policy = policy,
+        matrix_item = NULL, tsmatrix_series = NULL
+    )
+    workspace <- cruncher(
+        workspace = workspace, cruncher_bin_directory = cruncher_bin_directory,
+        param_file_path = fichier_param
+    )
 
     return(invisible(workspace))
 }