Merge pull request #259 from Crunch-io/siunitx

Siunitx

Author: 1beb

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/check-standard.yaml

@@ -0,0 +1,92 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Install tinytex
+        run: |
+          tinytex::install_tinytex()
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--no-build-vignettes", "--no-tests"), build_args = c("--no-build-vignettes", "--ignore-vignettes", "--no-manual"), error_on = "error", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Coverage
+        run: |
+          Rscript -e 'covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")'
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: results
+          path: check

.github/workflows/ci.yml

@@ -6,7 +6,7 @@ Description: In order to generate custom survey reports, this package provides
     'banners' (cross-tabulations) and codebooks of datasets in the Crunch
     (<https://crunch.io/>) web service. Reports can be written in 'PDF' format
     using 'LaTeX' or in Microsoft Excel '.xlsx' files.
-Version: 1.4.1
+Version: 1.4.2
 Authors@R: c(
     person("Persephone", "Tsebelis", role="aut"),
     person("Kamil", "Sedrowicz", role="aut"),
@@ -20,15 +20,18 @@ Depends:
     crunch,
 Imports:
     digest,
+    dplyr,
     httr,
     jsonlite,
     kableExtra (>= 1.1.0.9000),
     magrittr,
     methods,
     openxlsx,
     rlang,
+    stringi,
     tinytex
 Suggests:
+    arrow,
     covr,
     knitr,
     mockery, 

.github/workflows/internal_tests.yml

@@ -106,7 +106,10 @@ importFrom(stats,median)
 importFrom(stats,pnorm)
 importFrom(stats,quantile)
 importFrom(stats,weighted.mean)
+importFrom(utils,capture.output)
+importFrom(utils,head)
 importFrom(utils,installed.packages)
 importFrom(utils,modifyList)
 importFrom(utils,stack)
+importFrom(utils,tail)
 importFrom(utils,type.convert)

DESCRIPTION

@@ -1,6 +1,7 @@
 ## crunchtabs 1.4.2
 
 - INNOV-326 writeCodeBookLatex should not open by default. Add function argument open = FALSE. This avoids a situation in non-interactive sessions where the process would otherwise be stuck as it attempts to open a GTK program from a bash session. 
+- Small change in how appendices are automatically identified. Previous iterations prepared long tables with the longtabu package. However, this tex package overwrote numeric presentation options from siunitx. This has been changed to longtable, which respects siunitx. Now appendix long tables are identified by the length of lines in their tex (20 or more).
 
 ## crunchtabs 1.4.1
 

NAMESPACE

@@ -34,6 +34,7 @@
 #' @param logging Leave logs in the working directory, defaults to FALSE
 #' @param filename A string. The desired basename of the resulting file with no extension
 #' (i.e, "mycodebook")
+#' @param open Should the resulting PDF be opened? Defaults to FALSE
 #' @param ... Additional arguments passed to \link[kableExtra]{kable_styling} Unused.
 #' @md
 #'
@@ -42,7 +43,7 @@ writeCodeBookLatexGeneric <- function(
   table_of_contents = FALSE, sample_desc = NULL, field_period = NULL,
   preamble = NULL, suppress_zero_counts = FALSE, appendix = TRUE,
   logo = NULL, position = NULL, path = NULL, filename = NULL,
-  logging = FALSE, ...) {
+  logging = FALSE, open = FALSE, ...) {
 
   options("crunchtabs.codebook.suppress.zeros" = suppress_zero_counts)
 
@@ -118,7 +119,7 @@ writeCodeBookLatexGeneric <- function(
     body <- codeBookItemBody(x, meta = meta[meta$alias == nm,], ...) # A kable
 
     if (appendix & !is.list(body)) {
-      if (grepl("longtabu", body)) {
+      if (length(capture.output(body)) > 20) {
         appendices[[nm]] <- list()
 
         description <- codeBookItemTxtDescriptionGeneral(x, nm, meta)
@@ -266,6 +267,7 @@ writeCodeBookLatexGeneric <- function(
 #' @param x An R vector
 #' @param nm The alias of the current codeBookItem
 #' @param meta A specifically formatted data.frame with meta data.
+#' @param ... Further arguments, not used.
 #'
 #' @export
 codeBookItemTxtHeaderGeneral <- function(x, nm, meta, ...) {
@@ -372,3 +374,28 @@ codeBookItemTxtDescriptionGeneral <- function(x, nm, meta, ...) {
 
   tex
 }
+
+#' Get class name from arrow variable
+#'
+#' Arrow does not provide a method for class on it's variables. This function prints out
+#' the schema and captures the appropriate output.
+#'
+#' @param ds An arrow dataset
+#' @param variable A string identifying the variable
+get_class <- function(ds, variable) {
+  # nocov start
+  r <- utils::capture.output(ds$schema[[variable]])
+  r <- r[2]
+  r <- gsub(variable, "", r)
+  r <- gsub(": ", "", r)
+
+  if (r %in% c("string"))
+    return("character")
+  if (r %in% c("int32"))
+    return("integer")
+  if (r %in% c("float", "double"))
+    return("numeric")
+  if (grepl("dictionary", r))
+    return("factor")
+  # nocov end
+}

NEWS.md

@@ -3,6 +3,7 @@
 #' Create codebook item body.
 #'
 #' @param x A crunch dataset object
+#' @param meta A data.frame containing meta data. Must be provided for non-crunch datasets.
 #' @param ... Further arguments, not used.
 #' @export
 codeBookItemBody <- function(x, meta = NULL, ...) {
@@ -76,14 +77,25 @@ codeBookItemBody.CategoricalVariable <- function(x, meta = NULL, ...) { # nolint
     midrule_strip <- function(x) gsub("\\midrule", "", x, fixed = TRUE)
 
     alignment <- c("d", "l", "d", "c", "d", "l", "d")
-    names(k) <- curlyWrap(names(k))
+    # names(k) <- curlyWrap(names(k)) # al
+    # kableExtra::kable(
+    #   k, "latex",
+    #   booktabs = TRUE, align = scolumnAlign(k, alignment),
+    #   longtable = TRUE, linesep = "", escape = FALSE
+    # ) %>%
+    #   kable_styling_defaults(full_width = TRUE, ...) %>%
+    #   kableExtra::column_spec(c(2, 6), width = "1.75in", latex_column_spec = NULL) %>%
+    #   kableExtra::row_spec(
+    #     0,
+    #     extra_latex_after = "\\cmidrule(l){1-3}\\cmidrule(l){5-7}" # nolint
+    #   ) %>%
+    #   midrule_strip()
+
     kableExtra::kable(
       k, "latex",
-      booktabs = TRUE, align = scolumnAlign(k, alignment),
-      longtable = TRUE, linesep = "", escape = FALSE
+      booktabs = TRUE, longtable = TRUE, align = scolumnAlign(k, alignment),
+      linesep = "", escape = FALSE
     ) %>%
-      kable_styling_defaults(full_width = TRUE, ...) %>%
-      kableExtra::column_spec(c(2, 6), width = "1.75in", latex_column_spec = NULL) %>%
       kableExtra::row_spec(
         0,
         extra_latex_after = "\\cmidrule(l){1-3}\\cmidrule(l){5-7}" # nolint
@@ -92,7 +104,8 @@ codeBookItemBody.CategoricalVariable <- function(x, meta = NULL, ...) { # nolint
   } else {
     alignment <- c("d", "l", "d")
     names(k) <- curlyWrap(names(k))
-    kab <- kableExtra::kable(
+
+  kab <- kableExtra::kable(
       k, "latex",
       booktabs = TRUE, longtable = TRUE, align = scolumnAlign(k, alignment),
       linesep = "", escape = FALSE

R/codeBookGeneric.R

@@ -210,7 +210,7 @@ scolumnAlign <- function(k, alignment) {
       if (maxnchar > 6) {
         alignment[i] <- sprintf("S[table-format=%s]", maxnchar)
       } else {
-        alignment[i] <- c("J", "K", "d", "M", "N", "O")[maxnchar]
+        alignment[i] <- c("J", "K", "d", "M", "N", "O", "L", "M", "N")[maxnchar]
       }
     }
   }