Added problem set template and bibliography statistics helpers

.Rbuildignore

@@ -13,3 +13,4 @@
 ^pkgdown$
 ^cran-comments\.md$
 ^CRAN-RELEASE$
+^\.github$

.github/.gitignore

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

.github/workflows/prchecks.yml

@@ -61,6 +61,8 @@ jobs:
           remotes::install_github("crsh/citr")
           remotes::install_github("gadenbuie/xaringanExtra")
           remotes::install_github("giocomai/ganttrify")
+          utils::install.packages("roxygen2")
+          utils::install.packages("covr")
         shell: Rscript {0}
 
       - name: Document
@@ -76,3 +78,4 @@ jobs:
 
       - name: Calculate code coverage
         run: Rscript -e "covr::codecov()"
+        if: runner.os == 'macOS'

.github/workflows/pushrelease.yml

@@ -127,6 +127,13 @@ jobs:
         with:
           name: SyllabusExample
           path: Untitled/
+
+      - name: Save problem set sample as artifact
+        if: runner.os == 'macOS'
+        uses: actions/upload-artifact@v2
+        with:
+          name: ProblemSetExample
+          path: UntitledPS/
 
       - name: Remove Thesis project
         if: runner.os == 'macOS'
@@ -140,6 +147,10 @@ jobs:
         if: runner.os == 'macOS'
         run: Rscript -e 'unlink("Untitled", recursive = TRUE)'
 
+      - name: Remove problem set project
+        if: runner.os == 'macOS'
+        run: Rscript -e 'unlink("UntitledPS", recursive = TRUE)'
+
       - name: Calculate code coverage
         run: Rscript -e "covr::codecov()"
 
@@ -203,6 +214,17 @@ jobs:
           asset_name: IHEIDSyllabusExample.pdf
           asset_content_type: application/pdf
 
+      - name: Upload problem set Example Asset
+        id: upload-PS-example
+        uses: actions/upload-release-asset@v1.0.2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }}
+          asset_path: ProblemSetExample/IHEIDProblemSetExample.pdf
+          asset_name: IHEIDProblemSetExample.pdf
+          asset_content_type: application/pdf
+
       - name: Rename Mac release
         run: mv ./macOS/*.tgz iheiddown_macOS.tgz
 
@@ -258,7 +280,7 @@ jobs:
       # install packages needed
       - name: install required packages
         run: Rscript -e 'install.packages(c("rmarkdown"))'
-        
+
       # Render README.md using rmarkdown
       - name: render README
         run: Rscript -e 'rmarkdown::render("README.Rmd", output_format = "md_document")'
@@ -277,6 +299,8 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
+        with:
+          persist-credentials: false # add for deployment to work correctly
 
       - uses: r-lib/actions/setup-r@v1
 
@@ -305,9 +329,13 @@ jobs:
       - name: Install package
         run: R CMD INSTALL .
 
-      - name: Deploy package
-        run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Build site # build pkgdown site in separate step
+        run: Rscript -e 'pkgdown::build_site()'
 
+      - name: Deploy # deploy the docs folder to gh-pages
+        uses: JamesIves/github-pages-deploy-action@3.7.1
+        with:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          BRANCH: gh-pages
+          FOLDER: docs
+          CLEAN: true

DESCRIPTION

@@ -3,14 +3,16 @@ Title: For Writing Graduate Institute Geneva Documents
 Description: A set of tools to support writing various documents
     according to the Graduate Institute of International and Development Studies 
     conventions and regulations.
-    The most common use will be for writing and compiling theses or thesis chapters,
-    as drafts or for examination with all the correct preamble content.
-    However, the package also offers the creation of html presentation slides via 'xaringan',
-    and, for course instructors, also the ability to create a syllabus as a PDF.
+    The most common use will be for writing and compiling theses or thesis
+    chapters, as drafts or for examination with all the correct preamble
+    content. However, the package also offers the creation of html presentation
+    slides via 'xaringan', the capacity to write problem sets and, for course
+    instructors, the ability to create syllabi.
     The package includes additional functions for institutional color palettes
-    and an institutional 'ggplot' theme, as well as a function for word counts.
-Date: 2021-06-24
-Version: 0.8.2
+    and an institutional 'ggplot' theme, as well as a function for word counts
+    and a bibliographical analysis toolkit.
+Date: 2021-08-20
+Version: 0.8.3
 Authors@R: 
     c(person(given = "James",
            family = "Hollway",
@@ -30,10 +32,7 @@ License: MIT + file LICENSE
 Imports: 
     bookdown,
     dplyr,
-    roxygen2,
-    covr,
     ggplot2,
-    magrittr,
     rmarkdown,
     xaringan,
     crayon,
@@ -42,7 +41,14 @@ Imports:
     readr,
     rstudioapi,
     tibble,
-    tidytext
+    tidytext,
+    bib2df,
+    purrr,
+    stringr,
+    fs,
+    usethis,
+    gender,
+    remotes
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -5,18 +5,30 @@ export(advdate)
 export(bookdown_profile)
 export(chapter_pdf)
 export(count_words)
+export(fix_bib)
+export(get_used_bib)
 export(iheid_palette)
 export(iheid_palettes)
+export(mean_pages)
+export(mean_year)
+export(percent_female)
 export(preview_start)
 export(preview_stop)
+export(problemset_pdf)
 export(syllabus_pdf)
 export(theme_iheid)
 export(thesis_pdf)
+export(total_pages)
 import(crayon)
 import(dplyr)
+importFrom(bib2df,bib2df)
+importFrom(bib2df,df2bib)
 importFrom(bookdown,pdf_book)
 importFrom(bookdown,preview_chapter)
 importFrom(bookdown,render_book)
+importFrom(dplyr,filter)
+importFrom(dplyr,mutate)
+importFrom(fs,path_dir)
 importFrom(ggplot2,element_blank)
 importFrom(ggplot2,element_line)
 importFrom(ggplot2,element_rect)
@@ -28,13 +40,23 @@ importFrom(graphics,image)
 importFrom(graphics,par)
 importFrom(graphics,rect)
 importFrom(graphics,text)
+importFrom(purrr,map)
 importFrom(readr,read_lines)
 importFrom(rlang,.data)
 importFrom(rmarkdown,pdf_document)
 importFrom(rstudioapi,getSourceEditorContext)
 importFrom(servr,daemon_list)
 importFrom(servr,daemon_stop)
+importFrom(stats,na.omit)
+importFrom(stringr,fixed)
+importFrom(stringr,str_detect)
+importFrom(stringr,str_remove)
+importFrom(stringr,str_replace)
+importFrom(stringr,str_replace_all)
+importFrom(stringr,str_split)
 importFrom(tibble,as_tibble)
 importFrom(tidytext,unnest_tokens)
+importFrom(usethis,ui_info)
 importFrom(utils,file.edit)
+importFrom(utils,install.packages)
 importFrom(xaringan,inf_mr)

NEWS.md

@@ -1,3 +1,17 @@
+# iheiddown 0.8.3
+
+## Problem set template
+- Closed #94 by adding a problem set template to `{iheiddown}`
+
+## Thesis
+- Closed #76 by adding an option for line numbering for thesis output when the draft option is set to true
+
+## Package
+- Fixed #90 by solving the remaining issues of the package website deployment workflow
+- Closed #91 by removing unnecessary package dependencies following CRAN notes
+- Closed #93 by adding bibliography statistics family of functions
+
+
 # iheiddown 0.8.2
 
 - This release attends to the changes requested by CRAN:

R/_render.R

@@ -15,15 +15,16 @@ iheiddown::thesis_pdf("index.Rmd")
 #Come back to the original WD and copy the output while also renaming it
 setwd("..")
 date <- Sys.Date()
-name <- paste0("Thesis_Name_", date,".pdf")
+name <- paste0("Thesis_Name_", date, ".pdf")
 target_path <- "00-Example/versions"
-file.rename(file.path(target_path, name), file.path(target_path, "IHEIDThesisExample.pdf"))
+file.rename(file.path(target_path, name), file.path(target_path,
+                                                    "IHEIDThesisExample.pdf"))
 
 ############
 # Syllabus
 ############
 
-# Automatic rendering of thesis_pdf will run on a Windows VM
+# Automatic rendering of syllabus_pdf will run on a Windows VM
 #Step 1 Create an example project
 rmarkdown::draft(file = "Untitled", template = "Syllabus",
                  package = "iheiddown", create_dir = TRUE, edit = FALSE)
@@ -33,9 +34,29 @@ iheiddown::syllabus_pdf("Untitled.Rmd")
 #Come back to the original WD and copy the output while also renaming it
 setwd("..")
 date <- Sys.Date()
-name <- paste0("MINT001_Syllabus_", date,".pdf")
+name <- paste0("MINT001_Syllabus_", date, ".pdf")
 target_path <- "Untitled"
-file.rename(file.path(target_path, name), file.path(target_path, "IHEIDSyllabusExample.pdf"))
+file.rename(file.path(target_path, name), file.path(target_path,
+                                                    "IHEIDSyllabusExample.pdf"))
+
+##############
+# Problem Set
+##############
+
+# Automatic rendering of problemset_pdf will run on a Windows VM
+#Step 1 Create an example project
+rmarkdown::draft(file = "UntitledPS", template = "Problem_Set",
+                 package = "iheiddown", create_dir = TRUE, edit = FALSE)
+setwd("UntitledPS") # Since we can only knit from the WD
+#Step 2 render the example project and replace in template folder
+iheiddown::problemset_pdf("UntitledPS.Rmd")
+#Come back to the original WD and copy the output while also renaming it
+setwd("..")
+date <- Sys.Date()
+name <- paste0("MINT001_ProblemSet_", date, ".pdf")
+target_path <- "UntitledPS"
+file.rename(file.path(target_path, name),
+            file.path(target_path, "IHEIDProblemSetExample.pdf"))
 
 ############
 # Presentation
@@ -59,13 +80,18 @@ setwd("..")
 target_dir <- "docs/sample_output"
 dir.create(target_dir)
 # Thesis
-file.copy("00-Example/versions/IHEIDThesisExample.pdf", target_dir, overwrite = TRUE)
+file.copy("00-Example/versions/IHEIDThesisExample.pdf",
+          target_dir,
+          overwrite = TRUE)
 # Syllabus
 file.copy("Untitled/IHEIDSyllabusExample.pdf", target_dir, overwrite = TRUE)
+# Problem Set
+file.copy("UntitledPS/IHEIDProblemSetExample.pdf", target_dir, overwrite = TRUE)
 # Presentation
 file.copy("index/index.html", target_dir, overwrite = TRUE)
 file.copy("index/index_cache", target_dir, recursive = TRUE, overwrite = TRUE)
 file.copy("index/index_files", target_dir, recursive = TRUE, overwrite = TRUE)
 file.copy("index/assets", target_dir, recursive = TRUE, overwrite = TRUE)
 
-# Note, the directories generated will be erased further down the GitHub workflow
+# Note, the directories generated will be erased further down the GitHub
+# workflow

R/bibfix.R

@@ -0,0 +1,56 @@
+#' @rdname bibstats
+#' @importFrom stringr str_replace_all str_replace fixed
+#' @importFrom bib2df bib2df df2bib
+#' @importFrom purrr map
+#' @export
+fix_bib <- function(bib_file) {
+  if (missing(bib_file)) bib_file <- find_bib()
+  bib <- suppressMessages(bib2df::bib2df(bib_file))
+  bib$PAGES <- stringr::str_replace_all(bib$PAGES,
+                                        stringr::fixed("{\\textendash}"), "--")
+  bib$AUTHOR <- purrr::map(bib$AUTHOR, function(x) {
+    x <- stringr::str_replace(x, "^", "{")
+    x <- stringr::str_replace(x, "\\{\\{", "{")
+    x <- stringr::str_replace(x, "$", "}")
+    x <- stringr::str_replace(x, "\\}\\}", "}")
+  })
+  bib$EDITOR <- purrr::map(bib$EDITOR, function(x) {
+    x <- stringr::str_replace(x, "^", "{")
+    x <- stringr::str_replace(x, "\\{\\{", "{")
+    x <- stringr::str_replace(x, "$", "}")
+    x <- stringr::str_replace(x, "\\}\\}", "}")
+  })
+  bib2df::df2bib(bib, bib_file)
+}
+
+#' @rdname bibstats
+#' @importFrom readr read_lines
+#' @importFrom tibble as_tibble
+#' @importFrom dplyr mutate filter
+#' @importFrom stringr str_remove
+#' @export
+get_used_bib <- function(bib_file, rmd_file) {
+  if (missing(bib_file)) bib_file <- find_bib()
+  if (missing(rmd_file)) rmd_file <- rstudioapi::getSourceEditorContext()$path
+  bib <- suppressMessages(bib2df::bib2df(bib_file))
+  current_bibs <- readr::read_lines(rmd_file) %>%
+    tibble::as_tibble() %>%
+    remove_front_matter() %>%
+    remove_code_chunks() %>%
+    remove_inline_code() %>%
+    remove_html_comment() %>%
+    remove_bullets() %>%
+    get_biblines() %>%
+    dplyr::mutate(value = stringr::str_remove(.data$value, "@")) %>%
+    select(.data$value) %>%
+    as.vector()
+  current_bibs$value
+}
+
+remove_bullets <- function(x) {
+  dplyr::mutate(x, value = stringr::str_remove(.data$value, "^-[:space:]+"))
+}
+
+get_biblines <- function(x) {
+  dplyr::filter(x, grepl("@", .data$value))
+}