.Rbuildignore

@@ -2,12 +2,15 @@
 ^\.Rproj\.user$
 ^\.travis\.yml$
 ^Dockerfile$
+^appveyor\.yml$
 ^NEWS\.md$
 ^uw_thesis_rmd\.png$
 ^README\.md$
-^LICENSE$
+^LICENSE\.md$
 ^CONDUCT\.md$
 ^CONTRIBUTING\.md$
 ^\.Rhistory$
+^\.gitattributes$
+^\.gitignore$
 ^index$
-^LICENSE\.md$
+^fonts\.zip$

.gitattributes

@@ -0,0 +1,4 @@
+* text=auto
+data/* binary
+src/* text=lf
+R/* text=lf

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,27 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Your system (please complete the following information):**
+ - Paste in your output of `sessionInfo()`

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.travis.yml

@@ -6,12 +6,6 @@ matrix:
       sudo: required
       language: generic
       services: docker
-    - os: osx
-      language: r
-      cache: packages
-      pandoc_version: 1.17.2
-
-
 
 env:
  global:
@@ -20,24 +14,14 @@ env:
 warnings_are_errors:  false
 
 before_install:
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew tap caskroom/fonts  ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew cask install font-eb-garamond font-source-code-pro font-lato  ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr update --self  ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then sudo tlmgr install biblatex titling titlesec quotchap lettrine appendix units tocloft draftwatermark everypage wasysym logreq xstring collection-fontsrecommended texliveonfly   ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then R -e 'install.packages("devtools")'  ; fi
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then docker build -t $REPO . ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then R -e "devtools::install_github('benmarwick/huskydown')" ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then R -e "unlink('index', recursive = TRUE)" ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then R -e "rmarkdown::draft('index.Rmd', template = 'thesis', package = 'huskydown', create_dir = TRUE, edit = FALSE)"  ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then R -e "setwd('index'); bookdown::render_book('index.Rmd', huskydown::thesis_pdf(latex_engine = 'xelatex'))"  ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then R -e "file.exists('index/_book/thesis.pdf')"  ; fi
-  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then R -e "file.info('index/_book/thesis.pdf')"  ; fi
+
 
 
 # push our custom docker container to docker hub, env vars stored on travis-ci.org
 # don't forget to set these at https://travis-ci.org/.../...settings
 after_success:
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then docker login -e $DOCKER_EMAIL -u $DOCKER_USER -p $DOCKER_PASS ; fi
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then docker login  -u $DOCKER_USER -p $DOCKER_PASS ; fi
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then export REPO=$DOCKER_USER/huskydown ; fi
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then export TAG=`if [ "$TRAVIS_BRANCH" == "master" ]; then echo "latest"; else echo $TRAVIS_BRANCH ; fi`  ; fi
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then docker build -f Dockerfile -t $REPO:$COMMIT . ; fi

DESCRIPTION

@@ -1,24 +1,30 @@
 Package: huskydown
-Title: A R Markdown thesis template for the University of Washingtone
-Version: 0.0.4
+Title: An R Markdown thesis template for the University of Washington
+Version: 0.0.5
 Authors@R: c(
-    person("Chester", "Ismay", email = "chester.ismay@gmail.com", role = "cre"),
+    person("Chester", "Ismay", email = "chester.ismay@gmail.com", role = "aut"),
     person("Nick", "Solomon", email = "nick@nicksolomon.me", role = "aut"),
-    person("Ben", "Marwick", email = "benmarwick@gmail.com", role = "aut"))
+    person("Ben", "Marwick", email = "benmarwick@gmail.com", role = c("cre", "aut")))
 Description: Using the bookdown package and LaTeX and Word thesis templates from
     UW, this package aims to encourage reproducible research using
     simple Markdown syntax while embedding all of the R code to produce plots
     and analyses as well. Based on Chester Ismay's thesisdown.
-Maintainer: Ben Marwick <bmarwick@uw.edu>
+Maintainer: Ben Marwick <benmarwick@gmail.com>
 Depends:
-    R (>= 3.2.0),
-    devtools,
-    dplyr,
-    ggplot2,
+    R (>= 3.4.4)
+Imports:
     bookdown,
+    rmarkdown,
     knitr,
-    git2r
+    git2r,
+    tinytex,
+    devtools,
+    dplyr,
+    ggplot2
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.0.1
-License: MIT + file LICENSE
+RoxygenNote: 7.1.1
+SystemRequirements: pandoc (>= 1.18) - http://pandoc.org
+Suggests: 
+    testthat

Dockerfile

@@ -1,29 +1,24 @@
-# get the base image, the rocker/verse has R, RStudio and pandoc
-FROM rocker/verse:3.4.4
+# get the base image
+FROM rocker/verse:3.6.0
 
 # required
 MAINTAINER Ben Marwick <bmarwick@uw.edu>
 
+# get contents of GitHub repo
 COPY . /huskydown
 
 # go into the repo directory
 RUN . /etc/environment \
 
-  # Install linux depedendencies here
-  #  rocker/verse has xelatex 
-  && sudo apt-get update \
-  # install fonts
-  && sudo apt-get install fonts-ebgaramond -y \
-  && sudo git clone --depth 1 --branch release https://github.com/adobe-fonts/source-code-pro.git /usr/share/fonts/source-code-pro \
-  && sudo fc-cache -f -v \
-  && sudo apt-get install fonts-lato -y \
+&& sudo apt-get update \
 
-  # build this compendium package
-  && R -e "devtools::install('/huskydown', dep=TRUE)" \
+&& sudo unzip huskydown/inst/fonts.zip && cp fonts -r /usr/local/share/fonts \
+&& sudo fc-cache -f -v \
 
- # make a PhD thesis from the template, remove pre-built PDF,
- # then render new thesis into a PDF, then check it could work:
-  && R -e "rmarkdown::draft('index.Rmd', template = 'thesis', package = 'huskydown', create_dir = TRUE, edit = FALSE)" \
-  && R -e "if (file.exists('index/_book/thesis.pdf')) file.remove('index/_book/thesis.pdf')" \
-  && R -e "setwd('index');  bookdown::render_book('index.Rmd', huskydown::thesis_pdf(latex_engine = 'xelatex'))" \
-  && R -e "file.exists('index/_book/thesis.pdf')"
+&& R -e "devtools::install('/huskydown', dep=TRUE)" \
+
+&& R -e "if (dir.exists('index')) unlink('index', recursive = TRUE)" \
+&& R -e "rmarkdown::draft('index.Rmd', template = 'thesis', package = 'huskydown', create_dir = TRUE, edit = FALSE)" \
+&& R -e "if (file.exists('index/_book/thesis.pdf')) file.remove('index/_book/thesis.pdf')" \
+&& R -e "setwd('index');  bookdown::render_book('index.Rmd', huskydown::thesis_pdf(latex_engine = 'xelatex'))" \
+&& R -e "file.exists('index/_book/thesis.pdf')"

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2017
+YEAR: 2018
 COPYRIGHT HOLDER: Ben Marwick

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2018 Ben Marwick
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NEWS.md

@@ -1,3 +1,15 @@
+# huskydown 0.0.5
+
+- remove custom highlighting
+- make pandoc args available
+
+# huskydown 0.0.4
+
+- new version of Pandoc
+- Source-Code-Pro changed location on GitHub, so changed method of getting them
+- tinytex burst onto the scene, simplying LaTeX installs.
+
+
 # huskydown 0.0.4
 
 - CI on OSX and Linux, collect artefacts and issue PDF

R/huskydown.R

@@ -1,15 +1,5 @@
-#' huskydown: A package for creating undergraduate, Masters, and PhD theses
-#'using R Markdown
-#'
-#'
-#' @section thesis_gitbook:
-#' Creates an R Markdown thesis template as a webpage
-#' @section thesis_pdf:
-#' Creates an R Markdown thesis template as a PDF
-#' @section thesis_word:
-#' Creates an R Markdown thesis template as a Microsoft Word document
-#' @section thesis_epub:
-#' Creates an R Markdown thesis template as an ebook
-#' @docType package
-#' @name huskydown
-NULL
+#' huskydown: A package for creating undergraduate, Masters, and PhD theses
+#'using R Markdown
+#' @docType package
+#' @name huskydown
+NULL

R/thesis.R

@@ -1,7 +1,7 @@
 #' Creates an R Markdown PDF Thesis document
 #'
 #' This is a function called in output in the YAML of the driver Rmd file
-#' to specify using the Reed College Senior Thesis LaTeX template and cls files.
+#' to specify using the University of Washington Thesis LaTeX template and cls files.
 #'
 #' @export
 #' @param toc A Boolean (TRUE or FALSE) specifying whether table of contents should be created
@@ -15,14 +15,14 @@
 #' \dontrun{
 #'  output: huskydown::thesis_pdf
 #' }
-thesis_pdf <- function(toc = TRUE, toc_depth = 3, highlight = "default", ...){
+thesis_pdf <- function(toc = TRUE, toc_depth = 3, highlight = "default", pandoc_args = NULL, ...){
 
-  base <- pdf_book(template = "template.tex",
+  base <- bookdown::pdf_book(template = "template.tex",
     toc = toc,
     toc_depth = toc_depth,
     highlight = highlight,
     keep_tex = TRUE,
-    pandoc_args = "--chapters",
+    pandoc_args = c(pandoc_args, "--top-level-division=chapter"),
     ...)
 
   # Mostly copied from knitr::render_sweave
@@ -84,7 +84,7 @@ thesis_gitbook <- function(...){
 #' }
 thesis_word <- function(...){
 
-  base <- word_document2(...)
+  base <- bookdown::word_document2(...)
 
   # Mostly copied from knitr::render_sweave
   base$knitr$opts_chunk$comment <- NA