Pandoc Citations FTW (and more)

This release marks a number of major and minor improvements.

Major

• you can now use pandoc for citations, which causes less trouble than biblatex or natbib. Pandoc is used by default, but you can still manually opt-in to biblatex or natbib instead
• there is now only ONE template that is used to knit both the entire thesis and individual chapters

Minor

• overflowing code in code blocks now line wraps!
• most non-essential parameters now have sensible fall-back defaults, such that the thesis still knits if the relevant variables are missing from the YAML header (this is what allows us to now use the same template to knit individual chapters with a minimal YAML header)

Bug fixes

• the reference chapter now has correct running headings (this was temporarily broken when I added pandoc as an option to manage citations)
• many, many more tiny bug fixes..

Minor fixes and improvements

This release adds minor features and improvements.

New functionality

• the acknowledgements and/or abstract can now be included in the table of contents (#41)
• you can now include two different abstracts in the thesis (#39; e.g. you may need to include both an abstract in English and in non-English)

Minor changes and improvements

• dedication, acknowledgments, and abstract are now ordered in the YAML of index.Rmd in the order they appear in the thesis

Make Caching Allowed Again

This version deserved its own release, because it fixes an important bug:

The previous clean-up script by default deleted the _bookdown_files folder after the built process was completed. This had the unintended side-effect of removing the files stored when you set cache=TRUE in time-consuming code chunks (see #37).

This version fixes this issue: the _bookdown_files folder is no longer removed, unless you explicitly set allow_cache=FALSE in the knit_thesis function call in index.Rmd.

Minor updates and improvements

Hi all,

this is a minor release which adds some useful functionality, improves the documentation, and fixes minor bugs.

New functionality

• more of the front page layout can now be controlled from the YAML header in index.Rmd (font size of the title, size of whitespace before and after the university logo)
• overflowing lines in code blocks are now wrapped
• table of contents can now be linked just by the page number, instead of the entire heading, which is preferable when links are colored (thanks @shirdekel!)

Minor changes & improvements

• example bibliographies now live in a folder instead of the root directory
• improved documentation: the 'how to use' chapter now outlines the structure of oxforddown

Bug fixes

• abstract is only shown if provided (thanks @kasnder!)

Fix critical bug in clean-up script

This release fixes a critical bug in the script that cleans up miscellaneous files generated by LaTeX when building to PDF.

As pointed out in this issue, the old regex could inadvertently delete files that happened to have partly similar filenames to the files the clean-up script was meant to remove... 😱 This is now fixed!

Bug fixes

• fixed critical bug in clean-up script

New functionality

• added functionality to control link highlighting with either coloured text or borders around hyperlinks directly from index.Rmd
• added ability to set width of the university logo on the title page from index.Rmd

Minor changes

• the abbreviations file is now an R Markdown instead of Tex file
• changed default to not include separate abstract page
• bibliography settings have been moved further up in index.Rmd

Make the Knit button great again!

This is a major release that simplifies how you build your thesis, adds useful functionality and fixes a number of bugs.

Major changes

• To build the entire thesis, you now simply knit the index.Rmd file. You control the output format by commenting in or out the format you want in the YAML front matter.
• The build function used by the knit button can easily be customised by editing the corresponding R script. This removes the use of make, which simplifies the build process and streamlines it across operating systems (make can be a pain on Windows)

New functionality & documentation

• You can now hide or show line numbers by setting includeline-num to true or false in index.Rmd (thanks Ilse Pit!)
• You can now switch between the biblatex and natbib LaTeX packages for handling references, by setting corresponding options in index.Rmd, and you can also pass some options to these packages directly from index.Rmd
• The sample content now includes an example of how to include another paper in your thesis as an R Markdown child document
• You can now easily customise or replace the title page, so that it is easy to tweak oxforddown for use with another university's front matter - a section on how to do this has been added to the documentation

Minor changes and bug fixes

• The yaml options header_includes and in_header now works correctly (#17)
• The fix for header_includes etc also means that kableExtra now correctly includes its latex dependencies automatically when the library is loaded, so many of its dependencies have been removed from the oxforddown latex templates (#14)
• Fixed bug in hiding or showing hyperlink borders from index.Rmd (#18)
• oxforddown now uses the MIT license

Custom coloring and highlighting

NEW FUNCTIONALITY:

• you can now also use markdown attributes to apply custom font color and highlighting (see the customisations and extensions chapter for how)

Streamlined release

This release updates oxforddown with the main functionality and tricks I found that I needed as I was finishing my own thesis, and fixes bugs and inconsistencies noted by other users.

MAJOR CHANGES:

• The introduction chapter is now a chapter similar to other chapters - it should no longer be named _introduction.Rmd and is no longer a child of index.Rmd.
• In HTML output, the content in front-and-back-matter/_welcome-ebook.Rmd will be shown on the landing page (index.html), followed by the abstract and acknowledgements.

NEW FUNCTIONALITY

• you can now output to the great-looking BS4 book style, with make bs4book
• in PDF output you can now
  • control the location of page numbers and running headers, as well as spacing around code blocks, directly from the YAML header in index.Rmd
  • position images and plots where they are located in the text, with the chunk option fig.pos = 'H'
  • a new chapter explains tips and tricks needed to handle tables in PDF output (the oxforddown LaTeX template now includes all the latex packages used by the kableExtra R package)

MINOR CHANGES & BUG FIXES

• correction highlighting now uses the soul package - the previous solution had the problem that long lines would not be line wrapped
• the Makefile now automatically generates a docs/.nojekyll file when outputting to HTML format - this file is needed to deploy on GitHub pages
• you can now use more than one bibliography file
• a bug is fixed in the installation of required packages; and this is now also partitioned out into its own R script (scripts_and_filters/install_packages_if_missing.R)

Enjoy!

Stable release with bug fixes and minor new capabilities

As I've been finishing my own PhD thesis, I added a bunch of minor capabilities that were missing, and fixed a number of bugs. I've fixed enough of them now to warrant a new version number.

Version 1.1 includes:

• ability to set from the YAML in index.Rmd whether or not hyperlinks should be highlighted in PDF output with a coloured box (I've turned this off by default, as I found it was too distracting to read when printing)
• ability to set set from the YAML in index.Rmd whether DOI's should be included in the bibliography
• a note that the chunk option fig.scap can be used for short figure captions in the List of Figures in PDF output
• numerous misc bug fixes

Enjoy!

Pre-release for Zenodo DOI'ing

This is a pre-release to give the repo a DOI via Zenodo, to allow me to cite the repo.

The next proper release will include guidance in relation to tables.