302 lines
15 KiB
Markdown
302 lines
15 KiB
Markdown
---
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title: "Markdown bibliographic referencing workflow"
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date: "2023-07-14T20:21:29+03:00"
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author: "anybody"
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contributors: ["constantinos-miltiadis.md"]
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draft: false
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keywords:
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- guide
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- markdown guide
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abstract: |
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This article outlines a workflow for incorporating bibliographic citations/references in Markdown documents, and exporting new documents with compiled bibliographies according to specific citation styles. All tools involved in this pipeline are free, open source, and cross platform.
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---
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[Better Bibtex]: https://retorque.re/zotero-better-bibtex/ "an extension for Zotero for managing bibliographic data, especially for text-based document authoring toolchains"
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[Zotero]: https://www.zotero.org/ "free and open source, cross-platform citation management software."
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[Pandoc]: https://pandoc.org/ "universal document converter"
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<!-- try
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output: html_document
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bibliography: references.bib
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-->
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# Introduction
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This guide outlines a workflow for incorporating bibliographic referencing (citations and references) in  documents. The general idea is incorporating citation keys from a bibliography in a Markdown document, and then rendering citations and references by generating a new document against a bibliographic collection (`bib` file), and a citation style (`csl` file).
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The steps described in the following are:
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1. Installing required tools and software;
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1. creating and exporting a bibliography collection with [Zotero][];
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2. using citation keys in a Markdown document;
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3. getting a citation style file;
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4. exporting new documents (e.g. PDF, DOCX, MD, etc.) with [Pandoc][], where citations and bibliographic references are formatted as per any specific citation style.
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All tools involved in this workflow are free, open source, and cross-platform.
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---
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Note: A *citation* is used in the body of the text to refer to some external source. A *reference* is placed in the "References" or "Bibliography" section of the document providing the full information for a citation. Citations and references are formatted according to a citation style.
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For example, for an 'author-year' citation style like *Chicago* in-text citations look like: Khaled et al. (2018), or (Khaled et al. 2018). According to the same citation style, the reference for that citation is:
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- Khaled, Rilla, Jonathan Lessard, and Pippin Barr. ‘Documenting Trajectories in Design Space: A Methodology for Applied Game Design Research’. In _Proceedings of the 13th International Conference on the Foundations of Digital Games_, 1–10. Malmö Sweden: ACM, 2018. [https://doi.org/10.1145/3235765.3235767](https://doi.org/10.1145/3235765.3235767).
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# Requirements
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1. Some Markdown editor for authoring Markdown documents (see ).
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2. [Zotero][] -- free and open source cross platform citation management software.
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3. [Better Bibtex][] -- "an extension for Zotero ... that makes it easier to manage bibliographic data, especially for people authoring documents using text-based toolchains (e.g. based on [LaTeX](https://www.latex-project.org/) / [Markdown](https://www.markdownguide.org/)").
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4. [Pandoc][] -- "universal document converter"; command line tool for converting between different document formats (e.g. Markdown, PDF, DOCX, epub, etc.), and compiling bibliographic references.
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## Pandoc installation & upgrade {#pandoc-install}
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[Chocolatey]: https://chocolatey.org/ "Free and open source package manager for Windows."
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[Homebrew]: https://brew.sh/ "Free and open source package manager for macOS."
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Pandoc is a command line tool that can be installed via a downloadable installer or through the terminal (see [Installing pandoc](https://pandoc.org/installing.html)).
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To check if pandoc is installed, and which version is installed, open a terminal and do:
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```
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pandoc --version
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```
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If pandoc is not recognized as a valid command, go ahead and install pandoc. Otherwise, upgrade pandoc to the latest release.
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### Installation
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Installing via a terminal requires a package manager (e.g. [Chocolatey][] for Windows, or [Homebrew][] for macOS).
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- For Windows, using the package manager [Chocolatey] do:
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```
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choco install pandoc
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```
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- For macOS, using the package manager [Homebrew][], do:
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```
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brew install pandoc
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```
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### Upgrade
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To upgrade [Pandoc][], if it was installed via an installer, download and run the latest installer.
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If it was installed via terminal, it can be upgraded with a single command.
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- For Windows:
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```
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choco upgrade pandoc
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```
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- For macOS:
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```
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brew upgrade pandoc
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```
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Verify the version of your Pandoc installation with the command:
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```
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pandoc --version
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```
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# Create and export a bibliography collection
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This section outlines how to create a bibliography collection in Zotero and export it to a `bib` file.
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1. In Zotero, create a new collection (titled say `mycollection`).
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2. Add to your collection all items you want to reference (by drag and drop to collection, or right click > Add to Collection).
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3. With [Zotero][] and [Better Bibtex][] installed, each entry in your Zotero database should have a unique citation key displayed at the top of its Info section (image below). Use this key as in `@key` (or `@khaled2018`) to cite this item in your Markdown document ([further instructions below](#cite)).
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4. To export your reference collection, select the collection, right-click > Export Collection, select **Better BibLaTeX** (uncheck all options; background export optional):
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3. Save your collection (e.g. `mycollection.bib`). The resulting file is a dictionary of citation keys, each with its own citation metadata (you can preview the file with a text editor).
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Notes:
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- In case you modified your Zotero collection (e.g. added/removed items or edited existing items), re-export the collection and overwrite the previous `bib` file.
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- *Opt for the BibLaTeX export format.* The BibTeX export format will omit URLs associated with an entry!
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- The format of citation keys can be changed in the [Better Bibtex][] preferences (Zotero: Tools > Better BibTex > Open preferences). The format used in this example is `auth.lower+year`.
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# Using citation keys in Markdown documents {#cite}
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To add a citation in a Markdown file, just prefix a citation key (from Zotero) with the `@` sign, as in `@khaled2018`.
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Eventually, as described in the following steps, when the document is compiled (against a bibliography and a citation style), citation keys will be rendered according to the specified citation style, and a bibliographic reference will be added to the bibliography section of the document, per each unique cited document.
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For author-year type citation styles:
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- To add parentheses to a reference use square brackets, as in `[@khaled2018]` --> "(Khaled et al. 2018)")
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- For citing multiple sources at once separate keys with semicolons, as in `[@khaled2018;@graziano2019]` --> "(Khaled et al. 2018; Graziano et al. 2019)"
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- To supress the author name (in author-date citation styles) do `[-@khaled2018]` eg. "According to Khaled and colleagues [-@khaled2018]" will render as "According to Khaled and colleagues (2018)")
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- To add a page or a note before or after a citation do `[see @graziano2019, p.125]` --> (see Graziano et al. 2019, p.125)
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# Get a citation style file (CSL)
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Use a provided citation style file (CSL), or download one from [the official citation style repository](https://github.com/citation-style-language/styles) (GitHub repository), or from the [Zotero Style Repository](https://www.zotero.org/styles) (search interface).
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Notes:
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- [Zotero] includes a few CSL files for popular citation styles. These are located in the `styles` directory of the Zotero Data Directory (Zotero > Edit > Preferences > Advanced > Show Data Directory).
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- Zotero features a citation style editor (Tools > Style Editor), for modifying existing citation styles if needed.
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# Gather files and paths
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The next step is to gather all required files that will be used to compile a new document (Markdown document, citation style, and bibliography files) and make a note of their file paths.
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In addition, make sure that the path of any image referenced in the Markdown document is correct.
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Good practices:
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- Gather your Markdown document, bibliography, and CSL files in the same directory, e.g. `/mydocument/`.
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- Place images inside a subdirectory, e.g. `/mydocument/graphics/`
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- Make a subdirectory for exporting documents e.g. `/mydocument/export/`
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- Avoid using spaces in directory or file names.
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- It is recommended to write down these paths either in a comment section inside your document, or in a separate text file, as in:
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```
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<!-- Exporting notes
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Markdown document (md):
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"/path/to/mydocument/my-article.md"
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Bibliography file (bib):
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"/path/to/mydocument/mycollection.bib"
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Citation style file (csl):
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"/path/to/mydocument/reference-style.csl"
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Export directory:
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"/path/to/mydocument/export/"
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Pandoc export command: ...
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-->
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```
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Notes:
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- File paths can be either absolute (e.g. `c:/users/me/some-folder/some-file.md`), or relative (e.g. `/some-folder/some-file.md`). However, for relative paths pandoc commands will need to be executed from the base directory of these relative paths.
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- An easy way to get the absolute path of a file or directory, is to drag and drop it into a terminal, then select the path that will appear, right click, and copy.
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- Enclosing file paths within "quotes" is optional. However, doing so can bypass the need for escape characters in cases where file or directory names contain spaces.
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# Test Pandoc and Markdown document
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Open a terminal:
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- first, to check that [Pandoc][] is in order do:
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```
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pandoc --version
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```
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If the `pandoc` command is not recognized as valid go to [installation instructions](#pandoc-install).
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- to test that your Markdown document is in order do (this will not compile the bibliography):
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```
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For docx export:
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pandoc "/path/to/mydocument/my-article.md" -o "/path/to/mydocument/export/my-article.docx"
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or for pdf export:
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pandoc "/path/to/mydocument/my-article.md" -o "/path/to/mydocument/export/my-article.pdf"
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or for Markdown export:
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pandoc "path/to/my-article.md" -o "/path/to/export-document.md" --atx-headers --strip-comments --wrap=preserve -t markdown_mmd --standalone
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```
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# Compile document with bibliographic references
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To compile a new document including citations and bibliography add the options:
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| Pandoc option | Description |
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|-|-|
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| `--citeproc` | option for rendering citations/references|
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|`--csl` |option to specify citation style, followed by the path to the `CSL` file|
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| `--bib` | option to specify bibliography followed by the path to the `bib` file|
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To compile to PDF do:
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```
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pandoc "path/to/myarticle.md" --citeproc --bibliography "/path/to/mycollection.bib" --csl "/path/to/reference-style.csl" -o "/path/to/export-document.pdf"
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```
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*Note: Conversions to PDF format require a LaTeX installation.*
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---
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To compile to DOCX do:
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```
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pandoc "path/to/myarticle.md" --citeproc --bibliography "/path/to/mycollection.bib" --csl "/path/to/reference-style.csl" -o "/path/to/export-document.docx"
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```
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To compile to DOCX using a DOCX document as reference/template add the option:
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```
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--reference-doc="path/to/reference-document.docx"
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```
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*Note: Conversions to DOCX format will use Footnotes, not Endnotes.*
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---
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To compile to a new Markdown document (with references) do:
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```
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pandoc "path/to/myarticle.md" --citeproc --bibliography "/path/to/mycollection.bib" --csl "/path/to/reference-style.csl" -o "/path/to/export-document.md" --atx-headers --strip-comments --wrap=preserve -t markdown_mmd-citations --standalone
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```
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The additional options
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| Pandoc option | Description |
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|-|-|
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| `--atx-headers` | use common (ATX) formatting for Markdown headings |
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| `--strip-comments`| remove HTML comments(`<!-- comment-->`) |
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| `--wrap=preserve` | preserve line wrapping (by default pandoc will introduce line breaks)|
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| `-t markdown_mmd-citations` | `-t` (to) for specifying output format; ` markdown_mmd-citations` for `markdown_mmd` format *with* citations (by default Markdown exports don't render citations/bibliography)|
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| `--standalone`| export standalone (will also render frontmatter) |
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# Common Pandoc compilation errors
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Pandoc will not compile in case of errors. Some common errors include:
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- missing/wrong citation keys: [Pandoc][] will list all citation keys that were not found in the supplied bibliography file. Correct any potential citation key misspellings, or recompile your bibliography collection to include the missing citations.
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- file not found: check file paths
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- cannot write/open file: Pandoc is not able to overwrite files (such as PDF or DOCX) while they are open by other software.
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<!--
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```
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pandoc "path/to/myarticle.md" --citeproc --bibliography "C:\Users\cmilt\Nextcloud\Aalto-NC\Publications\2301 DiGRA\bib\digraNN2.bib" --csl "C:\Users\cmilt\Nextcloud\Aalto-NC\Publications\2301 DiGRA\csl\chicago-author-date-3.csl" -o "C:\Users\cmilt\gdj-temp\mdexport\exp.md" --atx-headers --strip-comments --wrap=preserve -t markdown_mmd-citations --standalone
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```
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-->
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# Pandoc command reference
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[pandoc options manual]: https://pandoc.org/MANUAL.html#options
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See also:
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- [Pandoc demos](https://pandoc.org/demos.html),
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- [Getting started with pandoc](https://pandoc.org/getting-started.html), and
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- [pandoc options manual][].
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A basic pandoc command example is:
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```
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pandoc "path/to/input.txt" -o "path/to/output.docx"
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```
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Additional options can be added to this command pattern to specify export parameters. Here is a brief list of some commonly used pandoc options (enclosing file paths inside quotation marks is optional):
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|Pandoc option | Description |
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|- |- |
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| `-i "path/to/input/file.ext"` | input file, followed by path to file including file extension (usually `-i` is omitted when input file is specified at the beginning of the command)|
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| `-o "/path/to/output/file.ext"` | output file, followed by path to file, including file extension|
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| `-f` | (from) for specifying input format, followed by option, see [pandoc options manual][]|
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| `-t` |(to) for specifying output format, followed by option, see [pandoc options manual][]|
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| `-s`, `--standalone` | to produce standalone file, which will render title, abstract, keywords, using data from front matter of the Markdown document|
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| `-C`, `--citeproc` | option to render citations; will expect bibliography and csl files |
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| `--bibliography "path/to/bibliography.bib"`| specify bibliography file |
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| `--csl "path/to/citation-style.csl"` |specify citation style file|
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| `--atx-headers` | use common (ATX) formatting for Markdown headings|
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| `--wrap=preserve` | option to preserve line wrapping for plain text output formats (other options: `auto`\|`none`)|
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| `--strip-comments` | remove HTML comments (`<!--a comment-->`)|
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| `--no-highlight` | Disables syntax highlighting for code blocks and inlines|
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# Specify bibliography placement
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By default, [pandoc][] will insert the bibliography at the end of the document. To force the bibliography to render at a specific location if needed -- for example before endnotes or appendix sections -- add the following to the target location for your bibliography:
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```
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... article body ...
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# Bibliography
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::: {#refs}
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:::
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# Some other appendix
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Lorem ipsum.
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```
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or
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```
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... article body ...
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# Bibliography
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<div id="refs"></div>
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# Some other appendix
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Lorem ipsum.
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```
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