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revision of MD Bib workflow

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@ -11,7 +11,7 @@ abstract: |
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.
---
[Better Bibtex]: https://retorque.re/zotero-better-bibtex/ "an extension for Zotero for managing bibliographic data, especially text-based document authoring toolchains"
[Better Bibtex]: https://retorque.re/zotero-better-bibtex/ "an extension for Zotero for managing bibliographic data, especially for text-based document authoring toolchains"
[Zotero]: https://www.zotero.org/ "free and open source, cross-platform citation management software."
[Pandoc]: https://pandoc.org/ "universal document converter"
@ -23,14 +23,16 @@ bibliography: references.bib
# Introduction
This guide outlines a workflow for incorporating bibliographic referencing (citations and references) in ![Markdown](article:md-formatting) documents. The general idea is incorporating citation keys in a Markdown document, and then rendering the bibliography by generating a new document against a bibliographic collection (`bib` file), and a citation style (`csl` file).
The following describes:
- creating and exporting a bibliography collection with [Zotero][];
- using citation keys in a Markdown document;
- getting a citation style file;
- exporting new documents (e.g. PDF, DOCX, MD, etc.) with [Pandoc][], where citations and bibliographic references are formatted as per any specific citation style.
This guide outlines a workflow for incorporating bibliographic referencing (citations and references) in ![Markdown](article:md-formatting) 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).
The steps described in the following are:
All tools involved are free, open source, and cross-platform.
1. Installing required tools and software;
1. creating and exporting a bibliography collection with [Zotero][];
2. using citation keys in a Markdown document;
3. getting a citation style file;
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.
All tools involved in this workflow are free, open source, and cross-platform.
---
@ -42,9 +44,8 @@ For example, for an 'author-year' citation style like *Chicago* in-text citation
1. Some Markdown editor for authoring Markdown documents (see ![Markdown guide](article:md-formatting)).
2. [Zotero][] -- free and open source cross platform citation management software.
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/)").
4. [Pandoc][] -- "universal document converter"; a command line tool for converting between different document formats (e.g. Markdown to PDF or DOCX), and compiling bibliographic references.
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/)").
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.
## Pandoc installation & upgrade {#pandoc-install}
@ -74,8 +75,7 @@ Installing via a terminal requires a package manager (e.g. [Chocolatey][] for Wi
### Upgrade
To upgrade [Pandoc][], if it was installed via an installer, download and run the latest installer.
To upgrade [Pandoc][], if it was installed via an installer, download and run the latest installer.
If it was installed via terminal, it can be upgraded with a single command.
- For Windows:
```
@ -86,7 +86,7 @@ If it was installed via terminal, it can be upgraded with a single command.
brew upgrade pandoc
```
Verify the version of pandoc with the command:
Verify the version of your Pandoc installation with the command:
```
pandoc --version
```
@ -102,7 +102,7 @@ This section outlines how to create a bibliography collection in Zotero and expo
![](/markdown-guide/zotero-citation-key.png)
4. To export your reference collection, select the collection, right-click > Export Collection, select **Better BibLaTeX** (uncheck all options; background export optional):
![](/markdown-guide/zotero-export-options.png)
3. Save your collection, e.g. as `mycollection.bib` . The resulting file is a set of citation keys, each with its own citation metadata (you can preview the file with a text editor).
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).
Notes:
- 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.
@ -114,26 +114,24 @@ Notes:
To add a citation in a Markdown file, just prefix a citation key (from Zotero) with the `@` sign, as in `@khaled2018`.
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.
When the document will be compiled against a bibliography and a citation style, citation keys will be rendered according to the specified citation style *and* a reference will be added to the bibliography section for each citation.
For author-year type citation styles:
For author-year type citation styles:
- To add parentheses to a reference use square brackets, as in `[@khaled2018]` --> "(Khaled et al. 2018)")
- For citing multiple sources at once separate keys with semicolons, as in `[@khaled2018;@graziano2019]` --> "(Khaled et al. 2018; Graziano et al. 2019)"
- 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)")
- To add a page or a note before or after a citation do `[see @graziano2019, p.125]` --> (see Graziano et al. 2019, p.125)
# Get a citation style file (CSL)
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).
Note: Zotero features a citation style editor (Tools > Style Editor), for modifying existing citation styles if needed.
Notes:
- [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).
- Zotero features a citation style editor (Tools > Style Editor), for modifying existing citation styles if needed.
# Gather files and paths
The next step is to make a note of the paths of your Markdown document, citation style, and bibliography files, which will be used to compile a new document.
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.
In addition, make sure that the path of any image referenced in the Markdown document is correct.
Good practices:
@ -157,45 +155,50 @@ Good practices:
Export directory:
"/path/to/mydocument/export/"
[Here you can also assemble the pandoc command for converting this document (discussed in the next sections), so that it can be easily reused.]
Pandoc export command: ...
-->
```
Notes:
- 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.
- 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.
- Enclosing file paths within "quotes" is optional. However, doing so can bypass the need for special characters in cases where file or directory names contain spaces.
# Test Pandoc and the Markdown document
- 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.
# Test Pandoc and Markdown document
Open a terminal:
- to test that [Pandoc][] works do (if the `pandoc` command is not recognized as valid go to [installation instructions](#pandoc-install):
- first, to check that [Pandoc][] is in order do:
```
pandoc --version
```
If the `pandoc` command is not recognized as valid go to [installation instructions](#pandoc-install).
- to test that your Markdown document is in order do (this will not compile the bibliography):
```
For docx export:
pandoc "/path/to/mydocument/my-article.md" -o /path/to/mydocument/export/my-article.docx"
pandoc "/path/to/mydocument/my-article.md" -o "/path/to/mydocument/export/my-article.docx"
or for pdf export:
pandoc "/path/to/mydocument/my-article.md" -o "/path/to/mydocument/export/my-article.pdf"
or for Markdown export:
pandoc "path/to/my-article.md" -o -o "/path/to/export-document.md" --atx-headers --strip-comments --wrap=preserve -t markdown_mmd-citations --standalone
pandoc "path/to/my-article.md" -o "/path/to/export-document.md" --atx-headers --strip-comments --wrap=preserve -t markdown_mmd --standalone
```
# Compile document with bibliographic references
To compile a new document file including citations and bibliography in Markdown do:
To compile a new document including citations and bibliography add the options:
| Pandoc option | Description |
|-|-|
| `--citeproc` | option for rendering citations/references|
|`--csl` |option to specify citation style, followed by the path to the `CSL` file|
| `--bib` | option to specify bibliography followed by the path to the `bib` file|
```
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
```
To compile to PDF do:
```
pandoc "path/to/myarticle.md" --citeproc --bibliography "/path/to/mycollection.bib" --csl "/path/to/reference-style.csl" -o "/path/to/export-document.pdf"
```
*Note: Conversions to PDF format require a LaTeX installation.*
---
To compile to DOCX do:
```
@ -206,8 +209,67 @@ To compile to DOCX using a DOCX document as reference/template add the option:
--reference-doc="path/to/reference-document.docx"
```
*Note: Conversions to *DOCX* format will use Footnotes, not Endnotes.*
*Note: Conversions to DOCX format will use Footnotes, not Endnotes.*
---
To compile to a new Markdown document (with references) do:
```
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
```
The additional options
| Pandoc option | Description |
|-|-|
| `--atx-headers` | use common (ATX) formatting for Markdown headings |
| `--strip-comments`| remove HTML comments(`<!-- comment-->`) |
| `--wrap=preserve` | preserve line wrapping (by default pandoc will introduce line breaks)|
| `-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)|
| `--standalone`| export standalone (will also render frontmatter) |
# Common Pandoc compilation errors
Pandoc will not compile in case of errors. Some common errors include:
- 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.
- file not found: check file paths
- cannot write/open file: Pandoc is not able to overwrite files (such as PDF or DOCX) while they are open by other software.
<!--
```
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
```
-->
# Pandoc command reference
[pandoc options manual]: https://pandoc.org/MANUAL.html#options
See also:
- [Pandoc demos](https://pandoc.org/demos.html),
- [Getting started with pandoc](https://pandoc.org/getting-started.html), and
- [pandoc options manual][].
A basic pandoc command example is:
```
pandoc "path/to/input.txt" -o "path/to/output.docx"
```
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):
|Pandoc option | Description |
|- |- |
| `-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)|
| `-o "/path/to/output/file.ext"` | output file, followed by path to file, including file extension|
| `-f` | (from) for specifying input format, followed by option, see [pandoc options manual][]|
| `-t` |(to) for specifying output format, followed by option, see [pandoc options manual][]|
| `-s`, `--standalone` | to produce standalone file, which will render title, abstract, keywords, using data from front matter of the Markdown document|
| `-C`, `--citeproc` | option to render citations; will expect bibliography and csl files |
| `--bibliography "path/to/bibliography.bib"`| specify bibliography file |
| `--csl "path/to/citation-style.csl"` |specify citation style file|
| `--atx-headers` | use common (ATX) formatting for Markdown headings|
| `--wrap=preserve` | option to preserve line wrapping for plain text output formats (other options: `auto`\|`none`)|
| `--strip-comments` | remove HTML comments (`<!--a comment-->`)|
| `--no-highlight` | Disables syntax highlighting for code blocks and inlines|
# Specify bibliography placement
@ -238,47 +300,3 @@ or
Lorem ipsum.
```
# Common errors
- missing/wrong citation keys: [Pandoc][] will list all citation keys that were not found in the supplied `bib` file. Correct any potential citation key misspellings, or recompile your bibliography collection to include the missing citations.
- file not found: check file paths
- cannot write/open file: Pandoc is not able to overwrite files (such as PDF or DOCX) while they are open by other software.
<!--
```
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
```
-->
# Pandoc command reference
[pandoc options manual]: https://pandoc.org/MANUAL.html#options
See also [Pandoc demos](https://pandoc.org/demos.html), [Getting started with pandoc](https://pandoc.org/getting-started.html), and [pandoc options manual][].
A basic pandoc command example is:
```
pandoc "path/to/input.txt" -o "path/to/output.docx"
```
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):
- `-i "path/to/input/file.ext"` (input file, followed by path to file including file extension)
- `-o "/path/to/output/file.ext"` (output file, followed by path to file, including file extension)
- `-f` (output format, followed by option, see [pandoc options manual][])
- `-t` (output format, followed by option, see [pandoc options manual][])
- `-s`, `--standalone` (will render title, abstract, keywords, using data from front matter of the Markdown document)
- `-C`, `--citeproc` (option to render citations; will expect bibliography and csl files)
- `--bibliography "path/to/bibliography.bib"`
- `--csl "path/to/citation-style.csl"` (citation style file)
- `--atx-headers` (for common Markdown heading format)
- `--wrap=auto`|`none`|`preserve` (line wrapping options for plain text formats)
- `--strip-comments[=true|false]` (remove HTML comments)
- `--no-highlight` (Disables syntax highlighting for code blocks and inlines)
<!--
- `--metadata-file=`_FILE_
- `--markdown-headings=setext`|`atx`
- `--template=`_FILE_|_URL_
-->