dendron-citations

tool for making Dendron work well with citing things using bibtex or Zotero

WORK IN PROGRESS. please use with care, since this will overwrite files in your dendron vault

The main script is dendron_gen_refs.py, which generates a vault of dendron notes corresponding to entries from a bibtex file

this allows the user to reference the dendron notes instead of raw bibtex item (such as when using PandocCiter), which lets us use backlink features from dendron to see where we have cited a paper

Note: I personally put all my references in a separate vault from my main vault, to avoid clutter. I highly recommend this, since this might also prevent you from accidentally overwriting things in your main vault.

Contents:

• Usage
• Installation
• Extras
• Roadmap

Usage:

to generate reference notes, run from anywhere:

dendron_gen_refs.py [cfg_path] [--<kwarg>=<val>]

Help and configuration

• --help : print help message and exit:

dendron_gen_refs.py --help

• --print_cfg : print to console an example config in either json or yaml (json by default):

dendron_gen_refs.py --print_cfg [--fmt=<format>]

Generation:

when running

dendron_gen_refs.py [cfg_path] [**kwargs]

cfg_path should be the location of a yaml or json config file any of those items can be overwritten as keyword arguments using --<keyword>=<value>

the expected config elements, types, and default values are:

	bib_filename : str = 'refs.bib'
	vault_loc : str = 'vault/'
	note_prefix : str = 'refs.'
	make_tag_notes : bool = True
	verbose : bool = False
	kebab_case_tag_names : bool = False
	template_path : Optional[str] = None

Examples:

dendron_gen_refs.py gen --bib_filename=<bibtex_file> --vault_loc=<output_dir>

Or, we could create a config file such as examples/custom_cfg.json and pass it in as

dendron_gen_refs.py gen <path_to_config_file>

Note: if you pass a config file, the script will change its directory to that of the config file, to allow paths to be specified relative to that file.

Installation:

Not yet on PyPi, due to instability. you can install with

pip install -e git+https://github.com/mivanit/dendron-citations.git#egg=dendron_citations

Note that this will place an executable dendron_gen_refs.py in your python Scripts folder (and thus hopefully in your path).

Dependencies:

• https://github.com/t-wissmann/biblib
  • not on pypi, installed from git repo
  • note: forked from https://github.com/aclements/biblib, which no longer works
• pyyaml
• chevron
  • python implementation of the mustache templating language
• pypandoc (optional)
  • for converting notes to markdown

Extras

tag notes

Not only can we use dendron backlinks to view where we have cited a certain paper, but we can additionally use the backlinks to see all papers by a given author, or all papers with a given keyword!

The argument --make_tag_notes, True by default, will enable the generation of notes for each tag, as long as the tag does not yet exists. Keywords will be processed into tags by removing spaces and other extra characters. Author tags will be of the format <first_char_of_first_name>-<last_name>, with all characters converted to ascii. The actual notes for author tags will contain the full author names.

templates

For now, you need to manually modify the template string DEFAULT_TEMPLATE in the file refs_vault_gen.py to suit your needs. The template is in Mustache format, with some extensions:

• Add the prefix _bln_ to the name of any iterable variable to get access to a boolean value that is true if the variable is not empty
• Lists of non-dict items are turned into lists of dicts, where each dict has a single key elt with the value of the item

For example, if keywords is a list of strings ['a', 'b'], we can use the template

{{#_bln_keywords}}# Keywords
{{/_bln_keywords}}
{{#keywords}}
 - #{{elt}}
{{/keywords}}

to print

# Keywords
 - a
 - b

or to return an empty string (with newlines) if keywords is empty.

vscode task

in order to have a vscode shortcut to running the dendron_gen_refs.py script, we can take advantage of VSCode Tasks and add the following task to .vscode/tasks.json:

{
	"label": "dendron-citations",
	"type": "shell",
	"command": "dendron_gen_refs.py {{your_config_file}}",
}

where {{your_config_file}} is the path to your config file relative to the root of the workspace -- for example, examples/custom_cfg.json

cross-vault links snippet

to allow simpler references to papers in a separate vault, without having to type [[dendron://refs-vault/<bibtex key>]], the user may create a vscode snippet in > Preferences > Configure User Snippets > markdown.json

"dendron-cite": {
	"prefix": "@",
	"body": [
		"[[dendron://refs-vault/refs.$1]]"
	],
	"description": "dendron reference citation"
},

Roadmap:

general

• implement a configuration system
• set up as an installable package
• turn this into a real vscode plugin
  • will probably use vscode-ext

bibtex integration

• given a bibtex file, generate a vault of dendron notes bibtex keys as filenames
• add tags and other things from bibtex to metadata
• optional generation of tag files
• "beneath" each note for the bibtex, add another note for the citation itself.
  • note that this will all break if the bibtex keys change!
• automatically convert PandocCiter style
  • this will allow for better searching for papers
• make citations work properly when compiling with Pandoc
  • probably best to do this as part of dendron-pandoc

zotero integration

do everything as for bibtex integration, but also:

• add links/copies in zotero to the dendron notes (when they exist)
• have zotero item materials inside dendron file
  • zotero notes, plaintext attachments inline
  • links to all other attachments
  • exclude the dendron file to avoid recursion, haha

Developing:

After cloning, run

make help

to see some utilities for developing (setting up a virtual environment, running type and style checkers, etc.)