I am using pandoc-include to break an otherwise big monolithic file into one root file including a set of smaller files.

This breaks however the autocompletion of cross-ref assets such as figures and listings.
(Citeproc citations still wotk throughout all files though, if PandocCiter.RootFile is set.)

I wished PandocCiter would account for such circumstance and still resolve cross-refs across file boundaries.

EDIT
To be clearer: All references (for tables, figures, listings, sections, etc. ...) as defined via cross-ref syntax in any markdown file should be resolved by PandocCiter in any other markdown file within the same project directory.

@notZaki thanks for this extremely helpful plugin!

In my Mac OS environment, autocomplement suggestion is shown in cases: ( @), [ @], [@] but not (@).
I want your product to suggest it in (@) case.
In our field citation is always in (), so I would not like to add extra space " ".

Any way that an option to use this together with pandoc-crossref could be added?

It can refer to different identifiers, uses for example the #sec, #fig, #tbl id to refer to headings, figures and tables respectively.

Thanks for this awesome and lightweight extension! I think it would be really handy to have support for:

1. a pop-up that shows the title, year, and author of a BibTeX citation on hover

2. jumping to where the citation is defined in the .bib file on cmd/control + click (i.e., similar to what the Markdown Notes extension does here).

What do you think?

Hi, thanks for this amazing extension!

I'm a little bit confused about the logic used in the search engine:

For example:

You can see the top few results are about Covid and aging.

But if I write covid a in the search box, only one candidate is left.

And when I wrote covid aging, it gave me the empty result

It feels hard to search the target citation when I have a large library and few keywords in mind.

Any thought?

Thank you!

Would be really useful to be able to specify more than one '.bib' file for autocompletion.
Thanks for the great extension, it's really nice.

Hi @notZaki !

Thanks for this nice plugin !
Would it be possible to dispaly citation as a footer after the .bib fetching ?
Just like with this Sublime plugin https://github.com/renerocksai/sublime_zk#location-of-your-bib-file (also uses Pandoc)

Thanks a lot !

PM

I was using Pandoc within Visual Studio to compile a Markdown document that contains literature citations. The specific problem arises after compilation: the resulting document displays each referenced bibliography entry twice, leading to duplicate references in the output. This issue persists despite the correct implementation of Markdown syntax for citations and the appropriate setup of the bibliography file (mybib.bib) and the CSL file (china-C.csl) which are correct. Additionally, the YAML header in the Markdown document seems to be correctly formatted with necessary fields like bibliography, csl, and other document settings. The problem appears to be related to the PandocCiter conversion process or possibly the settings or templates used during this conversion.

---
bibliography: ['bibliography.bib']

csl: [china-national-standard-gb-t-7714-2015-numeric-AuLower-Bilan.csl]

title: Test
link-citations: true
lang: en-US
figPrefix:
  - "Fig."
  - "Figs."
linkReferences: true
papersize: a4
colorlinks: true
links-as-notes: true
author: Author
abstract: Abstract
keywords: [nothing, nothingness]

---

Reference[@aidalaHousingStatusMedical2016]

The result of compilation is:

Reference[1]

[1]
Matthews R B, Gilbert N G, Roach A, et al. Agent-Based Land-Use Models: A Review of Applications[J/OL]. Landscape Ecology, 2007, 22(10): 1447–1459[2023–12–18]. https://doi.org/10.1007/s10980-007-9135-1. DOI:10.1007/s10980-007-9135-1[1]Matthews R B, Gilbert N G, Roach A, et al. Agent-based land-use models: A review of applications[J/OL]. Landscape Ecology, 2007, 22(10): 1447–1459[2023–12–18]. https://doi.org/10.1007/s10980-007-9135-1. DOI:10.1007/s10980-007-9135-1.

How can I fix it?

Problem
I use the latex markdown package. So to inject my markdown files I use /markdownInput. The Problem is that the bib file doesn't get loaded when only markdown files are open. I have to open a tex file so that the bib file gets loaded.

My configuration is

  "PandocCiter.DefaultBib": "sources.bib",
  "PandocCiter.ForgetUnusedBib": false,
  "PandocCiter.ShowLog": true,
  "PandocCiter.UseDefaultBib": true,
  "PandocCiter.ViewType": "browser",

Expected behavior
The bib file gets loaded when there is a markdown file open, so I don't need to open a tex file to cite in markdown.

Log files

PandocCiter is now activated
Looking for .bib file: sources.bib
Looking for .bib file: sources.bib
Showing 0 suggestions
Showing 0 suggestions
Looking for .bib file: sources.bib
Showing 0 suggestions
Looking for .bib file: sources.bib
Looking for .bib file: sources.bib
Looking for .bib file: sources.bib
Looking for .bib file: sources.bib
Looking for .bib file: sources.bib
# Here I opened my thesis.tex
Found .bib file /workspaces/markdown-thesis/sources.bib
Creating file watcher for .bib files.
Parsing .bib entries from /workspaces/markdown-thesis/sources.bib
Parsed 28 .bib entries from /workspaces/markdown-thesis/sources.bib.
Looking for .bib file: sources.bib
Found .bib file /workspaces/markdown-thesis/sources.bib
Adding .bib file /workspaces/markdown-thesis/sources.bib to bib file watcher.
Parsing .bib entries from /workspaces/markdown-thesis/sources.bib
Parsed 28 .bib entries from /workspaces/markdown-thesis/sources.bib.

No autocomplete suggestions and no preview available. I have followed the guidelines and enabled the Quick Suggestion recommended by ilcpm, however I absolutely cannot get this extension to work. Could someone please help me out?

While I'm at it, there is one more thing I would like to suggest :-) I usually do not create bibtex files on a project basis; most of the time I just use one bibtex file with my entire library.

PandocCiter allows me to do that, but I need to create a 'root file' that contains a YAML header pointing to the actual bibtex file. Rather than requiring an extra root file, I think it would be much easier if we could just directly point to a default bibtex file in the settings, something like "PandocCiter.DefaultLibrary": "~/Documents/library.bib". If the file I'm currently working on contains a YAML header pointing to a different bibtex file, then PandocCiter should prefer it over the default (or it should use both the default and project library, perhaps configurable by the user). I think this would be easier to set up and more intuitive.

Thanks for this extension!

It would be great if the Default Bib (and other appropriate settings?) could be set at the Folder level in Multi-Root Workspaces.

For example, I have a monorepo set up as a Workspace. Each package in the monorepo is set as a separate root Folder, and thus has it's own Folder-level settings that override the Workspace-level settings. Each package has it's own .bib file, so I would like to set the Default Bib for each package at the Folder-level.

Currently, none of the PandocCiter settings are available at the Folder-level (because all settings default to the window scope). However, appropriate settings can be made available at the Folder-level by using the multi-root workspace APIs to set them to resource scope: Adopting Multi Root Workspace APIs.

Hi, I have issues with your plugin when giving absolute path to a Dropbox file. I know I have saved the entries to the .bib file, however, pandoc-citer still states that no references are there. I tried all the possible paths. I assume the problem is related with the difference between linux ../.. and Windows ..\.. paths. Could you please clarify what should be the correct use?

The autocompletion of citations on BibTeX files is not working after updating to the latest version (v 0.10.0).

While other autocompletion, such as those on crossref on figures or tables, still works well.

I tried rolling back to version 0.9.3, and it works fine again.

OS: WSL2 on Windows 10
VSCode:1.78.2

First, thank you for this extension -- it's excellent!

I'm wondering if it would be possible for this extension to work on other pandoc-like language types. My particular use case is R Markdown, which I believe has a language id rmd provided by the vscode-R extension. Admittedly, I'm probably an edge case, so if there are local modifications I can make to get this to work, I'd appreciate any tips. The extension works fine if I temporarily change the language to "markdown" but I lose other features and toggling back and forth isn't the greatest.

Could you add round brackets to the characters that are allowed to be before the @ of a citation?
I'm not quite sure why round brackets wouldn't be allowed to be in front of @.
If there is any reason I would be happy to know!

It's a great extansion otherwise!
Thanks in advance

Thank you so much for making this awesome extension!
I was able to install this and use it in the markdown document but when I tried to export the document to another format such as pdf or docx using another extension "vscode-pandoc", the code (e.g., [@Author2008]) appears as it is, not the actual citation information. Am I missing something about this extension, or is it something that should be resolved with vscode-pandoc?

First of all, thanks for this great extension!

There's two minor things I've noticed in the display for the following bib file:

@article{Wrong,
annote = {This is a haiku
It has multiple newlines
That are not displayed},
author = {Author},
title = {{Wrongly displayed entry}}
}

@article{Correct,
author = {Author},
title = {{Correctly displayed entry}},
annote = {This is a haiku
It has a double newline.

It shows correctly}
}

Firstly, the order of the display follows the order of the attributes in the entry, not the one configured in PandocCiter.CitationFormat (i.e. annote should be displayed as last line). Secondly, the entry is formatted as a single line (even fields that contain newlines), unless one of the displayed entry has an empty line:

While investigating why the PandocCiter extension did not show any suggestions for the .bib file referenced in my YAML header I found the following IMO incorrect behavior:

Problem description

PandocCiter does not find my .bib file and provide suggestions if it is

• saved at the root of the directory currently open in VSCode ("project") and
• referenced by a relative path from a Markdown file in a subfolder of the project (e.g. ../bibliography.bib)

It appears PandocCiter resolves the relative path to the .bib file from the project root instead of the Markdown file that references it in the YAML header.

Expected behavior

PandocCiter should search for the referenced .bib file relative to the file in which it is referenced and not from the project root.

Steps to reproduce

I made a minimal sample project to test this with: pandoc-citer-example.zip

1. Unpack the zip so that you have a pandoc-citer-example folder with the subfolders draft and final, as well as the bibliography.bib file.
2. Open the folder pandoc-citer-example in VSCode
3. Open the document final/report.md with the PandocCiter extension installed and activated with default settings.
4. Start typing [@ anywhere in the document.
5. No citation keys are suggested :(

Additional Details

In my use case, I have a project folder for a seminar and subfolders with different Markdown documents (e.g. lecture notes, final report, etc.). I save a .bib (BibTeX, not BibLaTeX to be specific) at the project root so that I can cite the sources from this one file from all Markdown documents. I reference this file in the subfolders containing the Markdown documents in the Pandoc Markdown YAML header as bibliography: "bibliography.bib".

The PandocCiter output shows that the extension searches for a file one level above the root project (and does not find it), which leads me to believe the extension searches relative to the project root.

A workaround is to define (e.g. in the VSCode's project settings) a Default Bib file (e.g. './bibliography.bib'). However, this works only for one .bib file and is tedious to define for every project when the path is already specified in the Markdown documents YAML header.

Another "workaround" is to enclose the .bib path in square brackets: bibliography: ["../bibliography.bib"] as suggested in #5.

This seems very related to #32. Maybe what I experience is a side effect of the change mentioned in that issue? Fixing my problem by simply adding the square brackets seems like an easy fix and all examples in the README use these brackets. However, I think Pandoc allows bibliography paths without these brackets and #32 makes it seem like they should also be optional for this extension. If this is intended, IMO documentation should be added to make clear that adding square brackets makes the path relative to the document while no brackets make it relative to the project, as this is how it appears currently...

Install details:
Version: 1.85.1
Commit: 0ee08df0cf4527e40edc9aa28f4b5bd38bbff2b2
Date: 2023-12-13T09:47:11.635Z
Electron: 25.9.7
ElectronBuildId: 25551756
Chromium: 114.0.5735.289
Node.js: 18.15.0
V8: 11.4.183.29-electron.0
OS: Linux x64 6.6.9-arch1-1

My OS is Arch Linux and PandocCiter is at version v.0.10.3.

Anyways, thanks for the great extension, fixing one of the most annoying holes in my markdown writing pipeline <3

After struggling with markdown for complex documents I decided to try restructuredtext (with sphinx) and I'm liking it a lot. Sadly, no citation helper exist for this language yet.

I was wondering how difficult it would be to make your extension work with it. If in not wrong the differences in implementation with markdown are quite small: instead of @, rst require :cite: and rather than having the bibtex file declared in the yaml header, rst declares it at the bibliography insertion point .. bibliography:: refs.bib

More information please refer to:
https://sphinxcontrib-bibtex.readthedocs.io/en/latest/quickstart.html

Do you believe it would be possible to implement it easily?

This is great; is it possible to set it up so that the program recognizes .pmd files as markdown?
.pmd files are a python analog to R-markdown .rmd files, used with pweave (a python analog to knitr).

Being able to use PandocCiter would enable a really nice .pmd-based workflow for creating academic articles.

Is there any way to enable the extension for RMarkdown files?

Hi,

after installing Pandoc Citer, the extension seemingly doesn't parse my .bib-file, and no dropdown menu is produced when using [@] or [ctrl + space]. When checking for a log under the "Output"-tab, the log remains empty.

I'm running VSCode on Windows 10. After installing the extension, entries for Pandoc Citer are found in the settings.json. The extension vscode-pandoc is installed, and pandoc is also available via the command line.

Am I doing something wrong?

Here are the entries in the settings.json:

	// List of fields displayed in preview
	"PandocCiter.CitationFormat": [
		"author",
		"title",
		"journal",
		"publisher",
		"booktitle",
		"year"
	],

	// Path to default bib file
	"PandocCiter.DefaultBib": "",

	// Whether to forget bib file when changing documents
	"PandocCiter.ForgetUnusedBib": true,

	// Main document containing YAML for bibliography
	"PandocCiter.RootFile": "",

	// Should log be shown in Output panel
	"PandocCiter.ShowLog": false,

	// Whether to use the Default Bib
	"PandocCiter.UseDefaultBib": true,

	// How citation completions are shown
	"PandocCiter.ViewType": "inline",

Hi, me again.

I just noticed that PandocCiter only searches for the DefaultBib in the folder of the opened editor.

My defaultbib is in the root folder. My markdown files are in the folder and subfolders of the folder document. Right now PandocCiter is only searching for the bib file in the folder of the opened file e.g. /document/chapter01/...

I think when the bib file is relative specified than it would make sense to search the whole folder.
Something like this should do it:
vscode.workspace.findFiles(configuration.get('DefaultBib')).then(x => {bibFile = x[0]});

Maybe this is also useful if multiple defaultbibs are specified.

Is there a way to trigger the extension using another key or a keyboard shortcut? In particular, when using Quarto documents the popup conflict with the Quarto autocompletion that suggests cross-references within the document.
Thanks!

I've used sublime text for many years so it is difficult to change to a different editor. Your extension works so amazingly well on VSC. I would love if we had something similar for ST. I currently use citer which is seriously outdated but gets the job done. However, it is not as intuitive as PandocCiter. I am sure this is a major undertaking, but if it's possible, I and many others would appreciate it.

I just installed this and there seem to be no errors during installation. It just doesn't work for me. I also updated VSCode in case it was an issue with versions.Any ideas why this isn't working? I have the .bib file in the same folder so I have

bibliography: [./library.bib]

and also set a default .bib file just in case.

This is the output log so it seems to see my .bib file

Parsed 235 .bib entries from /home/../library.bib.
Looking for .bib file:/home/../library.bib.
Found .bib file /home/../library.bib.
.bib file /home/../library.bib. is already being watched.

Thoughts? Thanks for making this package.

It would be beneficial, if you would introduce a scope for the references (i.e. both for @reference and [@reference]) in order to be able to provide syntax highlight with the theme installed.

At the moment the references to citations are the same colour as the main text, making the finding of references very difficult.

Hello,

I cannot get PandocCiter suggestions to show up in macOS, not in autompletion when I type, for example, @wa; neither when I select those three letters and press Ctrl + Space. Below are my vscode user settings. Thanks for your help.

  "PandocCiter.DefaultBib": "/Users/macbook/Documents/Dropbox/BibDesk/biblio-books.bib",
  "PandocCiter.UseDefaultBib": true,
  "PandocCiter.ForgetUnusedBib": true,
  "PandocCiter.ViewType": "browser",
  "PandocCiter.ShowLog": true,
  "PandocCiter.CitationFormat": [
    "author",
    "title",
    "journal",
    "publisher",
    "booktitle",
    "year"
  ],
  "[markdown]": {
    "editor.wordWrap": "on",
    "editor.quickSuggestions": true
  },
  "editor.snippetSuggestions": "top",
  "editor.suggestOnTriggerCharacters": "true",

If I use a single citation .bib file without square brackets the autocomplete function doesn't work.
Is there a solution without using square brackets?
Thanks!

Thanks for the amazing project!

I remembered that when I first used Pandoc Citer, multiple citekeys could show up at the same time which was the same as the demo figure in README.md, so I could pick one that I want in a breeze. However, I have no idea why only one citekey shows up currently, even though I can switch them use keyboard ↓ and ↑.

I'd like to show multiple citekeys simultaneously as previous. And the settings are as follows. Could you help with the small issue? Thanks so much!

My autocomplete was broken and I searched through my bibTex file for possible errors. Eventually I found that I had an entry for a twitter post where I included the Twitter handle as the author name (e.g. @authorname).

Removing the @ symbol fixed the problem with parsing my .bib file and thereby restored autocomplete functionality.

Even so, it is desirable to be able to include "@" symbol in the author field, as certain citation styles demand the inclusion of Twitter handles when citing posts.

First, thank you so much for this extension!

Pandoc provides the -@citekey syntax to suppress the name of the author(s) and only show the publication year in the converted document. This is very useful when the name of the author is already mentioned in the text. For example, "As Habermas mentioned earlier...[-@Habermas1991]" will turn into "As Habermas mentioned earlier...(1991)".

Currently, PandocCiter won't trigger if the @ is right after some text without a space to avoid problems with email addresses. Unfortunately, this means that no suggestions are triggered when I want to use Pandoc's syntax for suppressing author names. It would be great if you could:

1. Add an exception to the rule so that suggestions are triggered when typing -@
2. Expand the solution for #1 and add syntax highlighting for Pandoc citations with suppressed author names

Hi, first, a great extension. Thank you.

I encountered a "bug" when the markdown file is not in the vscode workspace directory.

I have the following files in my project folder:

project/
  docs/
    manuscript.md
    manuscript.bib

and the manuscript.md YAML metafile block containing:

bibliography: manuscript.bib

But, when I save manuscript.md after a change, the extension leaves a log:

Looking for file: c:\Users\...\project\manuscript.bib

and obviously not functioning properly.

My desired behavior of the extension is to cwd to the document's directory before running its functionality.

Thanks

Problem
I have to use a custom BibEntry for Standards but I can't select this custom BibEntry in autocompletion.
I noticed that the BibTex Entries are hardcoded in https://github.com/notZaki/PandocCiter/blob/master/src/providers/completer/citation.ts. The version of latex workshop https://github.com/James-Yu/LaTeX-Workshop/blob/master/src/providers/completer/citation.ts does read all the entries from the actual bibtex.

Expected behavior
I want to autocomplete custom BibEntries.

Thanks for this very useful extension!

Currently, in the YAML header, I have:

bibliography: ["file1.bib","file2.bib"]

And this works without problems, also with pandoc.
But if I try to format the entry in a more YAML-ly way, which is:

bibliography:
  - file1.bib
  - file2.bib

this gets ignored by the extension, even if the two formats describe the same array.
Am I missing something? Or is it a feature that I could ask to be implemented?
Thanks!
mario

Thank you for this absolutely brilliant extension. The native format for pandoc-citeproc is CSL JSON, and it would be wonderful if you could support the ability to read these files as well as BibTeX. I expect that many Pandoc users will be using your extension with Zotero and its Better BibTeX for Zotero extension, which can export directly to CSL JSON or CSL YAML to avoid the encoding issues that can come with BibTeX.