Newbie: Unable to resolve references with citeproc

Newbie: Unable to resolve references with citeproc

[Nigel Jones]

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I have a bibliography file with many citations, and a variety of jupyter 
notebooks which refer to these. Previously these were processed using 
jupyter book, but I now need to create raw notebook versions.

With that in mind I tried this

Create a simple bibliography 'bib.bib'

@article{smid_development_2021,
     title = {Development of the {Advanced} {Encryption} {Standard}},
     volume = {126},
     url = 
{https://www.nist.gov/publications/development-advanced-encryption-standard},
     abstract = {Strong cryptographic algorithms are essential for the 
protection of stored and transmitted data throughout the world.},
     language = {en},
     urldate = {2023-05-17},
     journal = {NIST},
     author = {Smid, Miles E. and Foti, James},
     month = aug,
     year = {2021},
     note = {Last Modified: 2021-10-14T05:10-04:00
 Publisher: Miles E. Smid, James Foti},
     file = {Full Text PDF:/Users/dasc/Zotero/storage/5YCK8JKG/Smid and 
Foti - 2021 - Development of the Advanced Encryption 
Standard.pdf:application/pdf},
}

Now create a simple notebook in lesson1.ipynb with a single reference of 
the form AES[@smid_development_2021] or in full:

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "364e8ef9-eebe-4da8-b3e2-0005c94392ae",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Test document for pandoc\n",
    "\n",
    "We have just one article on the development of 
AES[@smid_development_2021]\n",
    "\n",
    "# References\n",
    "\n"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.11.4"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}

I also want these citations in IEEE format, so download

https://github.com/citation-style-language/styles/blob/master/ieee.csl

I then experimented with pandoc, but so far I've nott been able to get 
references resolved.

I then invoke 

pandoc -f ipynb -t ipynb --citeproc lesson1.ipynb -o lesson1-withrefs.ipynb 
--bibliography bib.bib --csl ieee.csl

But the output virtually identical to input, other than minor metadata 
differences

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Test document for pandoc\n",
    "\n",
    "We have just one article on the development of 
AES[@smid_development_2021]\n",
    "\n",
    "# References\n",
    "\n"
   ],
   "id": "364e8ef9-eebe-4da8-b3e2-0005c94392ae"
  }
 ],
 "nbformat": 4,
 "nbformat_minor": 5,
 "metadata": {
  "kernelspec": {
   "name": "python3",
   "display_name": "Python 3 (ipykernel)",
   "language": "python"
  },
  "language_info": {
   "name": "python",
   "codemirror_mode": {
    "name": "ipython",
    "version": "3"
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.11.4"
  }
 }
}

I then tried other variations such as writing to html, or markdown (gfm), 
but wasn't able to get the references expanded.

I WAS able to process the bibliography references completely in another 
test using a markdown input file of 

---
# Reference
bibliography: references.bib
link-citations: true
csl: ieee.csl
nocite: "@*"
---

and appropriate invocation changes

So I presume I've made a really simple/silly mistake, but I've yet to 
figure out where.

Can anyone spot the obvious error?

Many thanks
Nigel Jones





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Re: Newbie: Unable to resolve references with citeproc

['Nick Bart' via pandoc-discuss]

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Try

-f ipynb+citations

For an explanation, see https://github.com/jgm/pandoc/issues/5295.

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