From mboxrd@z Thu Jan 1 00:00:00 1970 X-Msuck: nntp://news.gmane.io/gmane.text.pandoc/33042 Path: news.gmane.io!.POSTED.blaine.gmane.org!not-for-mail From: Nigel Jones Newsgroups: gmane.text.pandoc Subject: Newbie: Unable to resolve references with citeproc Date: Thu, 10 Aug 2023 09:19:35 -0700 (PDT) Message-ID: <683f39b2-7d09-4f6c-97da-0b04d42c34e0n@googlegroups.com> Reply-To: pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_Part_168_524439941.1691684375487" Injection-Info: ciao.gmane.io; posting-host="blaine.gmane.org:116.202.254.214"; logging-data="38855"; mail-complaints-to="usenet@ciao.gmane.io" To: pandoc-discuss Original-X-From: pandoc-discuss+bncBC26JDHUVIARBGM42STAMGQERQ4PRNQ-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org Thu Aug 10 18:19:43 2023 Return-path: Envelope-to: gtp-pandoc-discuss@m.gmane-mx.org Original-Received: from mail-pg1-f188.google.com ([209.85.215.188]) by ciao.gmane.io with esmtps (TLS1.3:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.92) (envelope-from ) id 1qU8Ny-0009w2-G1 for gtp-pandoc-discuss@m.gmane-mx.org; 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Thu, 10 Aug 2023 09:19:36 -0700 (PDT) X-Received: by 2002:a17:90a:d357:b0:263:8c8b:e7b2 with SMTP id i23-20020a17090ad35700b002638c8be7b2mr654742pjx.3.1691684376325; Thu, 10 Aug 2023 09:19:36 -0700 (PDT) X-Original-Sender: nigel.l.jones-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org Precedence: list Mailing-list: list pandoc-discuss-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org; contact pandoc-discuss+owners-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org List-ID: X-Google-Group-Id: 1007024079513 List-Post: , List-Help: , List-Archive: , List-Unsubscribe: , Xref: news.gmane.io gmane.text.pandoc:33042 Archived-At: ------=_Part_168_524439941.1691684375487 Content-Type: multipart/alternative; boundary="----=_Part_169_1033603082.1691684375487" ------=_Part_169_1033603082.1691684375487 Content-Type: text/plain; charset="UTF-8" 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 -- You received this message because you are subscribed to the Google Groups "pandoc-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org To view this discussion on the web visit https://groups.google.com/d/msgid/pandoc-discuss/683f39b2-7d09-4f6c-97da-0b04d42c34e0n%40googlegroups.com. ------=_Part_169_1033603082.1691684375487 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable I have a bibliography file with many citations, and a variety of jupyter no= tebooks 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,
=C2=A0 =C2=A0 =C2=A0title =3D {Development of the {Advanced} {E= ncryption} {Standard}},
=C2=A0 =C2=A0 =C2=A0volume =3D {126},
=C2= =A0 =C2=A0 =C2=A0url =3D {https://www.nist.gov/publications/development-adv= anced-encryption-standard},
=C2=A0 =C2=A0 =C2=A0abstract =3D {Strong c= ryptographic algorithms are essential for the protection of stored and tran= smitted data throughout the world.},
=C2=A0 =C2=A0 =C2=A0language =3D = {en},
=C2=A0 =C2=A0 =C2=A0urldate =3D {2023-05-17},
=C2=A0 =C2=A0= =C2=A0journal =3D {NIST},
=C2=A0 =C2=A0 =C2=A0author =3D {Smid, Miles= E. and Foti, James},
=C2=A0 =C2=A0 =C2=A0month =3D aug,
=C2=A0 = =C2=A0 =C2=A0year =3D {2021},
=C2=A0 =C2=A0 =C2=A0note =3D {Last Modif= ied: 2021-10-14T05:10-04:00
=C2=A0Publisher: Miles E. Smid, James Foti= },
=C2=A0 =C2=A0 =C2=A0file =3D {Full Text PDF:/Users/dasc/Zotero/stor= age/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 fo= rm AES[@smid_development_2021] or in full:

{
=C2=A0"cells": [
=C2=A0 {
=C2=A0 =C2=A0"cell_type": "code",
=C2=A0 =C2=A0"execution_count": null,
=C2=A0 =C2=A0"id": "364e8ef9-e= ebe-4da8-b3e2-0005c94392ae",
=C2=A0 =C2=A0"metadata": {},
=C2=A0 = =C2=A0"outputs": [],
=C2=A0 =C2=A0"source": [
=C2=A0 =C2=A0 "# Te= st document for pandoc\n",
=C2=A0 =C2=A0 "\n",
=C2=A0 =C2=A0 "We = have just one article on the development of AES[@smid_development_2021]\n",=
=C2=A0 =C2=A0 "\n",
=C2=A0 =C2=A0 "# References\n",
=C2=A0 = =C2=A0 "\n"
=C2=A0 =C2=A0]
=C2=A0 }
=C2=A0],
=C2=A0"met= adata": {
=C2=A0 "kernelspec": {
=C2=A0 =C2=A0"display_name": "Py= thon 3 (ipykernel)",
=C2=A0 =C2=A0"language": "python",
=C2=A0 = =C2=A0"name": "python3"
=C2=A0 },
=C2=A0 "language_info": {
= =C2=A0 =C2=A0"codemirror_mode": {
=C2=A0 =C2=A0 "name": "ipython",
=C2=A0 =C2=A0 "version": 3
=C2=A0 =C2=A0},
=C2=A0 =C2=A0"file_e= xtension": ".py",
=C2=A0 =C2=A0"mimetype": "text/x-python",
=C2= =A0 =C2=A0"name": "python",
=C2=A0 =C2=A0"nbconvert_exporter": "python= ",
=C2=A0 =C2=A0"pygments_lexer": "ipython3",
=C2=A0 =C2=A0"versi= on": "3.11.4"
=C2=A0 }
=C2=A0},
=C2=A0"nbformat": 4,
= =C2=A0"nbformat_minor": 5
}

I also wa= nt these citations in IEEE format, so download

h= ttps://github.com/citation-style-language/styles/blob/master/ieee.csl
=

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

I t= hen invoke=C2=A0

pandoc -f ipynb -t ipynb --cite= proc lesson1.ipynb -o lesson1-withrefs.ipynb --bibliography bib.bib --csl i= eee.csl

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

{
=C2=A0"cells": [
=C2=A0 {
=C2=A0 =C2=A0"cell_type": "code= ",
=C2=A0 =C2=A0"execution_count": null,
=C2=A0 =C2=A0"metadata":= {},
=C2=A0 =C2=A0"outputs": [],
=C2=A0 =C2=A0"source": [
= =C2=A0 =C2=A0 "# Test document for pandoc\n",
=C2=A0 =C2=A0 "\n",
=C2=A0 =C2=A0 "We have just one article on the development of AES[@smid_de= velopment_2021]\n",
=C2=A0 =C2=A0 "\n",
=C2=A0 =C2=A0 "# Referenc= es\n",
=C2=A0 =C2=A0 "\n"
=C2=A0 =C2=A0],
=C2=A0 =C2=A0"id":= "364e8ef9-eebe-4da8-b3e2-0005c94392ae"
=C2=A0 }
=C2=A0],
= =C2=A0"nbformat": 4,
=C2=A0"nbformat_minor": 5,
=C2=A0"metadata":= {
=C2=A0 "kernelspec": {
=C2=A0 =C2=A0"name": "python3",
= =C2=A0 =C2=A0"display_name": "Python 3 (ipykernel)",
=C2=A0 =C2=A0"lan= guage": "python"
=C2=A0 },
=C2=A0 "language_info": {
=C2=A0 = =C2=A0"name": "python",
=C2=A0 =C2=A0"codemirror_mode": {
=C2=A0 = =C2=A0 "name": "ipython",
=C2=A0 =C2=A0 "version": "3"
=C2=A0 =C2= =A0},
=C2=A0 =C2=A0"file_extension": ".py",
=C2=A0 =C2=A0"mimetyp= e": "text/x-python",
=C2=A0 =C2=A0"nbconvert_exporter": "python",
=C2=A0 =C2=A0"pygments_lexer": "ipython3",
=C2=A0 =C2=A0"version": "3= .11.4"
=C2=A0 }
=C2=A0}
}

I= then tried other variations such as writing to html, or markdown (gfm), bu= t 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=C2=A0

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

a= nd 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

<= br />



--
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