Have you tested with the latest version that has just been released? I think some of this should have been fixed.
Von: pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org <pandoc-...@googlegroups.com> Im Auftrag von Matthew Lynskey
Gesendet: Freitag, 20. November 2020 01:48
An: pandoc-discuss <pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org>
Betreff: Re: Pandoc Citation Error with Zotero BibTex Key for Short Note
I also am having a similar issue. I was able to make the citekey work with page numbers, but when I tested this out the same problem occurred.
I have attached my .md file, .bib file, and .docx output below.
Notice that the issue does not seem to manifest with page numbers correctly notated (as delineated above). However, when a source/citekey is listed without page numbers issues occur. Also, interestingly, it seems to have issues with titles with quotation marks. Notice in my documents how there is no punctuation issue with the book with no page numbers but there is a punctuation issue with both the book section and journal article without page numbers.
I too am grateful for any help you can provide.
Many thanks in advance.
On Thursday, November 19, 2020 at 6:00:06 PM UTC-5 Joshua wrote:
Sorry for underestimating what was needed! And thank you for taking the time to look.
Pandoc v2.11.1.1
CSL: chicago-note-bibliography.csl
Sample Input (Markdown):
Do plants perceive?^[On the subject of plant perception, see @runyonVolatileChemicalCues2006 and @gaglianoOutSightNot2012. To compare formatting for a book citation, see @TudgeTreeNaturalHistory2007. For a discussion of specifically optical perception in plants, see @baluskaVisionPlantsPlantSpecific2016.]
Sample Output (PDF):
[1] On the subject of plant perception, see Runyon, “Volatile Chemical Cues Guide Host Location and Host Selection by Parasitic Plants.” and Gagliano et al., “Out of Sight but Not Out of Mind.”. To compare formatting for a book citation, see Tudge, The Tree. For a discussion of specifically optical perception in plants, see Baluška and Mancuso, “Vision in Plants via Plant-Specific Ocelli?”.
Sample Bibliography (ExportedItems.bib):
@article{baluskaVisionPlantsPlantSpecific2016,
title = {Vision in {{Plants}} via {{Plant}}-{{Specific Ocelli}}?},
author = {Baluška, Frantisek and Mancuso, Stefano},
date = {2016-09},
journaltitle = {Trends in Plant Science},
volume = {21},
pages = {727--730},
issn = {13601385},
doi = {10/ghknts},
url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138516300930},
urldate = {2020-11-19},
langid = {english},
number = {9}
}
@article{gaglianoOutSightNot2012,
title = {Out of {{Sight}} but {{Not}} out of {{Mind}}: {{Alternative Means}} of {{Communication}} in {{Plants}}},
shorttitle = {Out of {{Sight}} but {{Not}} out of {{Mind}}},
author = {Gagliano, Monica and Renton, Michael and Duvdevani, Nili and Timmins, Matthew and Mancuso, Stefano},
editor = {Moora, Mari},
date = {2012-05-22},
journaltitle = {PLoS ONE},
volume = {7},
pages = {e37382},
issn = {1932-6203},
doi = {10/f3zvbt},
url = {https://dx.plos.org/10.1371/journal.pone.0037382},
urldate = {2020-11-19},
langid = {english},
number = {5}
}
@article{runyonVolatileChemicalCues2006,
title = {Volatile {{Chemical Cues Guide Host Location}} and {{Host Selection}} by {{Parasitic Plants}}},
author = {Runyon, J. B.},
date = {2006-09-29},
journaltitle = {Science},
volume = {313},
pages = {1964--1967},
issn = {0036-8075, 1095-9203},
doi = {10/dj7dcx},
url = {https://www.sciencemag.org/lookup/doi/10.1126/science.1131371},
urldate = {2020-11-19},
langid = {english},
number = {5795}
}
@book{tudgeTreeNaturalHistory2007,
title = {The {{Tree}}: {{A Natural History}} of {{What Trees Are}}, {{How They Live}}, and {{Why They Matter}}},
shorttitle = {The {{Tree}}},
author = {Tudge, Colin},
date = {2007},
publisher = {{Three Rivers Press}},
location = {{New York}},
isbn = {978-0-307-39539-9 0-307-39539-1},
langid = {english}
}
On Thursday, November 19, 2020 at 2:38:44 PM UTC-8 John MacFarlane wrote:
Very likely this is something we can improve, but we'd
need a complete recipe for reproducnig this: not
just the md input, but the bibliographic data and style
you used. (If it's user error, we could also determine
that from a complete example.)
Joshua <joshu...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> writes:
> I'd like to piggyback here. I have a similar problem, but without a locator
> (Pandoc v2.11.1.1).
>
> *Markdown input:*
>
> Do plants perceive?^[On the subject of plant perception, see
> @runyonVolatileChemicalCues2006 and @gaglianoOutSightNot2012. To compare
> formatting for a book citation, see @TudgeTreeNaturalHistory2007. For a
> discussion of specifically optical perception in plants, see
> @baluskaVisionPlantsPlantSpecific2016.]
>
> *Footnote output:*
>
> [1] On the subject of plant perception, see Runyon, “Volatile Chemical Cues
> Guide Host Location and Host Selection by Parasitic Plants.” and Gagliano
> et al., “Out of Sight but Not Out of Mind.”. To compare formatting for a
> book citation, see Tudge, *The Tree*. For a discussion of specifically
> optical perception in plants, see Baluška and Mancuso, “Vision in Plants
> via Plant-Specific Ocelli?”.
>
> So I'm getting a lot of rogue periods. I *assume* this is user error, but
> I've tried a bunch of things to no avail.
>
> Many thanks,
> Joshua
>
> On Monday, November 16, 2020 at 6:50:02 AM UTC-8 ma...-99kdpPDHh7+H5jm5YRNtOEB+6BGkLq7r@public.gmane.org
> wrote:
>
>> Pranesh,
>>
>> Thank you kindly for this additional clarification on citation formatting
>> for Pandoc. It is helpful to know this for in-line citations.
>>
>> Many thanks.
>>
>> Kind Regards,
>> Matt
>>
>> On Sunday, November 15, 2020 at 4:48:37 PM UTC-5 the.so...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org
>> wrote:
>>
>>> Dear Matthew,
>>> I just wanted to note that, given you are using chicago-note-bibliography
>>> which uses footnotes, you can also achieve the same result by writing:
>>>
>>> ```
>>> Test [@KearneyIntroduction2006, p. xvi]
>>> ```
>>>
>>> instead of:
>>>
>>> ```
>>> Test [^4]
>>>
>>> [^4]: @KearneyIntroduction2006 [p. xvi]
>>> ```
>>>
>>> Pandoc with the help of the CSL will automatically convert that (inline)
>>> citation into a footnote. That makes writing the citations easier.
>>> Another benefit of doing that is that if you ever need to change the
>>> citations into an inline-citation style, then you won't need to go and
>>> remove all the footnote references: you would only need to change the CSL
>>> file.
>>>
>>> Regards,
>>> Pranesh
>>> On Saturday, 14 November, 2020 at 1:34:35 am UTC+5:30
>>> ma...@noblecollective.org wrote:
>>>
>>>> Yes. This seems to work great. I gave it a shot on my end and it renders
>>>> it correctly. Many, many thanks for your help here!
>>>>
>>>> On Friday, November 13, 2020 at 1:28:16 PM UTC-5 fiddlosopher wrote:
>>>>
>>>>> The correct way to do the citation would be
>>>>>
>>>>> [^4]: @KearneyIntroduction2006 [p. xvi].
>>>>>
>>>>> This ensures that citeproc can tell you've got a locator, and that it's
>>>>> a page -- if you do this, all the punctuation will be correct (and don't
>>>>> worry, the 'p.' won't show in the final result, since the style says not to
>>>>> use it).
>>>>> On Friday, November 13, 2020 at 3:27:58 AM UTC-8
>>>>> ma...@noblecollective.org wrote:
>>>>>
>>>>>> Thank you so very much! This .csl is exactly the style I was looking
>>>>>> for. Many, many thanks for this!
>>>>>>
>>>>>> This still does not resolve the punctuation issue, especially with
>>>>>> Book Sections and Journal Articles (i.e., perhaps anything with quotations
>>>>>> marks). I will try to submit a bug report for this particular concern.
>>>>>>
>>>>>> Very thankful for all of your help here!
>>>>>>
>>>>>> On Thursday, November 12, 2020 at 11:44:17 PM UTC-5 Denis Maier wrote:
>>>>>>
>>>>>>> Hi, I guess you're using the chicago-note-bibliography.csl style,
>>>>>>> right? (I couldn't find a chicago-short-note.csl on the repo. Anyway, the
>>>>>>> results you're getting may look odd to you, but this is exactly what is
>>>>>>> requested by CMoS in its current iteration. They now want the author's name
>>>>>>> only where they would have had "ibid." before.
>>>>>>>
>>>>>>> It's quite easy to change this. This here (
>>>>>>> https://gist.github.com/denismaier/21168acf9e9287fc41f32c7351917111)
>>>>>>> should do what you want.
>>>>>>>
>>>>>>> Best,
>>>>>>> Denis
>>>>>>>
>>>>>>> Am 13.11.2020 um 03:46 schrieb Matthew Lynskey:
>>>>>>>
>>>>>>> Thanks for the help. I will try to go and submit a bug report for
>>>>>>> this.
>>>>>>>
>>>>>>> Attached are 1) references from Zotero in Better BibTex, 2) the
>>>>>>> "Test" md file, and 3) the Test.docx output.
>>>>>>>
>>>>>>> In terms of the style issue regarding the lack of a title. I don't
>>>>>>> understand code or .csl format and would not be able to tell if it is
>>>>>>> reading the style correctly. If it is, this seems like an odd format as I
>>>>>>> have not seen a short-subsequent style that left out the title and only had
>>>>>>> author's name. If this is the case, do you have any insight into a .csl
>>>>>>> style that would do short style every time? (see below for an example)
>>>>>>>
>>>>>>> [1]: Kearney, “Introduction,” xvi.
>>>>>>> [2]: Kearney, “Introduction,” 3.
>>>>>>> [3]: Kearney, “Introduction,” 35.
>>>>>>>
>>>>>>> I appreciate your help and guidance here.
>>>>>>> On Thursday, November 12, 2020 at 8:51:36 PM UTC-5 John MacFarlane
>>>>>>> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>> It would help to have the bibtex bibliography entry you're using
>>>>>>>> for the Kearney item, and the exact markdown citation you're
>>>>>>>> using.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> John MacFarlane <j...-TVLZxgkOlNX2fBVCVOL8/A@public.gmane.org> writes:
>>>>>>>>
>>>>>>>> > The second issue probably just reflects the style, which
>>>>>>>> > can use a shortened form when the work has just been cited.
>>>>>>>> > Do you have reason to believe pandoc is not following
>>>>>>>> > the rules in the csl file?
>>>>>>>> >
>>>>>>>> > The first issue may be something we can improve. Why
>>>>>>>> > don't you submit a bug report on our tracker, with
>>>>>>>> > full information sufficient for reproducing it, so we
>>>>>>>> > don't lose track? https://github.com/jgm/pandoc/issues
>>>>>>>> >
>>>>>>>> > Matthew Lynskey <ma...-99kdpPDHh7+H5jm5YRNtOEB+6BGkLq7r@public.gmane.org> writes:
>>>>>>>> >
>>>>>>>> >> Alright. I am upgraded to version 2.11.1.1. Thanks for the help
>>>>>>>> here.
>>>>>>>> >>
>>>>>>>> >> When I process the BibTex Key through Pandoc I end up with
>>>>>>>> citations like
>>>>>>>> >> below. The same issues as described above seem to be occurring.
>>>>>>>> (Notice the *punctuation
>>>>>>>> >> issue* [which seems to happen with journal articles/book sections
>>>>>>>> that have
>>>>>>>> >> quotation marks but works fairly good with books which get
>>>>>>>> italicized] and
>>>>>>>> >> also that the *second reference* does not produce the title only
>>>>>>>> the
>>>>>>>> >> author).
>>>>>>>> >>
>>>>>>>> >> [1] Kearney, “Introduction.”, xvi.
>>>>>>>> >> [2] Kearney, 3.
>>>>>>>> >>
>>>>>>>> >> Any thoughts?
>>>>>>>> >> On Thursday, November 12, 2020 at 7:05:26 PM UTC-5
>>>>>>>> jmuc...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org wrote:
>>>>>>>> >>
>>>>>>>> >>> "brew upgrade" should do it all by itself. Homebrew has version
>>>>>>>> 2.11.1.1
>>>>>>>> >>> as of my writing:
>>>>>>>> >>>
>>>>>>>> >>>
>>>>>>>> >>>
>>>>>>>> >>> On Thursday, 12 November 2020 at 18:01:10 UTC-5
>>>>>>>> ma...-99kdpPDHh7+H5jm5YRNtOEB+6BGkLq7r@public.gmane.org
>>>>>>>> >>> wrote:
>>>>>>>> >>>
>>>>>>>> >>>> Thanks for the advice here.
>>>>>>>> >>>>
>>>>>>>> >>>> I updated Pandoc via Terminal using *brew upgrade pandoc* but
>>>>>>>> it only
>>>>>>>> >>>> brought it to *pandoc 2.10.1*. Any advice on how to get it to
>>>>>>>> pandoc
>>>>>>>> >>>> 2.11.1.1?
>>>>>>>> >>>>
>>>>>>>> >>>> Again, I am a newbie here and would appreciate any guidance?
>>>>>>>> >>>>
>>>>>>>> >>>> Many thanks in advance!
>>>>>>>> >>>>
>>>>>>>> >>>> On Thursday, November 12, 2020 at 4:55:00 PM UTC-5 John
>>>>>>>> MacFarlane wrote:
>>>>>>>> >>>>
>>>>>>>> >>>>>
>>>>>>>> >>>>> Ah. Try getting the latest version of pandoc (2.11.1.1).
>>>>>>>> >>>>> Citation support was completely overhauled in 2.11
>>>>>>>> >>>>> (so the pandoc-citeproc filter is no longer necessary;
>>>>>>>> >>>>> instead, you use the --citeproc option). It should
>>>>>>>> >>>>> be much better in general, so see if you get the same
>>>>>>>> >>>>> results with the latest pandoc.
>>>>>>>> >>>>>
>>>>>>>> >>>>> Matthew Lynskey <ma...-99kdpPDHh7+H5jm5YRNtOEB+6BGkLq7r@public.gmane.org> writes:
>>>>>>>> >>>>>
>>>>>>>> >>>>> > Thanks for the question. I checked this in terminal and this
>>>>>>>> is what
>>>>>>>> >>>>> the
>>>>>>>> >>>>> > output is:
>>>>>>>> >>>>> >
>>>>>>>> >>>>> > pandoc 2.10.1
>>>>>>>> >>>>> >
>>>>>>>> >>>>> > Compiled with pandoc-types 1.21, texmath 0.12.0.2,
>>>>>>>> skylighting 0.8.5
>>>>>>>> >>>>> >
>>>>>>>> >>>>> > Copyright (C) 2006-2020 John MacFarlane
>>>>>>>> >>>>> >
>>>>>>>> >>>>> > On Thursday, November 12, 2020 at 4:10:28 PM UTC-5 John
>>>>>>>> MacFarlane
>>>>>>>> >>>>> wrote:
>>>>>>>> >>>>> >
>>>>>>>> >>>>> >>
>>>>>>>> >>>>> >>
>>>>>>>> >>>>> >> It's very important to know here what pandoc --version
>>>>>>>> says.
>>>>>>>> >>>>> >>
>>>>>>>> >>>>> >> Matthew Lynskey <ma...-99kdpPDHh7+H5jm5YRNtOMXa4x6EXUF0@public.gmane.orgg> writes:
>>>>>>>> >>>>> >>
>>>>>>>> >>>>> >> > Hello. I am fairly new to Pandoc. I am seeking to use the
>>>>>>>> Chicago
>>>>>>>> >>>>> Short
>>>>>>>> >>>>> >> > Note .csl from Zotero. I believe I have downloaded the
>>>>>>>> most recent
>>>>>>>> >>>>> >> version.
>>>>>>>> >>>>> >> > I am also using the BibTex citation key in a footnote of
>>>>>>>> a Markdown
>>>>>>>> >>>>> that
>>>>>>>> >>>>> >> > outputs to .docx. My goal is to process these through
>>>>>>>> Pandoc.
>>>>>>>> >>>>> >> >
>>>>>>>> >>>>> >> > When I use the .csl short note style and the citation key
>>>>>>>> and
>>>>>>>> >>>>> process it
>>>>>>>> >>>>> >> > through Pandoc (i.e., DocDown). I have two
>>>>>>>> (interrelated?) issues
>>>>>>>> >>>>> that
>>>>>>>> >>>>> >> come
>>>>>>>> >>>>> >> > up. I am trying to resolve and would appreciate any help
>>>>>>>> and
>>>>>>>> >>>>> guidance.
>>>>>>>> >>>>> >> >
>>>>>>>> >>>>> >> > 1. *Punctuation*: My BibTex key for the following
>>>>>>>> resource is
>>>>>>>> >>>>> >> > @KearneyIntroduction2006. This is a book section and when
>>>>>>>> I write
>>>>>>>> >>>>> >> > @KearneyIntroduction2006, xvi the .csl file output comes
>>>>>>>> out like
>>>>>>>> >>>>> this:
>>>>>>>> >>>>> >> >
>>>>>>>> >>>>> >> > Kearney, “Introduction.”, xvi
>>>>>>>> >>>>> >> >
>>>>>>>> >>>>> >> > I have added the comma but the period does not go away.
>>>>>>>> >>>>> Interestingly,
>>>>>>>> >>>>> >> when
>>>>>>>> >>>>> >> > I use a BibTex citation key for a book (an item that does
>>>>>>>> not have
>>>>>>>> >>>>> >> > quotation marks in its output like a journal or book
>>>>>>>> section), it
>>>>>>>> >>>>> seems
>>>>>>>> >>>>> >> to
>>>>>>>> >>>>> >> > work fine. For example,
>>>>>>>> @Hubscher-DavidsonTranslation2017, 3-4
>>>>>>>> >>>>> comes out
>>>>>>>> >>>>> >> > like Hubscher-Davidson, Translation and Emotion, 3-4.
>>>>>>>> Notice that I
>>>>>>>> >>>>> >> added
>>>>>>>> >>>>> >> > the comma and this time it removed (what I think would
>>>>>>>> be) a
>>>>>>>> >>>>> naturally
>>>>>>>> >>>>> >> > generated period by Zotero.
>>>>>>>> >>>>> >> >
>>>>>>>> >>>>> >> > 2. *Subsequent References*: Additionally, when I have two
>>>>>>>> >>>>> references
>>>>>>>> >>>>> >> > following each other in sequence I get the following
>>>>>>>> result.
>>>>>>>> >>>>> >> >
>>>>>>>> >>>>> >> > Hubscher-Davidson, *Translation and Emotion*, 3-4.
>>>>>>>> >>>>> >> > Hubscher-Davidson, 7.
>>>>>>>> >>>>> >> >
>>>>>>>> >>>>> >> > I do not want to use ibid style.
>>>>>>>> >>>>> >> >
>>>>>>>> >>>>> >> > *Ideally, I would like the short note to reproduce the
>>>>>>>> author and
>>>>>>>> >>>>> short
>>>>>>>> >>>>> >> > title each time.* (i.e., I would like to produce
>>>>>>>> Hubscher-Davidson,
>>>>>>>> >>>>> >> *Translation
>>>>>>>> >>>>> >> > and Emotion* for all citations and then point this short
>>>>>>>> reference
>>>>>>>> >>>>> to my
>>>>>>>> >>>>> >> > bibliography.)
>>>>>>>> >>>>> >> >
>>>>>>>> >>>>> >> > Does anyone have any guidance on this issue(s)?
>>>>>>>> >>>>> >> >
>>>>>>>> >>>>> >> > Thank you for any guidance. This might be a basic
>>>>>>>> question asked in
>>>>>>>> >>>>> >> > ignorance. I appreciate your help in guiding a novice
>>>>>>>> along this
>>>>>>>> >>>>> way. :)
>>>>>>>> >>>>> >> >
>>>>>>>> >>>>> >> > --
>>>>>>>> >>>>> >> > 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-discus...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org.
>>>>>>>> >>>>> >> > To view this discussion on the web visit
>>>>>>>> >>>>> >>
>>>>>>>> >>>>>
>>>>>>>> https://groups.google.com/d/msgid/pandoc-discuss/db3cff52-8ca3-4d81-91ae-6888eb10e451n%40googlegroups.com
>>>>>>>> >>>>> >> .
>>>>>>>> >>>>> >>
>>>>>>>> >>>>> >
>>>>>>>> >>>>> > --
>>>>>>>> >>>>> > You received this message because you are subscribed to the
>>>>>>>> >>>>> Groups "pandoc-discuss" group.
>>>>>>>> >>>>> > To unsubscribe from this group and stop receiving emails
>>>>>>>> from it, send
>>>>>>>> >>>>> an email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org.
>>>>>>>> >>>>> > To view this discussion on the web visit
>>>>>>>> >>>>>
>>>>>>>> https://groups.google.com/d/msgid/pandoc-discuss/9cd04da6-1664-4645-99da-da571caf40c2n%40googlegroups.com.
>>>>>>>>
>>>>>>>> >>>>>
>>>>>>>> >>>>>
>>>>>>>> >>>>
>>>>>>>> >>
>>>>>>>> >> --
>>>>>>>> >> 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-discus...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org.
>>>>>>>> >> To view this discussion on the web visit
>>>>>>>> https://groups.google.com/d/msgid/pandoc-discuss/515174f6-4a2f-4344-8118-7e4f28e8473an%40googlegroups.com.
>>>>>>>>
>>>>>>>>
>>>>>>> --
>>>>>>> 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-discus...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org.
>>>>>>>
>>>>>>> To view this discussion on the web visit
>>>>>>> https://groups.google.com/d/msgid/pandoc-discuss/0596fb72-9c56-49bb-a7bd-1ec7503e7ad3n%40googlegroups.com
>>>>>>> <https://groups.google.com/d/msgid/pandoc-discuss/0596fb72-9c56-49bb-a7bd-1ec7503e7ad3n%40googlegroups.com?utm_medium=email&utm_source=footer>
>>>>>>> .
>>>>>>>
>>>>>>>
>>>>>>>
>
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