pandoc not actually doing anything with citations - what am I doing wrong?

pandoc not actually doing anything with citations - what am I doing wrong?

[Cormac Relf]

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Hi,

Filtering through *pandoc-citeproc-0.3.0.1* and supplying a .csl and .bib 
file to *pandoc-1.12.3.1* fails to render pandoc-style markdown citations.

It just sanitises [ and ] to {[} and {]}, not transforming the [@:] 
references into anything usable. pandoc doesn't output any errors, just 
silently drops, even though the citekey matches the bib file.

I can't figure out what I'm doing wrong; it doesn't seem to detect any 
citations at all, since using gibberish as a citekey doesn't pull any 
errors either, and still sits in the PDF as "[@:gibberish]".
The references section is also empty.

How can Pandoc or I be so blind? What's happening here? I don't get it.

Here's my command:

pandoc -r markdown -s -S --latex-engine=xelatex --filter pandoc-citeproc --
csl=/Users/cormac/.pandoc/csl/aglc.csl --bibliography=/Users/cormac/Dropbox/
Papers/pandoc.bib --biblatex -o output.pdf input.md

input.md consists of:

# Header
...
... [@Kore:2013vb] ...
...
# References

and the referenced pandoc.bib, generated by Papers 3 on a Mac, is below. 
This is just random, I'm not a linguistics expert. The CSL is straight from 
Zotero's website.

%% Created using Papers on Tue, 04 Feb 2014.
%% http://papersapp.com/papers/

@article{Kore:2013vb,
author = {Kore, M and Shaba, V},
title = {{COMMON PATTERNS OF WORD-FORMATION IN BALKAN LANGUAGES: THE CASE 
OF DIMINUITIVE SUFFIXES}},
year = {2013},
read = {Yes},
rating = {0},
date-added = {2014-02-04T12:06:54GMT},
date-modified = {2014-02-04T12:08:54GMT},
abstract = {ABSTRACT This paper discusses some linguistic features which 
are common to Albanian, Slavic languages in the Balkans, Modern Greek and 
Romanian with a special emphasis on the use of diminutive suffixes, which 
are not only used to express smallness but also ...
},
url = 
{http://www.ajssh.leena-luna.co.jp/AJSSHPDFs/Vol.2(2)/AJSSH2013(2.2-37).pdf},
local-url = 
{file://localhost/Users/cormac/Dropbox/Papers/Library.papers3/Files/96/967AC40C-AAA5-4FDA-8FAF-DBAE6B336D9E.pdf},
file = 
{{967AC40C-AAA5-4FDA-8FAF-DBAE6B336D9E.pdf:/Users/cormac/Dropbox/Papers/Library.papers3/Files/96/967AC40C-AAA5-4FDA-8FAF-DBAE6B336D9E.pdf:application/pdf}},
uri = 
{\url{papers3://publication/uuid/ED4C5C00-3D8E-4254-96CD-71B2457C2AC0}}
}


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Re: pandoc not actually doing anything with citations - what am I doing wrong?

[nickbart1980-Re5JQEeQqe8AvxtiuMwx3w]

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Try removing "--biblatex" from the command line.

"--biblatex" seems to convert @foo to \autocite{foo} before pandoc-citeproc 
even gets to see it.

@jgm - I wonder whether it'd be better to deactivate "--biblatex" (and 
"--natbib") when pandoc-citeproc is used … 

On Tuesday, February 4, 2014 1:32:27 PM UTC, Cormac Relf wrote:
>
> Hi,
>
> Filtering through *pandoc-citeproc-0.3.0.1* and supplying a .csl and .bib 
> file to *pandoc-1.12.3.1* fails to render pandoc-style markdown citations.
>
> It just sanitises [ and ] to {[} and {]}, not transforming the [@:] 
> references into anything usable. pandoc doesn't output any errors, just 
> silently drops, even though the citekey matches the bib file.
>
> I can't figure out what I'm doing wrong; it doesn't seem to detect any 
> citations at all, since using gibberish as a citekey doesn't pull any 
> errors either, and still sits in the PDF as "[@:gibberish]".
> The references section is also empty.
>
> How can Pandoc or I be so blind? What's happening here? I don't get it.
>
> Here's my command:
>
> pandoc -r markdown -s -S --latex-engine=xelatex --filter pandoc-citeproc 
> --csl=/Users/cormac/.pandoc/csl/aglc.csl --bibliography=/Users/cormac/
> Dropbox/Papers/pandoc.bib --biblatex -o output.pdf input.md
>
> input.md consists of:
>
> # Header
> ...
> ... [@Kore:2013vb] ...
> ...
> # References
>
> and the referenced pandoc.bib, generated by Papers 3 on a Mac, is below. 
> This is just random, I'm not a linguistics expert. The CSL is straight from 
> Zotero's website.
>
> %% Created using Papers on Tue, 04 Feb 2014.
> %% http://papersapp.com/papers/
>
> @article{Kore:2013vb,
> author = {Kore, M and Shaba, V},
> title = {{COMMON PATTERNS OF WORD-FORMATION IN BALKAN LANGUAGES: THE CASE 
> OF DIMINUITIVE SUFFIXES}},
> year = {2013},
> read = {Yes},
> rating = {0},
> date-added = {2014-02-04T12:06:54GMT},
> date-modified = {2014-02-04T12:08:54GMT},
> abstract = {ABSTRACT This paper discusses some linguistic features which 
> are common to Albanian, Slavic languages in the Balkans, Modern Greek and 
> Romanian with a special emphasis on the use of diminutive suffixes, which 
> are not only used to express smallness but also ...
> },
> url = {
> http://www.ajssh.leena-luna.co.jp/AJSSHPDFs/Vol.2(2)/AJSSH2013(2.2-37).pdf
> },
> local-url = 
> {file://localhost/Users/cormac/Dropbox/Papers/Library.papers3/Files/96/967AC40C-AAA5-4FDA-8FAF-DBAE6B336D9E.pdf},
> file = 
> {{967AC40C-AAA5-4FDA-8FAF-DBAE6B336D9E.pdf:/Users/cormac/Dropbox/Papers/Library.papers3/Files/96/967AC40C-AAA5-4FDA-8FAF-DBAE6B336D9E.pdf:application/pdf}},
> uri = 
> {\url{papers3://publication/uuid/ED4C5C00-3D8E-4254-96CD-71B2457C2AC0}}
> }
>
>
>

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Re: pandoc not actually doing anything with citations - what am I doing wrong?

[kurt.pfeifle-gM/Ye1E23mwN+BqQ9rBEUg]

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Hi,

I recently tested a lot of styles (~1000+) from Zotero and from Github's 
repository of citationstyles.org.

Am Dienstag, 4. Februar 2014 14:32:27 UTC+1 schrieb Cormac Relf:
  

> referenced pandoc.bib, generated by Papers 3 on a Mac, is below. This is 
> just random, I'm not a linguistics expert. The CSL is straight from 
> Zotero's website.
>

I do not see any style named aglc.csl on the Zotero website nor on Github. 
Note, that some of the *.csl files from there simply didn't work (none of 
the smaller ones with ~1600 Bytes or less did work -- they consist only of 
a small header, with no real style rules following afterwards.)

In case this should mean* australian-guide-to-legal-citation.csl *: I 
tested it, and it does its job.
 

> Here's my command:
>
> pandoc -r markdown -s -S --latex-engine=xelatex --filter pandoc-citeproc 
> --csl=/Users/cormac/.pandoc/csl/aglc.csl --bibliography=/Users/cormac/
> Dropbox/Papers/pandoc.bib --biblatex -o output.pdf input.md
>
 
This command should work as soon as you remove the "--biblatex" part from 
it. 

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Re: pandoc not actually doing anything with citations - what am I doing wrong?

[Cormac Relf]

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Indeed, should have pointed out that I renamed it to be shorter.

Both of you are right about --biblatex (thanks!), but there was actually 
another problem at hand on top of that. Papers 3 had a paper (a patent 
actually) which had a weird author field (numbers) and a citekey with 
nothing before the colon: [@:2008vo]. I don't think pandoc was recognising 
that as a citekey, even though that entry @patent{:2008vo, ...} existed in 
the bib file.

Is there supposed to be some sort of standard to how citekeys are laid out? 
I feel like it could be Papers messing up here. I don't think it's a really 
common thing to have no author, so not a big problem really.

Thanks for your help everyone,

Cormac

On Wednesday, February 5, 2014 4:13:19 AM UTC+11, kurt.p...-gM/Ye1E23mwN+BqQ9rBEUg@public.gmane.org 
wrote:
>
> Hi,
>
> I recently tested a lot of styles (~1000+) from Zotero and from Github's 
> repository of citationstyles.org.
>
> Am Dienstag, 4. Februar 2014 14:32:27 UTC+1 schrieb Cormac Relf:
>   
>
>> referenced pandoc.bib, generated by Papers 3 on a Mac, is below. This is 
>> just random, I'm not a linguistics expert. The CSL is straight from 
>> Zotero's website.
>>
>
> I do not see any style named aglc.csl on the Zotero website nor on Github. 
> Note, that some of the *.csl files from there simply didn't work (none of 
> the smaller ones with ~1600 Bytes or less did work -- they consist only of 
> a small header, with no real style rules following afterwards.)
>
> In case this should mean* australian-guide-to-legal-citation.csl *: I 
> tested it, and it does its job.
>  
>
>> Here's my command:
>>
>> pandoc -r markdown -s -S --latex-engine=xelatex --filter pandoc-citeproc 
>> --csl=/Users/cormac/.pandoc/csl/aglc.csl --bibliography=/Users/cormac/
>> Dropbox/Papers/pandoc.bib --biblatex -o output.pdf input.md
>>
>  
> This command should work as soon as you remove the "--biblatex" part from 
> it. 
>

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Re: pandoc not actually doing anything with citations - what am I doing wrong?

[Scot Mcphee]

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I have found one good way to check bib files to to load them into Bibdesk
and see what it complains about. Papers, in my experience, is particularly
notorious in producing illegal values in the bib file. I have now recently
ditched it entirely (after paying for the Papers3 upgrade!) because of this
and many other reasons to do with database reliability (well-documented in
a couple of posts on my blog). I switched to Mendeley, but even it won't
always produce a "clean" bib file. For example if your author is called
"O'Connell" you'll get a reference id of "O'Connell1999" which is
definitely illegal (also watch for the French, I had one - L'Hoir - with
the same problem). I manually adjust those when I find them in Mendeley to
omit the apostrophe.

Probably your reference is Anonymous, i.e. no author or an institutional
author? How the style handles the lack of an Author field in the body of
the bib will be up to the particular style, I suppose.

There are three nice side effects of moving over to Mendeley Desktop (sorry
to shill for it):

1.  it will automatically sync its database to a nominated .bib file so you
can always have one up to date with your research data.

2. it generates its citation keys in much nicer format, i.e. author date
(Mcphee2014) so you don't have to remember those awful random key
appendices that Papers tacks on, nor have the colon between the author and
the year. I had to do a bulk regexp search and replace on my documents to
make it work of course but that didn't take long and it's much nicer to use
now.

3. it's free if you have less than 2GB of PDFs.

One the downside, what it lacks is an internal search hook into the online
databases. You have to go to each one you use one by one and use their web
search facility individually and import results with the Mendeley
bookmarklet, which is slightly ugly. But that beats losing data to database
corruptions.

Scot



*Scot Mcphee. *
*Computer programmer. Classics PhD. Trouble-maker. Problem-solver.*
p 0412957414
e scot.mcphee-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org
let x=x http://crazymcphee.net/x/
inlustre monumentum est http://inlustre.net/


On 5 February 2014 10:21, Cormac Relf <cormacrelf-BUHhN+a2lJ4@public.gmane.org> wrote:

> Indeed, should have pointed out that I renamed it to be shorter.
>
> Both of you are right about --biblatex (thanks!), but there was actually
> another problem at hand on top of that. Papers 3 had a paper (a patent
> actually) which had a weird author field (numbers) and a citekey with
> nothing before the colon: [@:2008vo]. I don't think pandoc was recognising
> that as a citekey, even though that entry @patent{:2008vo, ...} existed in
> the bib file.
>
> Is there supposed to be some sort of standard to how citekeys are laid
> out? I feel like it could be Papers messing up here. I don't think it's a
> really common thing to have no author, so not a big problem really.
>
> Thanks for your help everyone,
>
> Cormac
>
> On Wednesday, February 5, 2014 4:13:19 AM UTC+11, kurt.p...-gM/Ye1E23mzyGubv3rZB4bnyvKbxsaOP@public.gmane.org:
>>
>> Hi,
>>
>> I recently tested a lot of styles (~1000+) from Zotero and from Github's
>> repository of citationstyles.org.
>>
>> Am Dienstag, 4. Februar 2014 14:32:27 UTC+1 schrieb Cormac Relf:
>>
>>
>>> referenced pandoc.bib, generated by Papers 3 on a Mac, is below. This is
>>> just random, I'm not a linguistics expert. The CSL is straight from
>>> Zotero's website.
>>>
>>
>> I do not see any style named aglc.csl on the Zotero website nor on
>> Github. Note, that some of the *.csl files from there simply didn't work
>> (none of the smaller ones with ~1600 Bytes or less did work -- they consist
>> only of a small header, with no real style rules following afterwards.)
>>
>> In case this should mean* australian-guide-to-legal-citation.csl *: I
>> tested it, and it does its job.
>>
>>
>>> Here's my command:
>>>
>>> pandoc -r markdown -s -S --latex-engine=xelatex --filter pandoc-citeproc
>>> --csl=/Users/cormac/.pandoc/csl/aglc.csl --bibliography=/Users/cormac/D
>>> ropbox/Papers/pandoc.bib --biblatex -o output.pdf input.md
>>>
>>
>> This command should work as soon as you remove the "--biblatex" partfrom it.
>>
>  --
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> .
>
> For more options, visit https://groups.google.com/groups/opt_out.
>

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Re: pandoc not actually doing anything with citations - what am I doing wrong?

[John MacFarlane]

Pandoc citation keys must begin with an underscore or a letter, and
can contain underscores, alphanumerics, and punctuation characters
that are followed by alphanumerics.


+++ Cormac Relf [Feb 04 14 16:21 ]:
>    Indeed, should have pointed out that I renamed it to be shorter.
>    Both of you are right about --biblatex (thanks!), but there was
>    actually another problem at hand on top of that. Papers 3 had a paper
>    (a patent actually) which had a weird author field (numbers) and a
>    citekey with nothing before the colon: [@:2008vo]. I don't think pandoc
>    was recognising that as a citekey, even though that entry
>    @patent{:2008vo, ...} existed in the bib file.
>    Is there supposed to be some sort of standard to how citekeys are laid
>    out? I feel like it could be Papers messing up here. I don't think it's
>    a really common thing to have no author, so not a big problem really.
>    Thanks for your help everyone,
>    Cormac
>    On Wednesday, February 5, 2014 4:13:19 AM UTC+11,
>    kurt.p...-gM/Ye1E23mwN+BqQ9rBEUg@public.gmane.org wrote:
> 
>    Hi,
>    I recently tested a lot of styles (~1000+) from Zotero and from
>    Github's repository of [1]citationstyles.org.
>    Am Dienstag, 4. Februar 2014 14:32:27 UTC+1 schrieb Cormac Relf:
> 
>    referenced pandoc.bib, generated by Papers 3 on a Mac, is below. This
>    is just random, I'm not a linguistics expert. The CSL is straight from
>    Zotero's website.
> 
>    I do not see any style named aglc.csl on the Zotero website nor on
>    Github. Note, that some of the *.csl files from there simply didn't
>    work (none of the smaller ones with ~1600 Bytes or less did work --
>    they consist only of a small header, with no real style rules following
>    afterwards.)
>    In case this should mean australian-guide-to-legal-citation.csl : I
>    tested it, and it does its job.
> 
>    Here's my command:
>    pandoc -r markdown -s -S --latex-engine=xelatex --filter
>    pandoc-citeproc --csl=/Users/cormac/.pandoc/csl/aglc.csl
>    --bibliography=/Users/cormac/Dropbox/Papers/pandoc.bib --biblatex -o
>    output.pdf input.md
> 
> 
>    This command should work as soon as you remove the "--biblatex" part
>    from it.
> 
>    --
>    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 post to this group, send email to pandoc-discuss-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>    To view this discussion on the web visit
>    [2]https://groups.google.com/d/msgid/pandoc-discuss/221119e1-f04c-42cc-
>    8aad-384ee8346e23%40googlegroups.com.
>    For more options, visit [3]https://groups.google.com/groups/opt_out.
> 
> References
> 
>    1. http://citationstyles.org/
>    2. https://groups.google.com/d/msgid/pandoc-discuss/221119e1-f04c-42cc-8aad-384ee8346e23%40googlegroups.com
>    3. https://groups.google.com/groups/opt_out

Re: pandoc not actually doing anything with citations - what am I doing wrong?

[Rintze Zelle]

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On Tuesday, February 4, 2014 12:13:19 PM UTC-5, kurt.p...-gM/Ye1E23mwN+BqQ9rBEUg@public.gmane.org 
wrote:
>
> I do not see any style named aglc.csl on the Zotero website nor on Github. 
> Note, that some of the *.csl files from there simply didn't work (none of 
> the smaller ones with ~1600 Bytes or less did work -- they consist only of 
> a small header, with no real style rules following afterwards.)
>

You mean styles like 
https://github.com/citation-style-language/styles/blob/master/dependent/3-biotech.csl 
? Dependent styles were specifically designed to work as aliases to 
"independent" styles, to eliminate the need to duplicate complete styles in 
case multiple journals use the same citation format. See 
http://citationstyles.org/downloads/specification.html#dependent-styles for 
more information.

Rintze 

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Re: pandoc not actually doing anything with citations - what am I doing wrong?

[kurt.pfeifle-gM/Ye1E23mwN+BqQ9rBEUg]

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Hi Rintze,

Am Donnerstag, 6. Februar 2014 21:38:15 UTC+1 schrieb Rintze Zelle:
>
> On Tuesday, February 4, 2014 12:13:19 PM UTC-5, kurt.p...-gM/Ye1E23mzyGubv3rZB4bnyvKbxsaOP@public.gmane.org:
>>
>> I do not see any style named aglc.csl on the Zotero website nor on 
>> Github. Note, that some of the *.csl files from there simply didn't work 
>> (none of the smaller ones with ~1600 Bytes or less did work -- they consist 
>> only of a small header, with no real style rules following afterwards.)
>>
>
> You mean styles like 
> https://github.com/citation-style-language/styles/blob/master/dependent/3-biotech.csl? Dependent styles were specifically designed to work as aliases to 
> "independent" styles, to eliminate the need to duplicate complete styles in 
> case multiple journals use the same citation format. See 
> http://citationstyles.org/downloads/specification.html#dependent-stylesfor more information.
>

Yes, probably most of these non-working csl files were "dependent" styles. 
(But not all.)

What i simply did was this: check out the Github repository of CSL styles 
and then:

    for i in *.csl; do
        [run my shellscript which creates a test sample of the citation 
style]
    done

I don't understand how these "dependent" styles are supposed to work. 
Probably not on the commandline and via a pandoc call, but only through 
some GUI tool... (I do not care at the moment, but I'll return to this 
topic later to research it further.)

 

>
> Rintze 
>

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Re: pandoc not actually doing anything with citations - what am I doing wrong?

[Kit Lloyd]

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I am also working with aglc.csl and have a problem that I hope maybe easy 
to solve.  

When identical citations are repeated immediately after one another then 
the second citation is replaced by "Ibid." - this works fine.  

When citations are separated by intervening citations then the following 
identical citation should comprise "authors_surname above n x", where x 
equates to the prior occurrence. This doesn't work (it simply prints the 
authors_surname).

I have tested the csl package and it works as expected, so it seems to be 
in the way I running citeproc.  (I am using the command line described 
above)

Can anyone point me in the right direction?





On Wednesday, 5 February 2014 04:21:44 UTC+4, Cormac Relf wrote:
>
> Indeed, should have pointed out that I renamed it to be shorter.
>
> Both of you are right about --biblatex (thanks!), but there was actually 
> another problem at hand on top of that. Papers 3 had a paper (a patent 
> actually) which had a weird author field (numbers) and a citekey with 
> nothing before the colon: [@:2008vo]. I don't think pandoc was recognising 
> that as a citekey, even though that entry @patent{:2008vo, ...} existed in 
> the bib file.
>
> Is there supposed to be some sort of standard to how citekeys are laid 
> out? I feel like it could be Papers messing up here. I don't think it's a 
> really common thing to have no author, so not a big problem really.
>
> Thanks for your help everyone,
>
> Cormac
>
> On Wednesday, February 5, 2014 4:13:19 AM UTC+11, kurt.p...-gM/Ye1E23mwN+BqQ9rBEUg@public.gmane.org 
> wrote:
>>
>> Hi,
>>
>> I recently tested a lot of styles (~1000+) from Zotero and from Github's 
>> repository of citationstyles.org.
>>
>> Am Dienstag, 4. Februar 2014 14:32:27 UTC+1 schrieb Cormac Relf:
>>   
>>
>>> referenced pandoc.bib, generated by Papers 3 on a Mac, is below. This is 
>>> just random, I'm not a linguistics expert. The CSL is straight from 
>>> Zotero's website.
>>>
>>
>> I do not see any style named aglc.csl on the Zotero website nor on 
>> Github. Note, that some of the *.csl files from there simply didn't work 
>> (none of the smaller ones with ~1600 Bytes or less did work -- they consist 
>> only of a small header, with no real style rules following afterwards.)
>>
>> In case this should mean* australian-guide-to-legal-citation.csl *: I 
>> tested it, and it does its job.
>>  
>>
>>> Here's my command:
>>>
>>> pandoc -r markdown -s -S --latex-engine=xelatex --filter pandoc-citeproc 
>>> --csl=/Users/cormac/.pandoc/csl/aglc.csl --bibliography=/Users/cormac/
>>> Dropbox/Papers/pandoc.bib --biblatex -o output.pdf input.md
>>>
>>  
>> This command should work as soon as you remove the "--biblatex" part 
>> from it. 
>>
>

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pandoc not actually doing anything with citations - what am I doing wrong?

[Kit Lloyd]

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Hi,

I was wondering whether you did finally manage to get aglc.csl to work as expected with pandoc-citeproc.  I seem to be stuck, aglc.csl seems to work fine when using the Zotero plugins, but not so well when using pandoc-citeproc.

Re: pandoc not actually doing anything with citations - what am I doing wrong?

[Cormac Relf]

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I don't even bother with aglc.csl any more. I manually follow AGLC3 in my
text editor with pandoc footnotes.

Best of luck.

On 3 April 2015 at 14:45, Kit Lloyd <kitlloyd-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:

> Hi,
>
> I was wondering whether you did finally manage to get aglc.csl to work as
> expected with pandoc-citeproc.  I seem to be stuck, aglc.csl seems to work
> fine when using the Zotero plugins, but not so well when using
> pandoc-citeproc.
>
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Re: pandoc not actually doing anything with citations - what am I doing wrong?

[Kit Lloyd]

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Glad its not just me.  

I do likewise, put the sources into zotero then drag the lot as formatted 
cites into a rtf file, convert to markdown. Use zotero to create the 
bibliography and convert to markdown.  Write the document in markdown using 
the formatted citations. Run it through a pandoc script with a custom latex 
template and out comes the pdf (or whatever format you desire).



On Sunday, 3 May 2015 13:38:34 UTC+10, Cormac Relf wrote:
>
> I don't even bother with aglc.csl any more. I manually follow AGLC3 in my 
> text editor with pandoc footnotes.
>
> Best of luck.
>
> On 3 April 2015 at 14:45, Kit Lloyd <kitl...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org <javascript:>> 
> wrote:
>
>> Hi,
>>
>> I was wondering whether you did finally manage to get aglc.csl to work as 
>> expected with pandoc-citeproc.  I seem to be stuck, aglc.csl seems to work 
>> fine when using the Zotero plugins, but not so well when using 
>> pandoc-citeproc.
>>
>> --
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>
>

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