org-cite citation commands

org-cite citation commands

[Vikas Rawal]

I have been a long time user of org-ref and am excited to see the
development of org-cite. Thanks a lot for this, Nicholas and others
who have been working on this. I have been wanting to give it a spin
for the last few days and finally got down to doing it.

I am aware that the documentation is still in the works and therefore
my apologies in advance if asking these questions is premature. I have
looked at Nicholas' mails which provide basic documentation and have
been trying to follow these.

What is the equivalent here of the various citation commands that something like biblatex or bibtex provide? The two most common citation commands I use are citet and citep (or parencite). These are used to produce the following kind of output using org-ref/biblatex:


-----
* citet

citet:john is an excellent resource.

will be exported as:

John (1990) is an excellent resource.

* citep

This is an excellent resource citep:john.

will be exported as

This is an excellent resource (John, 1990).

----

How does one achieve this using org-cite?

I am a bit lost with the citation styles that are inbuilt in oc-biblatex.el. Is it expected that we will have to write additional citation styles for getting these kinds of output?

Apologies if this is a naive or a premature question.

Many thanks to everyone.

Vikas

Re: org-cite citation commands

[John Kitchin]

[-- Attachment #1: Type: text/plain, Size: 2186 bytes --]

It sounds like you use natbib/bibtex (citet/citep are natbib commands I
think). In that case, my current understanding is that these are the
syntaxes for what you want, with the natbib exporter selected.

 [cite:@key]  -> \citep{key}

 [cite/t:@key]  -> \citet{key}

But, if you use the biblatex backend, these map to

 [cite:@key]  -> \autocite{key}

 [cite/t:@key]  -> \textcite{key}

There is not currently a way to get \citet and \citep with the biblatex
backend.

John

-----------------------------------
Professor John Kitchin (he/him/his)
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu



On Sat, Jul 17, 2021 at 7:41 AM Vikas Rawal <vikasrawal@gmail.com> wrote:

> I have been a long time user of org-ref and am excited to see the
> development of org-cite. Thanks a lot for this, Nicholas and others
> who have been working on this. I have been wanting to give it a spin
> for the last few days and finally got down to doing it.
>
> I am aware that the documentation is still in the works and therefore
> my apologies in advance if asking these questions is premature. I have
> looked at Nicholas' mails which provide basic documentation and have
> been trying to follow these.
>
> What is the equivalent here of the various citation commands that
> something like biblatex or bibtex provide? The two most common citation
> commands I use are citet and citep (or parencite). These are used to
> produce the following kind of output using org-ref/biblatex:
>
>
> -----
> * citet
>
> citet:john is an excellent resource.
>
> will be exported as:
>
> John (1990) is an excellent resource.
>
> * citep
>
> This is an excellent resource citep:john.
>
> will be exported as
>
> This is an excellent resource (John, 1990).
>
> ----
>
> How does one achieve this using org-cite?
>
> I am a bit lost with the citation styles that are inbuilt in
> oc-biblatex.el. Is it expected that we will have to write additional
> citation styles for getting these kinds of output?
>
> Apologies if this is a naive or a premature question.
>
> Many thanks to everyone.
>
> Vikas
>
>

[-- Attachment #2: Type: text/html, Size: 3026 bytes --]

Re: org-cite citation commands

[Bruce D'Arcus]

On Sat, Jul 17, 2021 at 7:41 AM Vikas Rawal <vikasrawal@gmail.com> wrote:

> What is the equivalent here of the various citation commands that something like biblatex or bibtex provide? The two most common citation commands I use are citet and citep (or parencite). These are used to produce the following kind of output using org-ref/biblatex:
>
>
> -----
> * citet

cite/t

> * citep

cite (no style; it's default)

> I am a bit lost with the citation styles that are inbuilt in oc-biblatex.el. Is it expected that we will have to write additional citation styles for getting these kinds of output?

No; there is already extensive style support, that works consistently
across the different export processors.

E.g. cite/t will produce the same output in natbib and biblatex (and
very soon, csl).

You can see the draft mapping of style here, though I need to update it.

https://github.com/bdarcus/bibtex-actions/wiki/Org-cite

Bruce

Re: org-cite citation commands

[Bruce D'Arcus]

We were posting at the same time :-)

On Sat, Jul 17, 2021 at 8:39 AM John Kitchin <jkitchin@andrew.cmu.edu> wrote:

> There is not currently a way to get \citet and \citep with the biblatex backend.

Yes, but \autocite andt \textcite produce the expected output, and
have the advantage they are independent of output format. As in, the
current behavior will work in an author-date style or a note-based
one.

So [cite:@key] and [cite/t:@key] should produce the expected output in
both biblatex and natbib.

Bruce

Re: org-cite citation commands

[András Simonyi]

Dear Vikas,

the CSL-based processor is in a bit of a flux in this respect, but as
for the natbib and biblatex processors I've extracted these
correspondences from the oc source code, which you might find useful.
(With the exception of the first, "fully nil" styles, one always has
to use the "/" separator between "cite" and the listed combinations,
for the default styles this means a double slash, e.g.,  [cite//b@key]
leads to  \citealp{key} using the natbib processor.

* Natbib

;; default style.
                                --> \citep
/ [bare|b]                      --> \citealp
/ [caps|c]                      --> \Citep
/ [full|f]                      --> \citep*
/ [bare-caps|bc]                --> \Citealp
/ [bare-full|bf]                --> \citealp*
/ [caps-full|cf]                --> \Citep*
/ [bare-caps-full|bcf]          --> \Citealp*

;; author style.
[author|a] / [caps|c]           --> \Citeauthor
[author|a] / [full|f]           --> \citeauthor*
[author|a]                      --> \citeauthor

;; noauthor style
[noauthor|na] / [bare|b]        --> \citeyear
[noauthor|na]                   --> \citeyearpar

;; nocite style.
[nocite|n]                      --> \nocite

;; text style.
[text|t] / [bare|b]             --> \citealt
[text|t] / [caps|c]             --> \Citet
[text|t] / [full|f]             --> \citet*
[text|t] / [bare-caps|bc]       --> \Citealt
[text|t] / [bare-full|bf]       --> \citealt*
[text|t] / [caps-full|cf]       --> \Citet*
[text|t] / [bare-caps-full|bcf] --> \Citealt*
[text|t]                        --> \citet

* biblatex

;; Default nil style.
                              --> autocite
/ [bare|b]                    --> cite
/ [caps|c]                    --> Autocite
/ [bare-caps|b]               --> Cite

;; author style.
[author|a] / [caps|c])        --> Citeauthor*
[author|a] / [full|f])        --> citeauthor
[author|a] / [caps-full|cf]   --> Citeauthor
[author|a]                    --> citeauthor*

;; locators style.
[locators|l] / [bare|b]       --> notecite
[locators|l] / [caps|c]       --> Pnotecite
[locators|l] / [bare-caps|bc] --> Notecite
[locators|l]                  --> pnotecite

;; noauthor style.
[noauthor|na]                 --> autocite*

;; nocite style.
[nocite|n]                    --> nocite

;; text style.
[text|t] / [caps|c])          --> Textcite
[text|t]                      --> textcite

best regards,
András


On Sat, 17 Jul 2021 at 13:41, Vikas Rawal <vikasrawal@gmail.com> wrote:
>
> I have been a long time user of org-ref and am excited to see the
> development of org-cite. Thanks a lot for this, Nicholas and others
> who have been working on this. I have been wanting to give it a spin
> for the last few days and finally got down to doing it.
>
> I am aware that the documentation is still in the works and therefore
> my apologies in advance if asking these questions is premature. I have
> looked at Nicholas' mails which provide basic documentation and have
> been trying to follow these.
>
> What is the equivalent here of the various citation commands that something like biblatex or bibtex provide? The two most common citation commands I use are citet and citep (or parencite). These are used to produce the following kind of output using org-ref/biblatex:
>
>
> -----
> * citet
>
> citet:john is an excellent resource.
>
> will be exported as:
>
> John (1990) is an excellent resource.
>
> * citep
>
> This is an excellent resource citep:john.
>
> will be exported as
>
> This is an excellent resource (John, 1990).
>
> ----
>
> How does one achieve this using org-cite?
>
> I am a bit lost with the citation styles that are inbuilt in oc-biblatex.el. Is it expected that we will have to write additional citation styles for getting these kinds of output?
>
> Apologies if this is a naive or a premature question.
>
> Many thanks to everyone.
>
> Vikas
>

Re: org-cite citation commands

[Vikas Rawal]

Thanks, Bruce and John. Indeed, I used biblatex with natbib=true
option, which gives me citet and citep in biblatex. But using
\autocite and \textcite is perfect.

I am noticing a few other issues at this stage.

I have a large biblatex database, and loading it using C-c C-x @ to
insert citations seems very slow (have not managed to load it thus
far). Org-ref used to be much faster in this. org-cite works fine with
a smaller biblatex database. I don't know if others have had the same
experience.

I understand that oc-biblatex.el loads biblatex in the background,
produces the citations and the bibliography, and inserts them in the
exported output. In that case, what are the possibilities of using
biblatex commands to configure the output? I realise that these will
not work since most of it would be LaTeX specific. Does that mean the
users will have to work with CSL styles to format the output even if
they are using oc-biblatex.el? I am still somewhat confused about how
this is going to work.

I notice that there is an option org-cite-biblatex-options which can
be customized to load biblatex with specific options. I have not yet
managed to test it. If somebody has already played around with it, it
would be useful to know what they could manage to do.

In my experience, biblatex and bibtex uniformly process the author
names whether they are written in the database file as "John Kitchin"
or "Kitchin, John". This does not seem to work with oc-biblatex.el at
least out of the box and the two are formatted differently.

Thanks again,

Vikas

Re: org-cite citation commands

[Vikas Rawal]

Thanks. This is very useful.

Vikas

On Sat, Jul 17, 2021 at 03:55:18PM +0200, András Simonyi wrote:
> Dear Vikas,
>
> the CSL-based processor is in a bit of a flux in this respect, but as
> for the natbib and biblatex processors I've extracted these
> correspondences from the oc source code, which you might find useful.
> (With the exception of the first, "fully nil" styles, one always has
> to use the "/" separator between "cite" and the listed combinations,
> for the default styles this means a double slash, e.g.,  [cite//b@key]
> leads to  \citealp{key} using the natbib processor.
>
> * Natbib
>
> ;; default style.
>                                 --> \citep
> / [bare|b]                      --> \citealp
> / [caps|c]                      --> \Citep
> / [full|f]                      --> \citep*
> / [bare-caps|bc]                --> \Citealp
> / [bare-full|bf]                --> \citealp*
> / [caps-full|cf]                --> \Citep*
> / [bare-caps-full|bcf]          --> \Citealp*
>
> ;; author style.
> [author|a] / [caps|c]           --> \Citeauthor
> [author|a] / [full|f]           --> \citeauthor*
> [author|a]                      --> \citeauthor
>
> ;; noauthor style
> [noauthor|na] / [bare|b]        --> \citeyear
> [noauthor|na]                   --> \citeyearpar
>
> ;; nocite style.
> [nocite|n]                      --> \nocite
>
> ;; text style.
> [text|t] / [bare|b]             --> \citealt
> [text|t] / [caps|c]             --> \Citet
> [text|t] / [full|f]             --> \citet*
> [text|t] / [bare-caps|bc]       --> \Citealt
> [text|t] / [bare-full|bf]       --> \citealt*
> [text|t] / [caps-full|cf]       --> \Citet*
> [text|t] / [bare-caps-full|bcf] --> \Citealt*
> [text|t]                        --> \citet
>
> * biblatex
>
> ;; Default nil style.
>                               --> autocite
> / [bare|b]                    --> cite
> / [caps|c]                    --> Autocite
> / [bare-caps|b]               --> Cite
>
> ;; author style.
> [author|a] / [caps|c])        --> Citeauthor*
> [author|a] / [full|f])        --> citeauthor
> [author|a] / [caps-full|cf]   --> Citeauthor
> [author|a]                    --> citeauthor*
>
> ;; locators style.
> [locators|l] / [bare|b]       --> notecite
> [locators|l] / [caps|c]       --> Pnotecite
> [locators|l] / [bare-caps|bc] --> Notecite
> [locators|l]                  --> pnotecite
>
> ;; noauthor style.
> [noauthor|na]                 --> autocite*
>
> ;; nocite style.
> [nocite|n]                    --> nocite
>
> ;; text style.
> [text|t] / [caps|c])          --> Textcite
> [text|t]                      --> textcite
>
> best regards,
> András
>
>
> On Sat, 17 Jul 2021 at 13:41, Vikas Rawal <vikasrawal@gmail.com> wrote:
> >
> > I have been a long time user of org-ref and am excited to see the
> > development of org-cite. Thanks a lot for this, Nicholas and others
> > who have been working on this. I have been wanting to give it a spin
> > for the last few days and finally got down to doing it.
> >
> > I am aware that the documentation is still in the works and therefore
> > my apologies in advance if asking these questions is premature. I have
> > looked at Nicholas' mails which provide basic documentation and have
> > been trying to follow these.
> >
> > What is the equivalent here of the various citation commands that something like biblatex or bibtex provide? The two most common citation commands I use are citet and citep (or parencite). These are used to produce the following kind of output using org-ref/biblatex:
> >
> >
> > -----
> > * citet
> >
> > citet:john is an excellent resource.
> >
> > will be exported as:
> >
> > John (1990) is an excellent resource.
> >
> > * citep
> >
> > This is an excellent resource citep:john.
> >
> > will be exported as
> >
> > This is an excellent resource (John, 1990).
> >
> > ----
> >
> > How does one achieve this using org-cite?
> >
> > I am a bit lost with the citation styles that are inbuilt in oc-biblatex.el. Is it expected that we will have to write additional citation styles for getting these kinds of output?
> >
> > Apologies if this is a naive or a premature question.
> >
> > Many thanks to everyone.
> >
> > Vikas
> >
>

Re: org-cite citation commands

[Bruce D'Arcus]

On Sat, Jul 17, 2021 at 10:20 AM Vikas Rawal <vikasrawal@gmail.com> wrote:

> Thanks, Bruce and John. Indeed, I used biblatex with natbib=true
> option, which gives me citet and citep in biblatex. But using
> \autocite and \textcite is perfect.
>
> I am noticing a few other issues at this stage.
>
> I have a large biblatex database, and loading it using C-c C-x @ to
> insert citations seems very slow (have not managed to load it thus
> far). Org-ref used to be much faster in this. org-cite works fine with
> a smaller biblatex database. I don't know if others have had the same
> experience.

Give this a try:

https://github.com/bdarcus/bibtex-actions#org-cite

I hope to see similar "insert processors" for ivy-bibtex and helm-bibtex.

Bottomline, it's trivial to replace that "basic" processor with much
better options.

See discussion on:

https://github.com/jkitchin/org-ref/issues/885

> I understand that oc-biblatex.el loads biblatex in the background,
> produces the citations and the bibliography, and inserts them in the
> exported output. In that case, what are the possibilities of using
> biblatex commands to configure the output?

To be precise, you mean what are the options to configure the
oc-biblatex export processor to use different or additional commands?

ATM, I don't believe there are any, and the alternative is to write
your own export processor, say basing it off the oc-biblatex one.

What, specifically, do you need, that is not currently supported?

The current processors are pretty comprehensive; see the note from Andras.

When designing this sort of thing, you basically have a choice.

You can just have styles that map directly to the output targets.

This has an obvious advantage if you only ever use one target.

But it has a major disadvantage if you want to use others.

So the approach we took here is to design a common set of styles and
substyles, and then map to output formats from there.

The result is the citations are more-or-less export format agnostic.

> I realise that these will
> not work since most of it would be LaTeX specific. Does that mean the
> users will have to work with CSL styles to format the output even if
> they are using oc-biblatex.el? I am still somewhat confused about how
> this is going to work.

CSL styles are analogous to BST files in bibtex; you use those with oc-csl.

When using that, citeproc-el handles the output processing, including for latex.

Basically, if you want consistent output formatting across latex and
other targets like HTML or OpenDocument, you want to use oc-csl.

Give it a try.

Note, though, that citeproc-el does not currently support cite/t or
some others, but that should be coming "soon".

HTH; let me know if anything is unclear.

Bruce

Re: org-cite citation commands

[John Kitchin]

[-- Attachment #1: Type: text/plain, Size: 3561 bytes --]

I made a video of my current org-cite setup at
https://www.youtube.com/watch?v=4ta4J20kpmM. You can also find a link to
the code to run it in the description there.

I don't intend this to be a final video (it is still a little rough!), it
is just to help people see what I am thinking about for the future of
org-ref, at least as far as the citations go.

John

-----------------------------------
Professor John Kitchin (he/him/his)
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu



On Sat, Jul 17, 2021 at 10:44 AM Bruce D'Arcus <bdarcus@gmail.com> wrote:

> On Sat, Jul 17, 2021 at 10:20 AM Vikas Rawal <vikasrawal@gmail.com> wrote:
>
> > Thanks, Bruce and John. Indeed, I used biblatex with natbib=true
> > option, which gives me citet and citep in biblatex. But using
> > \autocite and \textcite is perfect.
> >
> > I am noticing a few other issues at this stage.
> >
> > I have a large biblatex database, and loading it using C-c C-x @ to
> > insert citations seems very slow (have not managed to load it thus
> > far). Org-ref used to be much faster in this. org-cite works fine with
> > a smaller biblatex database. I don't know if others have had the same
> > experience.
>
> Give this a try:
>
> https://github.com/bdarcus/bibtex-actions#org-cite
>
> I hope to see similar "insert processors" for ivy-bibtex and helm-bibtex.
>
> Bottomline, it's trivial to replace that "basic" processor with much
> better options.
>
> See discussion on:
>
> https://github.com/jkitchin/org-ref/issues/885
>
> > I understand that oc-biblatex.el loads biblatex in the background,
> > produces the citations and the bibliography, and inserts them in the
> > exported output. In that case, what are the possibilities of using
> > biblatex commands to configure the output?
>
> To be precise, you mean what are the options to configure the
> oc-biblatex export processor to use different or additional commands?
>
> ATM, I don't believe there are any, and the alternative is to write
> your own export processor, say basing it off the oc-biblatex one.
>
> What, specifically, do you need, that is not currently supported?
>
> The current processors are pretty comprehensive; see the note from Andras.
>
> When designing this sort of thing, you basically have a choice.
>
> You can just have styles that map directly to the output targets.
>
> This has an obvious advantage if you only ever use one target.
>
> But it has a major disadvantage if you want to use others.
>
> So the approach we took here is to design a common set of styles and
> substyles, and then map to output formats from there.
>
> The result is the citations are more-or-less export format agnostic.
>
> > I realise that these will
> > not work since most of it would be LaTeX specific. Does that mean the
> > users will have to work with CSL styles to format the output even if
> > they are using oc-biblatex.el? I am still somewhat confused about how
> > this is going to work.
>
> CSL styles are analogous to BST files in bibtex; you use those with oc-csl.
>
> When using that, citeproc-el handles the output processing, including for
> latex.
>
> Basically, if you want consistent output formatting across latex and
> other targets like HTML or OpenDocument, you want to use oc-csl.
>
> Give it a try.
>
> Note, though, that citeproc-el does not currently support cite/t or
> some others, but that should be coming "soon".
>
> HTH; let me know if anything is unclear.
>
> Bruce
>

[-- Attachment #2: Type: text/html, Size: 4826 bytes --]

Re: org-cite citation commands

[Vikas Rawal]

This is very helpful already. Keenly looking forward to how this develops.

Vikas

On Sat, Jul 17, 2021 at 04:52:33PM -0400, John Kitchin wrote:
> I made a video of my current org-cite setup at https://www.youtube.com/watch?v=
> 4ta4J20kpmM. You can also find a link to the code to run it in the description
> there.
>
> I don't intend this to be a final video (it is still a little rough!), it is
> just to help people see what I am thinking about for the future of org-ref, at
> least as far as the citations go.
>
> John
>
> -----------------------------------
> Professor John Kitchin (he/him/his)
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> @johnkitchin
> http://kitchingroup.cheme.cmu.edu

Re: org-cite citation commands

[Bruce D'Arcus]

[-- Attachment #1: Type: text/plain, Size: 1509 bytes --]

Unlike John, I don't have a working demo of this particular smaller idea,
but as it relates to the styles/commands question, I thought I'd mention it.

So the idea is to use the style completion UI to show the user what the
options are, by including the export preview; for the tex export
processors, it would be the latex commands, and for CSL, would be the
rendered output.

While I don't have it running, this should definitely be doable.

I put an initial mockup here.

https://github.com/bdarcus/bibtex-actions/issues/168

Probably something like this should be added to oc-basic at some point.

On Sun, Jul 18, 2021, 12:10 AM Vikas Rawal <vikasrawal@gmail.com> wrote:

> This is very helpful already. Keenly looking forward to how this develops.
>
> Vikas
>
> On Sat, Jul 17, 2021 at 04:52:33PM -0400, John Kitchin wrote:
> > I made a video of my current org-cite setup at
> https://www.youtube.com/watch?v=
> > 4ta4J20kpmM. You can also find a link to the code to run it in the
> description
> > there.
> >
> > I don't intend this to be a final video (it is still a little rough!),
> it is
> > just to help people see what I am thinking about for the future of
> org-ref, at
> > least as far as the citations go.
> >
> > John
> >
> > -----------------------------------
> > Professor John Kitchin (he/him/his)
> > Doherty Hall A207F
> > Department of Chemical Engineering
> > Carnegie Mellon University
> > Pittsburgh, PA 15213
> > 412-268-7803
> > @johnkitchin
> > http://kitchingroup.cheme.cmu.edu
>

[-- Attachment #2: Type: text/html, Size: 2471 bytes --]