Re: citations: org-cite vs org-ref 3.0

[John Kitchin <jkitchin@andrew.cmu.edu>]

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On Sun, Mar 20, 2022 at 9:57 PM Timothy <tecosaur@gmail.com> wrote:

> Hi John,
>
> Thanks for your considered response.
>
> When you contrast org-cite and org-ref, you say:
>
> > With org-ref, bib(la)tex export is almost fully supported, and is easy,
>
> I find this odd as org-cite supports bib(la)tex export, and rather easily.
>
> ┌────
> │ #+bibliography: references.bib
> │ #+cite_export: biblatex authortitle/authortitle-ibid
> │
> │ [cite:@key] etc.
> │
> │ #+print_bibliography:
> └────
>
> The limitation which I think is on your mind is that not all bib(la)tex
> commands
> are supported, and not in the “usual” form. For instance, to get
> `pnotecite' one
> would use `[cite/locators:]'. However, to get a 1-to-1 name mapping, you
> can just
> customise `org-cite-biblatex-styles'. For instance, `parencite' is not
> currently
> available, but if I just add `("parencite" nil "parencite" nil nil)' I can
> then do
> `[cite/parencite:]' or if I replace the first `"parencite"' with
> `"paren"', just
> `[cite/paren:]'.
>

Yes, of course I mean the citation commands.


>
> A package could be created, say `org-cite-literal-biblatex' which is just
> a copy
> of `oc-biblatex.el' with a different default `org-cite-biblatex-styles' and
> `org-cite-biblatex-style-shortcuts' (or just sets those variables in
> `org-cite-biblatex'). As far as I can tell this would provide exactly the
> functionality you say org-cite can’t provide but org-ref does.
>

I wrote this package you suggest in org-ref-cite. In discussions during
that development, it was clear the preference was on the more abstracted,
and uniform syntax across backends cite commands in org-cite, and not this
kind of variant. Of course one can do this. It is not that org-cite can't
provide it, it is that it doesn't at this time. Even so, it is only a
partial solution to deprecating org-ref.


>
> You can already use `.bib' files, and so frankly I cannot myself see the
> point in
> org-ref’s existence beyond bifurcating the community on this. At this
> point the
> only remaining motivation I see is old documents and current users, and
> for this
> a migration tool seems more appropriate.


> I don’t mean to be overly critical, however this is my current honest
> assessment
> of the situation.
>
> –
> All the best,
> Timothy
>
> John Kitchin <jkitchin@andrew.cmu.edu> writes:
>
> > I do not think it is productive for the community to say or consider it
> > is a sad situation. Many good things have emerged from these
> > discussions, even if it is not yet consensus on a solution. It is a
> > complex problem, with many years of effort by many people on each side.
> > That is an indication of how ambitious this project is and that there
> > may be more than one solution that is needed. It pains me quite a bit
> > there is a sentiment of fractionation, and that I may be contributing to
> > it.
> >
> > My regular job workload the past few years has been crushing, and I have
> > not had the time to participate in this that I wish I had. I am not sure
> > I can add much here without sounding or feeling defensive about org-ref,
> > and my decision to continue supporting and developing it. I have thought
> > about this for most of the day, and in the (very long, apologies in
> > advance) response that follows I will do my best to provide a balanced
> > perspective (from my point of view) on the situation.
> >
> > Some specific context that is important to me is that I wrote org-ref
> > long ago to solve a specific problem for me in the preparation of
> > scientific publications that are destined for LaTeX export. I intended
> > it to provide nearly equivalent bib(la)tex citation export, and as
> > reasonable an export as possible for everything else. I use org-ref
> > professionally, and it is a complete solution for me. I simply cannot
> > compromise on the capability org-ref provides me, or wait for an
> > alternative complete solution in org-mode. I have work I have to do now,
> > and org-ref lets me do it. This alone is reason enough for me to
> > continue using, developing and supporting org-ref. I understand org is
> > not intended to be a substitute for writing LaTeX, but it is a fact of
> > my job that I have to do that.
> >
> > There are more than 8 years of legacy org-ref documents. I have written
> > 40+ scientific papers with it, and countless technical documents with
> > more than 8000 cite links among them. org-ref has exceeded 190K
> > downloads from MELPA, so I feel obligated to maintain org-ref for
> > myself, and those users. org-ref may be heavyweight in bundling a lot of
> > capability together that could be separated into individual packages,
> > but it is also convenient for people who need it, and a GitHUB issue or
> > pull request away from new features. I remain committed to supporting
> > this, and I do it in a way I can manage, hence the monolithic package
> > design.
> >
> > org-cite was also developed to solve some specific citation problems for
> > others that org-ref did not address well at the time it was started. I
> > believe those were issues like better pre/post note support, and
> > integration with CSL.
> >
> > I think org-ref and org-cite have different priorities, they solve
> > different problems with different approaches, and they have different
> > pros and cons. I believe there are mutually incompatible compromises one
> > must make here because the specific choices you make determine what is
> > easy and what is possible. There is not a direct mapping of bib(la)tex
> > and CSL as a citation processor. They are different programs and they
> > don’t share citation commands, or style information. It is inevitable
> > that something will be lost in the translation between these from a
> > single source like org, and whether that loss is acceptable depends on
> > what you need. For many things, close enough is ok for me, but for
> > manuscripts and proposals, they must be perfect, and in bib(la)tex form
> > for the journals I publish in. It is not that one thing is possible in
> > one and not the other; it is that you have to compromise one to do the
> > other no matter what you choose and that typically makes one thing or
> > the other easier to do. I am not even sure it is possible to do
> > everything one can do in bib(la)tex with CSL, for example, I don’t know
> > the equivalent of  in CSL. org-ref sides on making bib(la)tex
> > easy, and CSL is possible.
> >
> > With org-cite, CSL can be readily used across export backends, more
> > bibliography database formats are supported, and it is also possible to
> > get LaTeX export, although there is no goal to fully support all of
> > bib(la)tex. A pure org approach (e.g. org-files as bibliography
> > database) can be used, there are a lot of CSL styles to work with, and
> > you can develop or adapt your own style if needed. With reasonable
> > defaults this should be a straightforward introduction to using
> > citations for new users that works out of the box. I support that.
> >
> > With org-ref, bib(la)tex export is almost fully supported, and is easy,
> > and other exports via CSL are possible. Of course, you must have a
> > working LaTeX installation, only bibtex databases are supported, and
> > working knowledge of bib(la)tex is required to leverage this. Whether
> > you want it or not, you get a lot of extra utilities for getting bibtex
> > entries from a DOI, and support for cross-references, indexes,
> > glossaries and acronyms. This is a lot to ask of people who don’t need
> > it, and convenient for those who do. I support this.
> >
> > Which one of these approaches is right depends on what you want to be
> > easy. Neither is right or wrong, that is determined by what you need at
> > the time and what you prioritize in your solution. It is even possible
> > you need both approaches at different times. The two approaches are not
> > compatible, but it is org-mode after all, and you can certainly convert
> > back and forth between them for the most part.
> >
> > Both projects have benefited from this discussion a lot. org has
> > org-cite now, and org-ref now handles pre/post notes like org-cite does,
> > it supports CSL much better, and is even a little more modular, lighter
> > weight, and more easily integrated with other completion backends than
> > ivy or helm. That should broadly be viewed as a win-win situation.
> >
> > Here are some factors that have prevented me from deprecating org-ref. I
> > spent about a month and half trying to get a solution to this at
> > <https://github.com/jkitchin/org-ref-cite>, and I don’t make these
> > observations lightly. That solution was complete and highly functional
> > for org-cite, but as I describe below not a replacement for org-ref at
> > this time. I still welcome a new maintainer for this code.
> >
> > Cross-references are critical for me; without them, there is no path
> > forward for me with org-cite. I did work on a cross-reference approach
> > that leveraged org-cite syntax
> > (<https://github.com/jkitchin/org-ref-cite/issues/16>), but there was
> not
> > much appetite for the approach so I abandoned that. There are
> > cross-reference capabilities in org, that may be suitable for some
> > applications, but they do not come close to what org-ref offers, and
> > that the kind of technical documents I write require. For me, any
> > cross-reference capability would also have to support what is possible
> > in LaTeX, and preferrably look similar to the LaTeX commands. It has not
> > been possible to write an orthogonal package that could co-exist with
> > org-ref to address this; this would require a new syntax for
> > cross-references in my opinion. My opinion is that practically citations
> > and cross-references are just links to a place in your document (either
> > a figure/table/section/etc, or an entry in a bibliography). In org-ref,
> > both are represented by links; of course, they have different types and
> > functions, but they both have follow like actions. My opinion seems to
> > be in the minority on this.
> >
> > I do not like the abstraction away from LaTeX cite commands in org-cite.
> > This is an example of a compromise between LaTeX and CSL. They do not
> > share common citation commands, so you can either choose one or the
> > other, or make a new abstraction that generalizes them. I strongly favor
> > the LaTeX commands because I write for LaTeX export, and there is
> > extensive documentation for how to cite in LaTeX and what to expect.
> > Clearly org-cite favors using the standardized abstractions in org-cite,
> > and then mapping them to the LaTeX commands I think. My perspective on
> > this is partially one of an educator; I have taught a lot of people how
> > to use org-mode for technical writing. This layer of abstraction adds
> > additional complexity to documentation, and in teaching people what to
> > do. As a LaTeX-centric user, that abstraction adds an additional
> > cognitive load while writing I find unwelcome. I concede that it also
> > reflects “what I do”, that org is not LaTeX, and that others may have a
> > more CSL centric perspective. org-cite is for them. I can see that the
> > abstraction away from the LaTeX cite commands strengthens the org is not
> > LaTeX philosophy, and will serve part of the community well. If I wasn’t
> > required to generate LaTeX documents, and teach others how to do it, I
> > would not feel so strongly.
> >
> > It is my opinion that the modularity of org-cite is a challenge. I think
> > it is too difficult to configure, and difficult to support, even more so
> > than org-ref. I know my opinion differs from many on the list who want
> > modularity and configurability. I have supported org-ref since around
> > 2014, and even the modularity there (helm or ivy) has been a challenge
> > to support. org-ref has always been configurable, but monolithic. Still,
> > I learned a lot from Bruce (thank you!) that pushed me to redesign parts
> > of org-ref to be more modular and more easily pluggable to other
> > completion backends, and less specific on ivy/helm where practical.
> > There are limitations to this I learned about, compromises one has to
> > choose in doing it, and consequences in maintenance, support and
> > documentation from them. We still don’t fully agree on some of these
> > points, but org-ref is closer to that ideal than it was. Maybe one day I
> > will abandon ivy like I did helm many years ago and feel differently
> > about this, but that day is sufficiently far away that I don’t see it
> > now.
> >
> > Finally, the org-cite code is magnificent, and written at a level well
> > above my coding skills. I am grateful to those who wrote it, and
> > especially to Nicolas, for the opportunity to learn from it. The code I
> > wrote in org-ref-cite was challenging. org-cite uses (IMO) advanced
> > emacs-lisp techniques, and more complex data structures than I am
> > accustomed to. I learned a lot studying the org-cite code, but I will be
> > honest that I find it difficult to make contributions to. That gave me
> > pause in continuing to develop it. It is fair to say that org-cite
> > showed me some ways to address limitations of org-ref that I did not see
> > before, org-ref is better for it, and the writing community that uses
> > pre/post notes and biblatex is much better served as a result.
> >
> > Where does this leave me, org-ref and org-cite? I still have differences
> > of opinion on design choices between them, and those differences are
> > likely irreconcilable. These differences arise from my experiences in
> > writing, teaching, using, developing and supporting org-ref. For those
> > who need high fidelity LaTeX export like I do, I think org-ref is still
> > a superior solution. For everyone else, and especially if you do not
> > need sophisticated cross-references and don’t want the dependencies of
> > org-ref, org-cite is likely the better solution.
> >
> > I am content to agree to disagree on these points and move forward with
> > both packages because they solve different problems, are suitable for
> > different communities, and they continue to benefit each other. I can
> > see not everyone sees this as a positive situation though, and that has
> > weighed heavily upon me lately. These times are heavy enough. Anyway,
> > this turned out much longer than I expected, so thanks everyone who has
> > contributed to making org better, I hope I got things mostly correct,
> > you found it a fair assessment, we might still be friends, and thanks
> > for reading to the end.
> >
> > j
>

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