Re: org-ref 3 setup

2022-07-20 Thread John Kitchin
-ref-preprocessing (backend) (unless (eq backend 'latex) (org-ref-csl-preprocess-buffer backend))) (setq org-export-before-parsing-hook '(org-ref-preprocessing)) John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering

Re: @string abbreviation in bib file not honored in (basic) org-cite [and a minimal working example with natbib]

2022-07-12 Thread John Kitchin
; their LaTeX equivalent. > > best wishes, > András > > -- John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin https://kitchingroup.cheme.cmu.edu https://pointbreezepubs.gumroad.com/ pycse bookstore

Re: [PATCH] oc-csl: Add support for nocite citations

2022-07-03 Thread John Kitchin
do not understand. AFAIK, \nocite{*} is not a > valid LaTeX command. > > Best, > Ihor > > -- John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-

Re: We have asynchronous sessions, why have anything else?

2022-06-27 Thread John Kitchin
ow comes the next step, which is > definitely non-trivial. We need to take all that knowledge and > consolidate it into a single model from which we can define the > interfaces and associated APIs. A big job which will take considerable > time. > > -- John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin https://kitchingroup.cheme.cmu.edu https://pointbreezepubs.gumroad.com/ pycse bookstore

Re: org-ref3 export html with references of pages

2022-06-25 Thread John Kitchin
have to export it with C-c C-e rh to use the org-ref exporter. [image: image.png] John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin https

Re: Abbreviations support

2022-06-04 Thread John Kitchin
gt; acro-like support. Perhaps even support for a central abbreviations file. > Hmm, I > may think of trying a small MVP for that this weekend. > > All the best, > Timothy > -- John --- Professor John Kitchin (he/him/his) Dohert

Re: Trouble producing nicely aligned org tables from emacs-jupyter code blocks using latest org version

2022-05-18 Thread John Kitchin
often. 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 Wed, May 18, 2022 at 4:57 PM Richard Stanton

Re: Trouble producing nicely aligned org tables from emacs-jupyter code blocks using latest org version

2022-05-18 Thread John Kitchin
I use a function in an after execute hook for this: https://github.com/jkitchin/scimax/blob/master/scimax-org.el#L205 This works on a subtree, which has been fine for me. You could adapt it to only work in the results section. John --- Professor John Kitchin (he

Re: How to stop results being hidden when using ":results drawer"?

2022-05-13 Thread John Kitchin
-show-entry has a hard-coded line to hide drawers in it. Ihor Radchenko writes: > John Kitchin writes: > >> This does not change anything for me. >> >> The function that causes folding for me is `org-entry-show'. Presumably >> because of this line: (org-cycle-hi

Re: How to stop results being hidden when using ":results drawer"?

2022-05-12 Thread John Kitchin
e.org/80k0ar1lml@felesatra.moe/T/#u > > Does it help when you run > M-: (setq org-fold-core-first-unfold-functionsp nil) > before running the code block? > > Best, > Ihor -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http://kitchingroup.cheme.cmu.edu Pronouns: he/him/his

Re: How to stop results being hidden when using ":results drawer"?

2022-05-11 Thread John Kitchin
hm. what is xenops doing? That isn't a package I use, but my results drawers are also closed when opening a file. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412

Re: Org-ref not working when exporting to LaTeX

2022-05-11 Thread John Kitchin
processor. 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 Wed, May 11, 2022 at 2:15 PM Daniel Fleischer

Re: Citations using org-ref export to LaTeX incorrectly

2022-05-10 Thread John Kitchin
> blocks, but I'd rather use the new syntax if it works. > > Thank you much! > > -- > Daniel Fleming > > -- 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: [how to joint column/rows of tables that are in different files (id?)] (was: how to best correct exams (code matlab) using org mode (and tables))

2022-05-10 Thread John Kitchin
"Level" > #+END: > > Where the table uwe is located in a different file. However it seems > only to work for one table at the time, so if you have 20 tables in 20 > files that a bit complicated > > Any idea how to append column or rows from different table i

Re: how to best correct exams (code matlab) using org mode (and tables)

2022-05-09 Thread John Kitchin
egin_src > #+BEGIN: columnview :maxlevel 2 :skip-empty-rows t :indent nil :hlines 2 > :format "%5TODO(Status) %5Ap(Name) %5com(Comment) %5Ej1(Ej1/20) %5Ej2(Ej2/25) > %5Ej3(Ej3/55) %5Res(Result)" > #+END: > #+end_src > > What do others use? > > Regards

Re: Concatenate properties

2022-05-07 Thread John Kitchin
Where did you add that? 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 Fri, May 6, 2022 at 11:40

Re: Concatenate properties

2022-05-07 Thread John Kitchin
to > org-use-property-inheritance where the user can customise how to > accumulate parent properties. > > Best, > Ihor > -- John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mel

Re: Concatenate properties

2022-05-05 Thread John Kitchin
I believe this is hard coded in org-entry-get-with-inheritance. The fastest option would be an override advice with your own function that replaces (and value " ") with (and value ""), and maybe the two other " " with "". John ------

Re: [the culprit]

2022-04-26 Thread John Kitchin
alue)) #+END_SRC if you call it as M-x my-put, it just uses org-set-property. If you call it as C-u M-x my-put, it inserts the property before the point. It does not check you are in a property drawer, which could be a good idea. John --- Professor John Kitchin

Re: org-cite styles don't allow * in them

2022-04-22 Thread John Kitchin
I agree. 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 Fri, Apr 22, 2022 at 8:57 AM Bruce D'Arcus

Re: [PATCH] oc-basic: Detect malformed bibtex bibliographies

2022-04-20 Thread John Kitchin
I would see if you can cache the result and not do it more than needed; it can add a performance issue on large files. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA

Re: org-cite styles don't allow * in them

2022-04-17 Thread John Kitchin
On Sun, Apr 17, 2022 at 9:18 AM Ihor Radchenko wrote: > John Kitchin writes: > > > I am also not a fan of using Unicode here and prefer a simple ascii > > asterisk. That works fine for me so far, but I am not a heavy user of > bold > > markup and citations. > >

Re: org-cite styles don't allow * in them

2022-04-17 Thread John Kitchin
gt; However, I am not org-cite's maintainer. So, I would prefer to hear from > Nicolas before implementing anything myself. > > Best, > Ihor > -- John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical

Re: [BUG] org-cite does not support techreport, mastersthesis, phdthesis, and conference entries [9.5.2 (release_9.5.2-426-gf6813d @ /usr/share/emacs/site-lisp/org/)]

2022-04-08 Thread John Kitchin
--- 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 Fri, Apr 8, 2022 at 7:10 AM Eric S Fraga wrote: > On Fri

Re: org-cite styles don't allow * in them

2022-04-07 Thread John Kitchin
On Thu, Apr 7, 2022 at 12:17 AM Ihor Radchenko wrote: > "Bruce D'Arcus" writes: > > > On Sun, Apr 3, 2022 at 5:07 PM John Kitchin > wrote: > >> > >> I was looking into using latex commands as styles in org-cite, e.g. > >> > >> [cit

Re: org-cite styles don't allow * in them

2022-04-05 Thread John Kitchin
might also define links like cite:. 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 Tue, Apr 5, 2022

overlap between cite syntax and link activation

2022-04-03 Thread John Kitchin
LINK". I guess this means the activate-func is being used too aggressively. It looks like it is called after (re-search-forward org-link-any-re limit t). This does seem to match the cite syntax above. Does anyone else see this? John ------- Professor John

org-cite styles don't allow * in them

2022-04-03 Thread John Kitchin
I was looking into using latex commands as styles in org-cite, e.g. [cite/citet:@key]. That example works fine, but [cite/citet*:@key] is not allowed. Could that be allowed? John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical

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

2022-03-30 Thread John Kitchin
not a performance breaker, on say a moderate sized database and org-file. Getting high performance from large databases and large files with lots of citations (say a dissertation or big review article) takes some work. -- Professor John Kitchin Doherty Hall A207F Department of Chemical Eng

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

2022-03-27 Thread John Kitchin
Max Nikulin writes: > On 21/03/2022 18:51, John Kitchin wrote: >> citenum and bibentry are the only two I am not sure have a CSL analog. > > I read your messages once more and I should say that I feel some disagreement > of > this one (I removed most of it) and the earlie

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

2022-03-27 Thread John Kitchin
Nicolas Goaziou writes: > Hello, > > John Kitchin 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 soluti

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

2022-03-27 Thread John Kitchin
r to > cross-references. > >> For citations some values may be passed to specific citation backend >> overriding default value derived from style. > > In that situation, you can define a new style specific to the citation > back-end. > > Regards, -- Pr

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

2022-03-27 Thread John Kitchin
I have updated the readme in org-ref to indicate you can use both packages. Max Nikulin writes: > On 21/03/2022 18:51, John Kitchin wrote: >> Vikas Rawal writes: >>> >>> From the perspective of a user, this was only meant to express a >>> sentiment t

Re: [oc] provide style/citation preview?

2022-03-25 Thread John Kitchin
https://github.com/andras-simonyi/org-cite-csl-activate > > I think he was hoping to incorporate that into the oc-csl processor at > some point, and that would indeed be another approach to in-buffer > previewing. > > The issue I have is more just generating the preview content for > i

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

2022-03-21 Thread John Kitchin
ent for editing. >> >> Custom citation types may alleviate the issue with cross-references. It >> would be great to have more flexible links with arbitrary properties >> (and it would allow to consider citations and cross-references as >> special cases of links), but it

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

2022-03-21 Thread John Kitchin
; > Chris > >> >> Ivy-bibtex supports, for example, inserting of org-cite citations, but >> not via org-cite-insert. > > And I have `org-cite-insert` working straight out of the box. > >> >> So there are currently no org-cite processors for ivy-bi

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

2022-03-21 Thread John Kitchin
x actions. The commentary in this file also discusses some challenges in relying exclusively on completing-read. My opinion of course. I don't think you need a special processor for ivy-bibtex. It could be wired to insert org-cites on its own. > > Bruce -- Professor John Kitchin Dohe

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

2022-03-21 Thread John Kitchin
at the time. Maybe others will succeed in this another day. 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: citations: org-cite vs org-ref 3.0

2022-03-21 Thread John Kitchin
that be a situation > in which one is able to choose between the best of both and, as far as > possible, switch from one to the other. As far as I can tell, you can already do this. > > Thanks again for your time and effort, > > Vikas -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http://kitchingroup.cheme.cmu.edu Pronouns: he/him/his

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

2022-03-21 Thread John Kitchin
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, howeve

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

2022-03-20 Thread John Kitchin
rent citation systems cannot share org files. > > Indeed. >> >> What is the general view of the community about this? > > I don't know about the general view of the community, but, as a data > point, I find it very sad. > > That's not helpful, tho. > > Regard

Re: org-cite and org-ref-cite

2022-02-26 Thread John Kitchin
--- 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, Feb 26, 2022 at 8:42 AM Henrik Frisk wrote: > > > Den fre 25 feb. 2022 kl 13

Re: Footnote tooltips (an attempt)

2022-02-24 Thread John Kitchin
that is a nice solution. I probably should have read the docstring on org-footnote-get-definition a little more closely, it has the definition you need in it! John --- John Kitchin (he/his) Professor Doherty Hall A207F Department of Chemical Engineering Carnegie

Re: Footnote tooltips (an attempt)

2022-02-23 Thread John Kitchin
ock-fontified t 'font-lock-multiline t 'face 'org-footnote)) (advice-add 'org-activate-footnote-links :override 'footnote-tooltip) #+END_SRC John ------- John Kitchin (he/his) Professor Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon Universit

Re: processing of babel blocks and select_tags

2022-02-18 Thread John Kitchin
you want. 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 Fri, Feb 18, 2022 at 7:07 AM Eric S Fraga

Re: ob-powershell fixes, looking for original author

2022-02-18 Thread John Kitchin
I guess the author is here: https://list.orgmode.org/186354732.20201118123...@essential-it.be/ John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803

Re: ob-powershell fixes, looking for original author

2022-02-18 Thread John Kitchin
owever, the original did not have a license, so it is not possible to > proceed further, e.g. put it up on melpa. > Is the original author here on the list? I think they do not have a > contact address on github. Also posted on reddit to no avail. > > Regards, > Mois > -- John -

Re: org-ref-helm-insert-cite-link (using bibtex) when exporting to html

2022-02-17 Thread John Kitchin
I guess you are using the older org-ref version 2 here. If so, there isn't a real way to customize that, it comes from org-ref-get-html-bibliography which hard codes an unordered list. In version 3, you can use csl for this. John --- Professor John Kitchin (he

Re: org-ref-helm-insert-cite-link (using bibtex) when exporting to html

2022-02-17 Thread John Kitchin
There aren't enough details here to figure out what you mean. The bibliography formatting should be determined by the CSL style. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University

Re: Possible to robustly embed elisp links in source block table results?

2022-02-13 Thread John Kitchin
gt; > So in the first and third source block, org-mode teases me > that I can embed elisp links in that very nice table format > (first source block) with "complex" Lisp code (third source > block), but when I try to combine the two (second source > block), it slaps me in the

Re: Conversion to Jupyter notebooks

2022-02-07 Thread John Kitchin
. That should all be described in the commentary in the library. 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

Re: Missing the second '}'

2022-01-24 Thread John Kitchin
--- 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 Mon, Jan 24, 2022 at 11:02 AM Sharon Kimble wrote: > -BEGIN PGP SIGNED MESSAGE- >

Re: handling as special special block in derived export

2022-01-20 Thread John Kitchin
om; . fade-out))]] 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 Thu, Jan 20, 2022 at 10:21 AM Matt Price wrote: > > >

Re: handling as special special block in derived export

2022-01-19 Thread John Kitchin
ormat " " data-fragment src)) "\n" (r-stack "((src1 . fade-out) (src2 . fade-in) (src3 . fade-out))") #+END_SRC #+RESULTS: : #+BEGIN_EXPORT html : : : : : : #+END_EXPORT You could also make a link do that. John ----

Re: Playing down the text in org-mode

2022-01-13 Thread John Kitchin
this might be what you are looking for. The details are in this video description, and you can see what it looks like and does here https://www.youtube.com/watch?v=qBmvBkpzixs John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical

Re: Playing down the text in org-mode

2022-01-13 Thread John Kitchin
for something like that I think. I made a link for colorized text once ( https://kitchingroup.cheme.cmu.edu/blog/2016/11/08/New-color-link-in-org-9-0-using-font-lock-to-color-the-text/) that you might be able to adapt. John --- Professor John Kitchin (he/him/his) Doherty

Re: Bibliographies on export with ox-context and ox-epub

2022-01-12 Thread John Kitchin
These two packages can co-exist. This message means do not mix citations from both in a single org file; use one or the other. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh

Re: Cannot set invisible text property

2022-01-07 Thread John Kitchin
) #+BEGIN_SRC emacs-lisp (remove-from-invisibility-spec 'hide-this-stuff) #+END_SRC #+RESULTS: : ((org-hide-block . t) (org-link) (outline . t) t) John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon

Re: text after sub headings?

2021-12-23 Thread John Kitchin
You can also use drawers (as an alternative to inline tasks) for collapsible content. Another potential is to use blocks. You can define your own kind of blocks, or even just use an org block and it is collapsible. John --- Professor John Kitchin (he/him/his

Re: org-cite and export to ODT

2021-12-15 Thread John Kitchin
--- 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 Wed, Dec 15, 2021 at 6:58 PM Xianwen Chen (陈贤文) wrote: > Thank you John. I'm not s

Re: org-cite and export to ODT

2021-12-15 Thread John Kitchin
That code does not belong in your .emacs file. It should be in an emacs-lisp block in your org-file like it is in the example. You should run it from the org file. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical

Re: org-cite and export to ODT

2021-12-09 Thread John Kitchin
and bibliography . 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 Thu, Dec 9, 2021 at 4:54 AM Xianwen

Re: Raw Org AST snippets for "impossible" markup

2021-12-08 Thread John Kitchin
kup, you > > may try to trade it for +your soul+ compatibility and portability > > issues. The following almost works: > > Interesting, thank you. > > Yes, it is strange the new line added in `evilatex-emph' ... I have no > idea why that happens. > > Best regards,

Re: Looking for extensions of [[file:~/xx.org::My Target]]

2021-12-06 Thread John Kitchin
. You can learn more about it here: https://www.youtube.com/watch?v=H4sK5ld6Bw0 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

Re: Org-cite stuck in Helm minibuffer [9.5.1 (9.5.1-g36086a @ /home/dan/.emacs.d/elpa/org-9.5.1/)]

2021-12-06 Thread John Kitchin
something that is not a candidate but similar to one e.g. with fuzzy matching)). That happens with helm and ivy, probably selectrum, and other backends that try to improve on the vanilla completing-read interface. John --- Professor John Kitchin (he/him/his) Doherty

Re: Org-cite stuck in Helm minibuffer [9.5.1 (9.5.1-g36086a @ /home/dan/.emacs.d/elpa/org-9.5.1/)]

2021-12-06 Thread John Kitchin
be included) Other insert processors may use these backends natively, so this information may not apply to them. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268

Re: Org-cite stuck in Helm minibuffer [9.5.1 (9.5.1-g36086a @ /home/dan/.emacs.d/elpa/org-9.5.1/)]

2021-12-06 Thread John Kitchin
(if you use helm-mode), but it is actually the helm version of completing read, and not a helm selection command. Other completion backends use different bindings, e.g. ivy uses C-M-j I think. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department

Re: [fyi] extensible syntax, syntax features, parsing risk

2021-12-04 Thread John Kitchin
Is it related to https://lists.gnu.org/archive/html/emacs-orgmode/2010-08/msg00404.html I implemented that idea for fun once: https://kitchingroup.cheme.cmu.edu/blog/2015/02/05/Extending-the-org-mode-link-syntax-with-attributes/ John --- Professor John Kitchin

Re: Org-syntax: Intra-word markup

2021-12-04 Thread John Kitchin
e free to do what you want with the path, including parse it yourself to generate the output, and since it is a link, you could do all kinds of things to make it look the way you want with faces, overlays, etc. John --- Professor John Kitchin (he/h

Re: citeproc-org and org-ref 3

2021-12-03 Thread John Kitchin
n that each bibliographical reference is below its number link, and > it is not very nice. I wonder about the reason of this difference of > output, and a possible solution. > > Best wishes, > > Jo. > > Le 02/12/2021 à 18:35, John Kitchin a écrit : >> Glad to hear it is

Re: citeproc-org and org-ref 3

2021-12-02 Thread John Kitchin
o code it. >> >> No doubt that it should be for you and Ivan a piece of cake, but please >> do it only if you think that it is interesting and if you find the time >> to do it. >> >> Best wishes, >> >> Jo. >> >> PS in attachment, myb

Re: citeproc-org and org-ref 3

2021-12-01 Thread John Kitchin
configuration files in >> ..." prelude-personal-preload-dir) (mapc 'load (directory-files >> prelude-personal-preload-dir 't "^[^#.].*el$"))) >>(if (file-exists-p prelude-personal-preload-dir) (progn (message >> "[Prelude] Loading personal con

Re: citeproc-org and org-ref 3

2021-12-01 Thread John Kitchin
export..." >>> "/home/joseph/.emacs.d/personal/preload/myorgexport..." nil nil) >>> load("/home/joseph/.emacs.d/personal/preload/myorgexport...") >>> mapc(load ("/home/joseph/.emacs.d/personal/preload/myorgexport...")) >>>

Re: citeproc-org and org-ref 3

2021-11-30 Thread John Kitchin
-buffer))) (org-open-file (org-html-export-to-html))) 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: how to export red colored TeX to latex

2021-11-30 Thread John Kitchin
maybe @@latex:\textcolor{red}{$\delta \phi = \frac{2 m}{R}$}@@ will do. 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

Re: Bibliographies on export with ox-context and ox-epub

2021-11-24 Thread John Kitchin
-edition.csl #+csl-locale: en-US #+BEGIN_SRC emacs-lisp (require 'ox-epub) (let ((org-export-before-parsing-hook '(org-ref-csl-preprocess-buffer))) (org-open-file (org-epub-export-to-epub))) #+END_SRC John --- Professor John Kitchin (he/him/his) Doherty Hall A207F

Re: [Problems with org-ref-helm-insert-ref-link and org-id-get-create]

2021-11-18 Thread John Kitchin
the way you want. 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 Thu, Nov 18, 2021 at 2:46 AM Uwe

Re: [Problems with org-ref-helm-insert-ref-link and org-id-get-create]

2021-11-17 Thread John Kitchin
nfigure v3 with helm. 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 Wed, Nov 17, 2021 at 4:41 PM

Re: [Problems with org-ref-helm-insert-ref-link and org-id-get-create]

2021-11-17 Thread John Kitchin
using that? 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 Wed, Nov 17, 2021 at 1:58 PM Uwe Brauer

Re: [org-cite] CSL processor, APA Style, and no-date citations

2021-11-17 Thread John Kitchin
, or adapt the code in https://github.com/jkitchin/org-ref/blob/master/org-ref-natbib-bbl-citeproc.el to work off of the org-cites. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh

Re: [Problems with org-ref-helm-insert-ref-link and org-id-get-create] (was: insert automatically a reference to a section header and a link)

2021-11-17 Thread John Kitchin
--- 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 Wed, Nov 17, 2021 at 11:55 AM Uwe Brauer wrote: > > Pleas

Re: insert automatically a reference to a section header and a link

2021-11-17 Thread John Kitchin
(format "<>" (string-join (seq-take tokens (min 3 (length tokens))) "-" (insert (format "%s %s" label title you could also insert the leading * if you prefer. John --- Professor John Kitchin (he/him/his) Doherty Hall

Re: issue using org-export-before-parsing-hook in a src-block

2021-11-07 Thread John Kitchin
I should also add I see the same error if I just run #+BEGIN_SRC emacs-lisp (org-org-export-as-org) #+END_SRC and I see the same behavior with an emacs -q session. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering

issue using org-export-before-parsing-hook in a src-block

2021-11-07 Thread John Kitchin
no") (:tangle . "no") (:eval . "never-export")) "" nil 1 "(ref:%s)") nil "emacs-lisp") If I put :results silent that doesn't happen. Is this a bug? The org-file is empty in this case except for that block, but that doesn't seem to matter. Joh

org-store-link question

2021-11-03 Thread John Kitchin
ink is not an option anymore. Should the file link still be there? 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-ref 2 vs org-ref 3

2021-10-20 Thread John Kitchin
All the breaking changes are documented at https://github.com/jkitchin/org-ref/#breaking-changes-in-version-3. You can find configuration details at https://github.com/jkitchin/org-ref/#configuration. On Wed, Oct 20, 2021 at 2:59 AM Joseph Vidal-Rosset wrote: > > Dear John, > > I upgraded

Re: citeproc-style-parse: Symbol’s function definition is void: libxml-parse-xml-region

2021-10-18 Thread John Kitchin
This could mean you have an emacs that was not compiled with libxml. Type C-h v system-configuration-options and look for --with-xml2 to see if your emacs was built with it. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical

Re: Expanding how the new cite syntax is used to include cross-references - thoughts?

2021-10-12 Thread John Kitchin
--- 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 Tue, Oct 12, 2021 at 5:58 PM Bruce D'Arcus wrote: > On Tue, Oct 12, 2021 at 5:16 PM John Kitc

Re: Expanding how the new cite syntax is used to include cross-references - thoughts?

2021-10-12 Thread John Kitchin
e are some options to control if the clever parts are abbreviated and/or capitalized. This should be part of org-ref on Melpa next week. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pitt

Re: A minor suggestion about formatting citations

2021-10-11 Thread John Kitchin
you should probably trim each key, and re-add spaces where you want them in the function that does these kinds of things. Maybe that should even be controlled by a defcustom that allows 0-1 spaces. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F

Re: [org-cite] How to cite page number(s) in APA Style?

2021-10-05 Thread John Kitchin
Got it, thanks! 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 Tue, Oct 5, 2021 at 10:54 AM Bruce

Re: [org-cite] How to cite page number(s) in APA Style?

2021-10-05 Thread John Kitchin
meone-2021, then you need another bibliography entry with a different key for that, e.g. someone-2021-87 that might have page 87 in it? John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pitt

Re: Bare oc-csl author variants?

2021-10-05 Thread John Kitchin
These would be equivalent to things like \citeauthor{key} in natbib I think. 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

Re: Would it be possible to color horizontal lines in org mode?

2021-09-30 Thread John Kitchin
k (lambda () (font-lock-add-keywords > nil > '(("^-\\{5,\\}" 0 '(:foreground "red" > :weight bold)) > #+END_SRC > > -Alper > > On Tue, Sep 28, 2021 at 8:18 PM John Kitchin wr

Re: Would it be possible to color horizontal lines in org mode?

2021-09-28 Thread John Kitchin
bold in color. 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 Tue, Sep 28, 2021 at 4:00 AM Eric S Fraga wrote: > You could use

Re: Capture abort: Symbol’s function definition is void: turn-on-org-provide

2021-09-23 Thread John Kitchin
you should use describe-variable on org-capture-templates. Maybe some other package has added to it. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803

Re: [org-cite] citations in property drawers?

2021-09-15 Thread John Kitchin
mechanism. 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 Wed, Sep 15, 2021 at 1:11 PM Tom Gillespie

Re: emacs-jupyter does not send result form babel block

2021-09-08 Thread John Kitchin
s. I am not sure what the fix is for this. The code path from C-cC-c to executing the code, handling the request to the kernel, getting results and to the output is very hard to follow for me. I would post an issue at https://github.com/nnicandro/emacs-jupyter/issues. John ----

Re: Bug Re: Greater than, less than bug in emacs-lisp source block

2021-09-07 Thread John Kitchin
-syntax-entry ?< ".") > (modify-syntax-entry ?> ".") > > solves all the problems with languages that use these in an unbalanced > manner (comparison, assignment). I've had this configuration for years > now and it just works (for me). -- Professor John Kitchin Do

Re: Bug Re: Greater than, less than bug in emacs-lisp source block

2021-09-03 Thread John Kitchin
add-hook 'org-mode-hook #'scimax-fix-<>-syntax) 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

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