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

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

2021-09-03 Thread John Kitchin
isn't even something 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, Sep 3, 2021 at 7:42

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

2021-09-02 Thread John Kitchin
I think this issue is described in https://emacs.stackexchange.com/questions/50216/org-mode-code-block-parentheses-mismatch. There are also some solutions there. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering

Re: how to get multi-line author in ODT export?

2021-08-26 Thread John Kitchin
That is really nice, thanks for sharing it! 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, Aug

Re: how to get multi-line author in ODT export?

2021-08-26 Thread John Kitchin
Does something like this work for you: #+options: author:nil #+author: Test author - not shown in export @@odt:First author lineSecond line@@ Testing with content This exports to ODT like this for me: [image: image.png] John --- Professor John Kitchin (he/him

Re: [wip-cite-new] Merging tomorrow?

2021-08-20 Thread John Kitchin
I think bibtex-completion is agnostic of ivy or helm, and doesn't require either of them to work. You can use it for candidates to selectrum if you want, and the other many features it offers for notes, pdf, etc... On Fri, Aug 20, 2021 at 11:07 AM Bruce D'Arcus wrote: > I think so. > > I

too aggressive org-cite fontification?

2021-08-19 Thread John Kitchin
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: Function for retrieving the link of an Org Mode buffer

2021-08-14 Thread John Kitchin
lnkplist :desc (buffer-substring-no-properties (org-element-property :contents-begin lnk) (org-element-property :contents-end lnk) lnkplist))) John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie

Re: Custom function for killing the thing at point

2021-08-14 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, Aug 13, 2021 at 9:45 PM Ihor Radchenko wrote: > Rodrigo Morales wri

Re: [Q] How to programmatically get the description of a link?

2021-08-13 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, Aug 13, 2021 at 7:12 PM Rodrigo Morales < moralesrodrigo1...@gmail.com> wrote: > > *

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

2021-08-12 Thread John Kitchin
> As I have thought about this more, the line between citations and > > cross-references has blurred. In org-ref, they were handled the same > > way, with org-links (although each link had its own export function). > > For both cites and refs, the links are just pointers, and in both cases > > it

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

2021-08-11 Thread John Kitchin
mplicitly >> limits/collides with the #+link: keyword. > > Is there a workaround for this somehow, or an alternative that gets > the same thing in the end? > > Bruce -- 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: Expanding how the new cite syntax is used to include cross-references - thoughts?

2021-08-11 Thread John Kitchin
On Wed, Aug 11, 2021 at 10:32 AM Bruce D'Arcus wrote: > On Wed, Aug 11, 2021 at 9:53 AM John Kitchin > wrote: > > > > #+CAPTION: This is the caption for the next figure link (or table) > > > #+NAME: fig:SED-HR4049 > > > > > > [[./img/a.jpg]] >

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

2021-08-11 Thread John Kitchin
the target? I don't think metadata on the target helps with the cases described above, you can reference a label in different ways at different times to get different meanings. > > Bruce > > https://orgmode.org/manual/Images.html > https://orgmode.org/manual/Internal-Links.html

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

2021-08-11 Thread John Kitchin
"Bruce D'Arcus" writes: > Hi John, > > On Tue, Aug 10, 2021 at 8:58 PM John Kitchin wrote: > >> ... I would like what I call an orthogonal approach for cross-references, >> orthogonal in the sense that it can coexist with org-ref, but not require >>

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

2021-08-10 Thread John Kitchin
am curious what you all think. Is it a good idea? Worth waiting for or thinking of a better solution? John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @j

Re: Org-cite follow function for ebib

2021-08-09 Thread John Kitchin
hes. 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 Mon, Aug 9, 2021 at 6:45 AM Joost Kremers wrote: &

Re: add a heading w/ #+print_bibliography to parse tree on export

2021-07-30 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, Jul 30, 2021 at 8:18 PM Matt Price wrote: > Goal: > conditionally add a he

Re: [org-mode] make citation object available to org-cite-make-insert-processor SELECT-STYLE?

2021-07-29 Thread John Kitchin
my solution to this (which I think worked well) is to select the keys, and insert a default style, and then you run a command that updates the style. that way you can get the keys that are in the citation easily from org-element-context, and then I can make a preview for each style that is

Re: [BUG] Citations in tables are not exported

2021-07-29 Thread John Kitchin
It all looks good now! Thanks for the quick fix. 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: [BUG] Citations in tables are not exported

2021-07-29 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 Thu, Jul 29, 2021 at 8:26 AM Nicolas Goaziou wrote: > Hello, >

Re: org-cite-list-bibliography-files

2021-07-28 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, Jul 28, 2021 at 10:20 AM Titus von der Malsburg wrote

Re: org-cite-list-bibliography-files

2021-07-28 Thread John Kitchin
Could it be related to the variable org-mouse-1-follows-link? Today I added mouse-1 to the keymap that org-ref-cite uses so that might also resolve it for you. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering

org-ref-cite

2021-07-27 Thread John Kitchin
-ref-cite/issues. Thanks everyone who made this new cite syntax possible! 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-list-bibliography-files

2021-07-26 Thread John Kitchin
st week, there are cases where one might want > to combine them. > > https://lists.gnu.org/archive/html/emacs-orgmode/2021-07/msg00495.html > > It's just not the common case. > > Bruce -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering

Re: org-cite: how to include a cite with no key?

2021-07-19 Thread John Kitchin
On Mon, Jul 19, 2021 at 7:28 PM Emmanuel Charpentier < emm.charpent...@free.fr> wrote: > > In natbib there is \citetext{priv.\ comm.} which is used to add a > > textual citation to the bibliography that doesn't have a key > > associated with it. > > Hmmm... why should you bother to reference a

Re: should a BIBLIOGRAPHY keyword supercede org-cite-global-bibliography?

2021-07-19 Thread John Kitchin
The >> last one is of course a target for #+BIBLIOGRAPHY ; I'd tend to let the >> subject matter library as a file-specific #+BIBLIOGRAPHY (my subject >> matters tend to vary...), but this depends on your field. >> >> You may also think of this typology as books

org-cite: how to include a cite with no key?

2021-07-19 Thread John Kitchin
, but something like this seems like a reasonable solution to me. [cite/text:@ private communication] John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803

should a BIBLIOGRAPHY keyword supercede org-cite-global-bibliography?

2021-07-19 Thread John Kitchin
-global-bibliography. Is there a scenario where the union of those makes sense? 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: [BUG] Citations in tables are not exported

2021-07-18 Thread John Kitchin
ting to ASCII, I see this: > > #+begin_example > Schulte, Eric, and Dan Davison. 2011. “Active Documents with Org-Mode.” > /Computing in Science Engineering/ 13 (3):66–73. > > (Schulte and Davison 2011) > > > [cite/a:@SchulteActiveOrg] >

Re: org-cite citation commands

2021-07-17 Thread John Kitchin
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

2021-07-17 Thread John Kitchin
blatex 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

could we support * in a cite style.

2021-07-16 Thread John Kitchin
[cite/author/star:@swain-2016-chemd] or [cite/author-star:@swain-2016-chemd] IMO. 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: help with a regexp

2021-07-15 Thread John Kitchin
solution in my opinion would be for org-mode to not recognize [cite:...] as a link. Other ideas? Thanks, Stephen Berman writes: > On Wed, 14 Jul 2021 20:43:24 -0400 John Kitchin > wrote: > >> Hi all, I could use a bit of help with a regexp. I am trying to fine tune >>

help with a regexp

2021-07-14 Thread John Kitchin
[[ can prefix it to be a cite link in org-ref, but not 1 [. right now the cite: in the org-cite syntax is getting flagged as bad cite link which I want to avoid. is this doable? John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical

Re: [wip-cite-new] Merging tomorrow?

2021-07-13 Thread John Kitchin
-20210712/) 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, Jul 7, 2021 at 8:18 PM Nicolas

Re: [BUG] org-goto slows down org-set-property

2021-07-13 Thread John Kitchin
This link ( https://stackoverflow.com/questions/36926513/are-there-elisp-functions-that-list-markers-in-a-given-buffer) suggests there is not a good way to find all the markers associated with a buffer. John --- Professor John Kitchin (he/him/his) Doherty Hall

Re: [wip-cite-new] Merging tomorrow?

2021-07-08 Thread John Kitchin
My intuition is that crossrefs are separate from the citations. In org-ref, they are separate link types like ref:xxx, pageref:xxx. eqref:xxx, etc. They also use a different source of candidates than cites do. John --- Professor John Kitchin (he/him/his) Doherty

Re: LaTeX-producing code : how to export results to HTML/ODT

2021-07-07 Thread John Kitchin
egral", caption="This is an equation.", data=*this*) "\\begin{equation} \\int_0^2 e^x dx \\end{equation}" #+END_SRC works better for latex. I guess that is always going to be some kind of limitation. John ------- Professor John Kitchin (he/him/his)

Re: LaTeX-producing code : how to export results to HTML/ODT

2021-07-06 Thread John Kitchin
quot;$\int_0^2 e^x dx$" #+END_SRC #+RESULTS: :results: #+name: eq-integral #+caption: This is an equation. $int_0^2 e^x dx$ :end: John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsbu

Re: add #+ATTR_SOMETHING to headline?

2021-07-06 Thread John Kitchin
something obvious, or is htis not possible? I notice that > none of the org-xxx-headline functions in ox-xxx.el seem to check for > attributes, so maybe this is by design? > > THanks, > > Matt > -- John --- Professor John Kitchin (he/him/h

Re: LaTeX-producing code : how to export results to HTML/ODT ?

2021-07-04 Thread John Kitchin
a}{b}\right)}\] :end: the key is the drawer 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://kitchingroup.cheme.cmu.edu

Re: LaTeX-producing code : how to export results to HTML/ODT ?

2021-07-04 Thread John Kitchin
n >HTML/ODF/whatever-but-not-LaTeX ? >- Wouldn't an option to allow these exports be a welcome addition to >the export structure (or possibly to the various exporters) ? > > > Thanks in advance, > -- John --- Professor John Kit

Re: [wip-cite-new] Quick note about citation insertion

2021-07-02 Thread John Kitchin
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, Jul 2, 2021 at 4:59 PM Bruce D'Arcus wrote: > > > On Fri, Jul 2, 2021, 4:14 PM Nicola

Re: Virtually prefix headlines according to content

2021-06-29 Thread John Kitchin
There might be some clever way to tie that onto fontlock, or some kind of hook to make it also work for entries as you create them. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsbur

Re: Export Org mode files to (gag, barf) MS Office?

2021-06-26 Thread John Kitchin
there is some code at https://github.com/jkitchin/scimax/blob/master/ox-word.el that does an ok job with pandoc. It isn't perfect though, and I don't think it ever will be. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical

Re: appearance of list as results from evaluating code blocks

2021-06-25 Thread John Kitchin
on" "c72a3a11-8982-4ead-a0bf-cb92a24a966c" "ns" "user" "value" "nil" "changed-namespaces" (dict) "repl-type" "clj") That is my best guess for why you don't see the output. This happens in the function ob-clojure-eval-w

Re: appearance of list as results from evaluating code blocks

2021-06-24 Thread John Kitchin
have to explicitly return a value to see it. #+BEGIN_SRC python :results value code return [1, 2, 3] #+END_SRC #+RESULTS: #+begin_src python [1, 2, 3] #+end_src John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering

Re: Large source block causes org-mode to be unusable

2021-06-21 Thread John Kitchin
any LaTeX formulas) > several times per second... > > Is there a way to make this fontify function to act "around my cursor" ? > > Best, > Leo -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 4

Re: [longlines] (was: example paper written in org completely)

2021-06-18 Thread John Kitchin
I never found a longline mode I liked and that is why I stick to good > old auto-fill with 70 chars. > > I wounder what you use to display the file (I am using a either a 14 > inch Thinkpad X1 or 13inch MacBookAir, so maybe that is the issue here). > > -- John ---

Re: A dictionary made in Org Mode

2021-06-18 Thread John Kitchin
ew of the files involved and > the final compilation, before printing all the work: > > https://vimeo.com/538137630 > > Best regards, > > Juan Manuel > > > -- John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of

Re: some progress matlab-kernel, a python path problem?

2021-06-16 Thread John Kitchin
spec > | raise NoSuchKernel(kernel_name) > | jupyter_client.kernelspec.NoSuchKernel: No such kernel named matlab > | > | Process kernel-matlab exited abnormally with code 1 > ` > > But the matlab_kernel is installed > > I am puzzled, any python guru could enlighten me please? > > Regards > > Uwe Brauer > > > -- 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-attach a directory?

2021-06-11 Thread John Kitchin
. I remember old > version org-mode can do this. But later delete this feature? I forget what > version is. > > I suggest to add this feature. > > On Jun 8, 2021, at 11:49 PM, John Kitchin wrote: > > Is it possible to attach a directory to an org heading? > > I have

Re: org-attach a directory?

2021-06-10 Thread John Kitchin
isn't that just org-attach-attach-mv? or what happens if you set org-attach-method to mv? John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin

Re: org-attach a directory?

2021-06-09 Thread John Kitchin
scimax-org-attach-attach-directory-cp dir) (delete-directory dir t t)) 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.chem

Re: org-attach a directory?

2021-06-08 Thread John Kitchin
, but what I was thinking of doing). Did I misunderstand what org-attach-set-directory does? John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin

org-attach a directory?

2021-06-08 Thread John Kitchin
Is it possible to attach a directory to an org heading? I have only seen how to attach a file so far. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803

Re: Hiding results using :post

2021-06-07 Thread John Kitchin
that code should work on most src-blocks though. 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 Mon, Jun 7

Re: Hiding results using :post

2021-06-07 Thread John Kitchin
args) (org-babel-remove-result))) I guess there are other ways that might work too. #+BEGIN_SRC jupyter-python :results hide print(5) #+END_SRC #+RESULTS: : 5 John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carne

Re: colored src blocks question

2021-06-01 Thread John Kitchin
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, Jun 1, 2021 at 2:52 PM Tom Gillespie wrote: > Hi John, > Are you perhaps missing the :ex

Re: Get list of top-level headings

2021-05-19 Thread John Kitchin
be noticeable! 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 19, 2021 at 10:19 AM Jonathan Gregory

Re: Get list of top-level headings

2021-05-19 Thread John Kitchin
) "LEVEL=1") #+END_SRC 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 19, 202

Re: Global variables in Org mode document with source blocks

2021-05-18 Thread John Kitchin
re, but i don't know if this is 100% reliable across all blocks. 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, May 18, 202

Re: could a :var header argument refer to a data table in another file?

2021-04-29 Thread John Kitchin
I don't know if it is in the manual. It would be great to have it in https://orgmode.org/manual/Environment-of-a-Code-Block.html. John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University

Re: could a :var header argument refer to a data table in another file?

2021-04-29 Thread John Kitchin
This syntax works for me. #+BEGIN_SRC python :var data=data.org:remote-table print(data) #+END_SRC John --- Professor John Kitchin (he/him/his) Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803

Re: wip-cite status question and feedback

2021-04-21 Thread John Kitchin
something similar is done in the bibtex-completion commands. Bruce D'Arcus writes: > On Wed, Apr 21, 2021 at 3:57 PM John Kitchin wrote: > >> I guess that the actions I use most often when "opening" a citation are, >> opening the pdf, going to the webpage for it, an

Re: wip-cite status question and feedback

2021-04-21 Thread John Kitchin
>>> - "fontification" is meant to give full access to face selection, what >>> is really displayed, additional keymaps, all using a single >>> function. >> >>> At the moment, I have no idea about what arguments would be u

Re: wip-cite status question and feedback

2021-04-21 Thread John Kitchin
ment I am citing (or even page in the document). > > I think that full citation object should be worth passing to the > citation backend. > > 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: Using backticks for the inline code delimeter?

2021-04-21 Thread John Kitchin
On a Mac, you might find these useful. I don't use the right command and option keys, so I redefine them as hyper and super. they are right under my thumb, and convenient. (setq mac-right-command-modifier 'hyper) (setq mac-right-option-modifier 'super) -- Professor John Kitchin Doherty Hall A207

Re: Using backticks for the inline code delimeter?

2021-04-20 Thread John Kitchin
ess just write a function that checks context? Presumably all the > overloaded keybindings do this already but I guess I don't really know how > they do so. > > I do in general wish it were easier to switch between writing markdown and > writing org, since I often have to write mar

Re: Font lock in org+elisp confused with ?\[

2021-04-02 Thread John Kitchin
ix it. 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 2, 2021 at 12:24 AM Tim Cross wrote: >

Re: References?? (feature idea)

2021-03-14 Thread John Kitchin
, and use (org-entry-get) on the heading to get the property value. John --- 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

Re: [EXT] Problem with org-ref

2021-03-10 Thread John Kitchin
thanks for the troubleshooting. I pushed a fix that should use the customizable pdf filename function instead. John --- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803

Re: contact management in emacs

2021-03-08 Thread John Kitchin
ync from my BBDB/Org solution to the phone, but >> I feel like I never found a good option. > > bbdb-vcard package is here: > https://melpa.org/packages/bbdb-vcard-20201016.1902.tar > > Jean -- 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

Re: state of the art in org-mode tables e.g. join, etc

2021-02-25 Thread John Kitchin
> > > > This should also be possible but I cannot get it to work now: > > #+begin_src R :var recipe=recipe :var nutrition=nutrition :colnames yes > :prologue sqldf(' :epilogue ') > select * from recipe, nutrition where recipe.type=nutrition.type > #+end_src > > > > > &g

Re: state of the art in org-mode tables e.g. join, etc

2021-02-24 Thread John Kitchin
org > > (especially look at the Pandas section 10) > > In that file I also tangle a python library "orgbabelhelper" that is > available in Conda and PyPi. I mainly use that to work with my tables. > > Best regards > Derek -- Professor John Kitchin Doherty Hall A207F Dep

Re: Citations with page numbers using helm-bibtex and org-ref

2021-02-21 Thread John Kitchin
ast. John --- 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 On Sun, Feb 21, 2021 at 12:13 PM Adam Sneller wrote: > Hi Bruce/John, > > Thanks for getting bac

Re: state of the art in org-mode tables e.g. join, etc

2021-02-21 Thread John Kitchin
3 | 9.0 | | tomatoe | 120 | tomatoe | 0.6 | 2.1 | 0.8 | 3.4 | | eggplant | 300 | eggplant | 2.5 | 3.2 | 0.8 | 8.6 | | tofu | 100 | tofu | 0.7 | 0.5 | 6.6 | 1.4 | John --- Professor John Kitchin Doherty Hall A207F Department of

Re: state of the art in org-mode tables e.g. join, etc

2021-02-21 Thread John Kitchin
lant 3002.53.2 0.8 8.6 : 3 tofu 1000.70.5 6.6 1.4 :end: John --- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnki

Re: Citations with page numbers using helm-bibtex and org-ref

2021-02-21 Thread John Kitchin
In org-ref you also handle this by annotations of the cite links, e.g. [[cite:book-key][p23]] and then bibtex or biblatex does the formatting. John --- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University

state of the art in org-mode tables e.g. join, etc

2021-02-20 Thread John Kitchin
ot;type-2") (cl-loop for row in data sum (nth 2 row))) #+END_SRC #+RESULTS: : 5.1005 I have spent a lot of time with Pandas in Python lately, and trying to think through what some analogues with org-tables would be. I would be very happy not to reinvent the wheel here! John

Re: How to associate a code block to another one so that it is executed beforehand?

2021-02-15 Thread John Kitchin
: foo : bar : John ------- 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 On Mon, Feb 15, 2021 at 4:01 PM Rodrigo Morale

Re: programatically generate an agenda

2021-02-14 Thread John Kitchin
hat function… > > Thanks a lot for any suggestion on how to do this. > > Best, > > Alan -- 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

Re: Auto-activate new <<>>

2021-02-08 Thread John Kitchin
I guess the place to do it is with an advice on org-activate-links. Maybe a simple after advice would do. John --- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803

Re: Get =#+RESULTS= without re-evaluating source code block?

2021-02-01 Thread John Kitchin
; > >> > > So, my question is: Is it possible to use the actual =#+RESULTS= code >> > > block instead of always evaluating it when referencing the results >> > > through a =:noweb= reference? >> > >> > Perhaps "Cache results of evaluation" (15.5 Evaluating Code Bloc

Re: Get =#+RESULTS= without re-evaluating source code block?

2021-01-27 Thread John Kitchin
lts of evaluation" (15.5 Evaluating Code Blocks, > in the Interwebs here [1] is for you. > > In short, add a header argument :cache yes to your code block. > > Cheers > > [1] https://orgmode.org/org.html#Evaluating-Code-Blocks > > - t > -- John --- 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

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