Re: [O] lisp babel

2016-04-11 Thread John Kitchin
e: hello-world > #+header: :var message="Hello World!" :exports both > #+begin_src lisp > (princ message) > #+end_src > > In the past, it worked. I thought either slime or sly were needed. > > I'm using org version release_8.3.4-718-g634e12.dirty and GNU Emacs 25

Re: [O] isbn-to-bibtex (from org-ref) fails

2016-04-04 Thread John Kitchin
. "Reading, Mass.") (author . "Feynman, Leighton, Sands.") (ed . "8th > print.") (year . "1996") (isbn . ["0201500647"]) ...)] > --8<---cut here---end------->8--- > > However, isbn-to-bibtex-lead gets me t

Re: [O] org-ref, abstracts

2016-04-04 Thread John Kitchin
I think thats what I mean. org-ref-arxiv hasn't been changed for at least two months I think. and the abstract is listed in the template here: https://github.com/jkitchin/org-ref/blob/2a8635d4662fbe77f43731edeac1b4ec1112d233/org-ref-arxiv.el#L103 Julien Cubizolles writes: > John

Re: [O] org-ref, abstracts

2016-04-04 Thread John Kitchin
no problem. I am not sure when that happened though ;) Julien Cubizolles writes: > John Kitchin writes: > > >> If the data exists, then arxiv-add-bibtex-entry could probably add the >> abstract if it existed. I am not too familiar with arxiv so I am not >> sure. >

Re: [O] [PATCH 1/3] add id attribute to example-block on html export.

2016-04-03 Thread John Kitchin
Thanks. I found this in etc/ORG-NEWS, in case any one else was looking for it ;) Nicolas Goaziou writes: > Hello, > > John Kitchin writes: > >> I am not sure what those should look like or where they go. How about: >> >> * New html id attributes on special, examp

Re: [O] [PATCH 1/3] add id attribute to example-block on html export.

2016-03-31 Thread John Kitchin
links to these elements in other places, e.g. text Nicolas Goaziou writes: > Hello, > > John Kitchin writes: > >> This allows you to hyperlink to the block. > > Applied the 3 patches, with minor changes (you seem to be using an > outdated Org so you were reverting changes

Re: [O] problem with ob-octave (matlab)

2016-03-31 Thread John Kitchin
ab code block... > Wrote /tmp/babel-2948rpV/ob-input-2948ACJ > Error reading results: (beginning-of-buffer) > Code block produced no output. > > > However the code can be executed in matlab giving > > > ans = > > a + b > a - b > > > Any comments? >

Re: [O] using info in a filter

2016-03-30 Thread John Kitchin
ok, thanks. Nicolas Goaziou writes: > Hello, > > John Kitchin writes: > >> How does one use the info in a filter? >> >> e.g. >> >> in (defun my-block-filter (data backend info)) >> >> data is the transcoded block string, and I want to add s

Re: [O] ob-clojure: possible to display results as soon as something is written to STDOUT?

2016-03-30 Thread John Kitchin
x/blob/master/jmax-org.el#L936 It looks like I just redefined the org-babel-execute:sh function after it was loaded. That may not be recommended good practice, but it works ;) I am not sure why it is commented out, maybe because I don't use it alot and its not well tested. You could alway

Re: [O] ob-clojure: possible to display results as soon as something is written to STDOUT?

2016-03-30 Thread John Kitchin
Hi Eric, >>> >>>>> Note: I am not sure if this is something related to Org-mode, or >>>>> ob-clojure or Cider. >>>> None of these directly. It's Emacs, basically: it has very minimal >>>> support for threading so the whol

Re: [O] ob-clojure: possible to display results as soon as something is written to STDOUT?

2016-03-30 Thread John Kitchin
threading so the whole process (Emacs) is waiting for the >> sub-process (Clojure) to finish before doing anything else. > > > Ok good, thanks for confirming! > > Take care, > > Fred -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie M

Re: [O] How to export table from a src block?

2016-03-28 Thread John Kitchin
rg-table-export "/tmp/mytable.csv" "orgtbl-to-csv") > #+END_SRC > > Any help appreciated! > > Bill -- 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: [O] no div/id on named example blocks in html export

2016-03-28 Thread John Kitchin
this. Thanks, Nicolas Goaziou writes: > Hello, > > John Kitchin writes: > >> I noticed that if I make a block like this: >> >> #+name: methane-smiles >> #+BEGIN_EXAMPLE >> C >> #+END_EXAMPLE >> >> There is no id="methane-smiles&quo

[O] [PATCH 3/3] add html attributes to special blocks.

2016-03-28 Thread John Kitchin
Enables #+attr_html and puts an id in when the special block is named. --- lisp/ox-html.el | 26 -- 1 file changed, 16 insertions(+), 10 deletions(-) diff --git a/lisp/ox-html.el b/lisp/ox-html.el index 5bdfc14..da67958 100644 --- a/lisp/ox-html.el +++ b/lisp/ox-html.el @@

[O] [PATCH 1/3] add id attribute to example-block on html export.

2016-03-28 Thread John Kitchin
This allows you to hyperlink to the block. --- lisp/ox-html.el | 15 --- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/lisp/ox-html.el b/lisp/ox-html.el index d07cdcc..92de209 100644 --- a/lisp/ox-html.el +++ b/lisp/ox-html.el @@ -2370,14 +2370,23 @@ contextual informa

[O] [PATCH 2/3] add html attributes to quote-block

2016-03-28 Thread John Kitchin
Enables #+attr_html: and puts a id attribute when the block is named into the html element. --- lisp/ox-html.el | 12 ++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/lisp/ox-html.el b/lisp/ox-html.el index 92de209..5bdfc14 100644 --- a/lisp/ox-html.el +++ b/lisp/ox-htm

Re: [O] headers on special blocks

2016-03-28 Thread John Kitchin
-molecular-data-in-org-mode.org It is kind of interesting I think. Nicolas Goaziou writes: > Hello, > > John Kitchin writes: > >> I am playing around with storing data in special blocks. For example, >> here is an example bit of "data" which is the CH4 (methane)

[O] using info in a filter

2016-03-28 Thread John Kitchin
case where it is easier to make a custom backend with a function like: (defun sb-format (sb contents info)) that builds up the output string? -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin

[O] headers on special blocks

2016-03-28 Thread John Kitchin
:name "methane-smiles" :parent nil)) but I haven't seen any documentation for headers on a special block. Thanks, -- 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: [O] switch parsing in babel

2016-03-28 Thread John Kitchin
Nicolas Goaziou writes: > Hello, > > John Kitchin writes: > >> I am trying to make a new source block that looks like this: >> >> #+BEGIN_SRC obabel -icml -osmi >> [CH4] >> #+END_SRC >> >> This gets parsed to: >> >> (src-b

[O] no div/id on named example blocks in html export

2016-03-27 Thread John Kitchin
to do that? -- 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

[O] switch parsing in babel

2016-03-27 Thread John Kitchin
-labels t :use-labels t :label-fmt nil :hiddenp nil :value "[CH4] \n" :post-blank 1 :post-affiliated 190 :parent nil)) Is that correct? I would have thought that 1. The first switch should be -icml 2. -osmi would also be a switch. If I go with -i -o, then they are both listed as switc

Re: [O] org-ref, abstracts

2016-03-23 Thread John Kitchin
Julien Cubizolles writes: > John Kitchin writes: > >> I am pretty sure the metadata from dx.doi.org doesn't contain any >> abstract information, so there is not a way to put anything useful in >> it. The abstract is often covered by copyright. > > I hadn'

Re: [O] org-ref, abstracts

2016-03-23 Thread John Kitchin
eate an abstract field in the bibtex entry. Is it > possible? If not, I think it would be a useful addition. > > J. Cubizolles -- 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: [O] adding a new org-element?

2016-03-22 Thread John Kitchin
Samuel W. Flint writes: > :: Eric S Fraga writes: > > ESF> On Monday, 21 Mar 2016 at 21:51, John Kitchin wrote: >>> Suppose one wanted to add a new org-element/syntax to org-mode. Where >>> would one start? > > ESF> I cannot help but I am curious: >

Re: [O] adding a new org-element?

2016-03-22 Thread John Kitchin
anted to mine papers that contained $(molecule inchi-key LFQSCWFLJHTTHZ-UHFFFAOYSA-N formula C2H5OH)$ and $(float id melting-point inchi-key LFQSCWFLJHTTHZ-UHFFFAOYSA-N value -173.2 units "degF")$, then you might link to the melting-point value somehow in a new paper without having to copy it. Anyway, the thoughts are still a little loose in my head. I want to try it, and write a paper with it, and see if it was useful enough to write another paper that way ;) -- 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: [O] adding a new org-element?

2016-03-22 Thread John Kitchin
Eric S Fraga writes: > On Tuesday, 22 Mar 2016 at 07:34, John Kitchin wrote: > > [...] > >> the elisp link is a good idea, but I am looking into an idea for a >> chemical markup language where you might have a $(molecule + data)$ and >> reaction descriptions $(mo

Re: [O] adding a new org-element?

2016-03-22 Thread John Kitchin
Eric S Fraga writes: > On Monday, 21 Mar 2016 at 21:51, John Kitchin wrote: >> Suppose one wanted to add a new org-element/syntax to org-mode. Where >> would one start? > > I cannot help but I am curious: > >> I am interested in something like the following synta

[O] adding a new org-element?

2016-03-21 Thread John Kitchin
Suppose one wanted to add a new org-element/syntax to org-mode. Where would one start? I am interested in something like the following syntax: $(arbitrary stuff inside the sexp)$ with a mechanism to call an export function to transcode it. Any pointers to getting started? -- Professor John

Re: [O] uncommnet-region behavior in org-src blocks

2016-03-20 Thread John Kitchin
I think you mean (setq org-src-tab-acts-natively t) right? It looks like the function I made basically does the same thing, by another mechanism! I still wonder why it doesn't work with RET though. John --- Professor John Kitchin Doherty Hall A207F Departme

Re: [O] args-out-of-range #

2016-03-19 Thread John Kitchin
tch-end 0)) (cite-re > > (format "^\\(%s:\\)" (regexp-opt ...))) cite-type) (if (and > > s (string-match cite-re s)) (progn (setq cite-type (match-string 1 s)) > > (remove-text-properties beg end (quote ...)) (add-text-properties beg > > end (list ... ...))

Re: [O] uncommnet-region behavior in org-src blocks

2016-03-19 Thread John Kitchin
tions of this, and they all seem to do that. One day I will have to learn how to get multiple modes active in one buffer ;) Ken Mankoff writes: > On 2016-03-19 at 13:20, Eric S Fraga wrote: >> On Saturday, 19 Mar 2016 at 12:44, John Kitchin wrote: >>> I noticed

Re: [O] No text in pdf output

2016-03-19 Thread John Kitchin
-base 2013.20140215-1 >> >> I must have missed out on some very basic stuff? >> >> Any help would be highly welcomed, >> >> -- >> Guido >> >> Yesterday upon the stair >> I met a man who wasn't there. >> He wasn't there again t

Re: [O] uncommnet-region behavior in org-src blocks

2016-03-19 Thread John Kitchin
sure, that is true. I am still surprised that "uncommenting" adds a # which in org is a comment. actually that seems to happen everywhere in the org-file! John --- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carne

[O] uncommnet-region behavior in org-src blocks

2016-03-19 Thread John Kitchin
I noticed that you try to uncomment a region in a src block a # gets inserted! #+BEGIN_SRC emacs-lisp ; test #+END_SRC If you select ; test and run uncomment-region you get this: #+BEGIN_SRC emacs-lisp # ; test #+END_SRC It also does that in Python. Any ideas why? -- Professor John Kitchin

Re: [O] using vref in latex export, and normal links in html export

2016-03-12 Thread John Kitchin
I guess these are defined in backends, e.g. org-latex-link. Alan Schmitt writes: > On 2016-03-11 16:05, Alan Schmitt writes: > >> On 2016-03-11 15:02, John Kitchin writes: >> >>> Try: >>> >>> (setq org-latex-prefer-user-labels t) >>> >

Re: [O] using vref in latex export, and normal links in html export

2016-03-12 Thread John Kitchin
ef{" "vref{" text))) > > (eval-after-load "ox-latex" > '(progn > (add-to-list 'org-export-filter-link-functions > 'sn/ox-latex-filter-varioref))) > --8<---cut here---end--->8--- -- 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: [O] set default width for figure floats?

2016-03-11 Thread John Kitchin
Rainer M Krug writes: > John Kitchin writes: > >> Maybe you want org-image-actual-width >> >> This sets teh width in org, if you have a working imagemagick. > > No - I don't want any scaling. They are graphs I have created in R and I > want to conserve the

Re: [O] using vref in latex export, and normal links in html export

2016-03-11 Thread John Kitchin
to "fig:log-expt-7", but this does > not work as the label assigned by org to the figure is > "fig:orgparagraph1". > > Here is a small example of a similar problem. Exporting this to latex > > This is a \ref{fig:foo} and this is a link [[fig:foo]] > > #+label

Re: [O] set default width for figure floats?

2016-03-11 Thread John Kitchin
t to let them keep their own > size. > > Is this possible (I'd like to avoid having to use #+ATTR_LATEX :width > before each - and even then I would have no idea to unset the value) > > Thanks, > > Rainer -- Professor John Kitchin Doherty Hall A207F Department of Chem

Re: [O] org-babel C math.h issue

2016-03-10 Thread John Kitchin
d\n",(int)sqrt(i)); >> #+END_SRC > > I get the same problem, Ubuntu 14.04.3 LTS, GNU Emacs 24.3.1, Org-mode > version 8.2.10. So maybe it got fixed at some point since these versions > are about two years old? -- Professor John Kitchin Doherty Hall A207F Department of Chemica

Re: [O] Example of Make file for Org Mode LaTeX to pdf

2016-03-06 Thread John Kitchin
ive > in the real world." -- Mary Shafer, NASA Dryden -- 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: [O] How to prevent loading of org-agenda-files?

2016-03-02 Thread John Kitchin
I guess the OP opens a new emacs instance, which might be loading agenda files each time on initialization? If that is the case, emacsclient is probably the solution. or Open files in a new frame. John --- Professor John Kitchin Doherty Hall A207F Department of

Re: [O] Use org-ref to query pubmed under emacs

2016-03-01 Thread John Kitchin
gt; keyboard frequently. > > > > >> On 1 Mar 2016, at 19:10, John Kitchin wrote: >> >> I don't think so. See >> https://github.com/jkitchin/org-ref/blob/master/org-ref-pubmed.Ella for what >> is possible. It is mostly links and functions that open a browse

Re: [O] Use org-ref to query pubmed under emacs

2016-03-01 Thread John Kitchin
I don't think so. See https://github.com/jkitchin/org-ref/blob/master/org-ref-pubmed.Ella for what is possible. It is mostly links and functions that open a browser to search. On March 1, 2016, at 4:38 AM, 童俊翔 wrote: Is it possible to use org-ref to query pubmed under emacs? Just like Pubmod.

Re: [O] How do I format numbers to an exported table to latex, produced by a code block?

2016-02-29 Thread John Kitchin
ant to export it to latex to produce a pdf but I want to format the >>> numbers of the table so I get, say >>> >>> | 123.456e-3 | 2.000 | >>> | 3.000 | 4.000 | >>> >>> on the exported pdf. >>> >>> How can I do it? >>

Re: [O] How to add a test?

2016-02-29 Thread John Kitchin
. See, > e.g., "test-org-footnote.el". > > Obviously YMMV and the more important thing is to have more tests. How > tests are written is a lesser matter. Feel free to ignore my > suggestions. > > Thank you for your work. > > > Regards, -- 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: [O] How to add left superscripts

2016-02-29 Thread John Kitchin
I knew there was a way to do this. I forgot the \nbsp, {} by itself does not work. Thanks for the reminder. John --- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803

Re: [O] melpa

2016-02-19 Thread John Kitchin
s '(("elpy" . "http://jorgenschaefer.github.io/packages/";) ("org" . "http://orgmode.org/elpa/";) ("gnu" . "http://elpa.gnu.org/packages/";) ("melpa-stable" . "http://melpa-stable.milkbox.net/packages/";) ("melpa&q

Re: [O] org-ref

2016-02-16 Thread John Kitchin
testing. The issue will make sure I don't forget it. Thanks. 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 O

Re: [O] org-ref

2016-02-16 Thread John Kitchin
Is \ref{fig2,fig3} legal LaTeX? 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 Tue, Feb 16, 2016 at 8:52 AM

Re: [O] tangling order

2016-02-16 Thread John Kitchin
eb 16, 2016 at 5:19 AM, Alan Schmitt < alan.schm...@polytechnique.org> wrote: > #+BEGIN_SRC foob :tangle foo.ml > let x = 1 > #+END_SRC > > #+BEGIN_SRC fooa :tangle foo.ml > let x = 2 > #+END_SRC > John ------- Professor John Kitchin Dohert

Re: [O] src code fontification in org 8.3

2016-02-15 Thread John Kitchin
Thanks. A rebuild of emacs did indeed fix it. 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 14, 2016

[O] src code fontification in org 8.3

2016-02-14 Thread John Kitchin
8.2.10 to 8.3 that would affect fontification? or some previous setting that would interfere with it? Thanks, -- 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: [O] Invalid function: org-babel-header-args-safe-fn in Melpa

2016-02-14 Thread John Kitchin
ge-initialize) (package-refresh-contents) (package-install 'pydoc) (package-install 'org-plus-contrib) (org-babel-do-load-languages 'org-babel-load-languages '((emacs-lisp . t) (R . t) )) (message "done") John --- Professor

Re: [O] What does the _ in `(defun org-element-section-parser (_) ...)' stands for?

2016-02-14 Thread John Kitchin
/Using-Lexical-Binding.html 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 Thu, Feb 11, 2016 at 12:33 PM, Nick

[O] Invalid function: org-babel-header-args-safe-fn in Melpa

2016-02-14 Thread John Kitchin
t;ob-R.el" (file-name-directory (locate-library "org"))) t) the problem goes away. I haven't been able to come up with a simple reproducible example. This happens when I start my jmax starter kit from scratch. It does not happen though if I st

Re: [O] What does the _ in `(defun org-element-section-parser (_) ...)' stands for?

2016-02-11 Thread John Kitchin
There is up to date ... And up to date😉 funnily enough I run a near bleeding edge version of Emacs from home brew and org 8.2.10 from Melpa. On Thursday, February 11, 2016, Thorsten Jolitz wrote: > John Kitchin > writes: > > > On Wed, Feb 10, 2016 at 3:13 PM, Thorsten Joli

Re: [O] What does the _ in `(defun org-element-section-parser (_) ...)' stands for?

2016-02-10 Thread John Kitchin
o errors from checkdoc. 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: [O] Visiting an Entry with an ID

2016-02-09 Thread John Kitchin
tp://stackoverflow.com/questions/35299171/org-mode-elisp-how-does-one-switch-the-buffer-when-using-an-id-to-visit-an-en > > Does anyone have an answer for this? -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 41

Re: [O] What does the _ in `(defun org-element-section-parser (_) ...)' stands for?

2016-02-09 Thread John Kitchin
ist, > just out of curiosity, a few functions in org-element.el contain _ in > their parameter list, but its not used in the body. > What does it stand for? -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213

Re: [O] org-ref no bibliography generated in pdf

2016-02-07 Thread John Kitchin
no reason. I do not actually use this code below. I have another function that probably does want texify does ;) maybe some extra stuff like running makeindex, etc Andreas Kiermeier writes: > On 7 February 2016 at 04:38, John Kitchin wrote: > >> that is why you don't ge

Re: [O] org-ref no bibliography generated in pdf

2016-02-06 Thread John Kitchin
ry %o %b" "pdflatex -shell-escape -interaction nonstopmode -output-directory %o %b")) John ------- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin

Re: [O] org-ref no bibliography generated in pdf

2016-02-06 Thread John Kitchin
Then Eric is probably right:what is org-latex-to-pdf-process set to? 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: [O] org-ref no bibliography generated in pdf

2016-02-06 Thread John Kitchin
It could also be you didn't specify a bibliographystyle. Try running M-x org-ref on the file. It checks that some things like that are correct. Sometimes it is helpful to manually build the puff at the command line. Org hides a lot of errors sometimes. On February 6, 2016, at 9:23 AM, Eric S Fr

Re: [O] references to arbitrary labels in org and export to latex

2016-02-05 Thread John Kitchin
would not give the bibliography style link references at the end > of the exported document that you are looking for. -- 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: [O] Attach a Word doc in org mode file

2016-01-29 Thread John Kitchin
is it possible to attach and then open in org mode files other that > plain text? > Thanks -- 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: [O] display org-link url

2016-01-29 Thread John Kitchin
; a "bubble" (I can't remember what it's really called :-( ) with the expanded > link > shown. I think you are looking for "tooltip" ;) -- 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: [O] Require feedback on an idea: move to a central server all my org file and edit from there?

2016-01-23 Thread John Kitchin
you might adapt this: https://github.com/bbatsov/super-save it saves buffers when they lose focus. You could also have them commit and push with a little more work. John --- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie

Re: [O] How to cite author-date including page number in org-mode?

2016-01-18 Thread John Kitchin
This will do what you want I think. [[citep:Fong:2006][p. 1445]] 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: [O] how to add some features in a newly added headline?

2016-01-16 Thread John Kitchin
to collapse > the properties drawer > (org-cycle) > (org-cycle) > (save-excursion ;-> add time stamp >(org-end-of-meta-data t) >(org-time-stamp-inactive '(16)) >(newline) >) > )

Re: [O] org-file using tramp + babel?

2016-01-15 Thread John Kitchin
!! Simple stuff works. It seems to run shell and python fine, although it doesn't load my bashrc file, so some things don't seem to work right that require that. Still, pretty awesome it worked at all! Thanks for the tip about the temp directory! Charles C. Berry writes: > On Thu, 14

[O] org-links in tags

2016-01-15 Thread John Kitchin
Hi all, I think there may be an issue with tags that are defined as links (at least in 8.2.10). For example, if I tag a heading :file:test:, the tags become a file link. This can probably be fixed by adding [^:] to the beginning of the org link regexps? -- Professor John Kitchin Doherty Hall

[O] org-file using tramp + babel?

2016-01-14 Thread John Kitchin
there. Some details (not sure they are relevant): I am running Emacs on a Mac, and opened a file on a remote Centos5 server. Thanks! -- 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: [O] Changing org-block background with org-src-fontify-natively

2016-01-14 Thread John Kitchin
27;s the face-variable that defines the background of > blocks with a specified language? > > Or does it interfere with my "(setq org-src-fontify-natively t)"? > > It would be fine to have both: org-src-fontify-natively *and* a > background colour I can set. -- Profess

Re: [O] org-ref-clean-bibtex-entry and UTF-8

2016-01-13 Thread John Kitchin
turn-off" this option in > org-ref-clean-bibtex-entry, so I do not get warnings about non-ascii > characters? > > Many thanks, > > Julian -- 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: [O] Changing org-block background with org-src-fontify-natively

2016-01-13 Thread John Kitchin
I guess that gives away I am still using 8.2.10! I have never figured out how to get a higher version of that through elpa/melpa/http://orgmode.org/elpa/. Nick Dokos writes: > John Kitchin writes: > >> That is pretty weird. It should be defined in org-faces.el. What org version

Re: [O] Changing org-block background with org-src-fontify-natively

2016-01-12 Thread John Kitchin
That is pretty weird. It should be defined in org-faces.el. What org version are you using? John --- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http

Re: [O] Changing org-block background with org-src-fontify-natively

2016-01-12 Thread John Kitchin
arl Voit writes: > * John Kitchin wrote: >> What do you have org-block-background set to? > > There is no org-block-background in my setup: C-h v org-block- > only offers org-block-entry-blocking and org-block-regexp. > > Org-mode version 8.3.2 (release_8.3.2-200-gc2eeac) > &

Re: [O] importing?

2016-01-10 Thread John Kitchin
You have some luck with pandoc html to orgmode. Raimund writes: > Good morning, > > I think I caught the exporting issues - but is there a way to, say, > import from html to org-mode? I couldn't find something about this in > the info pages. > > ray -- Professor John

Re: [O] [0] Run org-babel src block periodically

2016-01-03 Thread John Kitchin
ry 1 min > for next 1 hour, I would like to set a property like repeat for times to > repeat and keep the org file auto updated > > #+BEGIN_SRC shell :repeat 60 :repeat-every 60sec > tail -n 10 file > #+END_SRC > > Thank you, > -GP -- Professor John Kitchin Doherty H

Re: [O] How define a hook function for `org-babel-post-tangle-hook' for a single file?

2016-01-03 Thread John Kitchin
gled > > * Research > > - Emacs 25, Org Git current > - org-babel-post-tangle-hook > - File local variables and eval > > * Question > > What is the best way to do something like this? > > Sincerely, > > Grant Rettke -- Professor John Kitchin Doherty Hall A207F D

Re: [O] Changing org-block background with org-src-fontify-natively

2016-01-03 Thread John Kitchin
What do you have org-block-background set to? I use the leuven theme, which gives this a light yellow background for me. John --- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268

Re: [O] Publishing images to various sizes

2015-12-26 Thread John Kitchin
s? Probably something that > wraps around imagemagick's 'convert' command? > > When I publish images to my website, I want them to be available in > various sizes, so that I can choose the appropriate image for the > context in which it appears, and thus optimize bandwidt

Re: [O] Problem with org-ref

2015-12-25 Thread John Kitchin
That sounds ok. I pushed a change that sort of does what you ask for. If the "calculated" pdf doesn't exist then you should get prompted for a pdf, and pressing enter for the default (no pdf) should not add a pdf link. John --- Professor John Kitch

Re: [O] Problem with org-ref

2015-12-25 Thread John Kitchin
-entry-fr 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 Thu, Dec 24, 2015 at 10:16 PM, Andreas Kiermeier

Re: [O] Problem with org-ref

2015-12-24 Thread John Kitchin
bibnotes.org" > org-ref-default-bibliography '("~/../Dropbox/_biblio/refs.bib")) > > So, non-nil. > > Andreas > > On 25 December 2015 at 00:45, John Kitchin wrote: > >> >> On Thu, Dec 24, 2015 at 1:04 AM, Andreas Kiermeier < >> and

Re: [O] Problem with org-ref

2015-12-24 Thread John Kitchin
phy-notes variable set to? The default value is nil which would cause that error. 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: [O] Problem with org-ref

2015-12-23 Thread John Kitchin
be unescaped on windows because of the : in the path, which is also done now. I pushed these out. hopefully that makes some progress for you! or at least gives some hints on where to look for the problem. Merry Xmas! John ------- Professor John Kitchin Doherty Hall A2

Re: [O] Problem with org-ref

2015-12-23 Thread John Kitchin
depending on the base of the url. I did that on a Mac, and I haven't tested it on a windows or Linux machine. John --- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268

Re: [O] blog refurbised: how is it in 2015 ?

2015-12-23 Thread John Kitchin
> > John Kitchin writes: > >> I integrated org-mode to blogofile here: >> https://github.com/jkitchin/jmax/blob/master/user/blogofile.el > >> This lets me "publish" an org heading to the blog with a single key >> press, and it copies all the files,

Re: [O] Base 64 inline images in html export

2015-12-22 Thread John Kitchin
I can't recall if I pointed to this post before: http://kitchingroup.cheme.cmu.edu/blog/2015/05/09/Another-approach-to-embedding-org-source-in-html/ but it is similar to what you are trying to do. John --- Professor John Kitchin Doherty Hall A207F Departme

Re: [O] org-ref video

2015-12-22 Thread John Kitchin
Thanks! You might add your interpretation of the pronunciation here: http://tex.stackexchange.com/questions/17502/what-is-the-correct-pronunciation-of-tex-and-latex ;) John --- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie

Re: [O] org-ref video

2015-12-22 Thread John Kitchin
Thanks! B.V. Raghav writes: > Hi, > > I had been following the thread(s) about org-ref by the words, out of > curiosity. However, this video shows how examplary the work is. Awesome > work sir. > > Thanks, > r -- Professor John Kitchin Doherty Hall A207F Department

[O] org-ref video

2015-12-22 Thread John Kitchin
to get a DOI from the PDF or url. 2. Tooltips on cite links The video shows how to use these to make a bibtex file, and then add citations and references in an org-file, followed by export to a pdf. Happy holidays and New Year to everyone! -- Professor John Kitchin Doherty Hall A207F Department

Re: [O] blog refurbised: how is it in 2015 ?

2015-12-22 Thread John Kitchin
zvxvDDbkja/L6UU > mZNPnFy+UPcmDneHBdTs3EouNicOuukYgIYhSClhzo8/H5W/MhqdpTAqZM3Rg/en > fqrm+q128F8UQqPKVchOPcURWBCFs0LoxPAH1uJkvE0yOeyFihVZwVpNazz8qJ0= > =setP > -END PGP SIGNATURE- -- 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: [O] org-ref on Melpa finally!

2015-12-17 Thread John Kitchin
citeproc is so experimental right now I don't think it is ready to be part of org-ref in melpa yet. It is in the git repo. If/when it becomes useful to use, we can figure out how to include it. Martin Yrjölä writes: > Hi! > > John Kitchin writes: >> I finally got org-ref

[O] org-ref on Melpa finally!

2015-12-17 Thread John Kitchin
Hi everyone, I finally got org-ref up on melpa. If you have been waiting to try it out for that, now is your chance! Happy Holidays! -- Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http

Re: [O] Converting paragraph to plain lis

2015-12-16 Thread John Kitchin
sse viverra > consectetur euismod. Donec non tempor turpis. > > to > > 1. Lorem ipsum dolor sit amet, consectetur adipiscing elit. > 2. Suspendisse viverra consectetur euismod. > 3. Donec non tempor turpis. > > In one key stroke, this would speed up my brain storming proc

Re: [O] Wrapping section within LaTeX environment

2015-12-14 Thread John Kitchin
Cool. You might want to change your string match to :correction: so you don't inadvertently wrap a section with the word correction in the body though. That seems like a possibility here. Xavier Garrido writes: > Le 14/12/2015 02:39, John Kitchin a écrit : >> could you provide a br

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