Re: [O] helm-bibtex questions
hmm strange still dosent work for me. here is the top section of my bib file
-*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-
@article{ackerman-1998-discr-clear,
author = {Ackerman, {S.A.} and Strabala, {K.I.} and Menzel,
{W.P.} and Frey, {R.A.} and Moeller, {C.C.} and
Gumley, {L.E.}},
title = {Discriminating Clear Sky From Clouds With Modis},
journal = {Journal of Geophysical Research},
volume = 103,
number = {D24},
pages = {32,141--32,157},
year = 1998,
shorttitle = {Discriminating clear sky from clouds with {MODIS}},
}
when i use the org ref clean i still get
bibtex-format-entry: Mandatory field `journal' is missing
also in the emacs menu the entry type is still bibtex. i tried restarting
emacs and still no go.
any clue? also do you prefer I continue this discussion on the github
org-ref site?
best!
Z
On Fri, Jun 26, 2015 at 5:28 PM, John Kitchin jkitc...@andrew.cmu.edu
wrote:
http://tex.stackexchange.com/questions/78455/does-emacs-support-editing-bibliography-files-for-biblatex
I think you need this in your bibtex file:
-*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-
Xebar Saram writes:
thanks so much again John
i did add this line
(bibtex-set-dialect 'biblatex)
in my init but that dosent seem to do much as i still get the journal
mandatory field missing error. anything else i can try?
best
Z
On Thu, Jun 25, 2015 at 2:09 PM, John Kitchin johnrkitc...@gmail.com
wrote:
I believe that is an emacs bibtex issue. You need some kind of line in
your bibtex file to specify it is the biblatex dialect.
On June 25, 2015, at 6:58 AM, Xebar Saram zelt...@gmail.com wrote:
Great, works well. one question though (and this may very well be due to
my inexperience). the jabref export i had used 'journaltitle' instead of
journal to be (to my understanding) compatible with the newer .bib files
used by biblatex (and biber). when i ran org-ref clean it gave an error
on
journal mandatory field missing. i had to replace all 'journaltitle'
to
'journal' to get it to work.
is this by design? does org-ref not support the new biblatex/biber .bib
file format?
kind regards
Itai
On Thu, Jun 25, 2015 at 12:03 AM, John Kitchin jkitc...@andrew.cmu.edu
wrote:
yes, there is a way ;)
First. Make sure you have a backup of the references. I like to keep
mine in a local git repo so you can undo any mistakes that get made.
I suggest you run these first:
%% (bibtex-validate-globally) ; checks for duplicate keys
%% (bibtex-validate)
I also recommend you run bibtex-sort (it is easier to spot duplicates
in
a sorted list).
and (org-ref-build-full-bibliography) - makes a pdf of all references.
to make sure everything is compliant and functional.
Then, put this next line at the top of your bibtex file. The t
argument to
org-ref-clean-bibtex-entry will preserve your existing keys.
% (bibtex-map-entries (lambda (key start end)
(org-ref-clean-bibtex-entry
t)))
Put your cursor at the end of that line, and type C-x C-e to run the
function, and
wait patiently. It took a few minutes on my 1300 entries, and I had to
restart it once on some entry.
when it is done, run (org-ref-build-full-bibliography) again to make
sure it works and review the ~200 page pdf ;). fix errors and repeat
until it builds ;)
Note if you want to change title cases in all entries you can use
% (bibtex-map-entries 'jmax-title-case-article)
% (bibtex-map-entries 'jmax-sentence-case-article)
I hope that helps!
Xebar Saram writes:
John
First of all thanks so much for the excellent
org-ref-clean-bibtex-entry
function i love it!
also your blog post on cleaning the bib file is a life saver
i have 800 references, is there a way to auto
make org-ref-clean-bibtex-entry go thorough my whole bib file instead
of me
going and cleaning it 1 by 1?
kind regards
Z.
On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg
malsb...@posteo.de
wrote:
Here is my CV in org-mode:
https://gist.github.com/tmalsburg/96084ba82281937c26b7
It’s a pretty straightforward org document except for one thing: the
key
to making this work was biblatex which can be used to create several
lists of references filtered according to keywords, author, etc.
This
allowed me to have separate sections for journal articles,
conference
presentations, etc. I store the relevant keywords in the tags
field of
the BibTeX entries and since biblatex doesn’t know this field, I
copy
the tags on-the-fly to the keywords field (see DeclareSourcemap in
the
LaTeX headers).
Titus
On 2015-06-22 Mon 07:28, Xebar Saram wrote:
Hi John
a bit off topic, but do you also write your academic CV in
orgmode or
lateX? in anycase would you mind sharing your org/latex CV
[O] comment org code block
Hi all i was wondering if anyone knew of a command or bind to quickly comment the entire content of an org code block (with the correct comment syntax)? thx! Z
Re: [O] problem with ox-pandoc export
On 2015-06-26 17:36, Nicolas Goaziou m...@nicolasgoaziou.fr writes: Hello, Alan Schmitt alan.schm...@polytechnique.org writes: Is there any reason why the options would disappear during export? Maybe ox-pandoc doesn't handle this meta-data. ox-pandoc does not do anything with that meta-data when generating the temporary org file. Shouldn't it inherited from the org exporter? Perhaps you're doing a body-only export. No, I just checked. Or you have `org-export-with-title' and al. set to nil... No, and I can reproduce this with an empty configuration. So I guess there is something fishy going on in the generation of the temporary org file. Thanks, Alan -- OpenPGP Key ID : 040D0A3B4ED2E5C7 Athmospheric CO₂ average (2015-05-30, Mauna Loa Observatory): 403.41 ppm signature.asc Description: PGP signature
Re: [O] more helm-bibtex/org-ref questions
Dear John, On Fri, 26-06-2015, at 22:58, John Kitchin jkitc...@andrew.cmu.edu wrote: You could have multiple file fields I suppose, and adapt [1] to give you a choice of which one to open. That is an intriguing suggestion. I'll try to play with it. Personally, I have one pdf per bibtex entry, named by the key of the entry, in a directory called bibtex-pdfs somewhere defined by org-ref-pdf-directory. There are ~1300 pdfs in there now. I always access them through helm bibtex. admittedly, I don't have the SI or other stuff around usually. I don't use bibtex to keep track of the directories where I write manuscripts either. I don't use bibtex to keep track of the dirs where I write manuscripts either, but SI et al I often do want to store. The SI more and more as time goes by, given the current policy of many journals of moving the methods details to SI ---I could merge PDFs into a single one, but that is another step. You could always make links to these other things in the associated notes entry. or put org-links in a bibtex field, and then you can open them with C-c o (if you setup links to work everywhere). That way, opening the pdf is easy, and opening the other things is just opening the entry and running the link open command. That is a great suggestion. However, I just realized that I would not be able to then open any of the links in an Android device (where I do part of my reading) or in, say, JabRef (I'd need to have a script run to reformat them, but then propagating changes both ways starts getting very cumbersome). I need to think some more about this. Thanks for your suggestions. Best, R. Ramon Diaz-Uriarte writes: Dear All, (I am not sure this is the appropriate place, but this is neither a bug report nor an feature request about helm-bibtex or org-ref, but a question from ignorance and I am learning quite a bit from the other helm-bibtex questions). How do people deal with multiple files that are logically associated to an entry? I've been used to keeping the main file, supplementary materials, associated code, etc, in a directory per entry. This kind of modus operandi is something I adopted (fell into?) easily with Zotero and Mendeley. But I am not sure that this is the best way to proceed. If I end up with multiple files per directory, helm-bibtex-find-pdf[1] cannot know which one I want to open. I could keep the main file in the general directory, so it is found directly by helm-bibtex-find-pdf and specify other files (of secondary usage) in the file field (and maybe open them via ebib when/if needed)? But this does not seem elegant. Another is to have an entry per file, with unique key, but this does not seem right. Thanks, R. [1] Thanks to Titus' help (https://github.com/tmalsburg/helm-bibtex/issues/53), opening a PDF that is given in the file field with the directory name is now within my reach. -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-25 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz
Re: [O] problem with ox-pandoc export
On 2015-06-27 12:07, Alan Schmitt alan.schm...@polytechnique.org writes: No, and I can reproduce this with an empty configuration. So I guess there is something fishy going on in the generation of the temporary org file. Here is an ECM to show the issue. Evaluate this code: #+begin_src emacs-lisp (org-export-define-derived-backend 'mytest 'org :translate-alist '((template . org-pandoc-template)) :export-block MYTEST :menu-entry '(?t test as/org-export-test)) (defun as/org-export-test (optional a s v b e) (org-export-to-file 'mytest (org-export-output-file-name (concat (make-temp-name .tmp) .org) s))) #+end_src Then try it with this file --8---cut here---start-8--- #+title: This is a title #+date: 1/2/3 * First section foo * Second section bar --8---cut here---end---8--- The resulting exported file is missing the title and date. Best, Alan -- OpenPGP Key ID : 040D0A3B4ED2E5C7 Athmospheric CO₂ average (2015-05-30, Mauna Loa Observatory): 403.41 ppm signature.asc Description: PGP signature
Re: [O] problem with ox-pandoc export
Alan Schmitt alan.schm...@polytechnique.org writes: On 2015-06-27 12:07, Alan Schmitt alan.schm...@polytechnique.org writes: No, and I can reproduce this with an empty configuration. So I guess there is something fishy going on in the generation of the temporary org file. Here is an ECM to show the issue. Evaluate this code: #+begin_src emacs-lisp (org-export-define-derived-backend 'mytest 'org :translate-alist '((template . org-pandoc-template)) :export-block MYTEST :menu-entry '(?t test as/org-export-test)) (defun as/org-export-test (optional a s v b e) (org-export-to-file 'mytest (org-export-output-file-name (concat (make-temp-name .tmp) .org) s))) #+end_src ox-org inserts meta-data in its template function (org-org-template). Since you're overriding it in the `mytest' back-end, you need to take care of that. Regards,
Re: [O] ox-odt roundtrip editing?
Hi Joakim, On 2015-06-26 at 07:45, joa...@verona.se wrote: I'm writing a manuscript for a publisher. The process looks like: - I write a chapter in org mode, export it to odt - I apply the styles the publisher wants to use with a libreoffice macro. This isn't particularily efficient, but I failed at modifying ox-odt to use custom templates. - I get back comments on the chapter from the publisher, that use the libreoffice annotation feature. Here I basically can't use org-mode anymore. Has someone attempted doing roundtrip editing ith libreoffice and org? That is, convert the odt file back to org, including the annotations, and edit fro there? Does this workflow describe what you want to do (but change DOCX to ODT)? https://lists.gnu.org/archive/html/emacs-orgmode/2015-06/msg00246.html -k.
Re: [O] comment org code block
This seems to work for some toy examples: (defun comment-org-in-src-block () (interactive) (org-edit-special) (comment-dwim nil) (org-edit-src-exit)) Xebar Saram writes: Hi all i was wondering if anyone knew of a command or bind to quickly comment the entire content of an org code block (with the correct comment syntax)? thx! Z -- 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] helm-bibtex questions
You need:
% -*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-
You probably have to close and reopen the file, and you will probably be
prompted for running local variables (or use C-x C-e after the command
above it
With this, it works fine for me.
This isn't really an org-ref problem, it is happening in
bibtex-clean-entry. it might be better to move it to github. I just
noticed a similar issue already there:
https://github.com/jkitchin/org-ref/issues/40
;)
Xebar Saram writes:
hmm strange still dosent work for me. here is the top section of my bib file
-*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-
@article{ackerman-1998-discr-clear,
author = {Ackerman, {S.A.} and Strabala, {K.I.} and Menzel,
{W.P.} and Frey, {R.A.} and Moeller, {C.C.} and
Gumley, {L.E.}},
title = {Discriminating Clear Sky From Clouds With Modis},
journal = {Journal of Geophysical Research},
volume = 103,
number = {D24},
pages = {32,141--32,157},
year = 1998,
shorttitle = {Discriminating clear sky from clouds with {MODIS}},
}
when i use the org ref clean i still get
bibtex-format-entry: Mandatory field `journal' is missing
also in the emacs menu the entry type is still bibtex. i tried restarting
emacs and still no go.
any clue? also do you prefer I continue this discussion on the github
org-ref site?
best!
Z
On Fri, Jun 26, 2015 at 5:28 PM, John Kitchin jkitc...@andrew.cmu.edu
wrote:
http://tex.stackexchange.com/questions/78455/does-emacs-support-editing-bibliography-files-for-biblatex
I think you need this in your bibtex file:
-*- mode:bibtex; eval: (bibtex-set-dialect 'biblatex); -*-
Xebar Saram writes:
thanks so much again John
i did add this line
(bibtex-set-dialect 'biblatex)
in my init but that dosent seem to do much as i still get the journal
mandatory field missing error. anything else i can try?
best
Z
On Thu, Jun 25, 2015 at 2:09 PM, John Kitchin johnrkitc...@gmail.com
wrote:
I believe that is an emacs bibtex issue. You need some kind of line in
your bibtex file to specify it is the biblatex dialect.
On June 25, 2015, at 6:58 AM, Xebar Saram zelt...@gmail.com wrote:
Great, works well. one question though (and this may very well be due to
my inexperience). the jabref export i had used 'journaltitle' instead of
journal to be (to my understanding) compatible with the newer .bib files
used by biblatex (and biber). when i ran org-ref clean it gave an error
on
journal mandatory field missing. i had to replace all 'journaltitle'
to
'journal' to get it to work.
is this by design? does org-ref not support the new biblatex/biber .bib
file format?
kind regards
Itai
On Thu, Jun 25, 2015 at 12:03 AM, John Kitchin jkitc...@andrew.cmu.edu
wrote:
yes, there is a way ;)
First. Make sure you have a backup of the references. I like to keep
mine in a local git repo so you can undo any mistakes that get made.
I suggest you run these first:
%% (bibtex-validate-globally) ; checks for duplicate keys
%% (bibtex-validate)
I also recommend you run bibtex-sort (it is easier to spot duplicates
in
a sorted list).
and (org-ref-build-full-bibliography) - makes a pdf of all references.
to make sure everything is compliant and functional.
Then, put this next line at the top of your bibtex file. The t
argument to
org-ref-clean-bibtex-entry will preserve your existing keys.
% (bibtex-map-entries (lambda (key start end)
(org-ref-clean-bibtex-entry
t)))
Put your cursor at the end of that line, and type C-x C-e to run the
function, and
wait patiently. It took a few minutes on my 1300 entries, and I had to
restart it once on some entry.
when it is done, run (org-ref-build-full-bibliography) again to make
sure it works and review the ~200 page pdf ;). fix errors and repeat
until it builds ;)
Note if you want to change title cases in all entries you can use
% (bibtex-map-entries 'jmax-title-case-article)
% (bibtex-map-entries 'jmax-sentence-case-article)
I hope that helps!
Xebar Saram writes:
John
First of all thanks so much for the excellent
org-ref-clean-bibtex-entry
function i love it!
also your blog post on cleaning the bib file is a life saver
i have 800 references, is there a way to auto
make org-ref-clean-bibtex-entry go thorough my whole bib file instead
of me
going and cleaning it 1 by 1?
kind regards
Z.
On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg
malsb...@posteo.de
wrote:
Here is my CV in org-mode:
https://gist.github.com/tmalsburg/96084ba82281937c26b7
It’s a pretty straightforward org document except for one thing: the
key
to making this work was biblatex which can be used to create several
lists of references filtered according to keywords, author, etc.
This
allowed me
Re: [O] comment org code block
(defun comment-org-in-src-block () (interactive) (org-edit-special) (mark-whole-buffer) (comment-dwim nil) (org-edit-src-exit)) ;) Xebar Saram writes: wow wonderful! this works flawlessly when i select the region inside the code block and run the command. I wonder if any lisp wizards out there can modify Johns code and make it auto select all lines *inside* the current block and then comment it? could be useful to other people i assume. thx again On Sat, Jun 27, 2015 at 2:32 PM, John Kitchin jkitc...@andrew.cmu.edu wrote: This seems to work for some toy examples: (defun comment-org-in-src-block () (interactive) (org-edit-special) (comment-dwim nil) (org-edit-src-exit)) Xebar Saram writes: Hi all i was wondering if anyone knew of a command or bind to quickly comment the entire content of an org code block (with the correct comment syntax)? thx! Z -- 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 -- 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] ox-odt roundtrip editing?
joa...@verona.se writes: I'm writing a manuscript for a publisher. The process looks like: - I write a chapter in org mode, export it to odt - I apply the styles the publisher wants to use with a libreoffice macro. This isn't particularily efficient, but I failed at modifying ox-odt to use custom templates. - I get back comments on the chapter from the publisher, that use the libreoffice annotation feature. Here I basically can't use org-mode anymore. Has someone attempted doing roundtrip editing ith libreoffice and org? That is, convert the odt file back to org, including the annotations, and edit fro there? There is no such functionality in Org. Why not send ox-ascii output whilst editing. Tell them to just edit and use ediff when you get it back. It would still require manual work to adapt the notes. But I'd guess that's always the case. Presumably, you could also use ox-org to get a cleaner version of your file that you could send. Cheers, Rasmus -- Vote for proprietary math!
Re: [O] comment org code block
wow wonderful! this works flawlessly when i select the region inside the code block and run the command. I wonder if any lisp wizards out there can modify Johns code and make it auto select all lines *inside* the current block and then comment it? could be useful to other people i assume. thx again On Sat, Jun 27, 2015 at 2:32 PM, John Kitchin jkitc...@andrew.cmu.edu wrote: This seems to work for some toy examples: (defun comment-org-in-src-block () (interactive) (org-edit-special) (comment-dwim nil) (org-edit-src-exit)) Xebar Saram writes: Hi all i was wondering if anyone knew of a command or bind to quickly comment the entire content of an org code block (with the correct comment syntax)? thx! Z -- 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] ox-odt roundtrip editing?
Ken Mankoff mank...@gmail.com writes: Hi Joakim, On 2015-06-26 at 07:45, joa...@verona.se wrote: I'm writing a manuscript for a publisher. The process looks like: - I write a chapter in org mode, export it to odt - I apply the styles the publisher wants to use with a libreoffice macro. This isn't particularily efficient, but I failed at modifying ox-odt to use custom templates. - I get back comments on the chapter from the publisher, that use the libreoffice annotation feature. Here I basically can't use org-mode anymore. Has someone attempted doing roundtrip editing ith libreoffice and org? That is, convert the odt file back to org, including the annotations, and edit fro there? Does this workflow describe what you want to do (but change DOCX to ODT)? https://lists.gnu.org/archive/html/emacs-orgmode/2015-06/msg00246.html It seems so. I'm not quite sure, I will have a close look. Thanks! -k. -- Joakim Verona
[O] org-mobile agenda truncated
I'm noticing something with mobile org and wonder if others have the same experience. An item that is in the Agenda View is truncated (only first 10 lines shown) when viewed under the Agenda views... selector, but that same item when viewed in its actual .org file is complete. I don't see where this happens in the code, nor a preference to set the number of lines before truncation, etc. Do other people using Mobile Org see shortened entries in the mobile Agenda? -k.
