Re: [O] helm-bibtex questions

[Xebar Saram]

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 
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 
> > 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  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  >
> >> 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 entr

Re: [O] HTML/images zipped?

[Nick Dokos]

John Kitchin  writes:

> hm... maybe it has been a while since I ran that ;) I pushed some
> changes that seem to have it working on a small test file.
>

Yes, it does not fail any longer. Thanks!

> This code is somewhat on the border of a filter/custom export. There are
> probably links that will now work with it, I have not tested it super
> thoroughly.
>
> Notably, it does not preserve relative paths, but rather renames files
> and images and replaces the links in the org-file with the new
> names. It was too hard to figure out how to preserve the paths when I
> wrote this originally.
>

OK. I'm just kicking the tires for now.

> Nick Dokos writes:
>
>> John Kitchin  writes:
>>
>>> I did something like this for org-files:
>>> https://github.com/jkitchin/jmax/blob/master/ox-archive.el
>>>
>>
>> I tried this on some arbitrary org file (not containing any references) and 
>> I got an error:
>>

-- 
Nick

[O] [PATCH] org-add-planning-info: Improve deletion handling

[Kyle Meyer]

Hello,

I've attached a patch that fixes up a few issues I've noticed with
org-add-planning-info.  The main one (in terms what I actually see when
editing Org files) is that, when org-adapt-indentation is nil, closing a
repeating TODO heading adds an extra space before the planning info
entry when it cycles back to TODO.  For example, marking

* TODO h
SCHEDULED: <2015-06-26 Fri +1w>

as DONE inserts an extra space before SCHEDULED:

* TODO h
 SCHEDULED: <2015-07-03 Fri +1w>
:PROPERTIES:
:LAST_REPEAT: [2015-06-26 Fri 23:38]
:END:
:LOGBOOK:
- State "DONE"   from "TODO"   [2015-06-26 Fri 23:38]
:END:

>From 6315be9e7a83cd9837807c2eb87ed7b3c6b70997 Mon Sep 17 00:00:00 2001
From: Kyle Meyer 
Date: Fri, 26 Jun 2015 21:33:34 -0400
Subject: [PATCH] org-add-planning-info: Improve deletion handling

* lisp/org.el (org-add-planning-info): Reset point before each
  planning entry search.  Clean up extra spaces.

* testing/lisp/test-org.el (test-org/add-planning-info): Add tests.

- Reposition save-excursion call to reset point every dolist
  iteration.  Otherwise, the order of the entries to be removed
  matters, and a call like

  (org-add-planning-info nil nil 'scheduled 'deadline)

  on

  DEADLINE: <2015-06-26 Fri> SCHEDULED: <2015-06-26 Fri>

  will fail to remove the deadline entry.

- Delete leading white space even when at the beginning of the line so
  that, when org-adapt-indentation is nil, a space is not inserted
  when removing the leading planning info entry.

  This prevents headings with repeating entries like

  SCHEDULED: <2015-06-26 Fri +1w>

  from being closed and recycled with an extra space in front of
  SCHEDULED.

- Add leading white space to the planning info entry regexp to prevent
  leftover white space when removing entries other than the first
  entry.
---
 lisp/org.el  |  35 ++-
 testing/lisp/test-org.el | 159 +++
 2 files changed, 178 insertions(+), 16 deletions(-)

diff --git a/lisp/org.el b/lisp/org.el
index 02f5c22..5a7d6d3 100755
--- a/lisp/org.el
+++ b/lisp/org.el
@@ -13478,23 +13478,26 @@ (defun org-add-planning-info (what &optional time &rest remove)
 	  (skip-chars-forward " \t")
 	  ;; Check if we have to remove something.
 	  (dolist (type (if what (cons what remove) remove))
-		(when (save-excursion
-			(re-search-forward
-			 (case type
-			   (closed org-closed-time-regexp)
-			   (deadline org-deadline-time-regexp)
-			   (scheduled org-scheduled-time-regexp)
-			   (otherwise (error "Invalid planning type: %s" type)))
-			 (line-end-position) t))
-		  (replace-match "")
-		  (when (looking-at "--+<[^>]+>") (replace-match ""))
-		  (when (and (not what) (eq type 'closed))
-		(save-excursion
-		  (beginning-of-line)
-		  (if (looking-at "[ \t]*$")
-			  (delete-region (point) (1+ (point-at-eol)))
+		(save-excursion
+		  (when (re-search-forward
+			 (concat
+			  " *"
+			  (case type
+			(closed org-closed-time-regexp)
+			(deadline org-deadline-time-regexp)
+			(scheduled org-scheduled-time-regexp)
+			(otherwise
+			 (error "Invalid planning type: %s" type
+			 (line-end-position) t)
+		(replace-match "")
+		(when (looking-at "--+<[^>]+>") (replace-match ""))
+		(when (and (not what) (eq type 'closed))
+		  (save-excursion
+			(beginning-of-line)
+			(if (looking-at "[ \t]*$")
+			(delete-region (point) (1+ (point-at-eol
 		;; Remove leading white spaces.
-		(when (and (not (bolp)) (looking-at "[ \t]+")) (replace-match ""
+		(when (looking-at "[ \t]+") (replace-match ""
 	 ((not what) (throw 'exit nil)) ; Nothing to do.
 	 (t (insert-before-markers "\n")
 		(backward-char 1)
diff --git a/testing/lisp/test-org.el b/testing/lisp/test-org.el
index 35905d3..437b594 100644
--- a/testing/lisp/test-org.el
+++ b/testing/lisp/test-org.el
@@ -2858,6 +2858,165 @@ (ert-deftest test-org/at-planning-p ()
 	 "* Headline\n*** Inlinetask\n*** END\nDEADLINE: <2014-03-04 tue.>"
(let ((org-inlinetask-min-level 3)) (org-at-planning-p))
 
+(ert-deftest test-org/add-planning-info ()
+  "Test `org-add-planning-info'."
+  ;; Create deadline when `org-adapt-indentation' is non-nil.
+  (should
+   (equal "* H\n  DEADLINE: <2015-06-25>\nParagraph"
+	  (org-test-with-temp-text "* H\nParagraph"
+	(let ((org-adapt-indentation t))
+	  (org-add-planning-info 'deadline "<2015-06-25 Thu>"))
+	(replace-regexp-in-string
+	 "\\( [.A-Za-z]+\\)>" "" (buffer-string)
+	 nil nil 1
+  ;; Create deadline when `org-adapt-indentation' is nil.
+  (should
+   (equal "* H\nDEADLINE: <2015-06-25>\nParagraph"
+	  (org-test-with-temp-text "* H\nParagraph"
+	(let ((org-adapt-indentation nil))
+	  (org-add-planning-info 'deadline "<2015-06-25 Thu>"))
+	(replace-regexp-in-string
+	 "\\( [.A-Za-z]+\\)>" "" (buffer-string)
+	 nil nil 1
+  ;; Update dea

Re: [O] HTML/images zipped?

[John Kitchin]

hm... maybe it has been a while since I ran that ;) I pushed some
changes that seem to have it working on a small test file.

This code is somewhat on the border of a filter/custom export. There are
probably links that will now work with it, I have not tested it super
thoroughly.

Notably, it does not preserve relative paths, but rather renames files
and images and replaces the links in the org-file with the new
names. It was too hard to figure out how to preserve the paths when I
wrote this originally.

Nick Dokos writes:

> John Kitchin  writes:
>
>> I did something like this for org-files:
>> https://github.com/jkitchin/jmax/blob/master/ox-archive.el
>>
>
> I tried this on some arbitrary org file (not containing any references) and I 
> got an error:
>
> Debugger entered--Lisp error: (wrong-type-argument stringp nil)
>   file-name-directory(nil)
>   (let* ((temporary-file-directory (file-name-directory (buffer-file-name))) 
> (tempname (make-temp-file "extract-bib")) (contents (buffer-string)) (cb 
> (current-buffer)) basename texfile bibfile results) (find-file tempname) 
> (insert contents) (setq basename (file-name-sans-extension 
> (file-name-nondirectory buffer-file-name)) texfile (concat tempname ".tex") 
> bibfile (concat tempname ".bib")) (save-excursion (goto-char (point-min)) (if 
> (re-search-forward "^bibliography:" (point-max) (quote end)) nil (insert 
> (format "\nbibliography:%s" (mapconcat (quote identity) 
> reftex-default-bibliography ",") (save-buffer) 
> (org-latex-export-to-latex) (find-file texfile) (reftex-parse-all) 
> (reftex-create-bibtex-file bibfile) (save-buffer) (setq results 
> (buffer-string)) (kill-buffer (concat basename ".bib")) (kill-buffer (concat 
> basename ".tex")) (kill-buffer basename) (delete-file bibfile) (delete-file 
> texfile) (delete-file tempname) (switch-to-buffer cb) (if (not (string= "" 
> results)) (progn (save-excursion (goto-char (point-max)) (insert "\n\n") 
> (org-insert-heading) (insert (format " Bibtex entries\n\n#+BEGIN_SRC text 
> :tangle %s\n%s\n#+END_SRC" (concat (file-name-sans-extension ...) ".bib") 
> results))
>   org-ref-extract-bibtex-entries()
>   (let* ((org-file (buffer-name)) (org-file-abs-path (buffer-file-name)) 
> (base-name (file-name-sans-extension org-file)) (org-archive (if (string= 
> zip-base-name "") (concat base-name "-" (format-time-string "%Y-%m-%d" 
> (current-time))) zip-base-name)) (org-archive-zip (concat org-archive 
> ".zip")) link-list) (if (file-exists-p org-archive-zip) (progn (delete-file 
> org-archive-zip))) (if (file-exists-p org-archive) (progn (delete-directory 
> org-archive t))) (make-directory org-archive t) (setq link-list (let 
> ((parsetree (org-element-parse-buffer)) (counter 0)) (org-element-map 
> parsetree (quote link) (function (lambda (link) (let* (... ... ... ... ... 
> ... ... ...) (message ...) (cond ... ... ...))) (message (format 
> "\n\nlink-list: %s\n\n" link-list)) (let ((counter 0)) (defalias (quote 
> ox-mrkup-filter-link) (function (lambda (text back-end info) (message 
> "handing link %s: %s\n" counter text) (let ((link ...)) (message "  %s 
> replacement is %s\n" counter link) (if (not ...) (progn ... ...) (setq output 
> ...)) (setq counter (+ counter 1)) output (let 
> ((org-export-filter-link-functions (quote (ox-mrkup-filter-link 
> (org-org-export-as-org))) (switch-to-buffer "*Org ORG Export*") (insert 
> (format "# archived from %s on %s\n" org-file-abs-path (format-time-string 
> "%Y-%m-%d" (current-time (org-ref-extract-bibtex-entries) (write-file 
> (expand-file-name org-file org-archive)) (shell-command (concat "zip -v -r " 
> org-archive-zip " *")) (rename-file org-archive-zip (concat "../" org-archive 
> ".zip")) (switch-to-buffer org-file) (delete-directory org-archive t) 
> org-archive-zip)
>   ox-archive-create-zip("foo")
> ...
>
> I think there is a bug in ox-archive-create-zip:
>
> --8<---cut here---start->8---
> ...
> (switch-to-buffer "*Org ORG Export*")
> (insert (format "# archived from %s on %s\n"
>   org-file-abs-path
>   (format-time-string "%Y-%m-%d" (current-time
>
> ;; add bibliography references if they exist.
> (org-ref-extract-bibtex-entries)
> ...
> --8<---cut here---end--->8---
>
> because the first thing that org-ref-extract-bibtex-entries does is
>
> --8<---cut here---start->8---
>   (let* ((temporary-file-directory (file-name-directory (buffer-file-name)))
> --8<---cut here---end--->8---
>
> and (buffer-file-name) returns nil on the *Org ORG Export* buffer.
> But since you obviously use this code successfully, I wonder why
> you don't hit this.
>
> Thanks for any help,
> Nick

--
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnk

Re: [O] HTML/images zipped?

[Nick Dokos]

John Kitchin  writes:

> I did something like this for org-files:
> https://github.com/jkitchin/jmax/blob/master/ox-archive.el
>

I tried this on some arbitrary org file (not containing any references) and I 
got an error:

Debugger entered--Lisp error: (wrong-type-argument stringp nil)
  file-name-directory(nil)
  (let* ((temporary-file-directory (file-name-directory (buffer-file-name))) 
(tempname (make-temp-file "extract-bib")) (contents (buffer-string)) (cb 
(current-buffer)) basename texfile bibfile results) (find-file tempname) 
(insert contents) (setq basename (file-name-sans-extension 
(file-name-nondirectory buffer-file-name)) texfile (concat tempname ".tex") 
bibfile (concat tempname ".bib")) (save-excursion (goto-char (point-min)) (if 
(re-search-forward "^bibliography:" (point-max) (quote end)) nil (insert 
(format "\nbibliography:%s" (mapconcat (quote identity) 
reftex-default-bibliography ",") (save-buffer) (org-latex-export-to-latex) 
(find-file texfile) (reftex-parse-all) (reftex-create-bibtex-file bibfile) 
(save-buffer) (setq results (buffer-string)) (kill-buffer (concat basename 
".bib")) (kill-buffer (concat basename ".tex")) (kill-buffer basename) 
(delete-file bibfile) (delete-file texfile) (delete-file tempname) 
(switch-to-buffer cb) (if (not (string= "" results)) (progn (save-excursion 
(goto-char (point-max)) (insert "\n\n") (org-insert-heading) (insert (format " 
Bibtex entries\n\n#+BEGIN_SRC text :tangle %s\n%s\n#+END_SRC" (concat 
(file-name-sans-extension ...) ".bib") results))
  org-ref-extract-bibtex-entries()
  (let* ((org-file (buffer-name)) (org-file-abs-path (buffer-file-name)) 
(base-name (file-name-sans-extension org-file)) (org-archive (if (string= 
zip-base-name "") (concat base-name "-" (format-time-string "%Y-%m-%d" 
(current-time))) zip-base-name)) (org-archive-zip (concat org-archive ".zip")) 
link-list) (if (file-exists-p org-archive-zip) (progn (delete-file 
org-archive-zip))) (if (file-exists-p org-archive) (progn (delete-directory 
org-archive t))) (make-directory org-archive t) (setq link-list (let 
((parsetree (org-element-parse-buffer)) (counter 0)) (org-element-map parsetree 
(quote link) (function (lambda (link) (let* (... ... ... ... ... ... ... ...) 
(message ...) (cond ... ... ...))) (message (format "\n\nlink-list: %s\n\n" 
link-list)) (let ((counter 0)) (defalias (quote ox-mrkup-filter-link) (function 
(lambda (text back-end info) (message "handing link %s: %s\n" counter text) 
(let ((link ...)) (message "  %s replacement is %s\n" counter link) (if (not 
...) (progn ... ...) (setq output ...)) (setq counter (+ counter 1)) output 
(let ((org-export-filter-link-functions (quote (ox-mrkup-filter-link 
(org-org-export-as-org))) (switch-to-buffer "*Org ORG Export*") (insert (format 
"# archived from %s on %s\n" org-file-abs-path (format-time-string "%Y-%m-%d" 
(current-time (org-ref-extract-bibtex-entries) (write-file 
(expand-file-name org-file org-archive)) (shell-command (concat "zip -v -r " 
org-archive-zip " *")) (rename-file org-archive-zip (concat "../" org-archive 
".zip")) (switch-to-buffer org-file) (delete-directory org-archive t) 
org-archive-zip)
  ox-archive-create-zip("foo")
...

I think there is a bug in ox-archive-create-zip:

--8<---cut here---start->8---
...
(switch-to-buffer "*Org ORG Export*")
(insert (format "# archived from %s on %s\n"
org-file-abs-path
(format-time-string "%Y-%m-%d" (current-time

;; add bibliography references if they exist. 
(org-ref-extract-bibtex-entries)
...
--8<---cut here---end--->8---

because the first thing that org-ref-extract-bibtex-entries does is

--8<---cut here---start->8---
  (let* ((temporary-file-directory (file-name-directory (buffer-file-name)))
--8<---cut here---end--->8---

and (buffer-file-name) returns nil on the *Org ORG Export* buffer.
But since you obviously use this code successfully, I wonder why
you don't hit this.

Thanks for any help,
Nick

Re: [O] Time-zone in dates

[Nicolas Goaziou]

Hello,

franc...@avalenn.eu writes:

> Timezones are strange beasts to deal with.

True.

> It is really simpler programmatically to deal with time offsets
> instead. The downside is that you cannot manage DST and other similar
> peculiarities but the API is much simpler to write.

However, time offsets are not very interesting. Org is (also) about
appointments, deadlines... so timezones are more accurate.

Also, Emacs contains "timezone.el", which, I assume, should take care of
all the heavy duty concerning these beasts, as far as an API is
concerned.

This requires care, but it should be doable, really, don't you think?

> Just please don't confuse timezones and time offsets especially in
> documentation as it is not the same thing and it can lead to
> confusion.
>
> I reread from time to time this note from W3C which explains the
> difference and why it matters :
> http://www.w3.org/TR/2005/NOTE-timezone-20051013/#d2e226

Thank you for the reference. I didn't know about it.


Regards,

-- 
Nicolas Goaziou

Re: [O] more helm-bibtex/org-ref questions

[John Kitchin]

You could have multiple file fields I suppose, and adapt [1] to give you
a choice of which one to open.

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.

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.

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.

--
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] more helm-bibtex/org-ref questions

[Ramon Diaz-Uriarte]

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] Time-zone in dates

[francois]

Hello,

On Fri, Jun 26, 2015 at 09:20:00PM +0200, Nicolas Goaziou wrote:
> Time zone information is interesting when users of different areas are
> exchanging Org documents.
> 
> I think it would be useful to have:
> 
>  - a keyword to specify time zone per document. This time zone would
>apply to every time stamp not defining their own time zone. Default
>value could be `local' so we would be backward compatible.
> 
>  - a way to specify a time zone per time stamp, overriding the previous
>keyword.
> 
> I think it would require to define a proper API for timestamps in order
> to ensure, e.g., comparisons are done right.

Timezones are strange beasts to deal with.

It is really simpler programmatically to deal with time offsets
instead. The downside is that you cannot manage DST and other similar
peculiarities but the API is much simpler to write.

Just please don't confuse timezones and time offsets especially in
documentation as it is not the same thing and it can lead to
confusion.

I reread from time to time this note from W3C which explains the
difference and why it matters :
http://www.w3.org/TR/2005/NOTE-timezone-20051013/#d2e226 

Regards,
François

Re: [O] HTML/images zipped?

[Peter Davis]

Thanks, John. That didn't solve it for me. I'll keep digging when I get
a chance.

Thank you.

-pd


John Kitchin  writes:

> I am not sure. I have this in my init file:
>
> (require 'ox-org)
>
> maybe that is required for you too?
>
> Peter Davis writes:
>
>> John Kitchin  writes:
>>
>>> I did something like this for org-files:
>>> https://github.com/jkitchin/jmax/blob/master/ox-archive.el
>>>
>>> You might use that as a starting point for html.
>>
>> I'm not lisp-savvy, but I've been experimenting with this. I get an
>> error:
>>
>> Unknown "nil" backend: Aborting export
>>
>> It seems to be coming from these lines:
>>
>>   (let ((org-export-filter-link-functions '(ox-mrkup-filter-link)))
>>   (org-org-export-as-org)))
>>
>> I'm not sure how or where backend is supposed to be defined.
>>
>> Also, I guess it would take some tweaking to export to HTML and save
>> that in the ZIP, instead of the original org file.
>>
>> Any hints welcome.
>>
>> Thanks!
>> -pd
>
> --
> 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] Time-zone in dates

[Nicolas Goaziou]

Hello,

Eric S Fraga  writes:

> In practice, I do not miss having time zone information in org.

Time zone information is interesting when users of different areas are
exchanging Org documents.

I think it would be useful to have:

 - a keyword to specify time zone per document. This time zone would
   apply to every time stamp not defining their own time zone. Default
   value could be `local' so we would be backward compatible.

 - a way to specify a time zone per time stamp, overriding the previous
   keyword.

I think it would require to define a proper API for timestamps in order
to ensure, e.g., comparisons are done right.


Regards,

-- 
Nicolas Goaziou

Re: [O] HTML/images zipped?

[John Kitchin]

I am not sure. I have this in my init file:

(require 'ox-org)

maybe that is required for you too?

Peter Davis writes:

> John Kitchin  writes:
>
>> I did something like this for org-files:
>> https://github.com/jkitchin/jmax/blob/master/ox-archive.el
>>
>> You might use that as a starting point for html.
>
> I'm not lisp-savvy, but I've been experimenting with this. I get an
> error:
>
> Unknown "nil" backend: Aborting export
>
> It seems to be coming from these lines:
>
>   (let ((org-export-filter-link-functions '(ox-mrkup-filter-link)))
>   (org-org-export-as-org)))
>
> I'm not sure how or where backend is supposed to be defined.
>
> Also, I guess it would take some tweaking to export to HTML and save
> that in the ZIP, instead of the original org file.
>
> Any hints welcome.
>
> Thanks!
> -pd

--
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

[John Kitchin]

In org-ref, I have a function that will copy a bibtex entry to the
clipboard in the helm menu for the cite link actions:

https://github.com/jkitchin/org-ref/blob/master/org-ref.el#L3363

And here a menu item to insert a bibtex entry and attach its pdf to an
email:

https://github.com/jkitchin/org-ref/blob/master/org-ref.el#L3382

exactly for those purposes!

>> 5. i love the insert formatted reference (f5) option and use it often
>> sending people references:
>> a. does it also auto send that to the clipboard?
>
> There is currently no way to copy references directly to the
> clipboard.  My recommendation is to use one of Emacs’ mail clients, then
> you don’t need the clipboard.  Mu4e is absolutely fantastic (especially
> when combined with helm-mu).
>
>> b. it cuts most of the authors name and leaves only the first few. is there
>> a switch to get it to print all authors. is that a latex cite formatting
>> issue?
>
> Not sure what you mean by “cuts most of the authors”.  It doesn’t cut
> anything in my setup.  Could you please provide an example?  (Perhaps
> this is something for the issue tracker on Github.)
>
> Best wishes,
>
>   Titus
>
>
>>
>> best and thanks so much again
>>
>> Z
>>
>> On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg 
>> 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 template? it
>>> > would be helpful as a starting point for me if thats possible.
>>> >
>>> > kind regards and thanks so much in advance
>>> >
>>> > Z
>>> >
>>> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin 
>>> > wrote:
>>> >
>>> >> sweet! I did not know you could do that! I will be refactoring org-ref
>>> >> soon to do that instead of redefining the commands!
>>> >>
>>> >> 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, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
>>> >> malsb...@posteo.de> wrote:
>>> >>
>>> >>>
>>> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
>>> >>> > Hi again Titus
>>> >>> >
>>> >>> > 2 quick questions that arose from using helm-bitex today extensively:
>>> >>> >
>>> >>> > how does one exclude in the search items? for example i want to
>>> search
>>> >>> for
>>> >>> > xebar without keyword "progress" (I want to exclude in progress
>>> articles
>>> >>> > not published yet)
>>> >>> >
>>> >>> > is it possible to define default enter command in helm-bibtex ?
>>> >>>
>>> >>> Yes.  Helm uses the first action as the default action.  To move an
>>> >>> action to the top of the list you can use the following code:
>>> >>>
>>> >>>   (helm-delete-action-from-source "Insert BibTeX key"
>>> helm-source-bibtex)
>>> >>>   (helm-add-action-to-source "Insert BibTeX key"
>>> 'helm-bibtex-insert-key
>>> >>> helm-source-bibtex 0)
>>> >>>
>>> >>> The second argument in the second line is the function that executes
>>> the
>>> >>> action.  Here is a list of all actions and their functions:
>>> >>>
>>> >>>   Open PDF file (if present): helm-bibtex-open-pdf
>>> >>>   Open URL or DOI in browser: helm-bibtex-open-url-or-doi
>>> >>>   Insert citation: helm-bibtex-insert-citation
>>> >>>   Insert reference: helm-bibtex-insert-reference
>>> >>>   Insert BibTeX key: helm-bibtex-insert-key
>>> >>>   Insert BibTeX entry: helm-bibtex-insert-bibtex
>>> >>>   Attach PDF to email: helm-bibtex-add-PDF-attachment
>>> >>>   Edit notes: helm-bibtex-edit-notes
>>> >>>   Show entry: helm-bibtex-show-entry
>>> >>>
>>> >>> Best,
>>> >>>
>>> >>>   Titus
>>> >>>
>>> >>> >
>>> >>> > best
>>> >>> >
>>> >>> > Z
>>> >>> >
>>> >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <
>>> >>> malsb...@posteo.de>
>>> >>> > wrote:
>>> >>> >
>>> >>> >>
>>> >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
>>> >>> >> > Hi Titus and thx so much for the answers!
>>> >>> >> >
>>> >>> >> > i will in the future use the github page to make requests.
>>> >>> >> >
>>> >>> >> > "The number of matches will be displayed in the mode line. "
>

Re: [O] helm-bibtex questions

[Titus von der Malsburg]

On 2015-06-26 Fri 10:21, Titus von der Malsburg wrote:
> On 2015-06-26 Fri 00:21, Xebar Saram wrote:
>> Hi Titus
>>
>> Another round of helm-bibtex questions if you dont mind (question come
>> since i use it 50 times a day now ;-))
>
> No problem.  I’ve also learned a couple of things though this exchange.
>
>> 1. is there a way (or a keybind) to select all entries filtered? now to
>> select all my publications for example i have to use C-space
>> repeatedly.
>
> Key bindings are inherited from Helm so it’s useful to consult Helm’s
> documentation for question of that type.  I just checked and found that
> M-a selects all candidates.
>
>> 2. what is the syntax for greater then? for example all articles > 2012
>> (year)
>
> I’m afraid that’s not possible because 2012 is just another string for
> the purposes of matching.  But you may want to check Helm’s
> documentation and mailing lists.  Helm is full of surprises.

Of course you can use regular expressions to search for a range of
years:

  201[2-5]

Almost as good as >2012.

>
>> 4. i cant get helm-bibtex to search the biblatex field of pubstate. are
>> biblatex (biber) supported/ i have this in my config?
>>
>> (setq helm-bibtex-additional-search-fields '(pubstate))
>
> This works on my setup.  Helm-bibtex doesn’t really care whether
> something is a BibTeX or a Biblatex field.  You should be able to use
> any kind of field whether standard or not.  Note that additional search
> fields are not displayed in the results list (they are only used for
> matching).  Perhaps that’s why you thought it doesn’t work?
>
>> also on a related issue i assume one can define many fields in the above
>> example. since my elisp sucks would the syntax be this
>>
>> (setq helm-bibtex-additional-search-fields '(pubstate tags))
>
> This is correct.
>
>> or do you need to qoute them or use a , symbol?
>>
>> 5. i love the insert formatted reference (f5) option and use it often
>> sending people references:
>> a. does it also auto send that to the clipboard?
>
> There is currently no way to copy references directly to the
> clipboard.  My recommendation is to use one of Emacs’ mail clients, then
> you don’t need the clipboard.  Mu4e is absolutely fantastic (especially
> when combined with helm-mu).
>
>> b. it cuts most of the authors name and leaves only the first few. is there
>> a switch to get it to print all authors. is that a latex cite formatting
>> issue?
>
> Not sure what you mean by “cuts most of the authors”.  It doesn’t cut
> anything in my setup.  Could you please provide an example?  (Perhaps
> this is something for the issue tracker on Github.)
>
> Best wishes,
>
>   Titus
>
>
>>
>> best and thanks so much again
>>
>> Z
>>
>> On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg 
>> 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 template? it
>>> > would be helpful as a starting point for me if thats possible.
>>> >
>>> > kind regards and thanks so much in advance
>>> >
>>> > Z
>>> >
>>> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin 
>>> > wrote:
>>> >
>>> >> sweet! I did not know you could do that! I will be refactoring org-ref
>>> >> soon to do that instead of redefining the commands!
>>> >>
>>> >> 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, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
>>> >> malsb...@posteo.de> wrote:
>>> >>
>>> >>>
>>> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
>>> >>> > Hi again Titus
>>> >>> >
>>> >>> > 2 quick questions that arose from using helm-bitex today extensively:
>>> >>> >
>>> >>> > how does one exclude in the search items? for example i want to
>>> search
>>> >>> for
>>> >>> > xebar without keyword "progress" (I want to exclude in progress
>>> articles
>>> >>> > not published yet)
>>> >>> >
>>> >>> > is it possible to define default enter command in helm-bibtex ?
>>> >>>
>>> >>> Yes.  Helm uses the first action as 

Re: [O] HTML/images zipped?

[Peter Davis]

John Kitchin  writes:

> I did something like this for org-files:
> https://github.com/jkitchin/jmax/blob/master/ox-archive.el
>
> You might use that as a starting point for html.

I'm not lisp-savvy, but I've been experimenting with this. I get an
error:

Unknown "nil" backend: Aborting export

It seems to be coming from these lines:

  (let ((org-export-filter-link-functions '(ox-mrkup-filter-link)))
(org-org-export-as-org)))

I'm not sure how or where backend is supposed to be defined.

Also, I guess it would take some tweaking to export to HTML and save
that in the ZIP, instead of the original org file.

Any hints welcome.

Thanks!
-pd

Re: [O] helm-bibtex questions

[Titus von der Malsburg]

On 2015-06-26 Fri 00:21, Xebar Saram wrote:
> Hi Titus
>
> Another round of helm-bibtex questions if you dont mind (question come
> since i use it 50 times a day now ;-))

No problem.  I’ve also learned a couple of things though this exchange.

> 1. is there a way (or a keybind) to select all entries filtered? now to
> select all my publications for example i have to use C-space
> repeatedly.

Key bindings are inherited from Helm so it’s useful to consult Helm’s
documentation for question of that type.  I just checked and found that
M-a selects all candidates.

> 2. what is the syntax for greater then? for example all articles > 2012
> (year)

I’m afraid that’s not possible because 2012 is just another string for
the purposes of matching.  But you may want to check Helm’s
documentation and mailing lists.  Helm is full of surprises.

> 4. i cant get helm-bibtex to search the biblatex field of pubstate. are
> biblatex (biber) supported/ i have this in my config?
>
> (setq helm-bibtex-additional-search-fields '(pubstate))

This works on my setup.  Helm-bibtex doesn’t really care whether
something is a BibTeX or a Biblatex field.  You should be able to use
any kind of field whether standard or not.  Note that additional search
fields are not displayed in the results list (they are only used for
matching).  Perhaps that’s why you thought it doesn’t work?

> also on a related issue i assume one can define many fields in the above
> example. since my elisp sucks would the syntax be this
>
> (setq helm-bibtex-additional-search-fields '(pubstate tags))

This is correct.

> or do you need to qoute them or use a , symbol?
>
> 5. i love the insert formatted reference (f5) option and use it often
> sending people references:
> a. does it also auto send that to the clipboard?

There is currently no way to copy references directly to the
clipboard.  My recommendation is to use one of Emacs’ mail clients, then
you don’t need the clipboard.  Mu4e is absolutely fantastic (especially
when combined with helm-mu).

> b. it cuts most of the authors name and leaves only the first few. is there
> a switch to get it to print all authors. is that a latex cite formatting
> issue?

Not sure what you mean by “cuts most of the authors”.  It doesn’t cut
anything in my setup.  Could you please provide an example?  (Perhaps
this is something for the issue tracker on Github.)

Best wishes,

  Titus


>
> best and thanks so much again
>
> Z
>
> On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg 
> 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 template? it
>> > would be helpful as a starting point for me if thats possible.
>> >
>> > kind regards and thanks so much in advance
>> >
>> > Z
>> >
>> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin 
>> > wrote:
>> >
>> >> sweet! I did not know you could do that! I will be refactoring org-ref
>> >> soon to do that instead of redefining the commands!
>> >>
>> >> 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, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
>> >> malsb...@posteo.de> wrote:
>> >>
>> >>>
>> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
>> >>> > Hi again Titus
>> >>> >
>> >>> > 2 quick questions that arose from using helm-bitex today extensively:
>> >>> >
>> >>> > how does one exclude in the search items? for example i want to
>> search
>> >>> for
>> >>> > xebar without keyword "progress" (I want to exclude in progress
>> articles
>> >>> > not published yet)
>> >>> >
>> >>> > is it possible to define default enter command in helm-bibtex ?
>> >>>
>> >>> Yes.  Helm uses the first action as the default action.  To move an
>> >>> action to the top of the list you can use the following code:
>> >>>
>> >>>   (helm-delete-action-from-source "Insert BibTeX key"
>> helm-source-bibtex)
>> >>>   (helm-add-action-to-source "Insert BibTeX key"
>> 'helm-bibtex-insert-key
>> >>> helm-source-bibtex 0)
>> >>>
>> >>> The second ar

Re: [O] problem with ox-pandoc export

[Nicolas Goaziou]

Hello,

Alan Schmitt  writes:

> Is there any reason why the options would disappear during export?

Maybe "ox-pandoc" doesn't handle this meta-data. Perhaps you're doing
a "body-only" export. Or you have `org-export-with-title' and al. set to
nil...


Regards,

-- 
Nicolas Goaziou

Re: [O] Turn off html entities in md export

[Rasmus]

Rustom Mody  writes:

> How to say (to ox-md) "Leave tables as they are"  ?

See org-element-interpret-data and e.g. org-org-identity.

Rasmus

-- 
And when I’m finished thinking, I have to die a lot

Re: [O] Time-zone in dates

[Eric S Fraga]

On Friday, 26 Jun 2015 at 10:38, J. David Boyd wrote:

[...]

> I can see that being a real pain.  The simple way would 'just' be to convert
> everything to UTC in the background for comparison.

Having spent a year essentially commuting between Australia and the UK a
couple of years ago, I can tell you that there is no "simple"
solution... :(

The simplest solution for me was firstly to use org (of course :-), then
put in all time stamps as "local" time and finally ensure that the time
zone setting for the computer itself, e.g. a laptop, matched where I was
at the time.  This turns out to be more human oriented than having to
worry about time zones, especially when it comes to extra complications
like summer time.

In practice, I do not miss having time zone information in org.

YMMV, of course!

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.1, Org release_8.3beta-1247-ga833d3

Re: [O] Turn off html entities in md export

[Nicolas Goaziou]

Rustom Mody  writes:

> As https://bitbucket.org/tutorials/markdowndemo/overview#markdown-header-tab
> shows
> bitbucket md tables are very similar to org tables (and html  is
> disallowed)
>
> How to say (to ox-md) "Leave tables as they are"  ?

Write a derived export backend, e.g., ox-md-bb.el that will translate
tables properly according to Bitbucket rules.

You can also use a hook that will turn Org tables into Bitbucket
markdown tables and wrap them within a #+begin_md...#+end_md block.


Regards,

Re: [O] Turn off html entities in md export

[Rustom Mody]

On Fri, Jun 26, 2015 at 1:24 PM, Nicolas Goaziou 
wrote:

> Hello,
>
> Rustom Mody  writes:
>
> > Bitbucket does not allow html entities in markdown
> > See https://bitbucket.org/rustom/vit-projects/wiki/emacs
> > and search for &#
> >
> > So how to turn off html entities in md export?
>
> It depends on where these entities are coming from.
>
> Anyway, vanilla Markdown supports HTML so anything "ox-md" cannot
> translate into Markdown syntax (e.g., tables) is exported as pure HTML.
>

As https://bitbucket.org/tutorials/markdowndemo/overview#markdown-header-tab
shows
bitbucket md tables are very similar to org tables (and html  is
disallowed)

How to say (to ox-md) "Leave tables as they are"  ?

[O] old ob-clojure in orgmode.org/elpa/?

[Julien Chastang]

Hello

Is there a reason why ob-clojure.el is out-of-date in orgmode.org/elpa/? It
does not have any reference to cider, and is therefore more than a year
old, I believe. It is also out-of-sync with
orgmode.org/cgit.cgi/org-mode.git. Am I missing something concerning how
current orgmode.org/elpa/ should be?

Many Thanks.

-- 
Julien Chastang
Scientific Software Developer
Unidata-UCAR

[O] [PATCH] org-mobile: Tiny fix in creating index.org file

[Sergey Gordienko]

* lisp/org-mobile.el (org-mobile-create-index-file):
Eliminate cloning of `#+READONLY' property in the `index.org' file.
A sublists of `org-todo-keywords' don't need to contain the `|'.

TINYCHANGE
---
 lisp/org-mobile.el | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lisp/org-mobile.el b/lisp/org-mobile.el
index 2c13802..293de79 100644
--- a/lisp/org-mobile.el
+++ b/lisp/org-mobile.el
@@ -439,14 +439,14 @@ agenda view showing the flagged items."
(if org-mobile-use-encryption
org-mobile-encryption-tempfile
  target-file)
+  (insert "#+READONLY\n")
   (while (setq entry (pop def-todo))
-   (insert "#+READONLY\n")
(setq kwds (mapcar (lambda (x) (if (string-match "(" x)
   (substring x 0 (match-beginning 0))
 x))
   (cdr entry)))
(insert "#+TODO: " (mapconcat 'identity kwds " ") "\n")
-   (setq dwds (member "|" kwds)
+   (setq dwds (or (member "|" kwds) (last kwds))
  twds (org-delete-all dwds kwds)
  todo-kwds (org-delete-all twds todo-kwds)
  done-kwds (org-delete-all dwds done-kwds)))
-- 
1.9.5 (Apple Git-50.3)

Re: [O] HTML/images zipped?

[Peter Davis]

Thanks, John. I will take a closer look at both of these.

Cheers,
-pd

On 6/26/15 10:24 AM, John Kitchin wrote:

I did something like this for org-files:
https://github.com/jkitchin/jmax/blob/master/ox-archive.el

You might use that as a starting point for html.

Also, my blogofile code
(https://github.com/jkitchin/jmax/blob/master/user/blogofile.el) does
something like this to publish org to blogofile.



Rasmus writes:


Peter Davis  writes:


Is there any way to export HTML with all references images,
etc. packaged in a ZIP file?

My guess is that at the moment your best bet is hacking some together with
ox-publish.  See org-publish-project-alist.

Hope it helps,
Rasmus

PS: On the list, we have talked about a .borg format that might serve for
similar situation but it's at an idea stage at the moment.

--
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] Time-zone in dates

[J. David Boyd]

Eric S Fraga  writes:

> On Friday, 26 Jun 2015 at 16:40, Oleg Sivokon wrote:
>> Hello, list.
>>
>> I was looking for a way to add time-zone to the date recrod, something
>> like: <2015-07-05 Sun 20:00 GMT+0>.  I was told that it's very likely
>> that the functionality isn't there, so I wonder if it's really so, and
>> if indeed so, then what would it take to add it?
>
> It is indeed so.  What would it take?  Somebody to program the
> functionality in but this is a major challenge as time stamps are a
> fundamental building block of org and it would likely need to be upwards
> compatible...

I can see that being a real pain.  The simple way would 'just' be to convert
everything to UTC in the background for comparison.

Nothing I want to do!

Dave

Re: [O] Time-zone in dates

[Left Right]

On Fri, Jun 26, 2015 at 5:12 PM, Eric S Fraga  wrote:
> Somebody to program the
> functionality in but this is a major challenge as time stamps are a
> fundamental building block of org and it would likely need to be upwards
> compatible...
> --
> : Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.1, Org release_8.3beta-1247-ga833d3

Thanks for the info, Eric. I imagined this wouldn't be easy, but I
would be interested to know whether there might be some suggestions,
possibly to split the work up into stages. For example, perhaps, at
first one could only live with dates typed in in that format, but the
calendar wouldn't offer an interface to input them. Perhaps there
could be even more fine-grained stages. I'm also not entirely sure,
but I have a feeling that that might be a problem as well: does
interoperability with Calc require certain date format? Would Calc
have to also have to support this, once added?

Thanks.

Oleg

Re: [O] HTML/images zipped?

[John Kitchin]

That is a cool idea. Here is some code for data uris that worked on with
org-mode earlier this summer. You could definitely hack a filter that
embedded the image uri directly into the exported html.

http://kitchingroup.cheme.cmu.edu/blog/2015/05/09/Another-approach-to-embedding-org-source-in-html/

Peter Davis writes:

> phillip.l...@newcastle.ac.uk (Phillip Lord) writes:
>
>> data-uri's is probably what you want. There is no standard format for
>> zipping multiple HTML files together, while including images (or video's
>> or audio) directly into the HTML works reasonably well.
>>
>> I found a snippet to get ox-html to do this -- it would be a good
>> feature to add properly though!
>
> Thanks, Phillip. That sounds like an interesting possibility. I've never
> worked with data-uri's. Can you post or send that snippet? I don't seem
> to be finding it on my initial searches.
>
> Thanks,
> -pd

--
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

[John Kitchin]

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 
> 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  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 
>> 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 template?
>>> it
>>> >> > would be helpful as a starting point for me if thats possible.
>>> >> >
>>> >> > kind regards and thanks so much in advance
>>> >> >
>>> >> > Z
>>> >> >
>>> >> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin <
>>> jkitc...@andrew.cmu.edu>
>>> >> > wrote:
>>> >> >
>>> >> >> sweet! I did not know you could do that! I will be refactoring
>>> org-ref
>>> >> >> soon to do that instead of redefining the commands!
>>> >> >>
>>> >> >> 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] HTML/images zipped?

[John Kitchin]

I did something like this for org-files:
https://github.com/jkitchin/jmax/blob/master/ox-archive.el

You might use that as a starting point for html.

Also, my blogofile code
(https://github.com/jkitchin/jmax/blob/master/user/blogofile.el) does
something like this to publish org to blogofile.



Rasmus writes:

> Peter Davis  writes:
>
>> Is there any way to export HTML with all references images,
>> etc. packaged in a ZIP file?
>
> My guess is that at the moment your best bet is hacking some together with
> ox-publish.  See org-publish-project-alist.
>
> Hope it helps,
> Rasmus
>
> PS: On the list, we have talked about a .borg format that might serve for
> similar situation but it's at an idea stage at the moment.

--
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] Time-zone in dates

[Eric S Fraga]

On Friday, 26 Jun 2015 at 16:40, Oleg Sivokon wrote:
> Hello, list.
>
> I was looking for a way to add time-zone to the date recrod, something
> like: <2015-07-05 Sun 20:00 GMT+0>.  I was told that it's very likely
> that the functionality isn't there, so I wonder if it's really so, and
> if indeed so, then what would it take to add it?

It is indeed so.  What would it take?  Somebody to program the
functionality in but this is a major challenge as time stamps are a
fundamental building block of org and it would likely need to be upwards
compatible...
-- 
: Eric S Fraga (0xFFFCF67D), Emacs 25.0.50.1, Org release_8.3beta-1247-ga833d3

Re: [O] HTML/images zipped?

[Peter Davis]

phillip.l...@newcastle.ac.uk (Phillip Lord) writes:

> data-uri's is probably what you want. There is no standard format for
> zipping multiple HTML files together, while including images (or video's
> or audio) directly into the HTML works reasonably well.
>
> I found a snippet to get ox-html to do this -- it would be a good
> feature to add properly though!

Thanks, Phillip. That sounds like an interesting possibility. I've never
worked with data-uri's. Can you post or send that snippet? I don't seem
to be finding it on my initial searches.

Thanks,
-pd

Re: [O] HTML/images zipped?

[Peter Davis]

Rasmus  writes:

> Peter Davis  writes:
>
>> Is there any way to export HTML with all references images,
>> etc. packaged in a ZIP file?
>
> My guess is that at the moment your best bet is hacking some together with
> ox-publish.  See org-publish-project-alist.

Thanks, Rasmus. I'll take a look when I have a chance, but for now, I'll
have to zip the files by hand.

Thanks!
-pd

Re: [O] HTML/images zipped?

[Phillip Lord]

data-uri's is probably what you want. There is no standard format for
zipping multiple HTML files together, while including images (or video's
or audio) directly into the HTML works reasonably well.

I found a snippet to get ox-html to do this -- it would be a good
feature to add properly though!


Peter Davis  writes:

> Is there any way to export HTML with all references images,
> etc. packaged in a ZIP file?
>
> Thank you.
>
> -pd
>
>
>
>

-- 
Phillip Lord,   Phone: +44 (0) 191 208 7827
Lecturer in Bioinformatics, Email: phillip.l...@newcastle.ac.uk
School of Computing Science,
http://homepages.cs.ncl.ac.uk/phillip.lord
Room 914 Claremont Tower,   skype: russet_apples
Newcastle University,   twitter: phillord
NE1 7RU 

Re: [O] Turn off html entities in md export

[Rustom Mody]

On Fri, Jun 26, 2015 at 2:13 PM, Nicolas Goaziou 
wrote:

> Rustom Mody  writes:
>
> > Simple basic thing
> > ... becomes …
> > -- becomes –
> > etc
>
> In this particular case, see `org-export-with-special-strings'.
>
>
Thanks Nicolas
Thats a help

[O] Time-zone in dates

[Oleg Sivokon]

Hello, list.

I was looking for a way to add time-zone to the date recrod, something
like: <2015-07-05 Sun 20:00 GMT+0>.  I was told that it's very likely
that the functionality isn't there, so I wonder if it's really so, and
if indeed so, then what would it take to add it?

I've asked the same question here:
http://emacs.stackexchange.com/questions/13463/specify-timezone-in-org-date-format
just in case you saw it earlier.

Best.

Oleg

Re: [O] Org-Mode and iCloud Reminders

[Ken Mankoff]

On 2015-06-26 at 00:38, Yuri Niyazov  wrote:
> what do you use for rem->org?

https://lists.gnu.org/archive/html/emacs-orgmode/2015-05/msg00556.html

Re: [O] HTML/images zipped?

[Rasmus]

Peter Davis  writes:

> Is there any way to export HTML with all references images,
> etc. packaged in a ZIP file?

My guess is that at the moment your best bet is hacking some together with
ox-publish.  See org-publish-project-alist.

Hope it helps,
Rasmus

PS: On the list, we have talked about a .borg format that might serve for
similar situation but it's at an idea stage at the moment.

-- 
This message is brought to you by the department of redundant departments

[O] HTML/images zipped?

[Peter Davis]

Is there any way to export HTML with all references images,
etc. packaged in a ZIP file?

Thank you.

-pd

[O] problem with ox-pandoc export

[Alan Schmitt]

Hello,

I’m having some issues with the ox-pandoc export and I would like to
have some help from people who understand derived backends to debug it.
Here is the github issue about it: 
https://github.com/kawabata/ox-pandoc/issues/3

The problem is that file metadata (author, date, title) is not present
in the export.

The main function of the exporter looks like this:

#+begin_src emacs-lisp
  (org-export-to-file 'pandoc (org-export-output-file-name
   (concat (make-temp-name ".tmp") ".org") s)
a s v b e (lambda (f) (org-pandoc-run-to-buffer-or-file f format s 
buf-or-open)))
#+end_src

If I read this correctly, it exports the org file to a temporary file
(which happens to be in org format), and then calls another function to
actually call pandoc. I think the problem is that the temporary file
created does not have the metadata in it.

For instance, 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---

results in this temporary file

--8<---cut here---start->8---


* First section
foo

* Second section
bar
--8<---cut here---end--->8---

The derived backend is defined like this:

#+begin_src emacs-lisp
(org-export-define-derived-backend 'pandoc 'org
  :translate-alist '((template . org-pandoc-template))
  :export-block "PANDOC"
  :menu-entry
  `(?p "export via pandoc"
   ,org-pandoc-menu-entry)
  :options-alist
  '((:pandoc-options "PANDOC_OPTIONS" nil nil space)
(:pandoc-metadata "PANDOC_METADATA" nil nil space)
(:pandoc-variables "PANDOC_VARIABLES" nil nil space)
(:epub-chapter-level "EPUB_CHAPTER_LEVEL" nil nil t)
(:epub-cover-image "EPUB_COVER" nil nil t)
(:epub-embed-font "EPUB_EMBED_FONT" nil nil newline)
(:epub-meta "EPUB_META" nil nil newline)
(:epub-css "EPUB_CSS" nil nil newline)
(:epub-rights "EPUB_RIGHTS" nil nil newline)
(:bibliography "BIBLIOGRAPHY")))
#+end_src

Is there any reason why the options would disappear during export?

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] can't assign to hline relative reference:

[Marijn Schouten (hkBst)]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

On 26-06-15 14:22, Nicolas Goaziou wrote:
> Hello,
> 
> "Marijn Schouten (hkBst)"  writes:
> 
>> Through irc I found someone who tested this with the latest
>> development version as of now and it instead produces the error: can't
>> assign to hline relative reference. That also does not seem like the
>> right behavior to me.
>>
>> Could someone shed some light on the situation?
> 
> See .
> 
> Regards,

Thanks Nicolas for that link.

It says that there is a known issue with hline references on the left side of 
table formulas, but I did not quite understand the details.

There seems to be a proposed fix by interpreting said references as ranges with 
the same on both sides, for example @II$2 would become @II$2..@II$2 and would 
then be interpreted properly. Was the issue with this fix that it does not work 
in all cases?

There also seems to be some counterintuitive use of these references that is 
useful to some people and included in the tests and fixing the issue would 
interfere with that use. If I said that right, could someone explain the 
details of this?

There was a mention that fixing the issue might involve rewriting much of 
org-table. Is that a concern?

Marijn
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Re: [O] Bug: org-mode breaks flyspell [8.2.10 (release_8.2.10 @ /usr/share/emacs/24.4/lisp/org/)]

[Reuben Thomas]

On 26 June 2015 at 13:05, Nicolas Goaziou  wrote:

> Hello,
>
> Reuben Thomas  writes:
>
> > Tested using “emacs -Q”, so you can ignore the details of my setup:
> >
> > Start up Emacs, M-x flyspell-mode dat
> >
> > The mis-spelled (I’m using English, not Latin as my default language)
> > “dat” is underwiggled.
> >
> > Type Backspace a SPACE
> >
> > The word is now “data”, and (in English or Latin!) is now correct, so
> not underwiggled.
> >
> > M-x org-mode and repeat the exercise: the underwiggle on the letters of
> > “dat” remains after I have typed the “a”.
>
> Thank you.
>
> Apparently, this issue cannot be reproduced on latest development
> version of Org. You may want to switch to development version of Org or
> wait for 8.3 to be released.
>

​Thanks, it's good to know the bug's been fixed.

-- 
http://rrt.sc3d.org

Re: [O] Export to Latex without \author{}

[Rasmus]

Lei Zhe  writes:

> I am trying to export a beamer from org-mode with my own \author
> command defined.
> But when I export, org-mode always generates another \author after my
> \author, which destroys the author list.
> I tried:
> 1. #+author:
> 2. #+bind: latex-export-with-author ""
> 3. move #+author before my author command.
> But none of them did make it. The \author{} always appears in the
> place after my author command!

Does "#+options: author:nil" work for you?

Rasmus

-- 
When the facts change, I change my mind. What do you do, sir?

Re: [O] can't assign to hline relative reference:

[Nicolas Goaziou]

Hello,

"Marijn Schouten (hkBst)"  writes:

> Through irc I found someone who tested this with the latest
> development version as of now and it instead produces the error: can't
> assign to hline relative reference. That also does not seem like the
> right behavior to me.
>
> Could someone shed some light on the situation?

See .

Regards,

-- 
Nicolas Goaziou

[O] can't assign to hline relative reference:

[Marijn Schouten (hkBst)]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear list,

Consider the following small org table:

|   | grade | weight | weighed grade |
|---+---++---|
|   | 5 | 10 |50 |
|---+---++---|
| total |   || 0 |
#+TBLFM: @II$2=vsum(@I$2..@II-1$2)::$4=$2*$3

In the version of org (8.2.10) distributed with emacs 24.5, evaluating this 
table does not produces the expected result of column 2 being summed to a total 
of 5. Instead depending on point both the second and first columns will get an 
additional 5.

Through irc I found someone who tested this with the latest development version 
as of now and it instead produces the error: can't assign to hline relative 
reference. That also does not seem like the right behavior to me.

Could someone shed some light on the situation?

Marijn 

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[O] Export to Latex without \author{}

[Lei Zhe]

Dear orgers,

I am trying to export a beamer from org-mode with my own \author
command defined.
But when I export, org-mode always generates another \author after my
\author, which destroys the author list.
I tried:
1. #+author:
2. #+bind: latex-export-with-author ""
3. move #+author before my author command.
But none of them did make it. The \author{} always appears in the
place after my author command!

Then I tried to filter using:
(defun delete-empty-author (contents backend info)
  (when (eq backend 'beamer)
  (replace-regexp-in-string "author{}" "" contents)))
(add-to-list 'org-export-filter-keyword-functions 'delete-empty-author)
(add-to-list 'org-export-filter-plain-text-functions 'delete-empty-author)
(add-to-list 'org-export-filter-comment-functions 'delete-empty-author)

But it seems like that none of the filter functions is right.
So how can i solve this kind of problem?

llcc

Re: [O] Bug: org-mode breaks flyspell [8.2.10 (release_8.2.10 @ /usr/share/emacs/24.4/lisp/org/)]

[Nicolas Goaziou]

Hello,

Reuben Thomas  writes:

> Tested using “emacs -Q”, so you can ignore the details of my setup:
>
> Start up Emacs, M-x flyspell-mode dat
>
> The mis-spelled (I’m using English, not Latin as my default language)
> “dat” is underwiggled.
>
> Type Backspace a SPACE
>
> The word is now “data”, and (in English or Latin!) is now correct, so not 
> underwiggled.
>
> M-x org-mode and repeat the exercise: the underwiggle on the letters of
> “dat” remains after I have typed the “a”.

Thank you.

Apparently, this issue cannot be reproduced on latest development
version of Org. You may want to switch to development version of Org or
wait for 8.3 to be released.

Regards,

-- 
Nicolas Goaziou

[O] Bug: org-mode breaks flyspell [8.2.10 (release_8.2.10 @ /usr/share/emacs/24.4/lisp/org/)]

[Reuben Thomas]

Remember to cover the basics, that is, what you expected to happen and
what in fact did happen.  You don't know how to make a good report?  See

 http://orgmode.org/manual/Feedback.html#Feedback

Your bug report will be posted to the Org-mode mailing list.


Tested using “emacs -Q”, so you can ignore the details of my setup:

Start up Emacs, M-x flyspell-mode dat

The mis-spelled (I’m using English, not Latin as my default language)
“dat” is underwiggled.

Type Backspace a SPACE

The word is now “data”, and (in English or Latin!) is now correct, so not 
underwiggled.

M-x org-mode and repeat the exercise: the underwiggle on the letters of
“dat” remains after I have typed the “a”.

Emacs  : GNU Emacs 24.4.1 (x86_64-pc-linux-gnu, GTK+ Version 3.10.8)
 of 2014-11-21 on skwd, modified by Debian
Package: Org-mode version 8.2.10 (release_8.2.10 @ 
/usr/share/emacs/24.4/lisp/org/)

current state:
==
(setq
 org-export-backends '(ascii html icalendar latex odt)
 org-tab-first-hook '(org-hide-block-toggle-maybe 
org-src-native-tab-command-maybe org-babel-hide-result-toggle-maybe 
org-babel-header-arg-expand)
 org-latex-classes '(("article" "\\documentclass[11pt]{article}" 
("\\section{%s}" . "\\section*{%s}") ("\\subsection{%s}" . "\\subsection*{%s}")
  ("\\subsubsection{%s}" . "\\subsubsection*{%s}") 
("\\paragraph{%s}" . "\\paragraph*{%s}")
  ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
 ("report" "\\documentclass[11pt]{report}" ("\\part{%s}" . 
"\\part*{%s}") ("\\chapter{%s}" . "\\chapter*{%s}")
  ("\\section{%s}" . "\\section*{%s}") ("\\subsection{%s}" 
. "\\subsection*{%s}") ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
 ("book" "\\documentclass[11pt]{book}" ("\\part{%s}" . 
"\\part*{%s}") ("\\chapter{%s}" . "\\chapter*{%s}")
  ("\\section{%s}" . "\\section*{%s}") ("\\subsection{%s}" 
. "\\subsection*{%s}") ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))
 ("scrartcl" "\\documentclass{scrartcl}" ("\\section{%s}" . 
"\\section*{%s}") ("\\subsection{%s}" . "\\subsection*{%s}")
  ("\\subsubsection{%s}" . "\\subsubsection*{%s}") 
("\\paragraph{%s}" . "\\paragraph*{%s}")
  ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
 )
 org-latex-default-packages-alist '(("postscript" "ucs" nil) ("" "pifont" nil) 
("utf8x" "inputenc" t) ("T1" "fontenc" t) ("" "fixltx2e" nil)
("" "graphicx" t) ("" "longtable" nil) ("" 
"float" nil) ("" "wrapfig" nil) ("" "rotating" nil) ("normalem" "ulem" t)
("" "amsmath" t) ("" "textcomp" t) ("" 
"marvosym" t) ("" "wasysym" t) ("" "amssymb" t) ("" "hyperref" nil)
"\\tolerance=1000" ("" "palatino" nil))
 org-speed-command-hook '(org-speed-command-default-hook 
org-babel-speed-command-hook)
 org-occur-hook '(org-first-headline-recenter)
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-html-format-drawer-function '(lambda (name contents) contents)
 org-latex-format-inlinetask-function 'ignore
 org-confirm-shell-link-function 'yes-or-no-p
 org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default
 org-export-with-section-numbers nil
 org-file-apps '((auto-mode . emacs) ("\\.mm\\'" . default) ("\\.x?html?\\'" . 
default) ("\\.pdf\\'" . default) (t . "xdg-open %s")
 (system . "xdg-open %s"))
 org-export-with-toc nil
 org-latex-format-headline-function 'org-latex-format-headline-default-function
 org-default-notes-file "~/Notes/Notes.org"
 org-startup-indented t
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 org-latex-format-drawer-function '(lambda (name contents) contents)
 org-odt-format-headline-function 'ignore
 org-from-is-user-regexp "\\"
 org-src-mode-hook '(org-src-babel-configure-edit-buffer 
org-src-mode-configure-edit-buffer)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-babel-pre-tangle-hook '(save-buffer)
 org-mode-hook '((lambda nil (local-set-key "\351" (quote 
org-toggle-iimage-in-org))) window-margin-mode
 #[nil "\300\301\302\303\304$\207" [org-add-hook 
change-major-mode-hook org-show-block-all append local] 5]
 #[nil "\300\301\302\303\304$\207" [org-add-hook 
change-major-mode-hook org-babel-show-result-all append local] 5]
 org-babel-result-hide-spec org-babel-hide-all-hashes 
turn-on-eldoc-mode)
 org-ascii-format-drawer-function '(lambda (name contents width) contents)
 org-odt-format-inlinetask-function 'ignore
 org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point 
org-babel-execute-safely-maybe)
 org-directory "~/Notes"
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers 
org-cycle-hide-inline-tasks org-cycle-show-empty-lines
 

[O] ox-odt roundtrip editing?

[joakim]

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?

-- 
Joakim Verona

Re: [O] Turn off html entities in md export

[Nicolas Goaziou]

Rustom Mody  writes:

> Simple basic thing
> ... becomes …
> -- becomes –
> etc

In this particular case, see `org-export-with-special-strings'.

> For systems (bitbucket is just a common example) that simply does not work
> because of security or whatever reasons
> See
> https://bitbucket.org/site/master/issue/6930/support-some-or-all-html-in-markdown-bb
> for BB users clamoring but BB not likely to listen

In the worst case, you might need to implement a derived export back-end
applying Bitbucket constraints.

Regards,

Re: [O] Turn off html entities in md export

[Rustom Mody]

On Fri, Jun 26, 2015 at 1:24 PM, Nicolas Goaziou 
wrote:

> Hello,
>
> Rustom Mody  writes:
>
> > Bitbucket does not allow html entities in markdown
> > See https://bitbucket.org/rustom/vit-projects/wiki/emacs
> > and search for &#
> >
> > So how to turn off html entities in md export?
>
> It depends on where these entities are coming from.
>

Simple basic thing
... becomes …
-- becomes –
etc


>
> Anyway, vanilla Markdown supports HTML so anything "ox-md" cannot
> translate into Markdown syntax (e.g., tables) is exported as pure HTML.
>

For systems (bitbucket is just a common example) that simply does not work
because of security or whatever reasons
See
https://bitbucket.org/site/master/issue/6930/support-some-or-all-html-in-markdown-bb
for BB users clamoring but BB not likely to listen


> > And if thats not available any tips on how to hook say a sed-filter to
> > ox-md export?
>
> See filters in (info "(org)Advanced configuration").
>

Thanks
Will try to check that out

Re: [O] Turn off html entities in md export

[Nicolas Goaziou]

Hello,

Rustom Mody  writes:

> Bitbucket does not allow html entities in markdown
> See https://bitbucket.org/rustom/vit-projects/wiki/emacs
> and search for &#
>
> So how to turn off html entities in md export?

It depends on where these entities are coming from. 

Anyway, vanilla Markdown supports HTML so anything "ox-md" cannot
translate into Markdown syntax (e.g., tables) is exported as pure HTML.

> And if thats not available any tips on how to hook say a sed-filter to
> ox-md export?

See filters in (info "(org)Advanced configuration").


Regards,

-- 
Nicolas Goaziou

Re: [O] helm-bibtex questions

[Xebar Saram]

Hi Titus

Another round of helm-bibtex questions if you dont mind (question come
since i use it 50 times a day now ;-))

1. is there a way (or a keybind) to select all entries filtered? now to
select all my publications for example i have to use C-space repeatedly.

2. what is the syntax for greater then? for example all articles > 2012
(year)

4. i cant get helm-bibtex to search the biblatex field of pubstate. are
biblatex (biber) supported/ i have this in my config?

(setq helm-bibtex-additional-search-fields '(pubstate))

also on a related issue i assume one can define many fields in the above
example. since my elisp sucks would the syntax be this

(setq helm-bibtex-additional-search-fields '(pubstate tags))

or do you need to qoute them or use a , symbol?

5. i love the insert formatted reference (f5) option and use it often
sending people references:
a. does it also auto send that to the clipboard?
b. it cuts most of the authors name and leaves only the first few. is there
a switch to get it to print all authors. is that a latex cite formatting
issue?

best and thanks so much again

Z

On Mon, Jun 22, 2015 at 6:12 PM, Titus von der Malsburg 
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 template? it
> > would be helpful as a starting point for me if thats possible.
> >
> > kind regards and thanks so much in advance
> >
> > Z
> >
> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin 
> > wrote:
> >
> >> sweet! I did not know you could do that! I will be refactoring org-ref
> >> soon to do that instead of redefining the commands!
> >>
> >> 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, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
> >> malsb...@posteo.de> wrote:
> >>
> >>>
> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
> >>> > Hi again Titus
> >>> >
> >>> > 2 quick questions that arose from using helm-bitex today extensively:
> >>> >
> >>> > how does one exclude in the search items? for example i want to
> search
> >>> for
> >>> > xebar without keyword "progress" (I want to exclude in progress
> articles
> >>> > not published yet)
> >>> >
> >>> > is it possible to define default enter command in helm-bibtex ?
> >>>
> >>> Yes.  Helm uses the first action as the default action.  To move an
> >>> action to the top of the list you can use the following code:
> >>>
> >>>   (helm-delete-action-from-source "Insert BibTeX key"
> helm-source-bibtex)
> >>>   (helm-add-action-to-source "Insert BibTeX key"
> 'helm-bibtex-insert-key
> >>> helm-source-bibtex 0)
> >>>
> >>> The second argument in the second line is the function that executes
> the
> >>> action.  Here is a list of all actions and their functions:
> >>>
> >>>   Open PDF file (if present): helm-bibtex-open-pdf
> >>>   Open URL or DOI in browser: helm-bibtex-open-url-or-doi
> >>>   Insert citation: helm-bibtex-insert-citation
> >>>   Insert reference: helm-bibtex-insert-reference
> >>>   Insert BibTeX key: helm-bibtex-insert-key
> >>>   Insert BibTeX entry: helm-bibtex-insert-bibtex
> >>>   Attach PDF to email: helm-bibtex-add-PDF-attachment
> >>>   Edit notes: helm-bibtex-edit-notes
> >>>   Show entry: helm-bibtex-show-entry
> >>>
> >>> Best,
> >>>
> >>>   Titus
> >>>
> >>> >
> >>> > best
> >>> >
> >>> > Z
> >>> >
> >>> > On Thu, Jun 18, 2015 at 9:38 PM, Titus von der Malsburg <
> >>> malsb...@posteo.de>
> >>> > wrote:
> >>> >
> >>> >>
> >>> >> On 2015-06-18 Thu 04:32, Xebar Saram wrote:
> >>> >> > Hi Titus and thx so much for the answers!
> >>> >> >
> >>> >> > i will in the future use the github page to make requests.
> >>> >> >
> >>> >> > "The number of matches will be displayed in the mode line. "
> >>> >> >
> >>> >> > i see that now thx! :) the problem was(is) that its colored black
> on
> >>> my
> >>> >> > black modline BG which makes it invisible ;-) i assume thats an
> helm
> >>> >> config
> >>> >> > i need to change
> >>> >> >
> >>> >> >
> >>> >> > "If you don’t want to type these search expressions, you could
> 

Re: [O] Org-Mode and iCloud Reminders

[Rainer M Krug]

Ken Mankoff  writes:

> I have hopes for rem https://github.com/kykim/rem but right now it is
> easier to have rem->org than org->rem.

Why not use apples tools: see
e.g. [http://apple.stackexchange.com/a/113022/52198] for an example on
how to use Applescript to add reminders - you can use it from the
commandline and therefore also from emacs. (not tested - just read it!)

Cheers,

Rainer

>
>   -k. 
>
> Please excuse brevity. Sent from pocket computer with tiny non-haptic 
> feedback keyboard. 
>
>> On Jun 25, 2015, at 19:43, Yuri Niyazov  wrote:
>> 
>> Has anyone had any success with getting Mac OS X Reminders working
>> with org-mode? I found this blog post from a few years ago:
>> http://msnyder.info/posts/2012/05/icloud-reminders-orgmode/ and was
>> wondering if anyone's had much success with that or some other syncing
>> mechanism.
>> 
>> Thanks!
>> 

-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :   +33 - (0)9 53 10 27 44
Cell:   +33 - (0)6 85 62 59 98
Fax :   +33 - (0)9 58 10 27 44

Fax (D):+49 - (0)3 21 21 25 22 44

email:  rai...@krugs.de

Skype:  RMkrug

PGP: 0x0F52F982


signature.asc
Description: PGP signature

Re: [O] helm-bibtex questions

[Xebar Saram]

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 
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  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 
> 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 template?
>> it
>> >> > would be helpful as a starting point for me if thats possible.
>> >> >
>> >> > kind regards and thanks so much in advance
>> >> >
>> >> > Z
>> >> >
>> >> > On Sun, Jun 21, 2015 at 9:40 PM, John Kitchin <
>> jkitc...@andrew.cmu.edu>
>> >> > wrote:
>> >> >
>> >> >> sweet! I did not know you could do that! I will be refactoring
>> org-ref
>> >> >> soon to do that instead of redefining the commands!
>> >> >>
>> >> >> 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, Jun 21, 2015 at 2:29 PM, Titus von der Malsburg <
>> >> >> malsb...@posteo.de> wrote:
>> >> >>
>> >> >>>
>> >> >>> On 2015-06-19 Fri 03:56, Xebar Saram wrote:
>> >> >>> > Hi again Titus
>> >> >>> >
>> >> >>> > 2 quick questions that arose from using helm-bitex today
>> extensively:
>> >> >>> >
>> >> >>> > how does one exclude in the search items? for exam