Re: [O] Bug: org-edit-special does not indent the blank line after exit editing [9.0.3 (9.0.3-elpa @ /Users/Yomisuko/.emacs.d/elpa/org-20161224/)]

[Jiajian Huang]

Hi,

Thanks for you reply. I cannot understand the design of
`org-src-preserve-indentation`.

Setting it to `nil` cause what described in my previous mail.
Setting it to `t` lose the leading two spaces indentation/alignment in the
origin org buffer.

If it is `nil`, why inserting 2 leading spaces to the code in the org
buffer except the line containing only spaces?

How can I get

#+BEGIN_SRC python
a = 1
b = 2
for i in range(10):
# 6 spaces before '#'
#+END_SRC

after exit `org-edit-special` ?

Best regards,
Jiajian Huang

On Sat, Jan 7, 2017 at 12:31 AM, Nicolas Goaziou 
wrote:

> Hello,
>
> Jiajian Huang  writes:
>
> > Reproduce steps:
> >
> > Launch emacs by `emacs -Q`, eval the following snippet(assumed org 9.x
> > is installed via elpa)
> >
> > (package-initialize)
> > (require 'org)
> >
> > open a org buffer, input the source by  >
> > #+BEGIN_SRC python
> >
> > #+END_SRC
> >
> > use C-c ' to edit the block and input
> >
> > for i in range(10):  # input this line and 
> > # there are 4 spaces before the '#' now
> >
> > use C-c ' to close the source block buffer and back to org-mode, we can
> > see the first line of the block is indented 2 spaces by org while the
> blank
> > line
> > isn't.
>
> This is not a bug. See `org-src-preserve-indentation'.
>
> Regards,
>
> --
> Nicolas Goaziou
>

[O] bug#25132: 26.0.50; emacs hangs when loading org file with python source blocks

[npostavs]

tags 25132 confirmed
quit

The problem is that org updates its temporary fontification buffer from
its fontify rules which are called by jit-lock-function, which means
that inhibit-modification-hooks is bound to t.  Therefore, when
org-src-font-lock-fontify-block calls delete-region to remove leftover text from
the previous source block fontification, the `before-change-functions'
are not run.  In this case `syntax-ppss-flush-cache' is the important
function that doesn't get run, so `syntax-propertize--done' is still set
from before and messes up python.el's fontification routines.

  org-src-font-lock-fontify-block(#("python" 0 6 (fontified t)) 19 65)
  org-fontify-meta-lines-and-blocks-1(172)
  org-fontify-meta-lines-and-blocks(172)
  font-lock-fontify-keywords-region(1 172 nil)
  font-lock-default-fontify-region(1 172 nil)
  font-lock-fontify-region(1 172)
  ...
  jit-lock--run-functions(1 172)
  jit-lock-fontify-now(1 501)
  jit-lock-function(1)
  redisplay_internal\ \(C\ function\)()
  redisplay()
  sit-for(2)
  execute-extended-command(nil "25132-test" "25")
  funcall-interactively(execute-extended-command nil "25132-test" "25")
  call-interactively(execute-extended-command nil nil)
  command-execute(execute-extended-command)

(defun org-src-font-lock-fontify-block (lang start end)
  ...
  (with-current-buffer
  (get-buffer-create
   (concat " org-src-fontification:" (symbol-name lang-mode)))
(delete-region (point-min) (point-max)) ;<-- 
`syntax-propertize--done' not reset here!
(insert string " ") ;; so there's a final property change
(unless (eq major-mode lang-mode) (funcall lang-mode))
(org-font-lock-ensure)
...)
  ...)

(defun jit-lock-function (start)
  ...
  (jit-lock-fontify-now start (+ start jit-lock-chunk-size))
  ...)

(defun jit-lock-fontify-now ( start end)
  "Fontify current buffer from START to END.
Defaults to the whole buffer.  END can be out of bounds."
  (with-buffer-prepared-for-jit-lock
...))

  (defmacro with-buffer-prepared-for-jit-lock ( body)
"Execute BODY in current buffer, overriding several variables.
Preserves the `buffer-modified-p' state of the current buffer."
(declare (debug t))
`(let ((inhibit-point-motion-hooks t))
   (with-silent-modifications ; <-- binds inhibit-modification-hooks to 
t
 ,@body)))

[O] publishing subtrees

[Matt Price]

In my course repositories, I have all my lecture notes in one file, and all
my assignments in another.  So they have the form

* Lecture 1
** Slide 1
** Slide 2
* Lecture 2 ...

* Assignment 1
** Description
** Rubric
* Assignment 2...

I'd like to have publishing functions that, say, export all first-level
headings to html with ox-reveal, and uploads those to a location on the
web. Or, alternatively, export them all to org in a remote location ,where
they can be viewed on github or using jeyll or something.

Is anyone doing something like this already? Is it possible using hte
built-in publishing functions?

Thank you!

Matt

Re: [O] org-ref: citation types (insert full citation); bib style; bib scope

[Matt Price]

Wow, this is pretty awesome, thank you.

A couple of notes inline

On Fri, Jan 6, 2017 at 3:42 PM, John Kitchin 
wrote:
>
> New org-ref update ;)
>
> I overhauled the formatted citation support in org-ref today.
>
> Now, you can do the following things:
>
> 1. from the C-c ] interface (helm-bibtex, helm-cite or ivy-cite) you can
> mark some entries and choose an action that inserts formatted strings.
> The default backend for this is text, but you can change that to
> org, and add new backends to the variable
> org-ref-formatted-citation-formats. The backend is defined in the variable
> org-ref-formatted-citation-backend.
>
> It is better than it was (we used to use org-ref-reftex-format-citation
> which had limited fields and character codes). Now the templates use
> s-format and the bibtex-completion code, so you can access any bibtex
> field that is there. This is not a real substitute for a citation
> processor, e.g. if your template has ${volume}(${issue}), and those
> fields do not exist, they will just be empty, e.g. 5(). I don't have
> plans to address this limitation at this point.
>
As you say, it's imperfect, but still pretty good, thank you!

>
> 2. If you click on a citation link, you can select an action to copy the
> formatted entry for that key.


I had trouble with this. I constructed a minimal emacs config:

#+BEGIN_SRC emacs-lisp
;;; elpa interface
(setq package-archives ())
(add-to-list 'package-archives '("marmalade" . "
http://marmalade-repo.org/packages/;))
(add-to-list 'package-archives '("gnu" . "http://elpa.gnu.org/packages/;))
(add-to-list 'package-archives '("org" . "http://orgmode.org/elpa/;) t)
(add-to-list 'package-archives '("melpa" . "
http://melpa.milkbox.net/packages/;) t)
;; basic initialization, (require) non-ELPA packages, etc.
(package-initialize)

(require 'cl)
(require 'org)
(require 'helm-config)
(require 'helm)
(require 'helm-bibtex)

;; see org-ref for use of these variables
(setq org-ref-bibliography-notes "~/Bibliography/notes.org"
  org-ref-default-bibliography '("~/Bibliography/Bibliography.bib")
  org-ref-pdf-directory "~/Bibliography/files/")

(setq bibtex-completion-bibliography "~/Bibliography/Bibliography.bib"
  bibtex-completion-library-path "~/Bibliography/files"
  )

;; org-define-error
;; for whatever reason, org wasn't finding this
(defun org-define-error (name message)
  "Define NAME as a new error signal.
MESSAGE is a string that will be output to the echo area if such
an error is signaled without being caught by a `condition-case'.
Implements `define-error' for older emacsen."
  (if (fboundp 'define-error) (define-error name message)
(put name 'error-conditions
 (copy-sequence (cons name (get 'error 'error-conditions))

(setq org-ref-formatted-citation-backend "org")
(setq org-ref-completion-library 'org-ref-helm-bibtex)

(require 'org-ref)

#+END_SRC

The action proceeds without errors, but nothing seems to be copied ot the
clipboard.

>
> 3. On a bibtex entry, you can use the org-ref-bibtex-hydra/body to copy
> a formatted string of the entry.
>
this works great.  Obviously I need to learn how to use hydra...
>
>
> >> > Does anyone know what the other options are? In particular, for the
> >> syllabi
> >> > I'm currently creating I'd like to just insert the org-formatted
citation
> >> > information itself -- is this possible?
> >>
> >> Can you give an example?
> >>
> >>
> > I htink I'm looking for something impossible.  org-zotxt allowed me to
use
> > a link type "citation", which just inserted the full citation in org
syntax:
> >
> > Hayles, K. (1999). /How we became posthuman: virtual bodies in
cybernetics,
> > literature, and informatics/. Chicago, Ill.: University of Chicago
Press. [[
> >
http://search.library.utoronto.ca/details?7949488=5aaa42cf-ffd2-41e3-ac6b-60e649f9f289
> > ]]
>
> You would want to have these settings with a new org-ref:
> (setq org-ref-formatted-citation-backend "org")
>
> (setf (cdr (assoc "book" (cdr (assoc "org"
> org-ref-formatted-citation-formats
>  "${author} ${year}. /${title}/, ${address}:${publisher}. [[${url}]]")
>
> Then you can insert the citation and get this (there is no address for
> the publisher in my entry). With helm bibtex as the backend, you would
> type C-c ], select an entry, and press f8 (or tab and select the insert
> formatted action). In the ivy backend, you type M-o f. Both of them
> support multiple selections.

Yeah, this is awesome, thank you.  it's F7 though, not F8.
>
>
> There is not a way to control the casing of the title here, it is
> sentence cased by the bibtex-completion library. I also don't have plans
> to address that.
>
> >
> > rather than generating a link.  If I had an option to do this in my
> > syllabi, it would greatly simplify my work flow.
> >
> >
> >> > I'd like to be able to point my
> >> > students directly to my github repo, and it will ultimately be more
> >> > convenient to have the links already present in 

[O] Default application for org-reveal

[Florian Lindner]

Hello,

the Org Attach dispatcher offers a key "f" to open the attachment directory not 
in Emacs.

(defun org-attach-reveal ( if-exists)
  "Show the attachment directory of the current task.
This will attempt to use an external program to show the directory."
  (interactive "P")
  (let ((attach-dir (org-attach-dir (not if-exists
(and attach-dir (org-open-file attach-dir

On my two systems this is the same a F, it opens in dired. xdg-open . uses 
dolphin to open inode/directory. How does Emacs/org determine which
application to use? How can I influence it?

Thanks,
Florian

P.S. Why are file associations such a mess on Linux. Emacs? KDE and Thunderbird 
all use different applications to open the same file...

Re: [O] org-ref: citation types (insert full citation); bib style; bib scope

[John Kitchin]

New org-ref update ;)

I overhauled the formatted citation support in org-ref today.

Now, you can do the following things:

1. from the C-c ] interface (helm-bibtex, helm-cite or ivy-cite) you can
mark some entries and choose an action that inserts formatted strings.
The default backend for this is text, but you can change that to
org, and add new backends to the variable
org-ref-formatted-citation-formats. The backend is defined in the variable
org-ref-formatted-citation-backend.

It is better than it was (we used to use org-ref-reftex-format-citation
which had limited fields and character codes). Now the templates use
s-format and the bibtex-completion code, so you can access any bibtex
field that is there. This is not a real substitute for a citation
processor, e.g. if your template has ${volume}(${issue}), and those
fields do not exist, they will just be empty, e.g. 5(). I don't have
plans to address this limitation at this point. 

2. If you click on a citation link, you can select an action to copy the
formatted entry for that key.

3. On a bibtex entry, you can use the org-ref-bibtex-hydra/body to copy
a formatted string of the entry.


>> > Does anyone know what the other options are? In particular, for the
>> syllabi
>> > I'm currently creating I'd like to just insert the org-formatted citation
>> > information itself -- is this possible?
>>
>> Can you give an example?
>>
>>
> I htink I'm looking for something impossible.  org-zotxt allowed me to use
> a link type "citation", which just inserted the full citation in org syntax:
>
> Hayles, K. (1999). /How we became posthuman: virtual bodies in cybernetics,
> literature, and informatics/. Chicago, Ill.: University of Chicago Press. [[
> http://search.library.utoronto.ca/details?7949488=5aaa42cf-ffd2-41e3-ac6b-60e649f9f289
> ]]

You would want to have these settings with a new org-ref:
(setq org-ref-formatted-citation-backend "org")

(setf (cdr (assoc "book" (cdr (assoc "org"
org-ref-formatted-citation-formats
 "${author} ${year}. /${title}/, ${address}:${publisher}. [[${url}]]")

Then you can insert the citation and get this (there is no address for
the publisher in my entry). With helm bibtex as the backend, you would
type C-c ], select an entry, and press f8 (or tab and select the insert
formatted action). In the ivy backend, you type M-o f. Both of them
support multiple selections.

Dominik, C. 2014. /The org mode 8 reference manual - organize your life with 
gnu emacs/, :Samurai Media Limited. [[http://amazon.com/o/ASIN/9881327709/]]

There is not a way to control the casing of the title here, it is
sentence cased by the bibtex-completion library. I also don't have plans
to address that.

>
> rather than generating a link.  If I had an option to do this in my
> syllabi, it would greatly simplify my work flow.
>
>
>> > I'd like to be able to point my
>> > students directly to my github repo, and it will ultimately be more
>> > convenient to have the links already present in the source code, since
>> > github doesn't reoslve org-ref
>>
>> What I mean is, that I'd like to stop building course websites and instead
>> just point students to github repos where my docs live in an org format.
>> This means I reallywant the citatiion information, and not citation links.
>> E.g.:
>>
>
> https://github.com/titaniumbones/New113/blob/master/New113Syllabus.org#2017-01-26-thu-state-surveillance

Does this mean you have an entry with the url in it? Say you have it as
a misc entry.

@misc{ase,
  Title ={Atomic Simulation Environment},
  Howpublished = {https://wiki.fysik.dtu.dk/ase/},
  note = {The Atomic Simulation Environment is a set of Python libraries
  for running molecular simulations and analyzing the results.}
}

That entry type isn't defined in the formats (there should be a default
entry, but it isn't formatted the way you want), but you could add it like this:


(push '("misc" . "${author} ${year}. /${title}/, [[${howpublished}]]")(cdr 
(assoc "org"
org-ref-formatted-citation-formats)))

then insert a citation from the entry that looks like this:

 . /Atomic Simulation Environment/, [[https://wiki.fysik.dtu.dk/ase/]]


>> >
>> > * bib style
>> > When I right-click on a link and select "copy the formatted citation", I
>> > don't get the URL field, which my students need. I assume that's because
>> > I'm not using the right bibliographic style. How do I set the citation
>> > format?  Would I use the bibliographystyle link, or a header argument
>> > somewhere?


You don't use the bibliographystyle, it is mostly only for building PDF
from LaTeX.

There is some more advanced code in the citeproc directory of org-ref,
but it is early in development (and has been for a year or more ;), and
it has a really limited set of styles. It is still a long time before it
is production ready.

This code has been tested about 1/2 a day now. Try it out and let me
know if you have any troubles.

>>
>> Support for this is kind of 

[O] Versioning of worg content

[Stefan-W. Hahn]

Hello,

is their a defined proceeding of how to cope with incompatible changes of
org-mode in the examples at orgmode.org/worg?

Just stumbled about examples for org-agenda where org-agenda-ndays is still
used when I already using org 9.1 where the alias is removed.

With kind regards
Stefan

-- 
Stefan-W. Hahn  It is easy to make things.
It is hard to make things simple.

Re: [O] Cannot resize inline image

[John Kitchin]

Try:

#+attr_org: :width 400
[[./test.png]]

400 means 400 pixels wide. 

Young-whan writes:

> I'm very beginner at org-mode and learning and having fun with it these
> days.
>
> Now, I'm embedding an image, but I'd like to resize it.
>
> Googling shows me like this:
>
> #+attr_org: :width 40%
> [[./test.png]]
>
> However, that is not working to me at all.
>
> I'm using
>
> GNU Emacs 25.1.90.1 (x86_64-apple-darwin13.4.0, NS appkit-1265.21 Version
> 10.9.5 (Build 13F1911)) of 2016-11-28
>
> Org-mode version 8.2.10 (release_8.2.10 @
> /Applications/Emacs.app/Contents/Resources/lisp/org/)
>
> Anyone can help on this, please?
>
> C-c C-x C-v shows only original image size. What should I need to check
> more?


-- 
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] speeding up Babel Gnuplot

[Thierry Banel]

Le 06/01/2017 10:41, Nicolas Goaziou a écrit :
> Hello,
>
> Thierry Banel  writes:
>
>> By "going through the table" I mean going through this structure.
>> Remember the issue in the first place was a slow conversion of this
>> huge structure into a temporary file. Now we need to convert this huge
>> structure into a hash. Ok, let us assume hashing is faster than
>> writing to disk.
> Converting this huge structure into a temporary file is (relatively)
> slow because of `orgtbl-to-generic', isn't it? Computing the hash
> doesn't call this function.
>
> Why do you expect computing the hash to be slow?
>
>

I don't. I "assume hashing is faster than writing to disk."

Regards
Thierry

[O] Running a Babun Shell In Emacs

[42 147]

How does one run a Babun shell in Emacs?

Re: [O] [bug] Tests: 4 unexpected results

[Marco Wahl]

Hi,

Nicolas Goaziou  writes:

>> With the current master
>>
>> #+begin_src shell
>> make test
>> #+end_src
>>
>>
>> results in
>>
>> #+begin_quote
>> 4 unexpected results:
>>FAILED  test-org-list/move-item-down
>>FAILED  test-org-list/move-item-up
>>FAILED  test-org/custom-properties
>>FAILED  test-org/forward-paragraph
>> #+end_quote
>>
>> This looks like an issue with checking visibility of a location.
>
> I cannot reproduce it. The build bot
> (http://www.randomsample.de:4457/waterfall) cannot either.

Thanks.

This is strong evidence that the problem sits somewhere on my side.
Sorry for the noise.

http://www.randomsample.de:4457/waterfall looks nice!


Best regards

   Marco

[O] HTML width attribute gets added to a href instead of img

[Kaushal Modi]

Hello,

I am using the devel versions of org and emacs.

Org mode version 9.0.3 (release_9.0.3-180-g0d3683 @
/home/kmodi/usr_local/apps/6/emacs/master/share/emacs/site-lisp/org/)

Emacs version: GNU Emacs 26.0.50.4 (x86_64-unknown-linux-gnu, GTK+ Version
2.24.23)
 of 2017-01-06, built using commit 8f0376309ee37e4f1da21d78971c4df2df5fd7b6.

I believe that after this commit, the width attribute doesn't get added to
img tag as expected:
http://orgmode.org/cgit.cgi/org-mode.git/commit/?id=5ffb373a2ca6833617e344154c3dc1b877ec4784

Here is a MWE:

=
Below works as expected
#+ATTR_HTML: :width 10px
[[http://orgmode.org/img/org-mode-unicorn-logo.png]]

Below does not where the image is added as /link description/.
#+ATTR_HTML: :width 10px
[[http://orgmode.org][http://orgmode.org/img/org-mode-unicorn-logo.png]]
=

Here is just the body of the exported html for brevity:

=



Below works as expected



http://orgmode.org/img/org-mode-unicorn-logo.png;
alt="org-mode-unicorn-logo.png" width="10px" />




Below does not where the image is added as link description.



http://orgmode.org; width="10px">http://orgmode.org/img/org-mode-unicorn-logo.png;
alt="org-mode-unicorn-logo.png" />




Exported using http://www.gnu.org/software/emacs/;>Emacs 26.0.50.4 (http://orgmode.org;>Org mode 9.0.3) by Kaushal.Modi.


=

Note that in the latter case, the width property gets added to 'a' tag
instead of to the 'img' tag.
-- 

Kaushal Modi

Re: [O] org-ref: citation types (insert full citation); bib style; bib scope

[Matt Price]

On Fri, Jan 6, 2017 at 10:26 AM, John Kitchin 
wrote:

>
> Matt Price writes:
>
> > After several years, I'm finally trying to move to bibtex from zotero,
> > partly because org-zotxt has stopped working for me (both link insertion
> > and html export seem at least temporarily broken).
> >
> > The UI for org-ref is pretty fantastic, and I love it. I'm having trouble
> > getting the behaviour I want fro mthe actual links, though.  My needs may
> > be somewhat atypical but I'm hoping someone else has figured these
> > questions out already.
> >
> > * citation types
> > The org-ref manual talks about different citation types, but the external
> > link it suggests is not loading:
> > http://ctan.unixbrain.com/macros/latex/contrib/natbib/natnotes.pdf
>
> try: http://tug.ctan.org/macros/latex/contrib/natbib/natnotes.pdf


ok, thx.

>
>
> >
> > Does anyone know what the other options are? In particular, for the
> syllabi
> > I'm currently creating I'd like to just insert the org-formatted citation
> > information itself -- is this possible?
>
> Can you give an example?
>
>
I htink I'm looking for something impossible.  org-zotxt allowed me to use
a link type "citation", which just inserted the full citation in org syntax:

Hayles, K. (1999). /How we became posthuman: virtual bodies in cybernetics,
literature, and informatics/. Chicago, Ill.: University of Chicago Press. [[
http://search.library.utoronto.ca/details?7949488=5aaa42cf-ffd2-41e3-ac6b-60e649f9f289
]]

rather than generating a link.  If I had an option to do this in my
syllabi, it would greatly simplify my work flow.


> > I'd like to be able to point my
> > students directly to my github repo, and it will ultimately be more
> > convenient to have the links already present in the source code, since
> > github doesn't reoslve org-ref
>
> What I mean is, that I'd like to stop building course websites and instead
> just point students to github repos where my docs live in an org format.
> This means I reallywant the citatiion information, and not citation links.
> E.g.:
>

https://github.com/titaniumbones/New113/blob/master/New113Syllabus.org#2017-01-26-thu-state-surveillance



> >
> > * bib style
> > When I right-click on a link and select "copy the formatted citation", I
> > don't get the URL field, which my students need. I assume that's because
> > I'm not using the right bibliographic style. How do I set the citation
> > format?  Would I use the bibliographystyle link, or a header argument
> > somewhere?
>
> Support for this is kind of rudimentary, because it is really difficult
> to get properly formatted strings for all references.
>
> When you click on a cite link and select copy formatted entry what
> happens is the bibfile is opened to that entry and then the result of
> org-ref-bib-citation is copied. It is pretty simple, and limited. At the
> moment, I think helm-bibtex does the actual formatting if you load it,
> and it does not appear to be customizable. See
> bibtex-completion-apa-format-reference
>
> I will work on this a little bit and see if some improvements can be
> made.
>

thanks you John!

>
> >
> > Also, is it possible to set this option to use org formatting instead of
> > html formatting?
>
> You could use a function like this on a link to get something more
> customizable.
>
> (defun better-formatted-citation ()
>   (interactive)
>   (kill-new (org-ref-get-bibtex-entry-citation (car
> (org-ref-get-bibtex-key-and-file)
>
> see the variable org-ref-bibliography-entry-format, you can set this to
> be whatever format you want.
>
> ah, looks pretty simple, I should be able to do this.

> >
> > * Bibliography scope
> > I guess I don't really know how to build a bibliographic file to go with
> a
> > particular project.  At present I am using my full Zotero library
> exported
> > to bibtex as a default. Is there a way to just build the bibliography
> from
> > the set of sources cited in the paper?
>
> M-x org-ref-extract-bibtex-entries should put a new heading in the buffer
> with the relevant bibtex entries.
>
> excellent, thank you!


> >
> > Thanks everyone, and of course especially John for this amazing tool.
> >
> > Matt
>
>
> --
> 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] Bug: org-edit-special does not indent the blank line after exit editing [9.0.3 (9.0.3-elpa @ /Users/Yomisuko/.emacs.d/elpa/org-20161224/)]

[Nicolas Goaziou]

Hello,

Jiajian Huang  writes:

> Reproduce steps:
>
> Launch emacs by `emacs -Q`, eval the following snippet(assumed org 9.x
> is installed via elpa)
>
> (package-initialize)
> (require 'org)
>
> open a org buffer, input the source by 
> #+BEGIN_SRC python
>
> #+END_SRC
>
> use C-c ' to edit the block and input
>
> for i in range(10):  # input this line and 
> # there are 4 spaces before the '#' now
>
> use C-c ' to close the source block buffer and back to org-mode, we can
> see the first line of the block is indented 2 spaces by org while the blank
> line
> isn't.

This is not a bug. See `org-src-preserve-indentation'.

Regards,

-- 
Nicolas Goaziou

Re: [O] [bug] Tests: 4 unexpected results

[Nicolas Goaziou]

Hello,

Marco Wahl  writes:

> With the current master
>
> #+begin_src shell
> make test
> #+end_src
>
>
> results in
>
> #+begin_quote
> 4 unexpected results:
>FAILED  test-org-list/move-item-down
>FAILED  test-org-list/move-item-up
>FAILED  test-org/custom-properties
>FAILED  test-org/forward-paragraph
> #+end_quote
>
> This looks like an issue with checking visibility of a location.

I cannot reproduce it. The build bot
(http://www.randomsample.de:4457/waterfall) cannot either.

Regards,

-- 
Nicolas Goaziou

Re: [O] org-ref: citation types (insert full citation); bib style; bib scope

[John Kitchin]

That is possible. I am out now, but this afternoon I will send another note
on how to do it.


On Fri, Jan 6, 2017 at 11:05 AM Matt Price  wrote:

> On Fri, Jan 6, 2017 at 10:26 AM, John Kitchin 
> wrote:
>
>
>
>
> Matt Price writes:
>
>
>
>
>
> > After several years, I'm finally trying to move to bibtex from zotero,
>
>
> > partly because org-zotxt has stopped working for me (both link insertion
>
>
> > and html export seem at least temporarily broken).
>
>
> >
>
>
> > The UI for org-ref is pretty fantastic, and I love it. I'm having trouble
>
>
> > getting the behaviour I want fro mthe actual links, though.  My needs may
>
>
> > be somewhat atypical but I'm hoping someone else has figured these
>
>
> > questions out already.
>
>
> >
>
>
> > * citation types
>
>
> > The org-ref manual talks about different citation types, but the external
>
>
> > link it suggests is not loading:
>
>
> > http://ctan.unixbrain.com/macros/latex/contrib/natbib/natnotes.pdf
>
>
>
>
>
> try: http://tug.ctan.org/macros/latex/contrib/natbib/natnotes.pdf
>
>
> ok, thx.
>
>
>
>
>
>
>
> >
>
>
> > Does anyone know what the other options are? In particular, for the
> syllabi
>
>
> > I'm currently creating I'd like to just insert the org-formatted citation
>
>
> > information itself -- is this possible?
>
>
>
>
>
> Can you give an example?
>
>
>
>
> I htink I'm looking for something impossible.  org-zotxt allowed me to use
> a link type "citation", which just inserted the full citation in org syntax:
>
> Hayles, K. (1999). /How we became posthuman: virtual bodies in
> cybernetics, literature, and informatics/. Chicago, Ill.: University of
> Chicago Press. [[
> http://search.library.utoronto.ca/details?7949488=5aaa42cf-ffd2-41e3-ac6b-60e649f9f289
> ]]
>
> rather than generating a link.  If I had an option to do this in my
> syllabi, it would greatly simplify my work flow.
>
>
>
>
> > I'd like to be able to point my
>
>
> > students directly to my github repo, and it will ultimately be more
>
>
> > convenient to have the links already present in the source code, since
>
>
> > github doesn't reoslve org-ref
>
>
>
> What I mean is, that I'd like to stop building course websites and instead
> just point students to github repos where my docs live in an org format.
> This means I reallywant the citatiion information, and not citation links.
> E.g.:
>
>
>
> https://github.com/titaniumbones/New113/blob/master/New113Syllabus.org#2017-01-26-thu-state-surveillance
>
>
>
>
>
>
>
> >
>
>
> > * bib style
>
>
> > When I right-click on a link and select "copy the formatted citation", I
>
>
> > don't get the URL field, which my students need. I assume that's because
>
>
> > I'm not using the right bibliographic style. How do I set the citation
>
>
> > format?  Would I use the bibliographystyle link, or a header argument
>
>
> > somewhere?
>
>
>
>
>
> Support for this is kind of rudimentary, because it is really difficult
>
>
> to get properly formatted strings for all references.
>
>
>
>
>
> When you click on a cite link and select copy formatted entry what
>
>
> happens is the bibfile is opened to that entry and then the result of
>
>
> org-ref-bib-citation is copied. It is pretty simple, and limited. At the
>
>
> moment, I think helm-bibtex does the actual formatting if you load it,
>
>
> and it does not appear to be customizable. See
> bibtex-completion-apa-format-reference
>
>
>
>
>
> I will work on this a little bit and see if some improvements can be
>
>
> made.
>
>
> thanks you John!
>
>
>
>
>
>
> >
>
>
> > Also, is it possible to set this option to use org formatting instead of
>
>
> > html formatting?
>
>
>
>
>
> You could use a function like this on a link to get something more
>
>
> customizable.
>
>
>
>
>
> (defun better-formatted-citation ()
>
>
>   (interactive)
>
>
>   (kill-new (org-ref-get-bibtex-entry-citation (car
> (org-ref-get-bibtex-key-and-file)
>
>
>
>
>
> see the variable org-ref-bibliography-entry-format, you can set this to
>
>
> be whatever format you want.
>
>
>
> ah, looks pretty simple, I should be able to do this.
>
>
>
> >
>
>
> > * Bibliography scope
>
>
> > I guess I don't really know how to build a bibliographic file to go with
> a
>
>
> > particular project.  At present I am using my full Zotero library
> exported
>
>
> > to bibtex as a default. Is there a way to just build the bibliography
> from
>
>
> > the set of sources cited in the paper?
>
>
>
>
>
> M-x org-ref-extract-bibtex-entries should put a new heading in the buffer
>
>
> with the relevant bibtex entries.
>
>
>
> excellent, thank you!
>
>
>
>
> >
>
>
> > Thanks everyone, and of course especially John for this amazing tool.
>
>
> >
>
>
> > Matt
>
>
>
>
>
>
>
>
> --
>
>
> Professor John Kitchin
>
>
> Doherty Hall A207F
>
>
> Department of Chemical Engineering
>
>
> Carnegie Mellon University
>
>
> Pittsburgh, PA 15213
>
>
> 412-268-7803
>
>
> @johnkitchin
>
>
> http://kitchingroup.cheme.cmu.edu
>
>
>

Re: [O] org-ref: citation types (insert full citation); bib style; bib scope

[John Kitchin]

Matt Price writes:

> After several years, I'm finally trying to move to bibtex from zotero,
> partly because org-zotxt has stopped working for me (both link insertion
> and html export seem at least temporarily broken).
>
> The UI for org-ref is pretty fantastic, and I love it. I'm having trouble
> getting the behaviour I want fro mthe actual links, though.  My needs may
> be somewhat atypical but I'm hoping someone else has figured these
> questions out already.
>
> * citation types
> The org-ref manual talks about different citation types, but the external
> link it suggests is not loading:
> http://ctan.unixbrain.com/macros/latex/contrib/natbib/natnotes.pdf

try: http://tug.ctan.org/macros/latex/contrib/natbib/natnotes.pdf

>
> Does anyone know what the other options are? In particular, for the syllabi
> I'm currently creating I'd like to just insert the org-formatted citation
> information itself -- is this possible?

Can you give an example?

> I'd like to be able to point my
> students directly to my github repo, and it will ultimately be more
> convenient to have the links already present in the source code, since
> github doesn't reoslve org-ref

I do not follow what you want here. Another example would be helpful.

>
> * bib style
> When I right-click on a link and select "copy the formatted citation", I
> don't get the URL field, which my students need. I assume that's because
> I'm not using the right bibliographic style. How do I set the citation
> format?  Would I use the bibliographystyle link, or a header argument
> somewhere?

Support for this is kind of rudimentary, because it is really difficult
to get properly formatted strings for all references. 

When you click on a cite link and select copy formatted entry what
happens is the bibfile is opened to that entry and then the result of
org-ref-bib-citation is copied. It is pretty simple, and limited. At the
moment, I think helm-bibtex does the actual formatting if you load it,
and it does not appear to be customizable. See 
bibtex-completion-apa-format-reference

I will work on this a little bit and see if some improvements can be
made.

>
> Also, is it possible to set this option to use org formatting instead of
> html formatting?

You could use a function like this on a link to get something more
customizable.

(defun better-formatted-citation ()
  (interactive)
  (kill-new (org-ref-get-bibtex-entry-citation (car 
(org-ref-get-bibtex-key-and-file)

see the variable org-ref-bibliography-entry-format, you can set this to
be whatever format you want.

>
> * Bibliography scope
> I guess I don't really know how to build a bibliographic file to go with a
> particular project.  At present I am using my full Zotero library exported
> to bibtex as a default. Is there a way to just build the bibliography from
> the set of sources cited in the paper?

M-x org-ref-extract-bibtex-entries should put a new heading in the buffer
with the relevant bibtex entries.

>
> Thanks everyone, and of course especially John for this amazing tool.
>
> Matt


-- 
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] Automatic export of columnview

[Shawn Way]

I have an org table created using columnview that requires further processing 
for a report.  Is there a parameter that allows a columnview to be 
automatically exported to a file for futher processing using another language.

For example 

*** Tasks
  :PROPERTIES:
  :ID:   Units
  :VISIBILITY: folded
  :COLUMNS: %35ITEM %CREATED %Effort
  :END:


#+BEGIN: columnview :hlines 1 :id global
| ITEM| CREATED 
   | Effort |
|-++|
| Masterpak, MasterpakLT and PRO Standards Development| 
   ||
| Adminstrative   | 
   ||
| Present Changes to Applications | [2017-01-06 Fri 
06:45] |   3:00 |
| Masterpak   | 
   ||
| HAZOP   | [2016-12-10 Sat 
12:00] |  24:00 |
| Review Standard System Descriptions | [2016-12-10 Sat 
12:00] |   1:30 |
#+END

Would upon export, send this columnview table to a .csv file.

The next

#+BEGIN_SRC
#+END_SRC

Would then process the .csv file and produce the charts based on the further 
processed data.


Thank you kindly,

Shawn Way, PE
  

[O] Bug: org-edit-special does not indent the blank line after exit editing [9.0.3 (9.0.3-elpa @ /Users/Yomisuko/.emacs.d/elpa/org-20161224/)]

[Jiajian Huang]

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 mailing list.

Bug(maybe): org-edit-special under org 9.x does not preserve the leading
spaces in black line or dose not indent the blank line after exit editing.


Reproduce steps:

Launch emacs by `emacs -Q`, eval the following snippet(assumed org 9.x
is installed via elpa)

(package-initialize)
(require 'org)

open a org buffer, input the source by 
# there are 4 spaces before the '#' now

use C-c ' to close the source block buffer and back to org-mode, we can
see the first line of the block is indented 2 spaces by org while the blank
line
isn't.


​

Emacs  : GNU Emacs 25.1.1 (x86_64-apple-darwin16.3.0, Carbon Version 157
AppKit 1504.76)
 of 2016-12-23
Package: Org mode version 9.0.3 (9.0.3-elpa @
/Users/Yomisuko/.emacs.d/elpa/org-20161224/)

current state:
==
(setq
 org-tab-first-hook '(org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
 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-confirm-shell-link-function 'yes-or-no-p
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 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 '((closure
 (org-inlinetask-min-level buffer-face-mode-face org-mode-map
  org-tbl-menu org-org-menu org-struct-menu org-entities
  org-last-state org-id-track-globally org-clock-start-time
  texmathp-why remember-data-file
  org-agenda-tags-todo-honor-ignore-options iswitchb-temp-buflist
  calc-embedded-open-mode calc-embedded-open-formula
  calc-embedded-close-formula align-mode-rules-list
  org-emphasis-alist org-emphasis-regexp-components
  org-export-registered-backends org-modules
  org-babel-load-languages t)
 nil
 (add-hook (quote change-major-mode-hook) (quote org-show-block-all)
  (quote append) (quote local))
 )
#[0 "\300\301\302\303\304$\207"
  [add-hook change-major-mode-hook org-babel-show-result-all append
   local]
  5]
org-babel-result-hide-spec org-babel-hide-all-hashes)
 org-archive-hook '(org-attach-archive-delete-maybe)
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
 org-cycle-show-empty-lines
 org-optimize-window-after-visibility-change)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-link-parameters '(("id" :follow org-id-open)
  ("rmail" :follow org-rmail-open :store org-rmail-store-link)
  ("mhe" :follow org-mhe-open :store org-mhe-store-link)
  ("irc" :follow org-irc-visit :store org-irc-store-link)
  ("info" :follow org-info-open :export org-info-export :store
org-info-store-link)
  ("gnus" :follow org-gnus-open :store org-gnus-store-link)
  ("docview" :follow org-docview-open :export org-docview-export
:store org-docview-store-link)
  ("bibtex" :follow org-bibtex-open :store org-bibtex-store-link)
  ("bbdb" :follow org-bbdb-open :export org-bbdb-export
:complete org-bbdb-complete-link :store org-bbdb-store-link)
  ("w3m" :store org-w3m-store-link) ("file+sys") ("file+emacs")
  ("doi" :follow org--open-doi-link)
  ("elisp" :follow org--open-elisp-link)
  ("file" :complete org-file-complete-link)
  ("ftp" :follow
(lambda (path) (browse-url (concat "ftp:" path
  ("help" :follow org--open-help-link)
  ("http" :follow
(lambda (path) (browse-url (concat "http:" path
  ("https" :follow
(lambda (path) (browse-url (concat "https:" path
  ("mailto" :follow
(lambda (path) (browse-url (concat "mailto:; path
  ("message" :follow
(lambda (path) (browse-url (concat "message:" path
  ("news" :follow
(lambda (path) (browse-url (concat "news:; path
  ("shell" :follow org--open-shell-link))
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 )

Re: [O] Possible bug: Emacs hangs on (require 'org)

[Martin Zuther]

Hi!

About every third time I start Emacs, I also experience a very slow 
startup with org-mode 9.0.3 enabled.  I run "GNU Emacs 24.5.1 
(x86_64-pc-linux-gnu, GTK+ Version 3.18.9) of 2016-04-17 on lgw01-04, 
modified by Debian" on Linux Mint 18.1 Cinnamon.


Here is my minimal setup:

  ;;; Minimal setup to load latest 'org-mode'

  ;; activate debugging
  (setq debug-on-error t
debug-on-signal nil
debug-on-quit nil)

  ;; add latest org-mode to load path
  (add-to-list 'load-path "~/.emacs.d/elisp/org_9.0.3/lisp")
  (require 'org)

This bug is solved by disabling my network, but in contrast to Luke, I 
have access to a fast and stable network.


Normal startup time is below one second.  When the bug hits, it is 
around 2 minutes and 7 seconds, which to me looks suspiciously like a 
typical network timeout of 120 seconds.


Martin
--
www.mzuther.de
www.radix-musik.de

Re: [O] Bug: org-edit-special does not indent the blank line after exit editing [9.0.3 (9.0.3-elpa @ /Users/Yomisuko/.emacs.d/elpa/org-20161224/)]

[Jiajian Huang]

The issue is found in:
https://github.com/joaotavora/yasnippet/issues/761#issuecomment-270693995

On Fri, Jan 6, 2017 at 10:29 PM, Jiajian Huang  wrote:

> 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 mailing list.
> 
> Bug(maybe): org-edit-special under org 9.x does not preserve the leading
> spaces in black line or dose not indent the blank line after exit editing.
>
>
> Reproduce steps:
>
> Launch emacs by `emacs -Q`, eval the following snippet(assumed org 9.x
> is installed via elpa)
>
> (package-initialize)
> (require 'org)
>
> open a org buffer, input the source by 
> #+BEGIN_SRC python
>
> #+END_SRC
>
> use C-c ' to edit the block and input
>
> for i in range(10):  # input this line and 
> # there are 4 spaces before the '#' now
>
> use C-c ' to close the source block buffer and back to org-mode, we can
> see the first line of the block is indented 2 spaces by org while the
> blank line
> isn't.
>
>
> ​
>
> Emacs  : GNU Emacs 25.1.1 (x86_64-apple-darwin16.3.0, Carbon Version 157
> AppKit 1504.76)
>  of 2016-12-23
> Package: Org mode version 9.0.3 (9.0.3-elpa @
> /Users/Yomisuko/.emacs.d/elpa/org-20161224/)
>
> current state:
> ==
> (setq
>  org-tab-first-hook '(org-babel-hide-result-toggle-maybe
> org-babel-header-arg-expand)
>  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-confirm-shell-link-function 'yes-or-no-p
>  org-after-todo-state-change-hook '(org-clock-out-if-current)
>  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 '((closure
>  (org-inlinetask-min-level buffer-face-mode-face org-mode-map
>   org-tbl-menu org-org-menu org-struct-menu org-entities
>   org-last-state org-id-track-globally org-clock-start-time
>   texmathp-why remember-data-file
>   org-agenda-tags-todo-honor-ignore-options iswitchb-temp-buflist
>   calc-embedded-open-mode calc-embedded-open-formula
>   calc-embedded-close-formula align-mode-rules-list
>   org-emphasis-alist org-emphasis-regexp-components
>   org-export-registered-backends org-modules
>   org-babel-load-languages t)
>  nil
>  (add-hook (quote change-major-mode-hook) (quote org-show-block-all)
>   (quote append) (quote local))
>  )
> #[0 "\300\301\302\303\304$\207"
>   [add-hook change-major-mode-hook org-babel-show-result-all append
>local]
>   5]
> org-babel-result-hide-spec org-babel-hide-all-hashes)
>  org-archive-hook '(org-attach-archive-delete-maybe)
>  org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
>  org-cycle-show-empty-lines
>  org-optimize-window-after-visibility-change)
>  org-confirm-elisp-link-function 'yes-or-no-p
>  org-metadown-hook '(org-babel-pop-to-session-maybe)
>  org-link-parameters '(("id" :follow org-id-open)
>   ("rmail" :follow org-rmail-open :store org-rmail-store-link)
>   ("mhe" :follow org-mhe-open :store org-mhe-store-link)
>   ("irc" :follow org-irc-visit :store org-irc-store-link)
>   ("info" :follow org-info-open :export org-info-export :store
> org-info-store-link)
>   ("gnus" :follow org-gnus-open :store org-gnus-store-link)
>   ("docview" :follow org-docview-open :export org-docview-export
> :store org-docview-store-link)
>   ("bibtex" :follow org-bibtex-open :store org-bibtex-store-link)
>   ("bbdb" :follow org-bbdb-open :export org-bbdb-export
> :complete org-bbdb-complete-link :store org-bbdb-store-link)
>   ("w3m" :store org-w3m-store-link) ("file+sys") ("file+emacs")
>   ("doi" :follow org--open-doi-link)
>   ("elisp" :follow org--open-elisp-link)
>   ("file" :complete org-file-complete-link)
>   ("ftp" :follow
> (lambda (path) (browse-url (concat "ftp:" path
>   ("help" :follow org--open-help-link)
>   ("http" :follow
> (lambda (path) (browse-url (concat "http:" path
>   ("https" :follow
> (lambda (path) (browse-url (concat "https:" path
>   ("mailto" :follow
> (lambda (path) (browse-url (concat "mailto:; path
>   ("message" :follow
> (lambda (path) (browse-url (concat "message:" path
>   ("news" :follow
> (lambda (path) (browse-url (concat "news:; path
>   ("shell" :follow org--open-shell-link))
>  org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
>  )
>
>

Re: [O] transcluding some org-elements in multiple places

[Matt Price]

makes sense, will try to figure that out in the next couple of days.

On Thu, Jan 5, 2017 at 9:19 PM, John Kitchin 
wrote:

> It would be easy to have it export the plain text of the transcluded
> heading. to export the actual heading, I would setup a preprocessing hook
> that replaces the link with the content it points to.
>
> John
>
> On Thu, Jan 5, 2017 at 9:17 PM, Matt Price  wrote:
>
>>
>> Would be cool to somehow include in export. But that's a little too hard
>> for me to think about.  This is already pretty good. Thank you!
>>
>>
>
>

[O] org-ref: citation types (insert full citation); bib style; bib scope

[Matt Price]

After several years, I'm finally trying to move to bibtex from zotero,
partly because org-zotxt has stopped working for me (both link insertion
and html export seem at least temporarily broken).

The UI for org-ref is pretty fantastic, and I love it. I'm having trouble
getting the behaviour I want fro mthe actual links, though.  My needs may
be somewhat atypical but I'm hoping someone else has figured these
questions out already.

* citation types
The org-ref manual talks about different citation types, but the external
link it suggests is not loading:
http://ctan.unixbrain.com/macros/latex/contrib/natbib/natnotes.pdf

Does anyone know what the other options are? In particular, for the syllabi
I'm currently creating I'd like to just insert the org-formatted citation
information itself -- is this possible? I'd like to be able to point my
students directly to my github repo, and it will ultimately be more
convenient to have the links already present in the source code, since
github doesn't reoslve org-ref

* bib style
When I right-click on a link and select "copy the formatted citation", I
don't get the URL field, which my students need. I assume that's because
I'm not using the right bibliographic style. How do I set the citation
format?  Would I use the bibliographystyle link, or a header argument
somewhere?

Also, is it possible to set this option to use org formatting instead of
html formatting?

* Bibliography scope
I guess I don't really know how to build a bibliographic file to go with a
particular project.  At present I am using my full Zotero library exported
to bibtex as a default. Is there a way to just build the bibliography from
the set of sources cited in the paper?

Thanks everyone, and of course especially John for this amazing tool.

Matt

[O] [bug] Tests: 4 unexpected results

[Marco Wahl]

Hello,

With the current master

#+begin_src shell
make test
#+end_src

results in

#+begin_quote
4 unexpected results:
   FAILED  test-org-list/move-item-down
   FAILED  test-org-list/move-item-up
   FAILED  test-org/custom-properties
   FAILED  test-org/forward-paragraph
#+end_quote

This looks like an issue with checking visibility of a location.

(version)"GNU Emacs 26.0.50.1 (x86_64-unknown-linux-gnu, GTK+ Version
3.22.5) of 2017-01-04"

BTW I don't know how to fix this reasonably.


Best regards

   Marco

Re: [O] speeding up Babel Gnuplot

[Nicolas Goaziou]

Hello,

Thierry Banel  writes:

> By "going through the table" I mean going through this structure.
> Remember the issue in the first place was a slow conversion of this
> huge structure into a temporary file. Now we need to convert this huge
> structure into a hash. Ok, let us assume hashing is faster than
> writing to disk.

Converting this huge structure into a temporary file is (relatively)
slow because of `orgtbl-to-generic', isn't it? Computing the hash
doesn't call this function.

Why do you expect computing the hash to be slow?

Regards,

-- 
Nicolas Goaziou

Re: [O] [export] Markdown - Exporting headings

[Nicolas Goaziou]

Hello,


sergio ruiz  writes:

> For some reason, when I export headings under over 2 deep, I get an 
> unexpected  markdown export. For example:
>
> * First header
> ** second level
> *** Third level
>  Fourth level
>
>
> gives me:
>
> First header
> 
>
> second level
> 
>
> 1.  Third level
>
>     1.  Fourth level
>
>
> ideas?

This is a limitation of Mardown syntax. See

  (info "(org) Markdown export")

and `org-md-headline-style' variable.

Regards,

-- 
Nicolas Goaziou