Re: example paper written in org completely

[Uwe Brauer]

>>> "ESF" == Eric S Fraga  writes:

> On Thursday, 17 Jun 2021 at 18:33, Uwe Brauer wrote:
>> [1]  truth being told, a lot of mathematicians and I think physicists
>> don't upgrade very frequently so it might have been a
>> compatibility issue.  

> Funnily enough, just in the past hour or so, I ended up in panic
> mode.  I rely on one commercial software (not by choice).  I knew I had
> an up to date licence but the software insisted that I did not have a
> licence.  Turns out that the actual software itself was umpteen years
> old and I needed a newer version of the software (which I could
> download) to use with the updated licence (and of course the old licence
> had expired).

> Downloaded new version and everything is working.


I wonder what that software might be ;-)


> However, I work on a "if it ain't broke, don't fix it" approach.  And
> that's why I don't like commercial closed software reason #381.

> Time for a beer. ;-)

Cheers 


smime.p7s
Description: S/MIME cryptographic signature

BUG: org-table: table option “:missing” not working (in ob-gnuplot.el)

[Robert Klein]

Hi everyone,
 a bug report:


Emacs  : GNU Emacs 27.2 (build 1, x86_64-unknown-openbsd, GTK+ Version 2.24.33)
 of 2021-04-20
Package: Org mode version 9.4.6 (release_9.4.6-4-g093c94 @ 
/home/roklein/.emacs.d/org-mode/lisp/)


When trying to run a table with missing values with ob-gnuplot.el
there's a “:missing value” option.  ob-gnuplot is supposed to put the
“value” into the place of empty cell values before calling on gnuplot.
It doesn't do this currently.  Bi-secting suggests,
“9209aa3c9d456bcfdd9d8cd223367f7cfb6b3231 is the first bad commit”:

--  commit 9209aa3c9d456bcfdd9d8cd223367f7cfb6b3231
--  Author: Nicolas Goaziou 
--  --  Sun Aug 24 01:31:56 2014 +0200
--
--  org-table: Use "ox.el" internally for radio tables


By my reading:
- in ob-gnuplot.el:org-babel-gnuplot-process-vars :missing variable is
  read, used in
- ob-gnuplot.el:org-babel-gnuplot-quote-tsv-field, called from
- ob-gnuplot.el:org-babel-gnuplot-table-to-data
- used in org-table.el:orgtbl-to-generic (as (part of the) :fmt param)
- which calls org-table--to-generic-cell
- which calle org-table.el:org-table--generic-apply
- which I don't understand

my dotemacs and a sample org file are attached.

When running the code (e.g. C-c C-c on the #+Call: line), temporary
files are created in /tmp/babel-/gnuplot.

These files should have "?" (as choosen :missing).  In the current
version there is nothing, so gnuplot uses up the values in the following
columns and the resulting graph is wrong.

Also, I couldn't find this in the manual, but there's a thread “using
gnuplot's "splot" and "every" comma nds on org-mode table” on the
mailing list (2013/09/23 - 3013/09/25) about the :missing feature.

Thanks for any help.

Best regards
Robert



gp.org
Description: Binary data


dotemacs
Description: Binary data

algorithm capabilities for org-mode

[Christopher Dimech]

There exists the algorithmicx package on https://ctan.org/pkg/algorithmicx
that people use.  But it comes under the "LaTeX Project Public License".

It was done Szász János and released in 2005, but is today inactive.

It would be beneficial if org-mode could have similar functionality
for algorithms as a built-in capability.



- Christopher Dimech
Administrator General - Naiad Informatics - Gnu Project

Society has become too quick to pass judgement and declare someone
Persona Non-Grata, the most extreme form of censure a country can
bestow.

In a new era of destructive authoritarianism, I support Richard
Stallman.  Times of great crisis are also times of great
opportunity.  I call upon you to make this struggle yours as well !

https://stallmansupport.org/
https://www.fsf.org/ https://www.gnu.org/

Re: Problem inserting meeting in agenda using "pm" time indicators

[Nicolas Goaziou]

Hello,

Ihor Radchenko  writes:

> Eric S Fraga  writes:
>> When I try this now, with org up to date from git, I get this backtrace:
>>
>> ,
>> | Debugger entered--Lisp error: (error "Invalid duration format: \"3pm\"")
>
> Confirmed

Fixed

(hopefully)

Regards,
-- 
Nicolas Goaziou

Re: BUG: export options properties drawer position and planning dates

[Nicolas Goaziou]

Hello,

Michael Dauer  writes:

> Yes, you're right. The problem was with my sample. Forget about my 2.
>
> Any ideas how I can specify the inclusion of planning dates specifically on
> sub-tree level (not just once for the whole export) without custom exporter
> or export filter?

I think you cannot without using those tools.

Regards,
-- 
Nicolas Goaziou

example paper written in org completely

[Christopher Dimech]

The algorithmicx latex package has a very annoying licence, the LaTeX Project 
Public License.  Although a free software license, it incompatible with the GPL 
with many requirements.


- Christopher Dimech
Administrator General - Naiad Informatics - Gnu Project

Society has become too quick to pass judgement and declare someone
Persona Non-Grata, the most extreme form of censure a country can
bestow.

In a new era of destructive authoritarianism, I support Richard
Stallman.  Times of great crisis are also times of great
opportunity.  I call upon you to make this struggle yours as well !

https://stallmansupport.org/
https://www.fsf.org/ https://www.gnu.org/


> Sent: Friday, June 18, 2021 at 5:04 AM
> From: "Christopher Dimech" 
> To: "Eric S Fraga" 
> Cc: "Emacs Org mode mailing list" 
> Subject: example paper written in org completely
>
> > Sent: Friday, June 18, 2021 at 4:42 AM
> > From: "Eric S Fraga" 
> > To: "Christopher Dimech" 
> > Cc: "Emacs Org mode mailing list" 
> > Subject: Re: example paper written in org completely
> >
> > On Thursday, 17 Jun 2021 at 18:31, Christopher Dimech wrote:
> > > Hi Eric, could you provihe examples on how to write equations in org.
> > > Does org accept both tex and latex commands?
> >
> > If you look at the org file I mentioned (link in signature), you'll see
> > several examples of LaTeX equations in org.
>
> I can see paper.org on more inspection, thank you.
>
> > I don't use TeX directly, only LaTeX.
>
> It is a good thing that one does not have to specify tex or latex blocks
> to export in html using mathjax.
>
> Used to think that tex or latex blocks were necessary.
>
>
>
> > --
> > : Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-551-gf70e36
> > : Latest paper written in org: https://arxiv.org/abs/2106.05096
> >
>
>

example paper written in org completely

[Christopher Dimech]

> Sent: Friday, June 18, 2021 at 4:42 AM
> From: "Eric S Fraga" 
> To: "Christopher Dimech" 
> Cc: "Emacs Org mode mailing list" 
> Subject: Re: example paper written in org completely
>
> On Thursday, 17 Jun 2021 at 18:31, Christopher Dimech wrote:
> > Hi Eric, could you provihe examples on how to write equations in org.
> > Does org accept both tex and latex commands?
>
> If you look at the org file I mentioned (link in signature), you'll see
> several examples of LaTeX equations in org.

I can see paper.org on more inspection, thank you.

> I don't use TeX directly, only LaTeX.

It is a good thing that one does not have to specify tex or latex blocks
to export in html using mathjax.

Used to think that tex or latex blocks were necessary.



> --
> : Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-551-gf70e36
> : Latest paper written in org: https://arxiv.org/abs/2106.05096
>

Re: example paper written in org completely

[Eric S Fraga]

On Thursday, 17 Jun 2021 at 18:31, Christopher Dimech wrote:
> Hi Eric, could you provihe examples on how to write equations in org.
> Does org accept both tex and latex commands?

If you look at the org file I mentioned (link in signature), you'll see
several examples of LaTeX equations in org.

I don't use TeX directly, only LaTeX.

-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-551-gf70e36
: Latest paper written in org: https://arxiv.org/abs/2106.05096

Re: example paper written in org completely

[Eric S Fraga]

On Thursday, 17 Jun 2021 at 18:33, Uwe Brauer wrote:
> [1]  truth being told, a lot of mathematicians and I think physicists
>  don't upgrade very frequently so it might have been a
>  compatibility issue.  

Funnily enough, just in the past hour or so, I ended up in panic
mode.  I rely on one commercial software (not by choice).  I knew I had
an up to date licence but the software insisted that I did not have a
licence.  Turns out that the actual software itself was umpteen years
old and I needed a newer version of the software (which I could
download) to use with the updated licence (and of course the old licence
had expired).

Downloaded new version and everything is working.

However, I work on a "if it ain't broke, don't fix it" approach.  And
that's why I don't like commercial closed software reason #381.

Time for a beer. ;-)

-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-551-gf70e36
: Latest paper written in org: https://arxiv.org/abs/2106.05096

Re: example paper written in org completely

[Uwe Brauer]

>>> "GM" == Greg Minshall  writes:

> Eric,
> thanks very much for sharing.  it's nice that you also provide the .org
> file on arXiv -- good marketing material!  :) ah, and mention in the
> code appendix.  it's very useful to have the .org file as a model of how
> to do various things.

> i don't know if this is you, or is arXiv, but the ancillary files
> ("details" on the main page) claims to get .tar.gz (and, indeed,
> downloads as a .tar.gz file) but is, in fact, an uncompressed .tar file.

That is a arXiv thing. Let's put it this way: they don't rely on very
modern software (it took them ages to get a recent texlive version)[1]

Uwe Brauer 


Footnotes:
[1]  truth being told, a lot of mathematicians and I think physicists
 don't upgrade very frequently so it might have been a
 compatibility issue.  



smime.p7s
Description: S/MIME cryptographic signature

example paper written in org completely

[Christopher Dimech]

Hi Eric, could you provihe examples on how to write equations in org.
Does org accept both tex and latex commands?

- Christopher Dimech
Administrator General - Naiad Informatics - Gnu Project

Society has become too quick to pass judgement and declare someone
Persona Non-Grata, the most extreme form of censure a country can
bestow.

In a new era of destructive authoritarianism, I support Richard
Stallman.  Times of great crisis are also times of great
opportunity.  I call upon you to make this struggle yours as well !

https://stallmansupport.org/
https://www.fsf.org/ https://www.gnu.org/


> Sent: Friday, June 18, 2021 at 12:06 AM
> From: "Eric S Fraga" 
> To: "Emacs Org mode mailing list" 
> Subject: example paper written in org completely
>
> Dear all,
>
> for those that may be interested, my latest paper (well, preprint at
> this stage) is available if you are looking for an example of a
> numerical work where the paper is completely written in org, including
> data analysis and visualisation.  See signature for link.
>
> The arxiv deposit includes the complete org file as an ancillary file.
> --
> : Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-551-gf70e36
> : Latest paper written in org: https://arxiv.org/abs/2106.05096
>
>

Re: misaligned tab and spaces in src block

[Michael Dauer]

Hi Tim,

indent-tabs-mode was exactly what I was looking for.

Thank you,
Michael

Am Di., 25. Mai 2021 um 04:39 Uhr schrieb Tim Cross :

>
> Michael Dauer  writes:
>
> > Hi,
> >
> > #+begin_src elisp :results output
> > (aaa
> >  bbb (
> > #x09#x09#x09ccc))
> >   ccc
> > #+end_src
> > looks like this in the editor
> > (aaa
> >  bbb (
> > ccc))
> >   ccc
> >
> > Line 1-3 were indented automatically by pressing Tab. In line 4 I
> inserted 6 spaces manually. This is what I would expect to find in line 3
> too. But at my
> > surprise there are 3 tab chars in line 3. Line 2 was indented
> automatically with 1 space.
> >
> > 1. So why is line 3 indented with 3 tabs instead of 6 spaces?
> > 2. How can I prevent this?
> > 3. Why does a tab have a width between 1 and 2 spaces?
> > 4. How can I prevent this misalignment?
> >
> >I don't understand what  org-block face has fixed-pitch.
> >
> > Org mode version 9.4.6 (9.4.6-gcf30f7
> > (setq-default tab-width 2)
> > (setq org-src-fontify-natively t
> > org-src-window-setup 'current-window
> > org-src-strip-leading-and-trailing-blank-lines t
> > org-src-preserve-indentation t
> > org-src-tab-acts-natively t)
> >
>
> Are you editing the source block using org-edit-special (C-c ,)? If not,
> then you are not editing the source block with the correct syntax for
> elisp and this will throw out auto formatting.
>
> Your example block is invalid elisp code which is
> #+begin_src elisp :results output
>   (aaa
>bbb (
> #x09#x09#x09ccc))
>   ccc
> #+end_src
>
> but I don't see how you can get any output as it is not valid elisp. It
> is not clear to me what you are trying to do. You have 3 tab characters
> (#x09), so don't see why you would expect them to be spaces?
>
> If what you want is for hitting tab to insert only spaces, have a look
> at the variable indent-tab-mode. You can, for example, do
>
> (setq-default indent-tab-mode nil)
>
> to force use of spaces instead of tabs. However, be careful about doing
> this globally if you also want to contribute to projects where tabs are
> used as this will cause havoc with diffs and git. You can also set this
> on a per language (via mode hooks) or per project (via local variables).
>
> To get a better feel for how language modes align code etc, you really
> need to make sure the code you are trying to align is syntactically
> valid and you are using the correct coding style for the language.
> --
> Tim Cross
>
>
> --
> Confidentiality Notice:This email and any attachments it may contain are
> intended for the individual or entity above and may be confidential and
> protected by legal privilege. SmartPM Technologies, Inc. makes no
> warranties, express or implied, concerning the accuracy of the information
> contained herein, which is subject to change without notice. Unintended
> recipients should be aware that use of this e-mail or any of its
> attachments in any way is forbidden.
>

Calling code block from header in agenda

[Ken Mankoff]

Hello,

I'd like to `ctrl-c ctrl-c` on a TODO section header in the agenda and have a 
code block execute. Is this possible?

Outside the agenda I can CC on part of this header (the src_bash{date} part) 
and it evaluates. Elsewhere it asks for tags as usual.

** TODO foo src_bash{date}

In the agenda, it asks for tags regardless of where I CC.

I don't need the src_bash in the headline, but it seems like a security issue 
to have org-babel-execute-subtree invoked from the agenda. I figure someone 
could add src_elisp{(org-babel-execute-subtree)} to the headline if they need 
that.

  -k.

Re: example paper written in org completely

[Eric S Fraga]

On Thursday, 17 Jun 2021 at 16:38, Greg Minshall wrote:
> it's nice that you also provide the .org file on arXiv -- good
> marketing material!  :) ah, and mention in the code appendix.  

Thank you.  Credit where credit is due!  

I wanted to reference both org and Emacs in some way, not to mention
Eric Schulte et al.'s paper on using org for literate
programming.  These have all changed, dramatically for the better, how I
undertake my research.  So much has been made about org's time
management aspects in the wider community, which I do use extensively,
but less about the support in org but also Emacs for actual writing and
it is this support that is the killer feature for me.

-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-551-gf70e36
: Latest paper written in org: https://arxiv.org/abs/2106.05096

Re: example paper written in org completely

[Eric S Fraga]

On Thursday, 17 Jun 2021 at 16:38, Greg Minshall wrote:
> i don't know if this is you, or is arXiv, but the ancillary files
> ("details" on the main page) claims to get .tar.gz (and, indeed,
> downloads as a .tar.gz file) but is, in fact, an uncompressed .tar file.

Not me.  I uploaded the files following whatever instructions they gave
me.  I believe that I had the option of uploading either .tar or .tar.gz
and chose the former (as the files are not large).  Maybe the web site
is not quite consistent with what they ask of authors.

-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-551-gf70e36
: Latest paper written in org: https://arxiv.org/abs/2106.05096

Re: BUG: export options properties drawer position and planning dates

[Michael Dauer]

Yes, you're right. The problem was with my sample. Forget about my 2.

Any ideas how I can specify the inclusion of planning dates specifically on
sub-tree level (not just once for the whole export) without custom exporter
or export filter?

thx
m


Am Di., 15. Juni 2021 um 17:05 Uhr schrieb Nicolas Goaziou <
m...@nicolasgoaziou.fr>:

> Hello,
>
> Michael Dauer  writes:
>
> 
>
> [...]
>
> 
>
> I think we are mis-communicating. I saw the document you're re-posting.
> My question, however, is about the specific part demonstrating the
> following:
>
> >> > 2. This actually works when the scheduled date is (incorrectly) placed
> >> > below the drawer. It is not just treated as the first paragraph, but
> >> > omitted when the with-planning property of its node is nil, while
> normal
> >> > text would be exported.
>
> I'm trying to reproduce this, so I need minimal example, with
> instruction.
>
> Regards,
> --
> Nicolas Goaziou
>

Re: example paper written in org completely

[Samuel Banya]

Wow, that example with 3D modeling, aka "Laurana_tex.zip 
" is absolutely insane.

That's amazing!

I mention this because I like doing art on the side, and am getting into 
Blender just to produce reference images for sketching, etc. and find that 
fascinating that you could literally embed 3D models into a TeX document:
http://tug.org/texshowcase/

On Thu, Jun 17, 2021, at 8:06 AM, Eric S Fraga wrote:
> Dear all,
> 
> for those that may be interested, my latest paper (well, preprint at
> this stage) is available if you are looking for an example of a
> numerical work where the paper is completely written in org, including
> data analysis and visualisation.  See signature for link.
> 
> The arxiv deposit includes the complete org file as an ancillary file.
> -- 
> : Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-551-gf70e36
> : Latest paper written in org: https://arxiv.org/abs/2106.05096
> 
> 

Re: example paper written in org completely

[Greg Minshall]

Eric,

thanks very much for sharing.  it's nice that you also provide the .org
file on arXiv -- good marketing material!  :) ah, and mention in the
code appendix.  it's very useful to have the .org file as a model of how
to do various things.

i don't know if this is you, or is arXiv, but the ancillary files
("details" on the main page) claims to get .tar.gz (and, indeed,
downloads as a .tar.gz file) but is, in fact, an uncompressed .tar file.

cheers, Greg

Re: Bug: Duplicate logbook entry for repeated tasks [9.4.6 (9.4.6-gab9f2a @ /home/gustavo/.emacs.d/elpa/org-9.4.6/)]

[Gustavo Barros]

Hi Jeff,

On Wed, 16 Jun 2021 at 23:22, Jeff Kowalski  
wrote:


I can confirm the same is happening here for me with Org mode version 
9.4.6

(9.4.6-4-g093c94-elpa @ /home/jeff/.emacs.d/elpa/org-20210607/) on GNU
Emacs 28.0.50 (build 1, x86_64-pc-linux-gnu, GTK+ Version 3.24.20, 
cairo

version 1.16.0) of 2021-06-16
The duplicate LOGBOOK entries also seem to be messing up the graphical
display of habit records in the agenda.  Deleting the duplicates 
returns
the habit display to expected output.  I'd be happy to share details 
of
that symptom, but the root cause seems to clearly be the duplicates in 
the

LOGBOOK


Thanks for confirming and for the habits info.  So that's what was 
happening with my consistency graphs.  I had indeed been noticing they 
felt "off", but I eventually reverted to 9.4.4 because of the duplicate 
entries and forgot about it.  It seems then that this got solved for me 
not by the reverting itself but by me removing the duplicate entries in 
the LOGBOOK.


Would clocking reports be affected too? (I'm not personally an user of 
clocking, so I don't really know).


Perhaps a "lint" for LOGBOOK duplicates would be a good idea alongside 
with the fix, so that people could go about fixing their data with a 
little more convenience?


Best regards,
Gustavo.

Re: example paper written in org completely

[Juan Manuel Macías]

Hi Eric,

Eric S Fraga writes:

> Dear all,
>
> for those that may be interested, my latest paper (well, preprint at
> this stage) is available if you are looking for an example of a
> numerical work where the paper is completely written in org, including
> data analysis and visualisation.  See signature for link.
>
> The arxiv deposit includes the complete org file as an ancillary file.

Congratulations. Thanks for sharing your work.

By the way, I think it would be nice to create on the Worg website a
section called "Org Showcase" or similar, just like there is a "Tex
Showcase" on the Tex User Group website: http://tug.org/texshowcase/,
with samples of published books, articles or web pages, all written in
Org, to demonstrate the productivity of Org Mode.

What do you think?

Best regards,

Juan Manuel 

example paper written in org completely

[Eric S Fraga]

Dear all,

for those that may be interested, my latest paper (well, preprint at
this stage) is available if you are looking for an example of a
numerical work where the paper is completely written in org, including
data analysis and visualisation.  See signature for link.

The arxiv deposit includes the complete org file as an ancillary file.
-- 
: Eric S Fraga via Emacs 28.0.50, Org release_9.4.6-551-gf70e36
: Latest paper written in org: https://arxiv.org/abs/2106.05096