Re: [O] Open Peer-Review Reproducible Publication with Org and GRASS

[Samuel Wales]

On 6/3/16, Ken Mankoff  wrote:
> My
> goal was to create not just an open access publication, but a fully
> reproducible publication. This is an early announcement, and the paper may
> not pass peer review.

thank you, sincerely, for acting to help fix one of science's serious crises.

this stuff matters.  in biomedicine and related academic fields, it
matters profoundly.

ok, back to org/grass talk.

-- 
The Kafka Pandemic: http://thekafkapandemic.blogspot.com

The disease DOES progress.  MANY people have died from it.  And
ANYBODY can get it.

Denmark: free Karina Hansen NOW.

Re: [O] Open Peer-Review Reproducible Publication with Org and GRASS

[Daniele Pizzolli]

On Fri, Jun 03 2016, Ken Mankoff wrote:

> Hi Org and GRASS lists,
>
> I just wanted to let these two lists know that I've just posted a
> paper written in Org and using GRASS (text-mode) and Python for the
> analysis. My goal was to create not just an open access publication,
> but a fully reproducible publication. This is an early announcement,
> and the paper may not pass peer review.

Hello Ken,

Thanks for sharing, I had only a brief look.  In the meantime some
early thoughts while it downloads the data.

[]

> To make it easier to reproduce... including my emacs.org seems
> overkill. Including a Virtual Machine that contains everything,
> including my ~/.emacs.d/ and all the software and data seems like the
> right thing to do, but journals don't want to host a 20 GB VM with the
> publication.

Well, you need only the recipe to build the VM.  Fortunately there are
a lot of tools that help to do this.  Unfortunately there are too
many, and not all of them focus on the reproducible side...

In the meantime I saw few main problems in your current document:

- No "One build step"
- Hardcoded path, for example
  root = "/Users/mankoff/Documents/Papers/B/Brinkerhoff/"
- I did not found the Grass installation part, I guess I will have an
  error later...
- Missing latex toolchain installation

Are you interested in fixing those issues?  If yes please share your
progress or ideas.

Best,
Daniele

Re: [O] Open Peer-Review Reproducible Publication with Org and GRASS

[Daniele Pizzolli]

On Fri, Jun 03 2016, Brett Viren wrote:

> Thanks for your example.
>
> A few ideas:
>
> - When you begin developing your paper, or sometime before submission,
>   make a break from your personal ~/.emacs.d/ environment and begin
>   processing the .org in an explicitly configured Emacs session.  Submit
>   the needed, minimal, paper-specific Emacs setup as part of the
>   supplementary material.
>
> - Bundle the document building into a shell script which calls Emacs so
>   that you can assure that personal ~/.emacs.d/ is excluded and only the
>   paper-specific Emacs setup is used.  It also helps users to rebuild
>   the paper, especially if they may not yet be Emacs aficionados.

Hello,

nice, but I suggest to start from scratch in a Virtual Machine.

I am currently trying to develop a generic extensible template for
this.

Right now I did only custom tailored installation.

When I have something interesting I will share it.  In the meantime I
will follow thread related to this topic closely!

> - Instead of multi-GB VM image, provide a few kB Dockerfile which can be
>   used to build a Linux container with base OS and all required
>   applications needed to run the Babel code blocks.
>
> - The Dockerfile could go so far as to create a user account, get the
>   supplementary material from a repository or the publisher's web page,
>   unpack and run the shell script which calls Emacs to build the
>   document.  If you go this far then in principle just this Dockerfile
>   is enough to reproduce the paper - but this will rely on some binaries
>   to remain available (Docker base OS images and OS packages).
>
> The reliance on long-term availability of the Docker base OS image and
> binary packages is problematic for long term automated reproducibility.
> However, even after those bits disappear from the 'net the Dockerfile
> serves as a concise and explicit recipe for future humans to follow.

I think that using debian only packages and the debian archive you
will be able to reproduce the environment with few effort in the
future, but I did not ever tried hard.

I will suggest to use are Vagrant rather than Docker (because it is
simpler to star, expressive enough, supports free software only
provider (like libvirt)) and some shell scripts or ansible playbooks.

I do not know the licence of the data, but I suggest to make at least
one private mirror and use a variable to switch between the two.

You may also want to verify sha256sum and/or gpg signatures on the
data and on the code (that should be hosted using a source code
management system).

Best,
Daniele

Re: [O] org export of source code indentation issue with 8 spaces

[Dennis van Dok]

On 06-06-16 18:16, Charles C. Berry wrote:

> You want `#+BEGIN_SRC sh -i' to preserve indentation. See:
> 
> (info "(org) Literal examples")

Indeed. I was looking at older docementation :-/

Thanks,

Dennis

Re: [O] org export of source code indentation issue with 8 spaces

[Charles C. Berry]

On Mon, 6 Jun 2016, Dennis van Dok wrote:


Hi,

not sure what is causing this, but whenever I use source blocks
any indentation beyond 8 spaces seem to go wrong.

The most basic example:

#+BEGIN_SRC sh
 this
   is
 indented
   more and
 more
#+END_SRC


You want `#+BEGIN_SRC sh -i' to preserve indentation. See:

(info "(org) Literal examples")


HTH,

Chuck

[O] How to export org file into mobi or azw3 file?

[童俊翔]

Re: [O] flycheck orgmode on windows invalid output file name

[Eli Zaretskii]

> From: Guido Van Hoecke 
> Date: Mon, 6 Jun 2016 08:43:00 +0200
> Cc: help-gnu-emacs , orgmode 
> 
> >> Still, when editing elisp blocks from my elisp.org files, I keep
> >> hitting the '*' problem...
> >
> > What is "the '*' problem", exactly?
> >
> Filenames with '*'.

But I thought my suggested change fixed that, as the file names no
longer have '*'.  Right?

> Flycheck member lunaryorn accepted to implement your
> convert-standard-filename suggestion and implemented it in master.
> 
> Thanks again Eli.

You are welcome.

[O] org export of source code indentation issue with 8 spaces

[Dennis van Dok]

Hi,

not sure what is causing this, but whenever I use source blocks
any indentation beyond 8 spaces seem to go wrong.

The most basic example:

#+BEGIN_SRC sh
  this
is
  indented
more and
  more
#+END_SRC

exporting to ASCII gets me

,
| this
|   is
| indented
|   more and
|   more
`

As you can see the last 'more' aligns with the one above in
the output.

Anyone else see this or is it just me?

Thanks,

Dennis
-- 
D.H. van Dok :: System administrator :: www.nikhef.nl/grid ::
Phone +31 20 592 22 28 :: http://www.nikhef.nl/~dennisvd/

[O] Could org-babel-process-file-name support cygwin environment?

[Xi Shen]

Hi,

I have been using the latest version of the Emacs in cygwin
environment for a long time. Recently, I want to use the sql source
environment in the org-mode.

But I got some error from the "osql" tool on Windows environment. I
did some investigation, and I believe it is because this tool cannot
handle the input and output path Emacs handled to it in Unix form.

I checked the code,
https://github.com/jwiegley/org-mode/blob/fdd9b18598239dd0e8b18383ac930110d51ed22e/lisp/ob-sql.el#L115,
it will directly pass the path generated from
"org-babel-process-file-name" to osql, but
"org-babel-process-file-name" did not take cygwin environment into
account neither.

I think it would be very helpful if the "org-babel-process-file-name"
check the cygwin environment, and map the path using the "cygpath"
tool beforehand.


Thanks,
David

Re: [O] Open Peer-Review Reproducible Publication with Org and GRASS

[Christian Moe]

This is really interesting on several levels. Thanks for posting.

Yours,
Christian

Ken Mankoff writes:

> Hi Org and GRASS lists,
>
> I just wanted to let these two lists know that I've just posted a paper 
> written in Org and using GRASS (text-mode) and Python for the analysis. My 
> goal was to create not just an open access publication, but a fully 
> reproducible publication. This is an early announcement, and the paper may 
> not pass peer review.
>
> The Supplemental Material is the Org file with all the code to generate the 
> document, beginning with downloading the 3rd party data that is input to our 
> analysis, the GRASS code to perform the analysis, and the Python code to 
> regenerate the figures.
>
> I don't think I did a great job on the reproducible part because I have a 
> highly customized .emacs, etc. All the information necessary to replicate the 
> work should be in the Supplemental Material, but it might not be easy to do 
> so. Anyway, I think it is a step in the right direction.
>
> To make it easier to reproduce... including my emacs.org seems overkill. 
> Including a Virtual Machine that contains everything, including my 
> ~/.emacs.d/ and all the software and data seems like the right thing to do, 
> but journals don't want to host a 20 GB VM with the publication.
>
> Thanks to people on these two lists who have developed the software and 
> helped me use it.
>
>-k.
>
> http://www.the-cryosphere-discuss.net/tc-2016-113/

Re: [O] ob-csharp

[Rasmus]

thomas  writes:

> Hi,
>
> I'm sorry, I could not find the time yet to figure out how to
> "officially" contribute to Emacs (the papers are signed, though).

See here:

http://orgmode.org/worg/org-contribute.html

-- 
Tack, ni svenska vakttorn. Med plutonium tvingar vi dansken på knä!

Re: [O] ob-csharp

[thomas]

Hi,

I'm sorry, I could not find the time yet to figure out how to 
"officially" contribute to Emacs (the papers are signed, though).


In the meantime you can find ob-csharp on github:

https://github.com/thomas-villagers/ob-csharp

- thomas



On 07.09.2015 19:23, thomas wrote:

Hi,

could not find ob-csharp in org mode. I created one to make the pointy 
haired boss happy.


It's based on Eric's ob-java.el with some bits taken from other ob files.

It works for the simple examples following below.

Hope this is useful and I'm open for hints to improve the code.

- thomas



* ob-csharp Tests

** Hello World

#+BEGIN_SRC csharp
class HelloWorld {
  public static void Main()
  {
System.Console.WriteLine("Hello World!");
  }
}
#+END_SRC

#+RESULTS:
: Hello World!



** Tables

#+BEGIN_SRC csharp
class Table {
  public static void Main()
  {
for (char  c = 'a'; c < 'd'; c++)
  System.Console.Write("{0} ",c);
System.Console.WriteLine();
for (int i = 0; i < 3; i++)
  System.Console.Write("{0} ",i);
  }
}
#+END_SRC

#+RESULTS:
| a | b | c |
| 0 | 1 | 2 |

** Compiler flags and command line args

#+BEGIN_SRC csharp :cmpflag -warnaserror+
public class TestFlags {
  public static void Main()
  {
   int i;  // unused; throw error
   System.Console.WriteLine("You won't see this!");
  }
}
#+END_SRC

#+RESULTS:

#+BEGIN_SRC csharp :results verbatim  :cmdline --version
public class TestCmd {
  public static void Main()
  {
   System.Console.WriteLine("You won't see this!");
  }
}
#+END_SRC

#+RESULTS:
#+begin_example
Mono JIT compiler version 3.2.8 (Debian 3.2.8+dfsg-10)
Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. 
www.mono-project.com

TLS:   __thread
SIGSEGV:   altstack
Notifications: epoll
Architecture:  amd64
Disabled:  none
Misc:  softdebug
LLVM:  supported, not enabled.
GC:sgen
#+end_example

Re: [O] flycheck orgmode on windows invalid output file name

[Guido Van Hoecke]

On 6 June 2016 at 04:29, Eli Zaretskii  wrote:
>> From: Guido Van Hoecke 
>> Date: Sun, 5 Jun 2016 21:41:18 +0200
>> Cc: help-gnu-emacs , orgmode 
>>
>> For testing i went to change flycheck-temp-file-system in flycheck.el
>> so that it reads
>>
>> (setq tempfile (convert-standard-filename (expand-file-name
>> (file-name-nondirectory filename)
>>directory)))
>>
>> rather than the original
>>
>> (setq tempfile (expand-file-name (file-name-nondirectory filename)
>>directory))
>>
>> I than edebugged the flycheck-temp-file-system with the
>> "c:/Users/guivh/emacs-guivho/.flycheck_emacs-guivho.org[*Org Src
>> emacs-guivho.org[ emacs-lisp ]*]") filename, and it nicely produced a
>> tempfile where the '*'s are replaced by '!'s.
>>
>> Still, when editing elisp blocks from my elisp.org files, I keep
>> hitting the '*' problem...
>
> What is "the '*' problem", exactly?
>
Filenames with '*'.
Flycheck member lunaryorn accepted to implement your
convert-standard-filename suggestion and implemented it in master.

Thanks again Eli.

Guido