restarting an org-babel session?

restarting an org-babel session?

[John Kitchin]

Hi all,

Is it possible to restart an org-babel session from the current point?
What I mean is if you have a largish org-file with many session blocks,
and you want to go the end and continue it, you need to run each session
block before the end to recreate the "session".

I have a little function that does that more or less, but it seemed like
a common enough need that it might already exist.

thanks,
--
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: restarting an org-babel session?

[Ken Mankoff]

On 2015-03-19 at 10:26, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
> Is it possible to restart an org-babel session from the current point?
> What I mean is if you have a largish org-file with many session blocks,
> and you want to go the end and continue it, you need to run each session
> block before the end to recreate the "session".

I am surprised there is no easy way to have an Org file run every code block in order either on command or on export. It seems like this would be a key component of reproducible research and literate documents.

Maybe there is a way, but it isn't mentioned in the "Evaluating code blocks" section of the manual.

  -k.
  

Re: restarting an org-babel session?

[Thomas S. Dye]

Ken Mankoff <mankoff@gmail.com> writes:

> On 2015-03-19 at 10:26, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
>> Is it possible to restart an org-babel session from the current point?
>> What I mean is if you have a largish org-file with many session blocks,
>> and you want to go the end and continue it, you need to run each session
>> block before the end to recreate the "session".
>
> I am surprised there is no easy way to have an Org file run every code
> block in order either on command or on export. It seems like this
> would be a key component of reproducible research and literate
> documents.
>
> Maybe there is a way, but it isn't mentioned in the "Evaluating code
> blocks" section of the manual.
>
>   -k.

Would org-babel-execute-buffer work?

,--------------------------------------------------------------------
| org-babel-execute-buffer is an interactive autoloaded compiled Lisp
| function in `ob-core.el'.                                          
|                                                                    
| (org-babel-execute-buffer &optional ARG)                           
|                                                                    
| Execute source code blocks in a buffer.                            
| Call `org-babel-execute-src-block' on every source block in        
| the current buffer.                                                
`--------------------------------------------------------------------

hth,
Tom

-- 
Thomas S. Dye
http://www.tsdye.com

Re: restarting an org-babel session?

[Ken Mankoff]

On 2015-03-19 at 13:47, Thomas S. Dye <tsd@tsdye.com> wrote:
> Ken Mankoff <mankoff@gmail.com> writes:
>
>> On 2015-03-19 at 10:26, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
>>> Is it possible to restart an org-babel session from the current point?
>>> What I mean is if you have a largish org-file with many session blocks,
>>> and you want to go the end and continue it, you need to run each session
>>> block before the end to recreate the "session".
>>
>> I am surprised there is no easy way to have an Org file run every code
>> block in order either on command or on export. It seems like this
>> would be a key component of reproducible research and literate
>> documents.
>>
>> Maybe there is a way, but it isn't mentioned in the "Evaluating code
>> blocks" section of the manual.
>>
>>   -k.
>
> Would org-babel-execute-buffer work?
>

Yes that works perfectly.

Thanks,

  -k.

Re: restarting an org-babel session?

[John Kitchin]

That is an interesting one I did not know of. I would not want to always
run every block, some of them might not be part of a session, and it is
possible to have multiple named sessions in a buffer. It might be good
practice to not do that though ;)

I will share my way of doing this if nothing else comes up.

Thomas S. Dye writes:

> Ken Mankoff <mankoff@gmail.com> writes:
>
>> On 2015-03-19 at 10:26, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
>>> Is it possible to restart an org-babel session from the current point?
>>> What I mean is if you have a largish org-file with many session blocks,
>>> and you want to go the end and continue it, you need to run each session
>>> block before the end to recreate the "session".
>>
>> I am surprised there is no easy way to have an Org file run every code
>> block in order either on command or on export. It seems like this
>> would be a key component of reproducible research and literate
>> documents.
>>
>> Maybe there is a way, but it isn't mentioned in the "Evaluating code
>> blocks" section of the manual.
>>
>>   -k.
>
> Would org-babel-execute-buffer work?
>
> ,--------------------------------------------------------------------
> | org-babel-execute-buffer is an interactive autoloaded compiled Lisp
> | function in `ob-core.el'.
> |
> | (org-babel-execute-buffer &optional ARG)
> |
> | Execute source code blocks in a buffer.
> | Call `org-babel-execute-src-block' on every source block in
> | the current buffer.
> `--------------------------------------------------------------------
>
> hth,
> Tom

--
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: restarting an org-babel session?

[Thomas S. Dye]

Aloha all,

John Kitchin <jkitchin@andrew.cmu.edu> writes:

> That is an interesting one I did not know of. I would not want to always
> run every block, some of them might not be part of a session, and it is
> possible to have multiple named sessions in a buffer. It might be good
> practice to not do that though ;)

If org-babel-execute-buffer is too much, there is
org-babel-execute-subtree:

,---------------------------------------------------------------------
| org-babel-execute-subtree is an interactive autoloaded compiled Lisp
| function in `ob-core.el'.                                           
|                                                                     
| It is bound to C-c C-v s, C-c C-v C-s.                              
|                                                                     
| (org-babel-execute-subtree &optional ARG)                           
|                                                                     
| Execute source code blocks in a subtree.                            
| Call `org-babel-execute-src-block' on every source block in         
| the current subtree.                                                
`---------------------------------------------------------------------

For finer control, this might work:

,----------------------------------
| #+name: recreate-my-named-session
| #+header: :session my-named-session
| #+begin_src lang                 
| <<source-code-block-1>>          
| <<source-code-block-2>>          
| #+end_src                        
`----------------------------------

hth,
Tom

>
> I will share my way of doing this if nothing else comes up.
>
> Thomas S. Dye writes:
>
>> Ken Mankoff <mankoff@gmail.com> writes:
>>
>>> On 2015-03-19 at 10:26, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
>>>> Is it possible to restart an org-babel session from the current point?
>>>> What I mean is if you have a largish org-file with many session blocks,
>>>> and you want to go the end and continue it, you need to run each session
>>>> block before the end to recreate the "session".
>>>
>>> I am surprised there is no easy way to have an Org file run every code
>>> block in order either on command or on export. It seems like this
>>> would be a key component of reproducible research and literate
>>> documents.
>>>
>>> Maybe there is a way, but it isn't mentioned in the "Evaluating code
>>> blocks" section of the manual.
>>>
>>>   -k.
>>
>> Would org-babel-execute-buffer work?
>>
>> ,--------------------------------------------------------------------
>> | org-babel-execute-buffer is an interactive autoloaded compiled Lisp
>> | function in `ob-core.el'.
>> |
>> | (org-babel-execute-buffer &optional ARG)
>> |
>> | Execute source code blocks in a buffer.
>> | Call `org-babel-execute-src-block' on every source block in
>> | the current buffer.
>> `--------------------------------------------------------------------
>>
>> hth,
>> Tom
>
> --
> 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

-- 
T.S. Dye & Colleagues, Archaeologists
735 Bishop St, Suite 315, Honolulu, HI 96813
Tel: 808-529-0866, Fax: 808-529-0884
http://www.tsdye.com

Re: restarting an org-babel session?

[Andreas Leha]

Hi John,

tsd@tsdye.com (Thomas S. Dye) writes:
> Aloha all,
>
> John Kitchin <jkitchin@andrew.cmu.edu> writes:
>
>> That is an interesting one I did not know of. I would not want to always
>> run every block, some of them might not be part of a session, and it is
>> possible to have multiple named sessions in a buffer. It might be good
>> practice to not do that though ;)
>
> If org-babel-execute-buffer is too much, there is
> org-babel-execute-subtree:
>
> ,---------------------------------------------------------------------
> | org-babel-execute-subtree is an interactive autoloaded compiled Lisp
> | function in `ob-core.el'.                                           
> |                                                                     
> | It is bound to C-c C-v s, C-c C-v C-s.                              
> |                                                                     
> | (org-babel-execute-subtree &optional ARG)                           
> |                                                                     
> | Execute source code blocks in a subtree.                            
> | Call `org-babel-execute-src-block' on every source block in         
> | the current subtree.                                                
> `---------------------------------------------------------------------
>
> For finer control, this might work:
>
> ,----------------------------------
> | #+name: recreate-my-named-session
> | #+header: :session my-named-session
> | #+begin_src lang                 
> | <<source-code-block-1>>          
> | <<source-code-block-2>>          
> | #+end_src                        
> `----------------------------------
>

That's what I am doing.  But that is manual book-keeping.  It means
ultimate control but also the book-keeping to be accurate.  But I agree
with John, that org could be smart enough to execute the blocks of one
session.

> hth,
> Tom
>
>>
>> I will share my way of doing this if nothing else comes up.

Please do.  I would be interested in such a function, as well.

Thanks,
Andreas


>>
>> Thomas S. Dye writes:
>>
>>> Ken Mankoff <mankoff@gmail.com> writes:
>>>
>>>> On 2015-03-19 at 10:26, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
>>>>> Is it possible to restart an org-babel session from the current point?
>>>>> What I mean is if you have a largish org-file with many session blocks,
>>>>> and you want to go the end and continue it, you need to run each session
>>>>> block before the end to recreate the "session".
>>>>
>>>> I am surprised there is no easy way to have an Org file run every code
>>>> block in order either on command or on export. It seems like this
>>>> would be a key component of reproducible research and literate
>>>> documents.
>>>>
>>>> Maybe there is a way, but it isn't mentioned in the "Evaluating code
>>>> blocks" section of the manual.
>>>>
>>>>   -k.
>>>
>>> Would org-babel-execute-buffer work?
>>>
>>> ,--------------------------------------------------------------------
>>> | org-babel-execute-buffer is an interactive autoloaded compiled Lisp
>>> | function in `ob-core.el'.
>>> |
>>> | (org-babel-execute-buffer &optional ARG)
>>> |
>>> | Execute source code blocks in a buffer.
>>> | Call `org-babel-execute-src-block' on every source block in
>>> | the current buffer.
>>> `--------------------------------------------------------------------
>>>
>>> hth,
>>> Tom
>>
>> --
>> 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: restarting an org-babel session?

[John Kitchin]

Here is my solution so far:

http://kitchingroup.cheme.cmu.edu/blog/2015/03/19/Restarting-org-babel-sessions-in-org-mode-more-effectively/

It is a few functions that can go through the code blocks and
selectively rerun only the blocks that are in the session of the block
you run the restart command from. It is not tested too heavily, just
enough for this proof of concept.

j

Andreas Leha writes:

> Hi John,
>
> tsd@tsdye.com (Thomas S. Dye) writes:
>> Aloha all,
>>
>> John Kitchin <jkitchin@andrew.cmu.edu> writes:
>>
>>> That is an interesting one I did not know of. I would not want to always
>>> run every block, some of them might not be part of a session, and it is
>>> possible to have multiple named sessions in a buffer. It might be good
>>> practice to not do that though ;)
>>
>> If org-babel-execute-buffer is too much, there is
>> org-babel-execute-subtree:
>>
>> ,---------------------------------------------------------------------
>> | org-babel-execute-subtree is an interactive autoloaded compiled Lisp
>> | function in `ob-core.el'.
>> |
>> | It is bound to C-c C-v s, C-c C-v C-s.
>> |
>> | (org-babel-execute-subtree &optional ARG)
>> |
>> | Execute source code blocks in a subtree.
>> | Call `org-babel-execute-src-block' on every source block in
>> | the current subtree.
>> `---------------------------------------------------------------------
>>
>> For finer control, this might work:
>>
>> ,----------------------------------
>> | #+name: recreate-my-named-session
>> | #+header: :session my-named-session
>> | #+begin_src lang
>> | <<source-code-block-1>>
>> | <<source-code-block-2>>
>> | #+end_src
>> `----------------------------------
>>
>
> That's what I am doing.  But that is manual book-keeping.  It means
> ultimate control but also the book-keeping to be accurate.  But I agree
> with John, that org could be smart enough to execute the blocks of one
> session.
>
>> hth,
>> Tom
>>
>>>
>>> I will share my way of doing this if nothing else comes up.
>
> Please do.  I would be interested in such a function, as well.
>
> Thanks,
> Andreas
>
>
>>>
>>> Thomas S. Dye writes:
>>>
>>>> Ken Mankoff <mankoff@gmail.com> writes:
>>>>
>>>>> On 2015-03-19 at 10:26, John Kitchin <jkitchin@andrew.cmu.edu> wrote:
>>>>>> Is it possible to restart an org-babel session from the current point?
>>>>>> What I mean is if you have a largish org-file with many session blocks,
>>>>>> and you want to go the end and continue it, you need to run each session
>>>>>> block before the end to recreate the "session".
>>>>>
>>>>> I am surprised there is no easy way to have an Org file run every code
>>>>> block in order either on command or on export. It seems like this
>>>>> would be a key component of reproducible research and literate
>>>>> documents.
>>>>>
>>>>> Maybe there is a way, but it isn't mentioned in the "Evaluating code
>>>>> blocks" section of the manual.
>>>>>
>>>>>   -k.
>>>>
>>>> Would org-babel-execute-buffer work?
>>>>
>>>> ,--------------------------------------------------------------------
>>>> | org-babel-execute-buffer is an interactive autoloaded compiled Lisp
>>>> | function in `ob-core.el'.
>>>> |
>>>> | (org-babel-execute-buffer &optional ARG)
>>>> |
>>>> | Execute source code blocks in a buffer.
>>>> | Call `org-babel-execute-src-block' on every source block in
>>>> | the current buffer.
>>>> `--------------------------------------------------------------------
>>>>
>>>> hth,
>>>> Tom
>>>
>>> --
>>> Professor John Kitchin
>>> Doherty Hall A207F
>>> Department of Chemical Engineering
>>> Carnegie Mellon University
>>> Pittsburgh, PA 15213
>>> 412-268-7803
>>> @johnkitchin
>>> http://kitchingroup.cheme.cmu.edu

--
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu