Re: [O] restarting an org-babel session?
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, t...@tsdye.com (Thomas S. Dye) writes: Aloha all, John Kitchin jkitc...@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 mank...@gmail.com writes: On 2015-03-19 at 10:26, John Kitchin jkitc...@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
Re: [O] restarting an org-babel session?
Ken Mankoff mank...@gmail.com writes: On 2015-03-19 at 10:26, John Kitchin jkitc...@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: [O] restarting an org-babel session?
On 2015-03-19 at 10:26, John Kitchin jkitc...@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.
[O] restarting an org-babel session?
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: [O] restarting an org-babel session?
Aloha all, John Kitchin jkitc...@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 mank...@gmail.com writes: On 2015-03-19 at 10:26, John Kitchin jkitc...@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: [O] restarting an org-babel session?
On 2015-03-19 at 13:47, Thomas S. Dye t...@tsdye.com wrote: Ken Mankoff mank...@gmail.com writes: On 2015-03-19 at 10:26, John Kitchin jkitc...@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: [O] restarting an org-babel session?
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 mank...@gmail.com writes: On 2015-03-19 at 10:26, John Kitchin jkitc...@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: [O] restarting an org-babel session?
Hi John, t...@tsdye.com (Thomas S. Dye) writes: Aloha all, John Kitchin jkitc...@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 mank...@gmail.com writes: On 2015-03-19 at 10:26, John Kitchin jkitc...@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
