[O] Clean logs for all tasks

2012-09-19 Thread Ilya Zonov
Hello!

I have little question. Does cleaning logs feature exist in Org mode now? I
didn't find anything similar.

I have calendar.org file with some tasks which should be done every day or
week. Logging is on for them (in :LOGBOOK: drawer). After few month I have
too big file with many logs and only ten tasks. So I want to clean up logs
which are older one or two month for example.

If there are no cleaning logs feature in org-mode, I will try to write it.

Thanks.

-- 
*Илья Зонов* (*Ilya Zonov*) aka *puzan*
Нижний Новгород, Россия (Nizhny Novgorod, Russia)


Re: [O] Invalid function: with-parsed-tramp-file-name with Perl

2012-09-19 Thread Nick Dokos
Achim Gratz strom...@nexgo.de wrote:

 Nick Dokos writes:
  Loris Bennett loris.benn...@fu-berlin.de wrote:
  In the *Org-Babel Error Output* buffer, I get the following:
  
  /bin/bash: /scpc:x@xx:/tmp/sh-script-7472puH: No such file or 
  directory
 
 It would seem that you are trying to use a remote file with a local
 bash.  That won't work, especially since bash doesn't understand what
 that tramp syntax invoking scpc is about… You need to either invoke that
 script on the remote end or copy the file to local and source it there.
 
  But probably the best thing to do is to leave org out of it and try opening
  the file directly: it seems to be a tramp problem.
 
 Sort of, but it wouldn't exist without Babel if I decode the temporary
 filename correctly.
 

Duh - you are right. OTOH, I don't understand how this could ever have
worked.  IIUC, the OP says that he had *something* working, although
revisiting the thread I don't see what that was.

Nick



Re: [O] [PATCH] Don't force the style tag to be present in `org-agenda-export-html-style'

2012-09-19 Thread Sebastien Vauban
Hello Achim,

Achim Gratz wrote:
 Sebastien Vauban writes:
 The only solution is:
 - don't check for `style'
 - allow a pure `link' tag to be inserted in the header

 Well, the /only other/\TM solution then is to check for either style
 or link.  Or maybe I'm missing something.

Well, the last option (the one taken by my patch) was no to check anything...

Otherwise, we have to:

- check for `style' (that is, matches both `style' and `stylesheet'), as
  proposed by Bastien

- check for `style' or `link', as you propose.

Thanks for your input.

Best regards,
  Seb

-- 
Sebastien Vauban




Re: [O] Clean logs for all tasks

2012-09-19 Thread Samuel Wales
Hi Ilya,

That would be a great feature.  You might want to allow for specific
things to be cleaned but not others.  The variable value might look
like '(state clock note), for example.

You might also want to allow for cleaning up until one month ago, for example.

Finally, somehow putting hte old items into the archive might be desirable.

Samuel

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



Re: [O] New exporter: no custom timestamps

2012-09-19 Thread Nicolas Goaziou
Hello,

Bastien b...@altern.org writes:

 I suggest to fix this in org-e-html.el with the attached patch.

 There is another option: to set :raw-value for time-stamps, but
 this feels a bit clumsy, especially when there is a :range-end.

   (org-element-property :raw-value TIMESTAMP) 

I tend to think that :raw-value would be a good option. Timestamps
properties could be enriched. Besides common properties
(:begin, :end, :post-blank) timestamps objects may accept :

  - :type
  - :year-start
  - :year-end
  - :month-start
  - :month-end
  - :day-start
  - :day-end
  - :hour-start
  - :hour-end
  - :minute-start
  - :minute-end
  - :repeater-type (a symbol among: `cumulative', 'catch-up', 'restart'
corresponding to, respectively +, ++ .+ repeater marks)
  - :repeater-value
  - :raw-value

:*-end properties would be the same as :*-start properties when
timestamp isn't a range. Both would be nil (along with :repeater-*) when
type is `diary'.

By default back-ends would use :raw-value and `org-translate-time'.

:range-end property would be removed.

What do you think?


Regards,

-- 
Nicolas Goaziou



Re: [O] Problem with paragraph fill / tab in lists

2012-09-19 Thread Nick Dokos
Anthony Lander anth...@landerfamily.ca wrote:

 
 On 12-Sep-19, at 2:10 PM, Nick Dokos wrote:
 
  Bastien b...@altern.org wrote:
  
  Yes -- we'll never say it enough: don't use filladapt.el with org-mode.
  
  It's probably worth adding a paragraph about this in the org manual,
  section Miscellaneous/Interactions/Conflicts.
 
 Nick, the way to turn off filladapt for orgmode is to add the following to 
 .emacs:
 
   (add-hook 'org-mode-hook 'turn-off-filladapt-mode)
 
 That might save people some digging for how to do it.
 

Thanks for that. I added a question to the FAQ with a description of the
problem as I understand it and incorporating Anthony's suggestion above.
Please review and either fix or let me know of any problems.

Nick



Re: [O] Extra space between list items in HTML export

2012-09-19 Thread Richard Stanton
 From: Bastien Guerry [mailto:bastiengue...@gmail.com] On Behalf Of
 Bastien
 Sent: Wednesday, September 19, 2012 9:45 AM
 To: Richard Stanton
 Cc: nicholas.do...@hp.com; emacs-orgmode@gnu.org
 Subject: Re: Extra space between list items in HTML export
 
 Richard Stanton stan...@haas.berkeley.edu writes:
 
  Yes - I thought you were advocating changing this behavior, but
  rereading your message, I now don't think you were...
 
 Okay, looks good, sorry if I was unclear!

What you wrote was perfectly clear. It was my reading that had problems...



Re: [O] [OT] Xiki - could something like that be done with emacs+orgmode?

2012-09-19 Thread Andrew Hyatt
That's odd, I get No org-babel-execute function for sh!.  I think I
just hadn't require'd ob-sh, and when I did this fixed the problem.
Thanks!

My point about removing the boilerplate still stands, however.  If I
have some free time in the next month, I may try to see if I can get
it removed as I proposed above.

On Wed, Sep 19, 2012 at 2:27 AM, Sean O'Halpin sean.ohal...@gmail.com wrote:
 On Wed, Sep 19, 2012 at 4:37 AM, Andrew Hyatt ahy...@gmail.com wrote:

 The xiki video is interesting, and I immediately thought of babel.
 However, babel sh-mode doesn't have support for execution yet.

 Not sure what you mean by that. Place cursor in source block and hit C-c, e.g.

 #+BEGIN_ORG
 * Shell example

 #+begin_src sh
 date
 #+end_src

 #+RESULTS:
 : Wed Sep 19 07:24:17 BST 2012

 #+END_ORG

 Regards,
 Sean




Re: [O] Org-mode release 7.9

2012-09-19 Thread Bastien
Hi Achim,

Achim Gratz strom...@nexgo.de writes:

 However I suggest to lose the plural
 and just use `org-plus-contrib´.

Yes, that's fine for me.  Thanks,

-- 
 Bastien



Re: [O] [PATCH] Don't force the style tag to be present in `org-agenda-export-html-style'

2012-09-19 Thread Bastien


Hi Sébastien,

Sebastien Vauban
wxhgmqzgwmuf-genee64ty+gs+fvcfc7...@public.gmane.org writes:

 Well, the last option (the one taken by my patch) was no to check
 anything...

Yes, I agree.  I have now applied your patch.

Note that the root of the problem lies in htmlize.el, which puts 
style.../style within head.../head.  If you feel like, don't
hesitate to report this to the author.

Thanks for the patch,

-- 
 Bastien




Re: [O] [OT] Xiki - could something like that be done with emacs+orgmode?

2012-09-19 Thread Torsten Wagner
hi,

I gave Xiki a try and it turned out to be an dependency hell on arch
linux. After installing dozen of packages from AUR, I managed to get
it up and running.
Its nice and some of the ideas could be shamelessly stolen for
org/org-babel. E.g. the mouse-support is great and would fit well to
org if we think of emacs on tablets.

However, I think it is in a very very early stage and one would need
to see how it develops. I do not like the ruby-bridge. This looks to
me very fragile and I had bad experience with python. Those bridges
tend to break whenever there is a change on one of the sides ext.
language or emacs. It also changed the entire appearance resp. face of
my emacs session not sure why it did this. Feels a bit invasive and
alienating.

Nevertheless, its good that this kind of things get tested out and
maybe in a future release of Emacs, we can see some of the ideas in
the Emacs core.

Totti



On 20 September 2012 06:49, Andrew Hyatt ahy...@gmail.com wrote:
 That's odd, I get No org-babel-execute function for sh!.  I think I
 just hadn't require'd ob-sh, and when I did this fixed the problem.
 Thanks!

 My point about removing the boilerplate still stands, however.  If I
 have some free time in the next month, I may try to see if I can get
 it removed as I proposed above.

 On Wed, Sep 19, 2012 at 2:27 AM, Sean O'Halpin sean.ohal...@gmail.com wrote:
 On Wed, Sep 19, 2012 at 4:37 AM, Andrew Hyatt ahy...@gmail.com wrote:

 The xiki video is interesting, and I immediately thought of babel.
 However, babel sh-mode doesn't have support for execution yet.

 Not sure what you mean by that. Place cursor in source block and hit C-c, 
 e.g.

 #+BEGIN_ORG
 * Shell example

 #+begin_src sh
 date
 #+end_src

 #+RESULTS:
 : Wed Sep 19 07:24:17 BST 2012

 #+END_ORG

 Regards,
 Sean





Re: [O] [OT] Xiki - could something like that be done with emacs+orgmode?

2012-09-19 Thread Eric Schulte
Andrew Hyatt ahy...@gmail.com writes:

 That's odd, I get No org-babel-execute function for sh!.  I think I
 just hadn't require'd ob-sh, and when I did this fixed the problem.
 Thanks!


For security reasons evaluation is not turned on by default.  The
relevant chapter of the manual is a very good resource [1].


 My point about removing the boilerplate still stands, however.  If I
 have some free time in the next month, I may try to see if I can get
 it removed as I proposed above.


You can insert code-block templates by typing s TAB, and there exists
other methods of expressing code blocks (e.g., inline code blocks).

If you do want to experiment with different syntax, it should be fairly
easy to write a function which parses some sparse code syntax near the
point and then calls existing org-babel-execute functions to run the
code.  For example the following function will check to see if the
current line starts with a $, and if so, it will run the line in your
shell and insert the result immediately following the line.

;; -*- emacs-lisp -*-
(defun sparse-execute ()
  (interactive)
  (save-excursion
(goto-char (point-at-bol))
(if (string= (thing-at-point 'char) $)
(let ((result (org-babel-execute:sh
   (substring (thing-at-point 'line) 1) '(
  (goto-char (point-at-eol))
  (open-line 1) (forward-char 1)
  (let ((beg (point)))
(insert (format %s result))
(org-babel-examplize-region beg (point
  (error this line doesn't look executable

Cheers,

Footnotes: 
[1]  http://orgmode.org/manual/Working-With-Source-Code.html

-- 
Eric Schulte
http://cs.unm.edu/~eschulte



Re: [O] Using org-mode for laboratory notes.

2012-09-19 Thread Torsten Wagner
Hi,

one way which works rather differently is the combination of git and org-mode.
You could write your protocols in separate org-files and link to them
in your records.
org allows (at least it did a while ago) to link not only to a file
but also to a specific version of a file.
You could do small modification in the protocol-files as you need them
and check them into the git system.
Link to them and you will see the version you used for exactly this experiments.

Actually using something like git and a git sensitive link is
important if you might plan link to a lot of external files. Imaging
you overwrite a file by accident or because you can't remember you
referred to the original file already. A normal link would quietly
point to the new file and would not be in-sync with anything you
mentioned in your org-file.

Other benefits are gits diff, merge and change-recording capabilities.
If you set-up the git repro with entire lab-book on a server (a PC
reachable from all your other devices) you could easily add data from
within the lab, go to your office to add more data and at a certain
point merge all this together. Both PCs could work offline and only
need to be online for check-in and check-out new data.
Another benefit of combining org-mode and git... you can tag certain
versions of your lab book. E.g. tag them whenever you write a paper
and make a notice in org-mode. This enables you to get back to all the
measurement and reps. data evaluation results as you found them during
writing your paper, even years and many many changes later (e.g. you
might improved your data analysis method over time but for the paper
you still want to see the old stupid way how you dealt with the data).

Recently we got an org-file sensitive git-module, which makes merging
org-files much more nice.
Check here:

http://orgmode.org/worg/org-contrib/org-git-link.html
http://orgmode.org/worg/org-contrib/gsoc2012/student-projects/git-merge-tool/index.html

Albeit I have to say I like to do all kind of stuff in org-mode, I
faced problems using only org-mode as lab-notebook. Sometimes things
in a lab are to numerous and to verbose to type them all in as they
happen. Sometimes a little sketch, some quick scribbled note, etc.
contains the real important data sentences like Damn, Joe slammed
the door AGAIN, during an AFM measurement. Or in your case Uhh..
what are the funny little flakes in my buffer solutions I think
sometimes a keyboard still filters to much and hence org-mode might
not really contain all the necessary info.
As a summary:
org-mode as a lab-book will work fine if you are strict in using it
and force yourself to be verbose enough.

Hope thats helps

Totti

CC. There might be some legal issue with real lab books and electronic
once. Back in the good old time where scientists didn't publish each
and every result and where it could take many many months until some
discovery reached the other side of the planet, the laboratory books
where the legal evidence of the original work. If someone made a wrong
claim or someone accused someone else of falsify reporting, the
laboratory books where used to proof those claims. That is the reason,
you find e.g. nicely archived laboratory books of all the great
scientists of the Bell laboratories. Not sure how much this is still
relevant today.


On 20 September 2012 03:49, Eric Schulte eric.schu...@gmx.com wrote:
 Eric Lubeck eric.lub...@gmail.com writes:

 Hello Everybody,

 I had a look around the web for awhile, but couldn't find any
 information pertaining to my particular needs.  I hope somebody here
 will be able to help me out.

 Anyway, I've been looking around for quite a while for the proper
 system to set-up an electronic laboratory notebook in.  I will be
 using org-mode to document wet-lab experiments in addition to
 computational work.

 One of my particular concerns is this: I'm accustomed to using a
 chronological laboratory notebook for recording all of my data.  The
 agenda views in org-mode seem to provide a means to retrieve
 chronological information out of my outlines, but I would than need to
 timestamp every single entry in my outline.  Is there a means for
 doing this?  Currently I am manually typing C-u C-c ! , but it would
 be helpful to have something automatically configured to timestamp and
 place the time in a drawer for any entry in a particular file.


 I believe such automated functionality may exist (although I don't use
 it personally).  Take a look at this portion of the manual [1].


 My other question pertains to efficiently representing linked or
 nested data.  I'd like to record my detailed laboratory protocols in
 another outline.  As most of my day-to-day work is using these
 protocols with minimal modifications, I'd like to record in my primary
 outline a property or hyperlink that points to the primary protocol
 and suggests that this days experiment inherits from the main
 protocol with given modifications.  It would be really 

Re: [O] [New Latex Exporter][BABEL][BUG] lists and inline src

2012-09-19 Thread Eric Schulte
cbe...@tajo.ucsd.edu writes:

 Bastien b...@altern.org writes:

 Hi Chuck,

 cbe...@tajo.ucsd.edu writes:

 My apologies if this is already reported (I recall seeing something like
 this, but cannot find it in the archives).

 A list element starting with an inline src block is improperly
 parsed. 

 I cannot reproduce this with Org 7.9.1.

 I just did a git pull, trimmed my .emacs down to 

 (setq load-path (cons ~/elisp/org-mode/lisp load-path))
 (setq load-path (cons ~/elisp/org-mode/contrib/lisp load-path))

 renamed  customizations.el, started Aquamacs, loaded org-e-latex.el and
 reran 

 (org-export-to-buffer 'e-latex *Test e-LaTeX* nil nil t)

 I am still getting the same result.

 What else can I do to get to the bottom of this??


Hi Chuck,

Does this problem present itself when you execute the inline code block
interactively, or only when using the new latex exporter?  If the later
then it is a latex exporter bug and not a Babel bug.  I've updated the
subject line so that hopefully the latex export experts will notice this
message.

Cheers,


 Chuck



-- 
Eric Schulte
http://cs.unm.edu/~eschulte



Re: [O] New maintainer for MobileOrg on iOS

2012-09-19 Thread Ranmocy
Hi Richard,
I am just begin to watch the project after it expire right the time T.T
There is so many iOS apps live without App Store.
They just release on their own website.
I found that you open the source. 
Maybe you can have a try to post in news list (or HackerNews?)
to transfer ownership of the repository? 
Since you do not have Mac any more?

Feel sorry again to know it stopped developing.

--
Ranmocy Sheng





Re: [O] Using org-mode for laboratory notes.

2012-09-19 Thread Eric Lubeck
Hey, 

Thanks for the good idea.  I'll have to look into figuring that system out.

On the broader point of organizing the notebook, I am still having a bit of a 
dilemma coming up with an effective system.  My first thought was to just place 
all my work in a dated hierarchy, such as with org-datetree.  This would be 
simple and mirror a conventional notebook, but would loose a lot of the logical 
hierarchy possible with digital tools.  

On the other hand, organizing all my experiments as a non-linear outline is 
getting a bit messy.  I found myself navigating around headlines everyday 
searching for items I need to schedule for the next day.  As my notebook gets 
bigger, this system will probably get very inefficient.  If i properly tag and 
schedule my tasks for the day this should be less of a problem, but i still 
foresee potential chaos if I get lazy.  In addition to tasks I intend to record 
other observations in the notebook that may not be associated with a recent 
task, yet are important for me planning future experiments.  Without proper 
timestamps I could loose these observations over time.

This is where I came up with the idea of tagging all of my headlines with their 
entry date and timestamp.  Potentially such a system would enable me to view 
the logical hierarchy of an experiment, but also view my work in the 
conventional linear order. 

Anyone have any other ideas for reasonable systems?

I'm also a bit confused about the proper way to implement such a system.  I 
imagine I could hack together some auto-timestamp property, but than it would 
only apply to headlines, not to my nested observations in list form.  For this 
reason I have little used lists at all in org-mode, as it seems that any data 
that could potentially be nested, such as with different tasks or properties, 
must be converted back to headline form before it can be annotated.  Am I 
missing something?

Also, I have a general question about nesting headings demonstrated by the 
below example.

* Today's Experiment   :EXPERIMENT:
** Do today's Experiment :RATIONALE:
** Data link :DATA:
** Experiments are sad.  :DISCUSSION:
** Repeat, but change X Tomorrow  :FOLLOW-UP:
* Tomorrow's Experiment  :EXPERIMENT:
** Yesterday's Experiment Failed :RATIONALE:
*** Determine if X was the cause

In the above case I have two options, to either continually nest all follow-up 
experiments, or rely on a network of links to get me back to the data that led 
to the follow-up experiments.  Anybody have any advice on pursing either option?

Thanks for the help,
Eric Lubeck


On Wednesday, September 19, 2012 at 6:44 PM, Torsten Wagner wrote:

 Hi,
 
 one way which works rather differently is the combination of git and org-mode.
 You could write your protocols in separate org-files and link to them
 in your records.
 org allows (at least it did a while ago) to link not only to a file
 but also to a specific version of a file.
 You could do small modification in the protocol-files as you need them
 and check them into the git system.
 Link to them and you will see the version you used for exactly this 
 experiments.
 
 Actually using something like git and a git sensitive link is
 important if you might plan link to a lot of external files. Imaging
 you overwrite a file by accident or because you can't remember you
 referred to the original file already. A normal link would quietly
 point to the new file and would not be in-sync with anything you
 mentioned in your org-file.
 
 Other benefits are gits diff, merge and change-recording capabilities.
 If you set-up the git repro with entire lab-book on a server (a PC
 reachable from all your other devices) you could easily add data from
 within the lab, go to your office to add more data and at a certain
 point merge all this together. Both PCs could work offline and only
 need to be online for check-in and check-out new data.
 Another benefit of combining org-mode and git... you can tag certain
 versions of your lab book. E.g. tag them whenever you write a paper
 and make a notice in org-mode. This enables you to get back to all the
 measurement and reps. data evaluation results as you found them during
 writing your paper, even years and many many changes later (e.g. you
 might improved your data analysis method over time but for the paper
 you still want to see the old stupid way how you dealt with the data).
 
 Recently we got an org-file sensitive git-module, which makes merging
 org-files much more nice.
 Check here:
 
 http://orgmode.org/worg/org-contrib/org-git-link.html
 http://orgmode.org/worg/org-contrib/gsoc2012/student-projects/git-merge-tool/index.html
 
 Albeit I have to say I like to do all kind of stuff in org-mode, I
 faced problems using only org-mode as lab-notebook. Sometimes things
 in a lab are to numerous and to verbose to type them all in as they
 happen. Sometimes a little sketch, some quick scribbled note, etc.
 contains the real important data sentences like 

Re: [O] Using org-mode for laboratory notes.

2012-09-19 Thread John Hendy
On Wed, Sep 19, 2012 at 10:18 PM, Eric Lubeck eric.lub...@gmail.com wrote:
 Hey,

 Thanks for the good idea.  I'll have to look into figuring that system out.

 On the broader point of organizing the notebook, I am still having a bit of
 a dilemma coming up with an effective system.  My first thought was to just
 place all my work in a dated hierarchy, such as with org-datetree.  This
 would be simple and mirror a conventional notebook, but would loose a lot of
 the logical hierarchy possible with digital tools.

First off, this is great stuff. This type of discussion happens all
the time, at least in part due to me :) At least I think these
partially get at some of the struggles you're having:

- http://lists.gnu.org/archive/html/emacs-orgmode/2011-07/msg01173.html
- http://osdir.com/ml/emacs-orgmode-gnu/2012-01/msg00681.html


 On the other hand, organizing all my experiments as a non-linear outline is
 getting a bit messy.  I found myself navigating around headlines everyday
 searching for items I need to schedule for the next day.  As my notebook
 gets bigger, this system will probably get very inefficient.  If i properly
 tag and schedule my tasks for the day this should be less of a problem, but
 i still foresee potential chaos if I get lazy.  In addition to tasks I
 intend to record other observations in the notebook that may not be
 associated with a recent task, yet are important for me planning future
 experiments.  Without proper timestamps I could loose these observations
 over time.

Yup. Same with me. I'm in RD for a large-ish (80k employees
globally), worldwide science and technology place. Technical notebooks
are a big deal. I do everything in Org, then print, chop the margins,
and permanently double tape in bound books. I witness them across the
paper edge and have them witnessed by my lab mate. When the book is
full, it gets sent to the vault in who knows what building.

I have current projects. Then I have odds and end ideas that might or
might not be relevant. But my project specific work is often much more
broadly applicable to something else. For example, I might be trying
to create a particular feature because I'm assigned to do so on a
project... but as I'm finding that solution, I think it would be
really cool down the road for something else.

I currently organize by project and then archive when it's done... but
it'd be nice to easily call up these broader ideas later. I know I can
search with agenda and then `v a` to add in archives, but thing still
feel a bit weird and the whole heirarchical or non-linear thing really
resonates with me.

Prior to Org-mode, I was using TiddlyWiki, which is actually quite
neat. I was able to do everything in daily entries, but a plugin
allowed me to mark each section as pertaining to a particular project.
I could view things completely along a timeline by date or filter down
to just a project. And I could add whatever other tags so that I could
call up any entries with that tag.


 This is where I came up with the idea of tagging all of my headlines with
 their entry date and timestamp.  Potentially such a system would enable me
 to view the logical hierarchy of an experiment, but also view my work in the
 conventional linear order.

 Anyone have any other ideas for reasonable systems?

Per my request, Bastien awesomely added the ability to change sparse
tree searching timestamp types. Thus, inactive stamps can be filtered
out, which is great. Search by a tag and timestamps (I think combining
is possible) and you kind of have your solution.

I would think out your tags ahead of time. The problem, is that even
these get tough to manage. I can't forecast ahead of time what to call
a tag. If it has to do with laser processing of a material, do I tag
it :laser: or if the laser processing is for a particular product
idea, do I tag it with the product idea? How many product ideas are
reasonable? And would the tag be :cool-thing-some-could-use-to-x:?
Sometimes, anything much less specific really won't serve me long
term!


 I'm also a bit confused about the proper way to implement such a system.  I
 imagine I could hack together some auto-timestamp property, but than it
 would only apply to headlines, not to my nested observations in list form.
 For this reason I have little used lists at all in org-mode, as it seems
 that any data that could potentially be nested, such as with different tasks
 or properties, must be converted back to headline form before it can be
 annotated.  Am I missing something?


Nope, you're not missing anything. Headlines are where it's at. You
might check out this thread where some nifty capture templates were
presented. Completely changed how I use Org:
- http://osdir.com/ml/emacs-orgmode-gnu/2012-08/msg00396.html

Instead of entering things manually, this makes it *far* easier to
just use a quick capture template. As with some other power users
here, I've found myself shifting more toward using capture to enter
and 

Re: [O] Using org-mode for laboratory notes.

2012-09-19 Thread John Hendy
On Wed, Sep 19, 2012 at 8:44 PM, Torsten Wagner
torsten.wag...@gmail.com wrote:
 Hi,

 one way which works rather differently is the combination of git and org-mode.
 You could write your protocols in separate org-files and link to them
 in your records.
 org allows (at least it did a while ago) to link not only to a file
 but also to a specific version of a file.
 You could do small modification in the protocol-files as you need them
 and check them into the git system.
 Link to them and you will see the version you used for exactly this 
 experiments.

 Actually using something like git and a git sensitive link is
 important if you might plan link to a lot of external files. Imaging
 you overwrite a file by accident or because you can't remember you
 referred to the original file already. A normal link would quietly
 point to the new file and would not be in-sync with anything you
 mentioned in your org-file.

 Other benefits are gits diff, merge and change-recording capabilities.
 If you set-up the git repro with entire lab-book on a server (a PC
 reachable from all your other devices) you could easily add data from
 within the lab, go to your office to add more data and at a certain
 point merge all this together. Both PCs could work offline and only
 need to be online for check-in and check-out new data.
 Another benefit of combining org-mode and git... you can tag certain
 versions of your lab book. E.g. tag them whenever you write a paper
 and make a notice in org-mode. This enables you to get back to all the
 measurement and reps. data evaluation results as you found them during
 writing your paper, even years and many many changes later (e.g. you
 might improved your data analysis method over time but for the paper
 you still want to see the old stupid way how you dealt with the data).

 Recently we got an org-file sensitive git-module, which makes merging
 org-files much more nice.
 Check here:

 http://orgmode.org/worg/org-contrib/org-git-link.html
 http://orgmode.org/worg/org-contrib/gsoc2012/student-projects/git-merge-tool/index.html

Thanks for re-bringing this up. The video demo of org-merge was
*amazing.* I should really try that. Git scares me a bit, but it seems
amazingly powerful. I really like the idea of being able to have tons
of versions to look back to, especially if I start rearranging and
wonder where I put some tidbit. I've done a few org file overhauls
which have both helped and hurt for this reason. I know something
existed, but then can't find it.


 Albeit I have to say I like to do all kind of stuff in org-mode, I
 faced problems using only org-mode as lab-notebook. Sometimes things
 in a lab are to numerous and to verbose to type them all in as they
 happen. Sometimes a little sketch, some quick scribbled note, etc.
 contains the real important data sentences like Damn, Joe slammed
 the door AGAIN, during an AFM measurement. Or in your case Uhh..
 what are the funny little flakes in my buffer solutions I think
 sometimes a keyboard still filters to much and hence org-mode might
 not really contain all the necessary info.

True, though one could document via voice recorder and link to the audio file.

I also sketch on a whiteboard, take a pic with my tablet, and then put
the file in a folder called ip-pics which serves to hold a huge
repository of any experiment, equipment, or sketch pics used for my
intellectual property notebook. I'll trade having to do a bit of file
and device maneuvering (taking pictures/sketch on x, getting it into
the right directory for Org to find) for all of the other stuff Org
provides.

In other words, imagine gaining the ability to sketch on pen and paper
and losing the ability to
- easily rearrange
- tag
- log time
- create awesome exports with minor modifications to notes vs. typing
from handwriting
- the list goes literally on, and on, and on

 As a summary:
 org-mode as a lab-book will work fine if you are strict in using it
 and force yourself to be verbose enough.

Yup. I think writing more than you think you do and trying to
anticipate one's future self is huge. When I file contacts, for
example, I try to think of any possible words I might use. For a
machining shop, things like machining, machin, mill, lathe, molding.


 Hope thats helps

 Totti

 CC. There might be some legal issue with real lab books and electronic
 once. Back in the good old time where scientists didn't publish each
 and every result and where it could take many many months until some
 discovery reached the other side of the planet, the laboratory books
 where the legal evidence of the original work. If someone made a wrong
 claim or someone accused someone else of falsify reporting, the
 laboratory books where used to proof those claims. That is the reason,
 you find e.g. nicely archived laboratory books of all the great
 scientists of the Bell laboratories. Not sure how much this is still
 relevant today.


The large RD company I work at is currently 

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