[chimera-dev] how to write documentation for an extension

Eric Pettersen pett at cgl.ucsf.edu
Fri Jul 25 10:50:59 PDT 2014

Hi Jan,
	If the extension is of somewhat general interest, you could announce it on chimera-users and we could put a news item on the Chimera home page about it.


On Jul 25, 2014, at 10:33 AM, Jan Kosinski <kosinski at embl.de> wrote:

> Dear Elaine and Eric,
> Thanks a lot! I will probably get an example html page as Elaine suggests, edit it and then use Eric's option 3) to bundle the help with the extension!
> Jan
> On 07/25/2014 07:29 PM, Eric Pettersen wrote:
>> Hi Jan,
>>  You probably also want to know how to get your extension to display the help you write.  Unfortunately the "Help" example in the Programmer's Guide hasn't been written.  Here's what you need to know:
>>  To enable the Help button on a dialog (assuming you are using standard Chimera dialogs from chimera.baseDialog [i.e. ModelessDialog or ModalDialog], you set a class variable named "help" to some value (analogous to the class variable "buttons" for specifying what buttons to show).  The possible values are:
>>  1)  A path.  This is used for extensions whose documentation is bundled with Chimera and therefore probably isn't relevant to you.
>>  2)  An URL (e.g. "http://myhost.myschool.edu/mylab/me/tool/help.html").  Chimera will show that URL in a browser when the Help button is clicked.
>>  3)  A 2-tuple consisting of a path and a module.  The module can either be your actual extension module object or a string that can be combined with "import" to import your extension.  Your extension should have a "helpdir" folder in it, and the path will be interpreted relative to that folder.  So as an example, ("help.html", "myext") will use "import myext" to import your extension, determine where that is on the file system (using the module's __path__ variable) and then look in its "helpdir" folder to find help.html and show that in a browser.
>>  Let me know if you need more info.
>> --Eric
>>                         Eric Pettersen
>>                         UCSF Computer Graphics Lab
>>                         http://www.cgl.ucsf.edu
>> On Jul 25, 2014, at 10:00 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>>> Hi Jan,
>>> We do strive for a reasonable amount of consistency in the documentation that we ship, but there is no official guideline at this point.  We only have something like that for the extension’s GUI text:
>>> <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/frameguidelines.html>
>>> One reason is that the tools themselves vary considerably in complexity and organization, calling for variations on the basic documentation format.
>>> My advice would be to start with the HTML manpage from the most similar existing tool (click Help button, use browser to save HTML, then modify, at least if you are comfortable directly text-editing HTML).  If you are not comfortable working with HTML directly there are probably other  routes to ultimately generating HTML with a similar organization and style. 
>>> We don’t mandate anything specific, however, and the mere fact that you are actually thinking about documentation is a positive!  Of the various extensions distributed by others, some have little documentation, some are documented on websites, and some have non-HTML documentation (PDF, etc.).  My general impression is that most don’t include documentation in their download.
>>> <http://www.rbvi.ucsf.edu/chimera/plugins/plugins.html>
>>> Thanks for asking!
>>> Elaine
>>> -----
>>> Elaine C. Meng, Ph.D.                       
>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>> Department of Pharmaceutical Chemistry
>>> University of California, San Francisco
>>> On Jul 25, 2014, at 6:16 AM, Jan Kosinski <kosinski at embl.de> wrote:
>>>> Hi,
>>>> I wrote a custom extension and now I want to create a documentation page that upon clicking a Help button opens a web page similarly to some other Chimera tools.
>>>> Is there any html template, style guide or any important instructions I should follow for implementing it?
>>>> Thanks in advance,
>>>> Jan
>>> _______________________________________________
>>> Chimera-dev mailing list
>>> Chimera-dev at cgl.ucsf.edu
>>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev
> -- 
> Jan Kosinski, PhD
> Structural and Computational Biology Unit
> European Molecular Biology Laboratory (EMBL)
> Meyerhofstrasse 1
> 69117 Heidelberg
> Germany
> _______________________________________________
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> Chimera-dev at cgl.ucsf.edu
> http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev

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