[chimera-dev] chimerax - registering an external tool problem

[Greg Couch]

Hi Wolfgang,

I was expecting a full-time developer to answer this, but I'll get 
things started.

1) The bundle name should be ChimeraX-//name// .  The leading ChimeraX- 
will eventually be stripped in the Toolshed interface, but is useful 
because ChimeraX bundles share the same namespace as PyPI packages.  The 
package in your bundle is installed in ChimeraX's python's 
site-packages, so you should put in the chimerax namespace (e.g., 
chimerax.starmap), to avoid conflicts with PyPI packages.  Both cases, 
using the ChimeraX- prefix and the chimerax namespace, are optional -- 
whether or not a particular wheel is a ChimeraX bundle is determined by 
the ChimeraX classifiers.

2) Conrad should work with you on uploading things to the central 
Toolshed so others can discover your extension easier.  You will need an 
account of some sort.

3) Use 'bin/ChimeraX -m pip install *.whl' to install your wheel instead 
of bin/python3.5.  It automatically rebuilds the bundle cache.  If you 
do use python3.5, you will need to run the command 'toolshed refresh'.  
Then the 'ts list' will work.  FYI, we are going to remove the builtin 
ts alias.

4) Building binary packages is work.  Ideally, you will have a Mac OS X 
system with XCode, a Windows 10 system with Visual Studio 2015 
(community edition is okay), and a system for running a Linux docker 
image that we will provide (currently Debian 8 based, but that may 
change).  We will document the exact requirements and provide examples 
later.

     HTH,

     Greg


On 1/5/2017 8:13 AM, Wolfgang Lugmayr wrote:
> dear chimera developers,
>
> i'm currently porting one of our chimera 1.x plugins called starmap to 
> chimerax.
>
> basic questions:
> 1. should the package be e.g. chimerax-starmap or just starmap?
> 2. is there a recommended way when i should upload to the toolshed 
> repository?
>
> my current problem:
> i use chimerax's python3.5 pip to install and remove my tests.
> my test package is called chimerax.starmapx (+.__init.py__)
>
> i had a look at your toolshed and added test categories like follows 
> to the metadata (installed version):
> Classifier: ChimeraX :: Bundle :: Volume data :: 1,1 :: 
> chimerax.starmap :: chimerax.starmap ::
> Classifier: ChimeraX :: Tool :: StarMapX :: Volume data :: Run Rosetta 
> refinements
> Classifier: ChimeraX :: Command :: apix :: Volume data :: Run Rosetta 
> apix
> Requires-Dist: ChimeraX-Core (>=0.1)
> Requires-Dist: pyparsing
>
> i also used "General" instead of "Volume data" for debugging.
>
> i have overriden the BundleAPI get_class, start_tools, 
> register_command similar to blastprotein.
>
> unfortunatly my test plugin never shows up in chimerax (e.g. ts list) 
> and the command "stm apix" is not registered.
>
> i debugged the toolshed (standalone - not in chimerax) and if i print 
> the contents of line 720 - end of_load_bundle_infos()
> i get
> ...using SteamVR]], ChimeraX-StarMap (installed) [version: 0.1.2] [api 
> package: chimerax.starmap] [category: Volume data] [tool: StarMap 
> [categories: Volume data] [synopsis: Run Rosetta refinements]] 
> [command: apix [categories: Volume data] [synopsis: Run Rosetta 
> refinements]], ChimeraX-Stringdb (installed) [version: 0.1]...
> and a little bit before
> ('checking', <InstalledDistribution 'ChimeraX-StarMap' 0.1.2 at 
> '/projects/marlovits/lugmayr/workspace/ChimeraX/lib/python3.5/site-packages/ChimeraX_StarMap-0.1.2.dist-info'>) 
>
>
> do i miss something during the registration process?
>
> cheers,
> wolfgang
>
> ---
> Universitätsklinikum Hamburg-Eppendorf (UKE)
> @ Centre for Structral Systems Biology (CSSB)
> @ Institute of Molecular Biotechnology (IMBA)
> Dr. Bohr-Gasse 3-7 (Room 6.14)
> 1030 Vienna, Austria
> Tel.: +43 (1) 790 44-4649
> Email: w.lugmayr at uke.de
> http://www.cssb-hamburg.de/
>
> -- 
>
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