chimerax - registering an external tool problem
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@uke.de http://www.cssb-hamburg.de/ -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING
dear chimerax developers, i think i have tracked down the problem (centos7): when i removed the ~/.cache/ChimeraX directory everything runs fine now. first i tried to remove only the lock .cache/ChimeraX/0.1/toolshed/bundle_info.cache.lock but this file stays even when chimerax is closed. and is overwritten with a new timestamp when a new instance is started. i tested to start in parallel a global chimerax and my development instance and the "ts list" for both instances is correct. so i am not sure what messed up my chimerax cache. cheers, wolfgang On 01/05/2017 05:13 PM, 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@uke.de http://www.cssb-hamburg.de/
--
_____________________________________________________________________
Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________
SAVE PAPER - THINK BEFORE PRINTING
_______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
-- 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@uke.de http://www.cssb-hamburg.de/ -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING
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@uke.de http://www.cssb-hamburg.de/
--
_____________________________________________________________________
Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________
SAVE PAPER - THINK BEFORE PRINTING
_______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
participants (2)
-
Greg Couch -
Wolfgang Lugmayr