[chimerax-users] ChimeraX tool installationg

[Yongcheng MU]

Hi Eric,

I really appreciate your quick response. It really helps me a lot to
understand it. But I have another question, following your instructions, I
modified the _init_.py file but it still holds an error. I attached some
related information below.

Thank you for your time and help.

Best regards,
Yongcheng

On Thu, Feb 4, 2021 at 4:09 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Yongcheng,
> You probably know this, but in order to avoid registering all commands at
> startup, which would involve executing the code from dozens of bundles and
> make startup really slow, ChimeraX uses information from the Toolshed to
> know which bundles implement which commands and only when the time comes to
> actually execute a command does it invoke the bundle's code that fully
> registers the command, which then allows ChimeraX to know what arguments
> and keywords the command allows and what function the command executes so
> that it can parse the command text and call that function.
> So all that error text you got is indicating that there is an error in
> your command-registration function.  ChimeraX asks you to register your
> command by calling the register_command() method of your BundleAPI
> subclass.  Does the implementation of register_command() in your
> __init__.py look something like this?:
>
> from chimerax.core.toolshed import BundleAPI
>
> class CL_TensorFlowAPI(BundleAPI):
>
>     @staticmethod
>     def register_command(command_name, logger):
>         from . import cmd
>         cmd.register_command(command_name, logger)
>
> If it does, then the problem is that you have no cmd.py file in your
> bundle, producing the error:
>
> cannot import name 'cmd' from 'chimerax.CL_Tensorflow'
> (/Users/jackmu/Library/Application
> Support/ChimeraX/1.1/site-packages/chimerax/CL_Tensorflow/__init__.py))
>
> Let me know if you need further clarification.
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
> On Feb 4, 2021, at 10:45 AM, Yongcheng MU <ymu004 at odu.edu> wrote:
>
> Hello,
>
> Hope you are doing well. This is Yongcheng. I am writing this email
> because I am trying to install a Deep learning tool in ChimeraX, but I have
> some issues about it.
>
> I built and installed my code following the steps on the Chimera Guide
> website. I installed my code successfully, but when I run using command
> that I created, it hold some errors:
>
> *"RuntimeError: delayed command registration for 'CL_Tensorflow' failed
> (register_command() failed for command CL_Tensorflow in bundle
> ChimeraX-CL-Tensorflow:*
>
>
>
> *cannot import name 'cmd' from 'chimerax.CL_Tensorflow'
> (/Users/jackmu/Library/Application
> Support/ChimeraX/1.1/site-packages/chimerax/CL_Tensorflow/__init__.py))File
> "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py",
> line 2142, in lazy_register*
> *raise RuntimeError("delayed command registration for %r failed (%s)" %
> (cmd_name, e))"*
>
> *"During handling of the above exception, another exception occurred:*
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *Traceback (most recent call last):  File
> "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/cmd_line/tool.py",
> line 275, in execute    cmd.run(cmd_text)  File
> "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py",
> line 2746, in run    self._find_command_name(final,
> used_aliases=_used_aliases)  File
> "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py",
> line 2489, in _find_command_name    what.lazy_register(cmd_name)  File
> "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py",
> line 2142, in lazy_register    raise RuntimeError("delayed command
> registration for %r failed (%s)" % (cmd_name, e))RuntimeError: delayed
> command registration for 'CL_Tensorflow' failed (register_command() failed
> for command CL_Tensorflow in bundle ChimeraX-CL-Tensorflow:cannot import
> name 'cmd' from 'chimerax.CL_Tensorflow' (/Users/jackmu/Library/Application
> Support/ChimeraX/1.1/site-packages/chimerax/CL_Tensorflow/__init__.py))RuntimeError:
> delayed command registration for 'CL_Tensorflow' failed (register_command()
> failed for command CL_Tensorflow in bundle ChimeraX-CL-Tensorflow:cannot
> import name 'cmd' from 'chimerax.CL_Tensorflow'
> (/Users/jackmu/Library/Application
> Support/ChimeraX/1.1/site-packages/chimerax/CL_Tensorflow/__init__.py))File
> "/Users/jackmu/Desktop/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/core/commands/cli.py",
> line 2142, in lazy_register*
> *raise RuntimeError("delayed command registration for %r failed (%s)" %
> (cmd_name, e))"*
>
> I wonder if you know what's going on here, and how to fix it. Thank you so
> much for your time.
>
> Best regards,
> Yongcheng
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