Per https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8927 which broke on the same dependency (mdtraj), dealing with recursive pip was such a nightmare that ChimeraX’s pip command searches for the python executable _next to_ ChimeraX.exe and uses that instead of ChimeraX; toolshed_utils will have to do the same to fix this error. 

— Zach 


On Aug 30, 2023, at 14:40, Tom Goddard <goddard@sonic.net> wrote:

Hopefully Zach or Greg can help you with this pip install error.

Tom


On Aug 30, 2023, at 2:19 PM, BARRY E DEZONIA via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

OK, so we have now installed chimerax-daily on another system that already had it on there. We were getting similar errors as detailed in my earlier email. After carefully cleaning the system and removing and reinstalling the July 14 daily build we are still getting install errors for my plugin. Instead of the python 3.9 complaints they are now python3.11 complaints. So that part of the earlier problem was fixed by my cleanups. But it is still broken. We still have pip running problems. Even with upgrading chimerax's python's pip and making sure that the chimerax's pip's bin dir is in the path. The error message is basically "AssertionError: Cannot run __pip-runner__.py as a non-main module". I will post the (lengthy) log output of my plugin install process below. Please let us know what might be causing this. We were just going to install a new daily build but your website has been down today.

====================================================

UCSF ChimeraX version: 1.7.dev202307150241 (2023-07-15)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
devel install /home/crow/bphon/bphon/chimerax-plugin/tut_tool_qtrunning build
running build_py
running bdist_wheel
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/chimerax
creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt
copying build/lib/chimerax/tut_tool_qt/tool.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt
copying build/lib/chimerax/tut_tool_qt/__init__.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt
creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable
copying build/lib/chimerax/tut_tool_qt/Runnable/zncc.sh -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable
copying build/lib/chimerax/tut_tool_qt/Runnable/zncc.jar -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable
copying build/lib/chimerax/tut_tool_qt/Runnable/simCC.com -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable
copying build/lib/chimerax/tut_tool_qt/Runnable/simNC.com -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable
creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable
copying build/lib/chimerax/tut_tool_qt/Installable/install_traj2nmr.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable
creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr
copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/README.md -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr
copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/setup.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr
creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr
copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/session.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr
copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/ucsf.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr
copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/__init__.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr
copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/resonance.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr
copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/shifts.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr
copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/utils.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr
copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/LICENSE -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr
running install_egg_info
running egg_info
writing ChimeraX_BphonTool.egg-info/PKG-INFO
writing dependency_links to ChimeraX_BphonTool.egg-info/dependency_links.txt
writing requirements to ChimeraX_BphonTool.egg-info/requires.txt
writing top-level names to ChimeraX_BphonTool.egg-info/top_level.txt
reading manifest file 'ChimeraX_BphonTool.egg-info/SOURCES.txt'
writing manifest file 'ChimeraX_BphonTool.egg-info/SOURCES.txt'
Copying ChimeraX_BphonTool.egg-info to build/bdist.linux-x86_64/wheel/ChimeraX_BphonTool-0.4-py3.11.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/ChimeraX_BphonTool-0.4.dist-info/WHEEL
creating 'dist/ChimeraX_BphonTool-0.4-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'chimerax/tut_tool_qt/__init__.py'
adding 'chimerax/tut_tool_qt/tool.py'
adding 'chimerax/tut_tool_qt/Installable/install_traj2nmr.py'
adding 'chimerax/tut_tool_qt/Installable/traj2nmr/LICENSE'
adding 'chimerax/tut_tool_qt/Installable/traj2nmr/README.md'
adding 'chimerax/tut_tool_qt/Installable/traj2nmr/setup.py'
adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/__init__.py'
adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/resonance.py'
adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/session.py'
adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/shifts.py'
adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/ucsf.py'
adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/utils.py'
adding 'chimerax/tut_tool_qt/Runnable/simCC.com'
adding 'chimerax/tut_tool_qt/Runnable/simNC.com'
adding 'chimerax/tut_tool_qt/Runnable/zncc.jar'
adding 'chimerax/tut_tool_qt/Runnable/zncc.sh'
adding 'ChimeraX_BphonTool-0.4.dist-info/METADATA'
adding 'ChimeraX_BphonTool-0.4.dist-info/WHEEL'
adding 'ChimeraX_BphonTool-0.4.dist-info/top_level.txt'
adding 'ChimeraX_BphonTool-0.4.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Distribution is in /home/crow/bphon/bphon/chimerax-plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl
[toolshed install](help:user/commands/toolshed.html#install)
/home/crow/bphon/bphon/chimerax-
plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl

[toolshed install /home/crow/bphon/bphon/chimerax-
plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-
any.whl](cxcmd:toolshed install /home/crow/bphon/bphon/chimerax-
plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl)

Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 517, in _pip_install
results = _run_logged_pip(command, logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 583, in _run_logged_pip
raise RuntimeError(s)
RuntimeError: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing /home/crow/bphon/bphon/chimerax-plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl
Requirement already satisfied: ChimeraX-Core~=1.1 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.4) (1.7.dev202307150241)
Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.4) (1.30.2)
Collecting mdtraj (from ChimeraX-BphonTool==0.4)
Using cached mdtraj-1.9.9.tar.gz (2.2 MB)
Installing build dependencies: started
Installing build dependencies: finished with status 'error'
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> [22 lines of output]
ERROR:
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/__main__.py", line 1044, in <module>
    exit_code = init(sys.argv)
                ^^^^^^^^^^^^^^
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/__main__.py", line 801, in init
    runpy.run_path(opts.run_path)
  File "<frozen runpy>", line 291, in run_path
  File "<frozen runpy>", line 98, in _run_module_code
  File "<frozen runpy>", line 88, in _run_code
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/pip/__pip-
runner__.py", line 49, in <module>
    assert __name__ == "__main__", "Cannot run __pip-runner__.py as a non-main
module"
           ^^^^^^^^^^^^^^^^^^^^^^
AssertionError: Cannot run __pip-runner__.py as a non-main module


[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/devel.py", line 174, in _run
unbound_method(bb, *args, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/bundle_builder/bundle_builder.py", line 154, in make_install
run(session, cmd)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/toolshed.py", line 301, in toolshed_install
ts.install_bundle(bundles, logger, **kw)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 916, in install_bundle
_install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall, session=session, no_deps=no_deps)
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 252, in _install_bundle
results = _pip_install(
^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 520, in _pip_install
raise UserError(str(e))
chimerax.core.errors.UserError: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing /home/crow/bphon/bphon/chimerax-plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl
Requirement already satisfied: ChimeraX-Core~=1.1 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.4) (1.7.dev202307150241)
Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.4) (1.30.2)
Collecting mdtraj (from ChimeraX-BphonTool==0.4)
Using cached mdtraj-1.9.9.tar.gz (2.2 MB)
Installing build dependencies: started
Installing build dependencies: finished with status 'error'
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> [22 lines of output]
ERROR:
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/__main__.py", line 1044, in <module>
    exit_code = init(sys.argv)
                ^^^^^^^^^^^^^^
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/core/__main__.py", line 801, in init
    runpy.run_path(opts.run_path)
  File "<frozen runpy>", line 291, in run_path
  File "<frozen runpy>", line 98, in _run_module_code
  File "<frozen runpy>", line 88, in _run_code
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/pip/__pip-
runner__.py", line 49, in <module>
    assert __name__ == "__main__", "Cannot run __pip-runner__.py as a non-main
module"
           ^^^^^^^^^^^^^^^^^^^^^^
AssertionError: Cannot run __pip-runner__.py as a non-main module


[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

From: Tom Goddard <goddard@sonic.net>
Sent: Thursday, August 24, 2023 9:49 PM
To: BARRY E DEZONIA <barry.dezonia@wisc.edu>
Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Trouble installing plugin
 
The ChimeraX daily build is using Python 3.11 and your error message includes paths to Python 3.9.  It will probably cause havoc if you have both in your same ChimeraX installation.

ChimeraX developers Greg or Zach who know more about Linux would have to comment on whether it is even possible to install ChimeraX over another ChimeraX without the original copy being deleted.  And they also work on the "devel install" command.

Tom


On Aug 24, 2023, at 12:08 PM, BARRY E DEZONIA via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

It is possible that on my home machine I installed the latest daily build over an earlier daily build.
From: BARRY E DEZONIA via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Sent: Thursday, August 24, 2023 6:33 AM
To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] Trouble installing plugin
 
I am having trouble installing a plugin I am developing. It works on one system I am using at work and fails on my system at home. The home system has the latest daily build on it. The work system has an earlier daily build on it.

This is what I try to do inside chimerax:

devel install ~/dev/bphon/chimerax-plugin/tut_tool_qt

And this is the installation error:

open /usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.pyTraceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.py", line 49, in <module>
assert __name__ == "__main__", "Cannot run __pip-runner__.py as a non-main module"
AssertionError: Cannot run __pip-runner__.py as a non-main module

Error opening python file /usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.py

Any idea what is happening? I may have run into this problem some time ago on the work computer and fixed it but I honestly don't know.

Please forward this to the bugs email list of it should go there instead. Thanks.

Sorry for yet another question. You guy seems very busy with mail recently.
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