Re: Trouble installing plugin
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.
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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 http://simcc.com/ -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable copying build/lib/chimerax/tut_tool_qt/Runnable/simNC.com http://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 http://simcc.com/' adding 'chimerax/tut_tool_qt/Runnable/simNC.com http://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. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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OK. So, we decided to wipe some computers and start fresh to install our plugin. And using the daily build from a couple days ago and a daily build from 7-15 and always on a freshly built linux 20.04 system we are unable to install my plugin. However, it somehow installed in the past on my coworker's system (using 7-15 chimerax) and my system (using 6-6 chimerax). He and I can both repeatedly install and uninstall my plugin. But any clean system will not "devel install" the plugin. Below is the latest log output using the daily build from 7-15 (because we have one user successfully using it). I am at a real loss as to what is going on. FWIW the clean systems do also have python 2.7. I know recently you fixed a problem of installing a plugin on a system that has python 2.7 on it. Please let me know what I can do. Our plugin is alpha ready and if I can't get it easily installable then our project is at a standstill.
(Note that the pip upgrade message at the bottom of the log is unimportant. If we update pip as it says using its syntax pip will upgrade but "devel install" will still error out in the same way.)
devel install /home/solids/Downloads/bphon/chimerax-plugin/tut_tool_qtrunning build running build_py creating build creating build/lib creating build/lib/chimerax creating build/lib/chimerax/tut_tool_qt copying src/__init__.py -> build/lib/chimerax/tut_tool_qt copying src/tool.py -> build/lib/chimerax/tut_tool_qt creating build/lib/chimerax/tut_tool_qt/Installable copying src/Installable/install_traj2nmr.py -> build/lib/chimerax/tut_tool_qt/Installable creating build/lib/chimerax/tut_tool_qt/Installable/traj2nmr copying src/Installable/traj2nmr/README.md -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr copying src/Installable/traj2nmr/setup.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr copying src/Installable/traj2nmr/LICENSE -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr creating build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/session.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/resonance.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/ucsf.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/__init__.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/shifts.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/utils.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr creating build/lib/chimerax/tut_tool_qt/Runnable copying src/Runnable/simCC.com -> build/lib/chimerax/tut_tool_qt/Runnable copying src/Runnable/zncc.sh -> build/lib/chimerax/tut_tool_qt/Runnable copying src/Runnable/simNC.com -> build/lib/chimerax/tut_tool_qt/Runnable copying src/Runnable/zncc.jar -> build/lib/chimerax/tut_tool_qt/Runnable running bdist_wheel installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 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 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/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/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/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 copying build/lib/chimerax/tut_tool_qt/__init__.py -> 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 creating 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/zncc.sh -> 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 copying build/lib/chimerax/tut_tool_qt/Runnable/zncc.jar -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable running install_egg_info running egg_info creating ChimeraX_BphonTool.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 writing manifest file 'ChimeraX_BphonTool.egg-info/SOURCES.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/solids/Downloads/bphon/chimerax-plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl [toolshed install](help:user/commands/toolshed.html#install) /home/solids/Downloads/bphon/chimerax- plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl
[toolshed install /home/solids/Downloads/bphon/chimerax- plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none- any.whl](cxcmd:toolshed install /home/solids/Downloads/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 ./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 Downloading mdtraj-1.9.9.tar.gz (2.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 10.5 MB/s eta 0:00:00 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.
[notice] A new release of pip is available: 23.0 -> 23.2.1 [notice] To update, run: chimerax-daily -m pip install --upgrade 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 ./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 Downloading mdtraj-1.9.9.tar.gz (2.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 10.5 MB/s eta 0:00:00 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.
[notice] A new release of pip is available: 23.0 -> 23.2.1 [notice] To update, run: chimerax-daily -m pip install --upgrade pip ________________________________ From: Zach Pearson zjp@cgl.ucsf.edu Sent: Wednesday, August 30, 2023 4:48 PM To: Tom Goddard goddard@sonic.net; Gregory Couch gregc@cgl.ucsf.edu; BARRY E DEZONIA barry.dezonia@wisc.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Trouble installing plugin
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.comhttp://simcc.com/ -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable copying build/lib/chimerax/tut_tool_qt/Runnable/simNC.comhttp://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.comhttp://simcc.com/' adding 'chimerax/tut_tool_qt/Runnable/simNC.comhttp://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. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edumailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
If I had to hazard a guess I am wondering if someone made a change that affected the previous mdtraj install fix and mdtraj will no longer install. And since we have existing systems with mdtraj already installed our code never complains. Again we are successfully using daily builds 6-6 and 7-15 so maybe my idea is a red herring. ________________________________ From: BARRY E DEZONIA via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: Thursday, September 7, 2023 1:45 PM To: Zach Pearson zjp@cgl.ucsf.edu; Tom Goddard goddard@sonic.net; Gregory Couch gregc@cgl.ucsf.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: [chimerax-users] Re: Trouble installing plugin
OK. So, we decided to wipe some computers and start fresh to install our plugin. And using the daily build from a couple days ago and a daily build from 7-15 and always on a freshly built linux 20.04 system we are unable to install my plugin. However, it somehow installed in the past on my coworker's system (using 7-15 chimerax) and my system (using 6-6 chimerax). He and I can both repeatedly install and uninstall my plugin. But any clean system will not "devel install" the plugin. Below is the latest log output using the daily build from 7-15 (because we have one user successfully using it). I am at a real loss as to what is going on. FWIW the clean systems do also have python 2.7. I know recently you fixed a problem of installing a plugin on a system that has python 2.7 on it. Please let me know what I can do. Our plugin is alpha ready and if I can't get it easily installable then our project is at a standstill.
(Note that the pip upgrade message at the bottom of the log is unimportant. If we update pip as it says using its syntax pip will upgrade but "devel install" will still error out in the same way.)
devel install /home/solids/Downloads/bphon/chimerax-plugin/tut_tool_qtrunning build running build_py creating build creating build/lib creating build/lib/chimerax creating build/lib/chimerax/tut_tool_qt copying src/__init__.py -> build/lib/chimerax/tut_tool_qt copying src/tool.py -> build/lib/chimerax/tut_tool_qt creating build/lib/chimerax/tut_tool_qt/Installable copying src/Installable/install_traj2nmr.py -> build/lib/chimerax/tut_tool_qt/Installable creating build/lib/chimerax/tut_tool_qt/Installable/traj2nmr copying src/Installable/traj2nmr/README.md -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr copying src/Installable/traj2nmr/setup.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr copying src/Installable/traj2nmr/LICENSE -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr creating build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/session.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/resonance.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/ucsf.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/__init__.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/shifts.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/utils.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr creating build/lib/chimerax/tut_tool_qt/Runnable copying src/Runnable/simCC.com -> build/lib/chimerax/tut_tool_qt/Runnable copying src/Runnable/zncc.sh -> build/lib/chimerax/tut_tool_qt/Runnable copying src/Runnable/simNC.com -> build/lib/chimerax/tut_tool_qt/Runnable copying src/Runnable/zncc.jar -> build/lib/chimerax/tut_tool_qt/Runnable running bdist_wheel installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 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 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/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/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/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 copying build/lib/chimerax/tut_tool_qt/__init__.py -> 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 creating 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/zncc.sh -> 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 copying build/lib/chimerax/tut_tool_qt/Runnable/zncc.jar -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable running install_egg_info running egg_info creating ChimeraX_BphonTool.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 writing manifest file 'ChimeraX_BphonTool.egg-info/SOURCES.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/solids/Downloads/bphon/chimerax-plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl [toolshed install](help:user/commands/toolshed.html#install) /home/solids/Downloads/bphon/chimerax- plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl
[toolshed install /home/solids/Downloads/bphon/chimerax- plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none- any.whl](cxcmd:toolshed install /home/solids/Downloads/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 ./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 Downloading mdtraj-1.9.9.tar.gz (2.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 10.5 MB/s eta 0:00:00 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.
[notice] A new release of pip is available: 23.0 -> 23.2.1 [notice] To update, run: chimerax-daily -m pip install --upgrade 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 ./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 Downloading mdtraj-1.9.9.tar.gz (2.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 10.5 MB/s eta 0:00:00 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.
[notice] A new release of pip is available: 23.0 -> 23.2.1 [notice] To update, run: chimerax-daily -m pip install --upgrade pip ________________________________ From: Zach Pearson zjp@cgl.ucsf.edu Sent: Wednesday, August 30, 2023 4:48 PM To: Tom Goddard goddard@sonic.net; Gregory Couch gregc@cgl.ucsf.edu; BARRY E DEZONIA barry.dezonia@wisc.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Trouble installing plugin
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.comhttp://simcc.com/ -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable copying build/lib/chimerax/tut_tool_qt/Runnable/simNC.comhttp://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.comhttp://simcc.com/' adding 'chimerax/tut_tool_qt/Runnable/simNC.comhttp://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. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edumailto:chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
There is something weird going on in the ChimeraX when trying to install the mdtraj source code package. It works better in today's build, but I wouldn't considered it fixed yet. The bug is in ChimeraX's code that keeps its version of Python isolated from the system's Python.
If you happen to be using ChimeraX 1.6 on macOS, then you should not be experiencing this bug. mdtraj provides a macOS Python 3.9 binary package. And that bypasses all of the issues associated with installing a source package, and avoids the weirdness noted above. The ChimeraX daily build uses Python 3.11, so, at a minimum, you need a C++ compiler to install mdtraj. And that should be sufficient, the fact that it doesn't is a bug.
-- Greg
On 9/7/23 12:35, BARRY E DEZONIA wrote:
If I had to hazard a guess I am wondering if someone made a change that affected the previous mdtraj install fix and mdtraj will no longer install. And since we have existing systems with mdtraj already installed our code never complains. Again we are successfully using daily builds 6-6 and 7-15 so maybe my idea is a red herring.
*From:* BARRY E DEZONIA via ChimeraX-users chimerax-users@cgl.ucsf.edu *Sent:* Thursday, September 7, 2023 1:45 PM *To:* Zach Pearson zjp@cgl.ucsf.edu; Tom Goddard goddard@sonic.net; Gregory Couch gregc@cgl.ucsf.edu *Cc:* ChimeraX Users Help chimerax-users@cgl.ucsf.edu *Subject:* [chimerax-users] Re: Trouble installing plugin OK. So, we decided to wipe some computers and start fresh to install our plugin. And using the daily build from a couple days ago and a daily build from 7-15 and always on a freshly built linux 20.04 system we are unable to install my plugin. However, it somehow installed in the past on my coworker's system (using 7-15 chimerax) and my system (using 6-6 chimerax). He and I can both repeatedly install and uninstall my plugin. But any clean system will not "devel install" the plugin. Below is the latest log output using the daily build from 7-15 (because we have one user successfully using it). I am at a real loss as to what is going on. FWIW the clean systems do also have python 2.7. I know recently you fixed a problem of installing a plugin on a system that has python 2.7 on it. Please let me know what I can do. Our plugin is alpha ready and if I can't get it easily installable then our project is at a standstill.
(Note that the pip upgrade message at the bottom of the log is unimportant. If we update pip as it says using its syntax pip will upgrade but "devel install" will still error out in the same way.)
devel install /home/solids/Downloads/bphon/chimerax-plugin/tut_tool_qtrunning build running build_py creating build creating build/lib creating build/lib/chimerax creating build/lib/chimerax/tut_tool_qt copying src/__init__.py -> build/lib/chimerax/tut_tool_qt copying src/tool.py -> build/lib/chimerax/tut_tool_qt creating build/lib/chimerax/tut_tool_qt/Installable copying src/Installable/install_traj2nmr.py -> build/lib/chimerax/tut_tool_qt/Installable creating build/lib/chimerax/tut_tool_qt/Installable/traj2nmr copying src/Installable/traj2nmr/README.md -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr copying src/Installable/traj2nmr/setup.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr copying src/Installable/traj2nmr/LICENSE -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr creating build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/session.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/resonance.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/ucsf.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/__init__.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/shifts.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr copying src/Installable/traj2nmr/traj2nmr/utils.py -> build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr creating build/lib/chimerax/tut_tool_qt/Runnable copying src/Runnable/simCC.com -> build/lib/chimerax/tut_tool_qt/Runnable copying src/Runnable/zncc.sh -> build/lib/chimerax/tut_tool_qt/Runnable copying src/Runnable/simNC.com -> build/lib/chimerax/tut_tool_qt/Runnable copying src/Runnable/zncc.jar -> build/lib/chimerax/tut_tool_qt/Runnable running bdist_wheel installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 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 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/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/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/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 copying build/lib/chimerax/tut_tool_qt/__init__.py -> 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 creating 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/zncc.sh -> 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 copying build/lib/chimerax/tut_tool_qt/Runnable/zncc.jar -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable running install_egg_info running egg_info creating ChimeraX_BphonTool.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 writing manifest file 'ChimeraX_BphonTool.egg-info/SOURCES.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/solids/Downloads/bphon/chimerax-plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl [toolshed install](help:user/commands/toolshed.html#install) /home/solids/Downloads/bphon/chimerax- plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl
[toolshed install /home/solids/Downloads/bphon/chimerax- plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none- any.whl](cxcmd:toolshed install /home/solids/Downloads/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 ./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 Downloading mdtraj-1.9.9.tar.gz (2.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 10.5 MB/s eta 0:00:00 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.
[notice] A new release of pip is available: 23.0 -> 23.2.1 [notice] To update, run: chimerax-daily -m pip install --upgrade 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 ./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 Downloading mdtraj-1.9.9.tar.gz (2.2 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 10.5 MB/s eta 0:00:00 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.
[notice] A new release of pip is available: 23.0 -> 23.2.1 [notice] To update, run: chimerax-daily -m pip install --upgrade pip
*From:* Zach Pearson zjp@cgl.ucsf.edu *Sent:* Wednesday, August 30, 2023 4:48 PM *To:* Tom Goddard goddard@sonic.net; Gregory Couch gregc@cgl.ucsf.edu; BARRY E DEZONIA barry.dezonia@wisc.edu *Cc:* ChimeraX Users Help chimerax-users@cgl.ucsf.edu *Subject:* Re: [chimerax-users] Trouble installing plugin Per https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8927%C2%A0which 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 http://simcc.com/-> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable copying build/lib/chimerax/tut_tool_qt/Runnable/simNC.com http://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 http://simcc.com/' adding 'chimerax/tut_tool_qt/Runnable/simNC.com http://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. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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participants (3)
-
BARRY E DEZONIA -
Greg Couch -
Zach Pearson