Trouble with a daily build installing a plugin

[barry.dezonia@…]

Hello,

I am developing a plugin to be used in chimerax. We are using some components that have required the developers to fix some installing python modules from within chimerax  bugs so that we can make progress on our project.

Anyhow I have two Ubuntu 20.04 systems with different daily build versions of chimerax that behave differently when installing our plugin.

My system has this version of chimerax installed:

version 1.7.dev202306060017 (2023-06-06)

We needed this version because before this fix chimerax could not do "pip install mdtraj" correctly. Something to do with recursive module importing or something.

When I do "devel install <blah> <blah> <blah>" my plugin installs fine. It ends up in Tools :: General and I can launch and run it fine. I can also uninstall it with toolshed just fine too.

On the second system we are using chimerax from the daily build of July 14. This is because another bug was fixed that kept mdtraj from installing correctly if the system you were installing on also had python 2.7 in place. Or at least chimerax would try to run pip install under python 2.7.

On this system when I do "devel install ..." the plugin says it installed fine. But the plugin does not have any entry in Tools :: General. And when I use toolshed to try and uninstall it the program says the plugin is not installed.

Was there some change in the program between these two dates that would account for this behavior? I am going to list the install progress dump text from the failing system (July 14 build) below.

----------------------------------------------------------------------------------

devel install /home/harding/BPHON_installrunning 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/__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/docs
creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/docs/user
creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/docs/user/tools
copying build/lib/chimerax/tut_tool_qt/docs/user/tools/bphon.html -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/docs/user/tools
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-0.2-py3.11.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/ChimeraX_BphonTool-0.2.dist-info/WHEEL
creating 'dist/ChimeraX_BphonTool-0.2-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/docs/user/tools/bphon.html'
adding 'ChimeraX_BphonTool-0.2.dist-info/METADATA'
adding 'ChimeraX_BphonTool-0.2.dist-info/WHEEL'
adding 'ChimeraX_BphonTool-0.2.dist-info/top_level.txt'
adding 'ChimeraX_BphonTool-0.2.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Distribution is in /home/harding/BPHON_install/dist/ChimeraX_BphonTool-0.2-py3-none-any.whl
[toolshed install](help:user/commands/toolshed.html#install)
/home/harding/BPHON_install/dist/ChimeraX_BphonTool-0.2-py3-none-any.whl

[toolshed install
/home/harding/BPHON_install/dist/ChimeraX_BphonTool-0.2-py3-none-
any.whl](cxcmd:toolshed install
/home/harding/BPHON_install/dist/ChimeraX_BphonTool-0.2-py3-none-any.whl)

Errors may have occurred when running pip:
pip standard error:
---
DEPRECATION: Loading egg at /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/pandas-2.0.3-py3.11-linux-x86_64.egg is deprecated. pip 23.3 will enforce this behaviour change. A possible replacement is to use pip for package installation..
DEPRECATION: Loading egg at /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/traj2nmr-0.0.1-py3.11.egg is deprecated. pip 23.3 will enforce this behaviour change. A possible replacement is to use pip for package installation..
DEPRECATION: Loading egg at /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/nmrglue-0.9-py3.11.egg is deprecated. pip 23.3 will enforce this behaviour change. A possible replacement is to use pip for package installation..
DEPRECATION: Loading egg at /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/astunparse-1.6.3-py3.11.egg is deprecated. pip 23.3 will enforce this behaviour change. A possible replacement is to use pip for package installation..
DEPRECATION: Loading egg at /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/mdtraj-1.9.8-py3.11-linux-x86_64.egg is deprecated. pip 23.3 will enforce this behaviour change. A possible replacement is to use pip for package installation..
---
pip standard output:
---
Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing ./dist/ChimeraX_BphonTool-0.2-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==0.2) (1.7.dev202307150241)
Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.2) (1.30.2)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-UI~=1.0->ChimeraX-BphonTool==0.2) (1.1.1)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-UI~=1.0->ChimeraX-BphonTool==0.2) (1.2)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-UI~=1.0->ChimeraX-BphonTool==0.2) (1.0)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX-BphonTool==0.2) (1.1)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-Graphics~=1.0->ChimeraX-UI~=1.0->ChimeraX-BphonTool==0.2) (1.3)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-BphonTool==0.2) (1.0.1)
Installing collected packages: ChimeraX-BphonTool
Successfully installed ChimeraX-BphonTool-0.2
---
Successfully installed ChimeraX-BphonTool-0.2
No change in list of installed bundles

[pett]

Hi Barry,

The way plugins get installed in the daily build changed recently, and there is a problem if you installed plugins with a daily build before the change and then again after the change. You need to remove the directory where plugins are getting installed, which you can find with the "info path user versioned data" command in ChimeraX. Then you should be able to install plugins without this issue.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab