id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9415 Trouble with a daily build installing a plugin barry.dezonia@… Eric Pettersen "{{{ 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 "" 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 }}} " defect closed normal Tool Shed duplicate chimera-programmers all ChimeraX