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Opened 2 years ago
Last modified 2 years ago
#10027 assigned task
Installing a python module at plugin start/load
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Greg Couch, Tom Goddard, Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
This might not be a bug but it is definitely an email for the developers.
I am trying to build a plugin with a nice user experience. One aspect of that is that it will look for a plugin (traj2nmr) and if it is not installed it will install it. This was siggested by one of the developers some onths ago.
My process is kind of working. I am using a daily build (from June that I am loathe to update since all other aspects of our project works with it and I am the sole developer).
Anyhow my code installs the plugin and it ends up in /home/bdezonia/.local/share/ChimeraX/1.7/lib/python/traj2nmr-0.0.1-py3.9.egg.
Now when I start my app it can't import traj2nmr even after it just successfully installed. Python must not be looking in that directory above.
Someone told me to install tra2nmr in the chimerax.apps.user_dir. Maybe that is /home/bdezonia/.local/share/ChimeraX/1.7/site-packages/? Anyhow traj2nmr is not in there. And I'm not sure I am accurate about the value of chimerax.apps.user_dir I just mentioned.
It is not here either: /lib/ucsf-chimerax-daily/lib/python3.9. (Yes, I know 3.11 is the version expected but it was not back in June I think). We can't install here because the app installs traj2nmr at plugin startup and needs a directory the current user has permissions to write to.
Can you tell me where my traj2nmr package should get installed to so that it can be found by ChimeraX (e.g. its python I think)? The traj2nmr module is old and uses easyinstall and a "python setup.py install" approach. I don't have a lot of control where traj2nmr gets installed once it is running.
Any pointers appreciated. Let me know what other info you might need to help come up with a solution. Thanks.
Change History (11)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Third Party |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Type: | defect → task |
comment:2 by , 2 years ago
I would clear out /home/bdezonia/.local/share/ChimeraX/1.7 and get a more recent daily build. Greg and I have been working out how ChimeraX installs and finds its packages for the upcoming release, so the behavior will be closer to the actual behavior in 1.7 and if it _still_ doesn't work we need to know so we can fix it.
comment:3 by , 2 years ago
I believe this in reference to this thread: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/thread/2JK2LPAWFZSP2WM6IQEARE62GFS5KQV4/#2JK2LPAWFZSP2WM6IQEARE62GFS5KQV4 where I suggested various ways to install traj2nmr into ChimeraX's user plugin directory.
comment:4 by , 2 years ago
Well, not really "user plugin directory" but rather where ChimeraX's Python looks for user-installed modules.
comment:5 by , 2 years ago
OK. Thanks for all the feedback. I will start working on the issues a piece at a time.
It took me a while to be able to produce the install program string. It is a script I run and it is doing this:
cd /home/bdezonia/.local/share/ChimeraX/1.7/lib/python3.11/site-packages/chimerax/tut_tool_qt/Installable/traj2nmr; /usr/bin/chimerax-daily --nogui --script 'setup.py install --home="/home/bdezonia/.local/share/ChimeraX/1.7"' --exit
tut_tool_qt is my app and installable is a directory in it where I keep the traj2nmr source to be able to install from at runtime.
I did install yesterday's daily build. When I install my plugin it says "No bundles were installed" but it also says "Installed ChimeraX-BphonTool (0.4)" which is my plugin. The command is present in the Tools :: General menu. When I run the plugin it is trying to load and in my code where it tries to import traj2nmr it says it can't find it. But just a line or two earlier it is getting installed and I can see that code is being run because I can instrument the call. That is the "cd /home/bdezonia-blah-blah-blah ..." I mentioned above. Trying to uninstall then says "No change in list of installed bundles". And the plugin is still in Tools::General.
Note that if I install my plugin and then exit and then run it again it can't find traj2nmr. So it is not the case that some internal tracking variable has not been updated by the at-runtime plugin install.
Maybe the plugin is still in the Tools menu because it might have cruft from an earlier installation? When I installed the daily build I had to do some hand uninstallation. Before reinstall I had cleared /home/bdezonia/.local/share/ChimeraX/1.7 though.
Note that traj2nmr's egg file looks to be at:
/home/bdezonia/.local/share/ChimeraX/1.7/lib/python/traj2nmr-0.0.1-py3.11.egg
That's a lot of information for you to take in. I am going to continue doing some of your suggestions but please critique any issues you see. Thanks.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, October 20, 2023 11:55 AM
To: zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>; BARRY E DEZONIA <barry.dezonia@wisc.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #10027: Installing a python module at plugin start/load
#10027: Installing a python module at plugin start/load
--------------------------------------+--------------------------
Reporter: barry.dezonia@… | Owner: Zach Pearson
Type: task | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+--------------------------
Comment (by pett):
Well, not really "user plugin directory" but rather where ChimeraX's
Python looks for user-installed modules.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10027#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:6 by , 2 years ago
In response to the system paths chimerax is seeing here is the output from a python shell in chimerax:
import sys
sys.path
Out[2]:
['/home/bdezonia/.local/share/ChimeraX/1.7/lib/python3.11/site-packages',
'/usr/lib/ucsf-chimerax-daily/lib/python311.zip',
'/usr/lib/ucsf-chimerax-daily/lib/python3.11',
'/usr/lib/ucsf-chimerax-daily/lib/python3.11/lib-dynload',
'/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages']
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, October 20, 2023 1:17 PM
To: zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>; BARRY E DEZONIA <barry.dezonia@wisc.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #10027: Installing a python module at plugin start/load
#10027: Installing a python module at plugin start/load
--------------------------------------+--------------------------
Reporter: barry.dezonia@… | Owner: Zach Pearson
Type: task | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+--------------------------
Comment (by barry.dezonia@…):
{{{
OK. Thanks for all the feedback. I will start working on the issues a
piece at a time.
It took me a while to be able to produce the install program string. It is
a script I run and it is doing this:
cd /home/bdezonia/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/tut_tool_qt/Installable/traj2nmr; /usr/bin/chimerax-
daily --nogui --script 'setup.py install
--home="/home/bdezonia/.local/share/ChimeraX/1.7"' --exit
tut_tool_qt is my app and installable is a directory in it where I keep
the traj2nmr source to be able to install from at runtime.
I did install yesterday's daily build. When I install my plugin it says
"No bundles were installed" but it also says "Installed ChimeraX-BphonTool
(0.4)" which is my plugin. The command is present in the Tools :: General
menu. When I run the plugin it is trying to load and in my code where it
tries to import traj2nmr it says it can't find it. But just a line or two
earlier it is getting installed and I can see that code is being run
because I can instrument the call. That is the "cd /home/bdezonia-blah-
blah-blah ..." I mentioned above. Trying to uninstall then says "No change
in list of installed bundles". And the plugin is still in Tools::General.
Note that if I install my plugin and then exit and then run it again it
can't find traj2nmr. So it is not the case that some internal tracking
variable has not been updated by the at-runtime plugin install.
Maybe the plugin is still in the Tools menu because it might have cruft
from an earlier installation? When I installed the daily build I had to do
some hand uninstallation. Before reinstall I had cleared
/home/bdezonia/.local/share/ChimeraX/1.7 though.
Note that traj2nmr's egg file looks to be at:
/home/bdezonia/.local/share/ChimeraX/1.7/lib/python/traj2nmr-0.0.1-py3.11.egg
That's a lot of information for you to take in. I am going to continue
doing some of your suggestions but please critique any issues you see.
Thanks.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, October 20, 2023 11:55 AM
To: zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>; BARRY E DEZONIA
<barry.dezonia@wisc.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregc@cgl.ucsf.edu
<gregc@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #10027: Installing a python module at plugin
start/load
#10027: Installing a python module at plugin start/load
--------------------------------------+--------------------------
Reporter: barry.dezonia@… | Owner: Zach Pearson
Type: task | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+--------------------------
Comment (by pett):
Well, not really "user plugin directory" but rather where ChimeraX's
Python looks for user-installed modules.
--
Ticket URL:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10027#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
}}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10027#comment:5>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:7 by , 2 years ago
Using setuptools flags (--user --prefix=) the setup.py program the setuptools output is saying:
"Copying traj2nmr-0.0.1-py3.11.egg to /home/bdezonia/.local/share/ChimeraX/1.7/lib/python3.11/site-packages"
This looks perfect.
If I run once it cannot import traj2nmr. But if I exit and run a second time it does find it. I think this part of the mystery is fixed.
The remaining issues are why does my plugin say no bundles added and my uninstall result say my plugin was not installed. All the while I can run my plugin.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, October 20, 2023 1:41 PM
To: BARRY E DEZONIA <barry.dezonia@wisc.edu>; zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #10027: Installing a python module at plugin start/load
#10027: Installing a python module at plugin start/load
--------------------------------------+--------------------------
Reporter: barry.dezonia@… | Owner: Zach Pearson
Type: task | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+--------------------------
Comment (by barry.dezonia@…):
{{{
In response to the system paths chimerax is seeing here is the output from
a python shell in chimerax:
import sys
sys.path
Out[2]:
['/home/bdezonia/.local/share/ChimeraX/1.7/lib/python3.11/site-packages',
'/usr/lib/ucsf-chimerax-daily/lib/python311.zip',
'/usr/lib/ucsf-chimerax-daily/lib/python3.11',
'/usr/lib/ucsf-chimerax-daily/lib/python3.11/lib-dynload',
'/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages']
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, October 20, 2023 1:17 PM
To: zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>; BARRY E DEZONIA
<barry.dezonia@wisc.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregc@cgl.ucsf.edu
<gregc@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #10027: Installing a python module at plugin
start/load
#10027: Installing a python module at plugin start/load
--------------------------------------+--------------------------
Reporter: barry.dezonia@… | Owner: Zach Pearson
Type: task | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+--------------------------
Comment (by barry.dezonia@…):
{{{
OK. Thanks for all the feedback. I will start working on the issues a
piece at a time.
It took me a while to be able to produce the install program string. It
is
a script I run and it is doing this:
cd /home/bdezonia/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/tut_tool_qt/Installable/traj2nmr; /usr/bin/chimerax-
daily --nogui --script 'setup.py install
--home="/home/bdezonia/.local/share/ChimeraX/1.7"' --exit
tut_tool_qt is my app and installable is a directory in it where I keep
the traj2nmr source to be able to install from at runtime.
I did install yesterday's daily build. When I install my plugin it says
"No bundles were installed" but it also says "Installed ChimeraX-
BphonTool
(0.4)" which is my plugin. The command is present in the Tools :: General
menu. When I run the plugin it is trying to load and in my code where it
tries to import traj2nmr it says it can't find it. But just a line or two
earlier it is getting installed and I can see that code is being run
because I can instrument the call. That is the "cd /home/bdezonia-blah-
blah-blah ..." I mentioned above. Trying to uninstall then says "No
change
in list of installed bundles". And the plugin is still in Tools::General.
Note that if I install my plugin and then exit and then run it again it
can't find traj2nmr. So it is not the case that some internal tracking
variable has not been updated by the at-runtime plugin install.
Maybe the plugin is still in the Tools menu because it might have cruft
from an earlier installation? When I installed the daily build I had to
do
some hand uninstallation. Before reinstall I had cleared
/home/bdezonia/.local/share/ChimeraX/1.7 though.
Note that traj2nmr's egg file looks to be at:
/home/bdezonia/.local/share/ChimeraX/1.7/lib/python/traj2nmr-0.0.1-py3.11.egg
That's a lot of information for you to take in. I am going to continue
doing some of your suggestions but please critique any issues you see.
Thanks.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, October 20, 2023 11:55 AM
To: zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>; BARRY E DEZONIA
<barry.dezonia@wisc.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregc@cgl.ucsf.edu
<gregc@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #10027: Installing a python module at plugin
start/load
#10027: Installing a python module at plugin start/load
--------------------------------------+--------------------------
Reporter: barry.dezonia@… | Owner: Zach Pearson
Type: task | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+--------------------------
Comment (by pett):
Well, not really "user plugin directory" but rather where ChimeraX's
Python looks for user-installed modules.
--
Ticket URL:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10027#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
}}}
--
Ticket URL:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10027#comment:5>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
}}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10027#comment:6>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:8 by , 2 years ago
We can open a new bug if you like.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, October 20, 2023 2:42 PM
To: zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>; BARRY E DEZONIA <barry.dezonia@wisc.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #10027: Installing a python module at plugin start/load
#10027: Installing a python module at plugin start/load
--------------------------------------+--------------------------
Reporter: barry.dezonia@… | Owner: Zach Pearson
Type: task | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+--------------------------
Comment (by barry.dezonia@…):
{{{
Using setuptools flags (--user --prefix=) the setup.py program the
setuptools output is saying:
"Copying traj2nmr-0.0.1-py3.11.egg to
/home/bdezonia/.local/share/ChimeraX/1.7/lib/python3.11/site-packages"
This looks perfect.
If I run once it cannot import traj2nmr. But if I exit and run a second
time it does find it. I think this part of the mystery is fixed.
The remaining issues are why does my plugin say no bundles added and my
uninstall result say my plugin was not installed. All the while I can run
my plugin.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, October 20, 2023 1:41 PM
To: BARRY E DEZONIA <barry.dezonia@wisc.edu>; zjp@cgl.ucsf.edu
<zjp@cgl.ucsf.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregc@cgl.ucsf.edu
<gregc@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #10027: Installing a python module at plugin
start/load
#10027: Installing a python module at plugin start/load
--------------------------------------+--------------------------
Reporter: barry.dezonia@… | Owner: Zach Pearson
Type: task | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+--------------------------
Comment (by barry.dezonia@…):
{{{
In response to the system paths chimerax is seeing here is the output
from
a python shell in chimerax:
import sys
sys.path
Out[2]:
['/home/bdezonia/.local/share/ChimeraX/1.7/lib/python3.11/site-packages',
'/usr/lib/ucsf-chimerax-daily/lib/python311.zip',
'/usr/lib/ucsf-chimerax-daily/lib/python3.11',
'/usr/lib/ucsf-chimerax-daily/lib/python3.11/lib-dynload',
'/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages']
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, October 20, 2023 1:17 PM
To: zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>; BARRY E DEZONIA
<barry.dezonia@wisc.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregc@cgl.ucsf.edu
<gregc@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #10027: Installing a python module at plugin
start/load
#10027: Installing a python module at plugin start/load
--------------------------------------+--------------------------
Reporter: barry.dezonia@… | Owner: Zach Pearson
Type: task | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+--------------------------
Comment (by barry.dezonia@…):
{{{
OK. Thanks for all the feedback. I will start working on the issues a
piece at a time.
It took me a while to be able to produce the install program string. It
is
a script I run and it is doing this:
cd /home/bdezonia/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/tut_tool_qt/Installable/traj2nmr; /usr/bin/chimerax-
daily --nogui --script 'setup.py install
--home="/home/bdezonia/.local/share/ChimeraX/1.7"' --exit
tut_tool_qt is my app and installable is a directory in it where I keep
the traj2nmr source to be able to install from at runtime.
I did install yesterday's daily build. When I install my plugin it says
"No bundles were installed" but it also says "Installed ChimeraX-
BphonTool
(0.4)" which is my plugin. The command is present in the Tools ::
General
menu. When I run the plugin it is trying to load and in my code where it
tries to import traj2nmr it says it can't find it. But just a line or
two
earlier it is getting installed and I can see that code is being run
because I can instrument the call. That is the "cd /home/bdezonia-blah-
blah-blah ..." I mentioned above. Trying to uninstall then says "No
change
in list of installed bundles". And the plugin is still in
Tools::General.
Note that if I install my plugin and then exit and then run it again it
can't find traj2nmr. So it is not the case that some internal tracking
variable has not been updated by the at-runtime plugin install.
Maybe the plugin is still in the Tools menu because it might have cruft
from an earlier installation? When I installed the daily build I had to
do
some hand uninstallation. Before reinstall I had cleared
/home/bdezonia/.local/share/ChimeraX/1.7 though.
Note that traj2nmr's egg file looks to be at:
/home/bdezonia/.local/share/ChimeraX/1.7/lib/python/traj2nmr-0.0.1-py3.11.egg
That's a lot of information for you to take in. I am going to continue
doing some of your suggestions but please critique any issues you see.
Thanks.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, October 20, 2023 11:55 AM
To: zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>; BARRY E DEZONIA
<barry.dezonia@wisc.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregc@cgl.ucsf.edu
<gregc@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #10027: Installing a python module at plugin
start/load
#10027: Installing a python module at plugin start/load
--------------------------------------+--------------------------
Reporter: barry.dezonia@… | Owner: Zach Pearson
Type: task | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+--------------------------
Comment (by pett):
Well, not really "user plugin directory" but rather where ChimeraX's
Python looks for user-installed modules.
--
Ticket URL:
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ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
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}}}
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Ticket URL:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10027#comment:5>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
}}}
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Ticket URL:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10027#comment:6>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
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}}}
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Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10027#comment:7>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:9 by , 2 years ago
To get ChimeraX/Python to notice your newly installed bundle immediately, try this after the install:
import importlib
importlib.invalidate_caches()
comment:10 by , 2 years ago
Regarding importlib.invalidate_cache() I was sure that would work when I read it but alas it does not. In the worst case I can throw up a dialog quitting my app and telling the user to restart chimerax. But it sounds like that should not be necessary. Any pointers?
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, October 20, 2023 4:05 PM
To: zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>; BARRY E DEZONIA <barry.dezonia@wisc.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #10027: Installing a python module at plugin start/load
#10027: Installing a python module at plugin start/load
--------------------------------------+--------------------------
Reporter: barry.dezonia@… | Owner: Zach Pearson
Type: task | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+--------------------------
Comment (by pett):
To get ChimeraX/Python to notice your newly installed bundle immediately,
try this after the install:
import importlib
importlib.invalidate_caches()
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10027#comment:9>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:11 by , 2 years ago
Sorry for the noise. I think this cache invalidation problem is a python bug. I see a handful of posts from the python developers on similar topics and some hedging on how to solve things. I'll investigate a bit more.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, October 24, 2023 11:15 AM
To: zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>; BARRY E DEZONIA <barry.dezonia@wisc.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #10027: Installing a python module at plugin start/load
#10027: Installing a python module at plugin start/load
--------------------------------------+--------------------------
Reporter: barry.dezonia@… | Owner: Zach Pearson
Type: task | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+--------------------------
Comment (by barry.dezonia@…):
{{{
Regarding importlib.invalidate_cache() I was sure that would work when I
read it but alas it does not. In the worst case I can throw up a dialog
quitting my app and telling the user to restart chimerax. But it sounds
like that should not be necessary. Any pointers?
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, October 20, 2023 4:05 PM
To: zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>; BARRY E DEZONIA
<barry.dezonia@wisc.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; gregc@cgl.ucsf.edu
<gregc@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #10027: Installing a python module at plugin
start/load
#10027: Installing a python module at plugin start/load
--------------------------------------+--------------------------
Reporter: barry.dezonia@… | Owner: Zach Pearson
Type: task | Status: assigned
Priority: normal | Milestone:
Component: Third Party | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
--------------------------------------+--------------------------
Comment (by pett):
To get ChimeraX/Python to notice your newly installed bundle immediately,
try this after the install:
import importlib
importlib.invalidate_caches()
--
Ticket URL:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10027#comment:9>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
}}}
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/10027#comment:10>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
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Hi Barry,