Avogadro 2 1.102.0 prompts for an update and hangs on Pixi installation

Marco · October 24, 2025, 1:21pm

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I believe this to be a bug with Avogadro:
(Please describe your bug or issue)

Environment Information

Avogadro version: 1.102.0 AppImage
Operating system and version: Fedora 42

Actual Behavior

On startup, Avogadro shows an “update available” prompt even though it’s already the latest release.

When I try to install a Python extension, Avogadro attempts to run Pixi (which is not installed on my system) and then hangs indefinitely.

matterhorn103 · October 24, 2025, 1:33pm

I’ll let Geoff respond in more detail but note that Pixi is included within the AppImage bundle as of 1.102, so it isn’t necessary to have it on your system.

ghutchis · October 24, 2025, 1:49pm

Thanks for the bug report. I’m aware of the “update available” bug. We’ll release 1 1.102.1 to fix that one. (@matterhorn103 has suggested turning it off for Linux)

pixi is included as part of the AppImage, which is why it’s being used. Obviously it shouldn’t hang, but it would help to know:

what extension you’re trying to install
if there’s anything printed on the console / terminal

Marco · October 24, 2025, 1:56pm

I was trying to install avo_xtb, here is the terminal output, thanks!

terminal_output.txt (4.6 KB)

ghutchis · October 24, 2025, 1:59pm

Yes, I think avo_xtb could use an update for the new release (I have a pull request for @matterhorn103 Add pixi support or linux, mac, windows by ghutchis · Pull Request #74 · matterhorn103/avo_xtb · GitHub)

Marco · October 24, 2025, 2:07pm

Also, it seems that Avogadro can’t load the Python extensions that are already present, for example, I can’t find the ORCA input generator.
In the terminal output there are many lines like “Cannot load script …”.

ghutchis · October 24, 2025, 2:15pm

I can certainly start a build for an AppImage without pixi - the only thing I can think of is that it was unable to install the manifest to run the input generators or other scripts. So:

it finds pixi and tries to use it
it doesn’t have the pixi default environment

Since my 10 am meeting was cancelled, I’ll go spin that up.

github.com/OpenChemistry/avogadrolibs

For now, don't bundle pixi with the AppImage

master ← ghutchis:fix-appimage-pixi

opened 02:26PM - 24 Oct 25 UTC

ghutchis

+2 -2

Developer Certificate of Origin Version 1.1 Copyright (C) 2004, 2006 The Lin…ux Foundation and its contributors. 1 Letterman Drive Suite D4700 San Francisco, CA, 94129 Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Developer's Certificate of Origin 1.1 By making a contribution to this project, I certify that: (a) The contribution was created in whole or in part by me and I have the right to submit it under the open source license indicated in the file; or (b) The contribution is based upon previous work that, to the best of my knowledge, is covered under an appropriate open source license and I have the right under that license to submit that work with modifications, whether created in whole or in part by me, under the same open source license (unless I am permitted to submit under a different license), as indicated in the file; or (c) The contribution was provided directly to me by some other person who certified (a), (b) or (c) and I have not modified it. (d) I understand and agree that this project and the contribution are public and that a record of the contribution (including all personal information I submit with it, including my sign-off) is maintained indefinitely and may be redistributed consistent with this project or the open source license(s) involved.

ghutchis · October 24, 2025, 3:25pm

Okay, here’s the build:
https://github.com/OpenChemistry/avogadrolibs/actions/runs/18782803419/artifacts/4364541072

Javier_Cerezo · October 24, 2025, 4:44pm

Thanks for the thread, I actually got the same issues. I tried this new build, along with pixi installed via conda, but the problems persist:

The python plugins are not active (namely, the input generators)
The install bar remains forever

In my case, the issue with input generators is especially critical.

Many thanks for such a nice program!

Javier

ghutchis · October 24, 2025, 5:09pm

All I did in the build was remove pixi from the AppImage. If it’s available in your path, it will try to use it. So if you’re having problems with pixi, I’d remove it from your environment.

I suspect the problem is that the default environment isn’t getting installed for pixi to use. But I don’t have time to debug that right now.

(It should be installing a pyproject.toml in the plugin directory and then using that to create a default python environment.)

If Avogadro can’t find pixi it won’t use it.

ghutchis · October 24, 2025, 5:16pm

Actually, I’m thinking about this a bit more. I’d be curious for some opinions.

Pixi makes a bunch of things easier .. but many people already have conda or python set up to their liking.

So maybe for a 1.102.1 release, the default should be to use conda (or mamba etc.) if found. And use pixi only as a backup for users who don’t have it installed.

Thoughts?

JAVIER_CEREZO_BASTID · October 24, 2025, 6:38pm

Removing pixi leads to errors when trying to call it on startup. The program starts anyway, but input generators are still not showing up. They worked with previous versions and the Python scripts are already in the .local folder

Enviado desde Outlook para Android

ghutchis · October 24, 2025, 7:29pm

Can you please include the errors you’re seeing? If you’re using the new build and don’t have pixi it should not use it and defer to your python environment.

Marco · October 24, 2025, 8:13pm

I’m trying the latest AppImage, and now it doesn’t load any plugin.
The terminal output shows multiple lines like “Cannot load script […] Can’t find pixi in your path”

ghutchis · October 24, 2025, 8:53pm

Okay, I think I found that one thanks to your help.

Should be spun up in a few minutes:

github.com/OpenChemistry/avogadrolibs

Fix a bug with calling default python when pixi is not available

master ← ghutchis:fix-default-python

opened 08:45PM - 24 Oct 25 UTC

ghutchis

+10 -5

Developer Certificate of Origin Version 1.1 Copyright (C) 2004, 2006 The Lin…ux Foundation and its contributors. 1 Letterman Drive Suite D4700 San Francisco, CA, 94129 Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Developer's Certificate of Origin 1.1 By making a contribution to this project, I certify that: (a) The contribution was created in whole or in part by me and I have the right to submit it under the open source license indicated in the file; or (b) The contribution is based upon previous work that, to the best of my knowledge, is covered under an appropriate open source license and I have the right under that license to submit that work with modifications, whether created in whole or in part by me, under the same open source license (unless I am permitted to submit under a different license), as indicated in the file; or (c) The contribution was provided directly to me by some other person who certified (a), (b) or (c) and I have not modified it. (d) I understand and agree that this project and the contribution are public and that a record of the contribution (including all personal information I submit with it, including my sign-off) is maintained indefinitely and may be redistributed consistent with this project or the open source license(s) involved.

I’ll see if I can sort out another bug report about MMFF94 / GAFF force fields in the AppImage, but I’ll likely release a 1.102.1 release this weekend (including the update dialog fix).

ghutchis · October 24, 2025, 9:14pm

Okay, that should do it for python:
https://github.com/OpenChemistry/avogadrolibs/actions/runs/18791715744/artifacts/4367486206

Marco · October 25, 2025, 7:15am

I can confirm that it works now, thank you!

The only errors I get now in the terminal are that it can’t find the force field parameters for GAFF and MMFF94.

Edit: I’ve also noticed another issue:

I removed the OpenChemistry folder in ~/.local/share. When I try to install the avo_xtb plugin, the message window appears “Installing dependencies with…”, but now it uses pip instead of pixi. The process hangs, and the terminal shows the following messages:

qt.core.qobject.connect: QObject::connect: No such slot Avogadro::QtPlugins::DownloaderWidget::cancelInstallation()
qt.core.qobject.connect: QObject::connect: (receiver name: ‘DownloaderWidget’)
qt.core.qobject.connect: QObject::connect: No such slot Avogadro::QtPlugins::DownloaderWidget::installationFinished()
qt.core.qobject.connect: QObject::connect: (receiver name: ‘DownloaderWidget’)

However, I’ve noticed that if I wait for a while, then close and restart Avogadro, the XTB extension appears in the Extensions menu.

Then, when trying to install the crest or xtb plugins from the Extensions menu, their installation window closes unexpectedly without any message. The terminal shows multiple error and warning messages. I’ve attached the full output here:

xtb_crest_error.txt (10.1 KB)

Marco · October 25, 2025, 7:17am

That sounds like a good idea to me!

matterhorn103 · October 25, 2025, 11:07am

Just to note that it’s not just a problem with the avo_xtb plugin, I tested with the AppImage on my system and the same error occurs when trying to install the prerequisites for nanocar-avogadro:

qt.core.qobject.connect: QObject::connect: No such slot Avogadro::QtPlugins::DownloaderWidget::cancelInstallation()
qt.core.qobject.connect: QObject::connect:  (receiver name: 'DownloaderWidget')
qt.core.qobject.connect: QObject::connect: No such slot Avogadro::QtPlugins::DownloaderWidget::installationFinished()
qt.core.qobject.connect: QObject::connect:  (receiver name: 'DownloaderWidget')

matterhorn103 · October 25, 2025, 11:12am

avo_xtb very deliberately doesn’t actually have any dependencies, so I was confused as to why the problem is even arising.

What I guess is happening is that Avogadro/Pixi is trying to install the dev dependencies group from avo_xtb’s pyproject.toml. Since these aren’t required dependencies I’m not sure why it’s doing that – maybe that’s the default behaviour of Pixi?

For now, anyone who wants to install the avo_xtb plugin can click “No” when asked whether to install dependencies. The plugin doesn’t need them.

Edit: Having said that, if you choose “no” then the plugin doesn’t currently get installed, even though it’s downloaded, which I guess makes sense if it thinks that it can’t install it without deps.