Home   Manual

Input file gen still downloading scripts into the wrong directory

Scripts are being downloaded by 1.94 into the “other” directory rather than “commands” which is causing input file generation entries to not populate in the UI. Manually renaming the other directory to commands or otherwise moving these scripts successfully populates tgese entries on restart of avogadro.

Thanks for your message, I’d like to figure out what’s going on.

  • How did you install Avogadro? I ask because it seems like you’re not using the 1.94 release, which had some very specific code.
  • I assume based on your message that you’re using the plugin downloader to install the input generators. Can you attach a screenshot when it’s installing?

The plugin download code looks at a JSON file to know the “type” of different plugin scripts. The current JSON has no “other” listed.

{"name": "avogenerators", 
"repo": "https://github.com/OpenChemistry/avogenerators", 
"description": "Python input file generators for Avogadro 2", 
"updated_at": "2021-05-22T13:50:05Z", 
"branch": "master", 
"has_release": false, 
"release_version": "N/A", 
"zipball_url": "https://api.github.com/repos/OpenChemistry/avogenerators/zipball/master", "type": "inputGenerators"},

The other thing is that putting input generators into a “commands” directory doesn’t seem like it would work. Anything in the “commands” directory will be run with different API and ignored.

In order to end up in the new “Input” menu, input generators need to be in the “inputGenerators” directory.

Beyond how you installed it (e.g., are you sure you’re using 1.94 release?) can you show me screenshot of your Input menu?


How did you install Avogadro?

I used the flatpak link on the avogadro website.

Here’s what the about section:

The shortcut is using the following command to run avogadro: /usr/bin/flatpak run --branch=stable --arch=x86_64 --command=avogadro2 --file-forwarding org.openchemistry.Avogadro2 @@ %f @@

1.93 had been present before 1.94 so the directory structure from 1.93 was still there. Once the scripts were downloaded by avogadro, they were in the other directory. I restarted avogadro after this was done and only after moving the scripts from other to commands and re opening the program were they recognized. The weird part is that reversing that process or moving the scripts out of the ~/.local/share/OpenChemistry/Avogadro/ directory entirely doesn’t actually break things after the input generators are already recognized. It could be that it just doesn’t care what folder they’re in and takes a few restarts to recognize that they’re there? I have no idea.

I had to take a screenshot with my phone since printscreen won’t actually take a screenshot while the menu is open. Also is there supposed to be no background now? Everything behind it like the desktop just bleeds through:

That’s a bug fixed in the latest dev which will be released as 1.95. The code enables transparency, so it’s possible to save images with transparent background (e.g, for presentations, posters, etc.) but evidently, modern graphics cards and drivers take that to mean “make the window transparent.”

Right, makes sense. As I said, 1.94 (and later) should download things correctly.

It definitely cares what directory they’re in, but there could be a Flatpak or filesystem cache.

Just to clarify if you launch 1.94 from the Flatpak, open the Plugin Downloader and install generators, and some commands, where do they end up?


Yes its being lauched via flatpak. Other is where they ended up after downloading. It does not appear to be using that directory as temporary storage. The input generators didnt show up until the contents of the other directory were moved manually to commands though. After that, it didnt matter if they were there or not even after reboot of the system and theres nothing in flatpak’s cache directory. I suspect that the fact it was installed via flatpak has a lot to do with what I am seeing.

Also that transparency feature is pretty neat