Creating flatpak package #161
Comments
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Great news! This was on my todo list. |
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Thanks for your approval. I have a question on different coot sources. Each of Release-1.1.10 source in git repo and Release-1.1.10 one in the homepage has different md5 checksum. Should I use which source to build the flatpak package? |
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The one on lmb-mrc web site. The other (from github) contains a lot of extra devel stuff. However, I notice that there the Note that 1.1.11 is on the horizon (i.e. 2 to 8 weeks away). |
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I submitted PR to flathub as I confirmed the package built locally using the manifest I made worked. Coot v1.1.10 will be available on Flathub after review. @pemsley |
Add "and cryo-EM reconstructions" Let's talk about the domain id. I don't have a web server for the domain id. I understand that I should have. Is that your understanding too? I am OK with buying one. |
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I think the ID is merely for namespace purposes. Therefore, there is no need to purchase a web server. The domain name and ID are solely for identification, and there is no need to actually buy a domain or set up a server to publish an app on Flathub. |
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Remove |
OK, we will remove it when bumping to version 1.1.11. |
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Which icon file should I use for coot desktop app that appear in the menubar/launcher? I've chosen However, |
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I think I need to do a better job at properly comprehending the coordgen configuration of the rdkit, so that the correct libraries are linked. |
This one. But it doesn't have the ATP. I should if see if the ATP version can be used. |
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I think ATP version is better, too. It makes clear this app is related to Chemistry/Biology. |
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This file depicts a coot holding a ATP altough the format is png. https://github.com/pemsley/coot/blob/main/pixmaps/coot-icon.png |
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I see that you've been making progress. |
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Is flapak for non-gui apps? How about Servalcat? |
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As far as I know, Flatpak is mainly for packaging GUI apps, but I believe CLI apps can be used as a part of the packaged app. I think you can use servalcat as a module in a Coot package using Flatpak, and use it as a CLI command, too. The servalcat executable binary should be placed in |
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@pemsley https://flathub.org/apps/manage/io.github.pemsley.coot Could you do this when you have time? |
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Coot is now available on Flathub! |
I logged into flathub.org via github, but I can't see the page, haha
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This is excellent news. Thank you for your work. @eunos-1128 After the installation in Ubuntu 24.04, I ran Coot launched with the error |
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Are you using NVIDIA GPUs? if so, try |
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@eunos-1128 Yes, I am using Nvidia GPUs. I already have Nvidia driver 550-107-02 installed in flatpak. I have uninstalled and reinstalled nvidia-550-107-02 in flatpak and still got the same errors. and
The PyMOL from flatpak utilized Nvidia GPUs just fine, so I don't think there are any problems with the flatpak Nvidia driver. |
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I made a change to the Flatpak manifest and rebuilt coot. Could you reinstall coot and test it again? |
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@eunos-1128 Thanks! I just uninstalled and reinstalled Coot in flatpak and still got the same errors. |
@pemsley |
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It seems that this has not yet been reflected in the official Flathub build. Could you try the test build with the following command after uninstalling coot? |
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@eunos-1128 Thanks! I just tried the test build and got the same errors. |
You can choose x11 or Wayland on login screen like this (this is for lightDM but you should be able to do so also on other display managers). You might want to try logging in to your Arch Linux with X11 and verify whether XWayland causes some problems. |
Did you try it? |
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Yes... I did try it (at last). |
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Will you update the flatpak coot version to 1.1.11? Thanks! |
Sorry for delayed reply. Now I'm working on it. After finishing to update Coot on flathub, I'll note here. |
Can I remove this option for building Release-1.1.11 though it still remains in build script for 1.1.11? |
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https://github.com/pemsley/coot/blob/main/build-it-3-3#L3804-L3805 This issue of build failure due to not including For Flatpak builds I don't see any problem with changing the RDKit version from Can I get your opinion? |
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I've updated Coot on flathub to 1.1.11. In case one wants to use more recent version, commit |
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@eunos-1128 Thanks! I encountered the old error. "Unable to create a GL context" in the display window. |
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@jianghaizhu And related to your above messages, I will see if I can find out what is going wrong with the metal distances. |
Hooray!
That seems like a good thing to do. |
Try these ones first. flatpak run io.github.pemsley.coot --opengl-es
flatpak run io.github.pemsley.coot -- --opengl-esIn bumping to 1.1.11, it seemed that Python 3.12 was required, so I adopted GNOME Runtime 47, which ships with Python 3.12.8, instead of GNOME 46. With that, the version of gtk4 included in GNOME47 was also increased, and it seems that If the commands with 1. flatpak run --env=GDK_DEBUG=opengl io.github.pemsley.coot
2. flatpak run --env=GDK_DEBUG=gl-prefer-gl io.github.pemsley.coot
3. flatpak run --env=GDK_DEBUG=glx io.github.pemsley.coot
4. flatpak run --env=GDK_BACKEND=x11 --env=GDK_DEBUG=opengl io.github.pemsley.coot
5. flatpak run --env=GDK_BACKEND=x11 --env=GDK_DEBUG=gl-prefer-gl io.github.pemsley.coot
6. flatpak run --env=GDK_BACKEND=x11 --env=GDK_DEBUG=glx io.github.pemsley.cootCould you share each result of the commands here? |
How about this? I've shipped 1.1.11 with |
In 1.1.11, this option is no longer an option, it is now a non-optional dependency - because it was needed by the new ligand tools. So, I think you should see a warning saying unknown option or some such, when you run configure. |
OK, I will remove this option for running |
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Now you are invited to Coot flatpak repo for verifying Coot on Flathub. Please remember to complete the following procedures before the deadline, and after joining the repo try to login porovider verification with your GitHub account.
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@eunos-1128
For your 6 commands, only 2 and 5 worked. The rest failed. |
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After I launched Coot 1.1.11 with |
OK noted. Coot should handle |
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@jianghaizhu ... OK, but more importantly can you see things now? The error messages that you see are the framebuffers failing to be setup correctly. I see messages like that myself. They are harmless in Basic mode. I will make a not to clean them up with |
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It works fine so far with limited usage. |
@pemsley Could you deal with this within the expiration date? |
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Try this test build, in which the current stable build fault for NVIDIA OpenGL should be fixed. flatpak install --user https://dl.flathub.org/build-repo/155614/io.github.pemsley.coot.flatpakrefI guess running even without And can you share the log on running? |
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I got the same GL context error as @jianghaizhu with an Nvidia GPU on Ubuntu 22.04. The test build suggested by @eunos-1128 works for me, even without Coot opens with the following terminal output: |
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Thank you for your cooperation! I've merged the fixed one, which will be available as the stable build about 5-6 hours later on flathub. |
OK, I checked out https://github.com/flathub/io.github.pemsley.coot and followed the instructions. Coot starts up OK when I use I have a core dump don't know how to use the debugger (I mean I don't know where the binary is). Note that this part of the code is about as close as software gets to hardware, so the issue might actually be the graphics drivers and not coot. |
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I logged into Flathub, but I get this message:
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Like @pemsley I also see such a crash when trying to do a tandem refinement |
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Update: I have learned how to use the debugger in flatpak. I have added protection to stop |
Have you taken the following steps?
Could you tell me which commands you used to debug?
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Hello,
Thank you very much for your wonderful software.
I thought that if coot could be used with modern GUI app runtimes such as Flatpak or Snap, many people would be able to easily install without building from source.
Since, I have created a Flatpak manifest for Coot 1.1 (GTK4-based) (not yet complete though). I have also confirmed that it works on my local PC.
If I can get permission, I would like to register the package to Flathub so that many people can access this app.
Regards,
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