Official Debian package

pemsley / coot

Software for macromolecular model-building

http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

GNU General Public License v3.0

114 stars 46 forks source link

Official Debian package #120

Open alexmyczko opened 4 months ago

alexmyczko commented 4 months ago

There's the intent to package at https://bugs.debian.org/897673 and the current public state: https://salsa.debian.org/science-team/coot and then there's some success on a local machine that builds 1.1.07 and if software builds successfully, it's likely to also work and be packagable... (Using this place to keep track of the history of building the package)

correction: almost success

[100%] Linking CXX executable test-molecules-container
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libssm.so: undefined reference to `mmdb::Atom::Transform(double (&) [4][4])'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/libssm.so: undefined reference to `mmdb::Mat4Copy(double (&) [4][4], double (&) [4][4])'
collect2: error: ld returned 1 exit status

Just to see where we are: https://repology.org/project/coot/versions (comparisons are bad, Paul Watzlawik, Situation is Hopeless, But Not Serious, The Pursuit of Unhappiness)

pemsley commented 1 month ago

Should I add a workaround for when git is not available when autogen.sh is run?

This would be really nice to have.

OK, done (it seems to me).

I am thinking to release 1.1.09 in a week or so, for the record.

merkys commented 1 month ago

I noticed /usr/libexec/coot-bin has been renamed to /usr/libexec/Coot in 1.1.08, which went smoothly in Debian package update. However, were there any other important path changes? The main coot executable fails to launch for me after the update:

ERROR:: Failure to read or parse /usr/share/coot/ui/coot-gtk4.ui
No function named `on_active_map_ok_button_clicked`.

merkys commented 4 weeks ago

I noticed /usr/libexec/coot-bin has been renamed to /usr/libexec/Coot in 1.1.08, which went smoothly in Debian package update. However, were there any other important path changes? The main coot executable fails to launch for me after the update:
ERROR:: Failure to read or parse /usr/share/coot/ui/coot-gtk4.ui
No function named `on_active_map_ok_button_clicked`.

Commit https://github.com/pemsley/coot/commit/a0fbdb6c679b30c576f3ea8ff438f44ee50cc612 fixes this issue.

pemsley commented 4 weeks ago

Commit a0fbdb6c679b30c576f3ea8ff438f44ee50cc612 fixes this issue

Hmm. Yes. What do you need me to do?

For the record (1.1.09+) I have changed the coot shell script again. Now it is a minimal wrapper.

merkys commented 3 weeks ago

Hmm. Yes. What do you need me to do?

Noting, actually. I just described the failure as I thought you were not aware of it. I have not tried the master branch before bothering you. Then I did some bisecting and noticed there was a fix in post-1.1.08.

For the record (1.1.09+) I have changed the coot shell script again. Now it is a minimal wrapper.

OK. I think layla also needs a thin wrapper in Debian to set the LD_LIBRARY_PATH accordingly.

pemsley commented 2 weeks ago

Would it be OK to build Coot for the Hurd without --with-sound? Is that a "doable" thing in Debian-land?

alexmyczko commented 2 weeks ago

@pemsley debian/rules file is a makefile. technically that is no problem to do.

pemsley commented 2 weeks ago

I am working on XDG base today and will hopefully get that done and release 1.1.09 tomorrow.

merkys commented 2 weeks ago

Would it be OK to build Coot for the Hurd without --with-sound? Is that a "doable" thing in Debian-land?

To add to @alexmyczko reply, architecture-specific build options are an usual practice in Debian. I will try to do so for the next upload.

jianghaizhu commented 2 days ago

How do I install the Debian Coot package in Ubuntu 22.04? Apt couldn't find Coot since it is in SID.

merkys commented 2 days ago

@jianghaizhu Coot is slated to appear in the next Ubuntu release. New packages are not included into already released Ubuntu releases.

jianghaizhu commented 2 days ago

@merkys Thanks! I see. Will it be available for the next 22.0 minor update or 24.0 versions?

I guess I will have to either compile it from the source code or use Linuxbrew for now.

merkys commented 1 day ago

@merkys Thanks! I see. Will it be available for the next 22.0 minor update or 24.0 versions?

It will appear in Ubuntu 24.10.

I guess I will have to either compile it from the source code or use Linuxbrew for now.

Another option would be to install Debian sid in Apptainer/Singularity or another type of container.

alexmyczko commented 1 day ago

another to use abp: https://github.com/alexmyczko/autoexec.bat/blob/master/abp

during manual test easy for debian 12, not so much for ubuntu 22.04