openbabel-3.1* in Rawhide

[Antonio T. sagitter]

@fedora
These are some information for upgrading to openbabel3.

@epel7


Are we definitely interested?

Links of Copr projects to get srpms for testing:

It's also opened a bugzilla ticket (#1628243) for building openbabel-2.4.1 on epel7 openbabel3-3.1.1: https://copr.fedorainfracloud.org/coprs/sagitter/Openbabel-3/

openbabel2-2.4.1: https://copr.fedorainfracloud.org/coprs/sagitter/ForTesting/

On 9/1/21 10:35 AM, Mamoru TASAKA wrote:

Antonio T. sagitter wrote on 2021/09/01 16:58:

You're right, i underestimated the issue.




Thank you.

Probably, Avogadro is not compatible with openbabel3 but Avogadro2 should be. I try to keep a separated 'openbabel2' package as new rpm, and then upgrade current 'openbabel' to the release 3+

There is useful information on debian:
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946263

On 8/31/21 8:05 PM, Alexander Ploumistos wrote:

On Tue, Aug 31, 2021 at 6:08 PM Antonio T. sagitter
<sagit...@fedoraproject.org> wrote:

On 8/31/21 5:27 PM, Alexander Ploumistos wrote:

Which software are not ready for openbabel-3 yet?

We must decide if go forward with most recent software or stay stationary.

Almost two years ago (how time flies!), when the subject had been
first broached, Dominik provided this list:

Link-time dependencies:
IQmol
avogadro
ghemical

Okay with debian patch:

https://sources.debian.org/src/ghemical/3.0.0-5/debian/patches/openbabel3.patch/

I've applied this to Fedora git source.

gnome-chemistry-utils

debian says only a small modification is needed:
https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946263#20

kalzium
molsketch

xdrawchem

https://github.com/bryanherger/xdrawchem/pull/17

Run-time dependencies:
avogadro2
chemtool
molsketch


At the time, I think only Molsketch was compatible with Open Babel 3.
After getting version 3.1.1 to build[1], I spent a few weekends trying
to modify gnome-chemistry-utils, but due to lack of time I didn't go
very far and looking at the code in my files, I'm not really sure what
I've actually done, I don't remember much. Personally, I use avogadro*
a lot, which you maintain (and therefore I don't worry about it ;) )
and GChemCalc (almost daily) and sometimes GSpectrum from g-c-u,
neither of which is indispensable, though both are quite handy. I
haven't checked any of the other programs on that list recently, but
about a year ago, not much had changed.

I can leave to you an openbabel-3 srpm or Copr builds of it for your tests.

One week is a minimal time, no problem if you need more time.

As far as I can tell, Molsketch will use whichever version of Open
Babel is installed on the system and users of a couple of other
distros have been building it against v3 without any problems, so I
don't expect any either. Just please let me know when you've built it
in Rawhide and I'll do the rebuild then - hopefully the new version
will also be out by that time.


Best regards,
A.


1. https://copr.fedorainfracloud.org/coprs/alexpl/openbabel/builds/

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Antonio Trande
Fedora Project
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