Hello Antonio,

On Tue, Aug 31, 2021 at 5:03 PM Antonio T. sagitter <sagitter(a)fedoraproject.org&gt; wrote: > > openbabel-3.1.1 is ready for Rawhide branch. 'libopenbabel' soname is > updated from 5 to 7, all dependent packages will need a rebuild at least: What about the packages that haven't been ported to work with Open Babel 3.* yet?

Do you intend to keep v2 around in some form?

> $ repoquery --whatrequires openbabel-devel --disablerepo=* > --enablerepo=*-source > > molsketch-0:0.7.2-1.fc34.src I'm waiting for Hendrik to release a new version sometime soon, at worst let it FTBFS and I'll deal with it in time.

All the best, A. _______________________________________________ devel mailing list -- devel(a)lists.fedoraproject.org To unsubscribe send an email to devel-leave(a)lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure

On Tue, Aug 31, 2021 at 6:08 PM Antonio T. sagitter <sagitter(a)fedoraproject.org&gt; wrote: > > On 8/31/21 5:27 PM, Alexander Ploumistos wrote: >> > > We must decide if go forward with most recent software or stay stationary. > Which software are not ready for openbabel-3 yet? Almost two years ago (how time flies!), when the subject had been first broached, Dominik provided this list: Link-time dependencies: IQmol avogadro ghemical gnome-chemistry-utils kalzium molsketch xdrawchem 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/

Antonio T. sagitter wrote on 2021/09/01 16:58: > You're right, i underestimated the issue. > 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+ > > Thank you. There is useful information on debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946263

Antonio T. sagitter wrote on 2021/09/01 16:58: > You're right, i underestimated the issue. > 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+ > > Thank you. 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 >> <sagitter(a)fedoraproject.org&gt; wrote: >>> >>> On 8/31/21 5:27 PM, Alexander Ploumistos wrote: >>>> >>> >>> We must decide if go forward with most recent software or stay >>> stationary. >>> Which software are not ready for openbabel-3 yet? >> >> 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... 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/ >> >

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

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

I will try with a Fedora 34 VM later and report back.

On Sat, Sep 25, 2021 at 5:10 PM Alexander Ploumistos <alex.ploumistos(a)gmail.com&gt; wrote: > I built the latest avogadro2 and avogadro2-libs from the srpm in your > copr for F34 and I hit some graphical glitches again. On Wayland, > Avogadro2 for X11 has a transparent canvas, whereas the other one (I > guess Wayland) doesn't, but as soon as I add a fourth atom to the > drawing, it crashes: > > /usr/include/c++/11/bits/stl_vector.h:1045: std::vector<_Tp, > _Alloc>::reference std::vector<_Tp, > _Alloc>::operator[](std::vector<_Tp, _Alloc>::size_type) [with _Tp = > Eigen::Matrix<double, 3, 1>; _Alloc = > std::allocator<Eigen::Matrix<double, 3, 1> >; std::vector<_Tp, > _Alloc>::reference = Eigen::Matrix<double, 3, 1>&; std::vector<_Tp, > _Alloc>::size_type = long unsigned int]: Assertion '__n < > this->size()' failed. > Aborted (core dumped) I don't know if this is the same as the inchi-related abort, but that one is caused by this code, on lines 178-180 of molecule_smiles.cpp, in Molecule::ToInChI(): std::string s = ostream.str(); s[s.length() - 1] = '\0'; // Abort happens here return ( QString( s.c_str() ) ); The abort happens because s is the empty string, so s.length() == 0, and assigning to s[-1] just isn't a good idea. I'm pretty sure that line isn't needed anyway. Isn't s.c_str() guaranteed to provide a null-terminated C string?

Returns a pointer to an array that contains a null-terminated sequence of characters (i.e., a C-string) representing the current value of the string object.

We are ready to push openbabel3 in Rawhide

Hello Antonio, On Sun, Oct 24, 2021 at 3:05 PM Antonio T. sagitter <sagitter(a)fedoraproject.org&gt; wrote: > > We are ready to push openbabel3 in Rawhide Will it be just Rawhide? Will you please let us know when the build is done in order to rebuild dependent packages?

Are we saying goodbye to Avogadro 1.x? Thank you for all the work you've put into this, A. _______________________________________________ devel mailing list -- devel(a)lists.fedoraproject.org To unsubscribe send an email to devel-leave(a)lists.fedoraproject.org Fedora Code of Conduct: https://docs.fedoraproject.org/en-US/project/code-of-conduct/ List Guidelines: https://fedoraproject.org/wiki/Mailing_list_guidelines List Archives: https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.org Do not reply to spam on the list, report it: https://pagure.io/fedora-infrastructure

On Fri, Nov 5, 2021 at 9:23 PM Antonio T. sagitter <sagitter(a)fedoraproject.org&gt; wrote: > > On 10/24/21 15:11, Alexander Ploumistos wrote: >> Hello Antonio, >> >> On Sun, Oct 24, 2021 at 3:05 PM Antonio T. sagitter >> <sagitter(a)fedoraproject.org&gt; wrote: >>> >>> We are ready to push openbabel3 in Rawhide >> >> Will it be just Rawhide? Will you please let us know when the build is >> done in order to rebuild dependent packages? > > Within 24 hours i will create a side-tag in Rawhide. Thanks Antonio, I'll probably be able to do the rebuild on Sunday night.

On Sat, Sep 25, 2021 at 5:05 PM Alexander Ploumistos <alex.ploumistos(a)gmail.com&gt; wrote: > > I will try with a Fedora 34 VM later and report back. I got pretty much the same results on F34. I think xdrawchem works better with Open Babel 3 than it does with Open Babel 2, at least as far as structure cleanup goes (I installed the current version in F34). With Open Babel 2, SMILES output is also asterisks and trying InChi output crashes the program, so nothing changed there. gnome-chemistry-utils programs can't find the required shared object files in F34 either.

On 9/26/21 10:22, Antonio T. sagitter wrote: > I moved the openbabel's libraries under a private lib directory. > 'desktop' files are modified for working in this sense. Sorry, i meant gchemistry's libraries under a private lib directory. > > Let me check again Avogadro2.