8:14 a.m.
Hi everyone,
I've finally admitted to myself that I have no time to take good care
of openbabel:
https://src.fedoraproject.org/rpms/openbabel
It has one FTBFS bug in rawhide (related to cmake macro changes)
and two requests to update. One in Fedora to move to the recent 3.x
series and one for EPEL to update from 2.3 to 2.4.
It has 9 consumers in Fedora:
avogadro
avogadro2
chemtool
ghemical
gnome-chemistry-utils
IQmol
kalzium
molsketch
xdrawchem
Hopefully, one of their maintainers (Bcc'd) or someone from SciTech SIG
(Cc'd) can pick this up.
I'll orphan it in a few days if nobody responds here with their
FAS ID.
Regards,
--
Fedora https://getfedora.org | RPM Fusion http://rpmfusion.org
There should be a science of discontent. People need hard times and
oppression to develop psychic muscles.
-- from "Collected Sayings of Muad'Dib" by the Princess Irulan
12:18 p.m.
Hello Dominik and everyone else,
The next release of Molsketch is going to build against Open Babel
3.x, so I started working on updating the openbabel package around the
time version 3.1.1 came out, which supposedly fixed some issues
related to packaging on linux. Based on your spec file, I was trying
to see which patches were obsolete, what else might be required to get
it to build with as many features as possible and then test the
"abandonware" that depends on it. Unfortunately (fortunately?), the
local lockdown was lifted and I was among the people authorized back
in the lab and I got swamped with work, so I didn't get very far. I
got the base stuff building at some point, but I had trouble with some
runtime dependencies. In the meantime, there's been the CMake change
and I don't know if what I got building still does.
I am currently on vacation until the last week of August and away from
my systems, so I can't test things, or comment on the issues I
encountered. That being said, I think that of the packagers involved,
I am the least qualified to take up openbabel and I haven't touched
RHEL or CentOS in years, so I have no idea what's going on there and
what's required to maintain the EPEL branches. I'd be happy to
co-maintain the Fedora ones and help out as much as I can. Given the
time of the year in the Northern Hemisphere, do you think you could
hold on to the package a little longer (e.g. until the beginning of
September), so that people who are interested might get the chance to
get our act together?
Thank you for everything you've done so far,
A.
4:04 a.m.
Alexander Ploumistos wrote:
The next release of Molsketch is going to build against Open Babel
3.x, so I started working on updating the openbabel package around the
time version 3.1.1 came out, which supposedly fixed some issues
related to packaging on linux. Based on your spec file, I was trying
to see which patches were obsolete, what else might be required to get
it to build with as many features as possible and then test the
"abandonware" that depends on it. Unfortunately (fortunately?), the
local lockdown was lifted and I was among the people authorized back
in the lab and I got swamped with work, so I didn't get very far. I
got the base stuff building at some point, but I had trouble with some
runtime dependencies. In the meantime, there's been the CMake change
and I don't know if what I got building still does.
We will likely also need an openbabel2 compatibility package then, because I
doubt that everything will build against OpenBabel 3 without non-trivial
porting.
Kevin Kofler
3:59 p.m.
On Friday, 31 July 2020 at 11:04, Kevin Kofler wrote:
[...]
We will likely also need an openbabel2 compatibility package then,
because I
doubt that everything will build against OpenBabel 3 without non-trivial
porting.
This is the porting guide:
https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html#...
It doesn't look too bad from a cursory look.
Regards,
Dominik
--
Fedora https://getfedora.org | RPM Fusion http://rpmfusion.org
There should be a science of discontent. People need hard times and
oppression to develop psychic muscles.
-- from "Collected Sayings of Muad'Dib" by the Princess Irulan
5:06 p.m.
Dominik 'Rathann' Mierzejewski wrote:
This is the porting guide:
https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html#...
It doesn't look too bad from a cursory look.
To me, this list looks like a classic incompatible major version of a
library that is nontrivial to port to and that some packages will never get
ported to, requiring a compatibility library.
I see that the CLI and the Python modules have been renamed entirely, that
the C++ interface has renamed and removed methods (which I assume are also
renamed and removed in the Python bindings), and that there is even a major
API design change (the "Handling of implicit hydrogens" part). This type of
changes is not trivial to port to.
Kevin Kofler
4:03 p.m.
On Thursday, 30 July 2020 at 19:18, Alexander Ploumistos wrote:
[...]
Given the time of the year in the Northern Hemisphere, do you think
you could hold on to the package a little longer (e.g. until the
beginning of September), so that people who are interested might get
the chance to get our act together?
Sure thing, though I probably won't have time to do anything with the
package in the meantime.
Thank you for everything you've done so far,
You're welcome! I've enjoyed maintaining a lot of packages over the
years, but it's time to let go of those I have no interest in anymore.
Openbabel is one of them.
Regards,
Dominik
--
Fedora https://getfedora.org | RPM Fusion http://rpmfusion.org
There should be a science of discontent. People need hard times and
oppression to develop psychic muscles.
-- from "Collected Sayings of Muad'Dib" by the Princess Irulan
6:53 p.m.
Hello everyone,
I've finally managed to find some time and get the latest Open Babel
snapshot to build in F32 and rawhide. The spec file is ugly with a
bunch of comments still in it and I've realized that documentation
upstream is lacking, especially concerning build options and bindings.
So far, I've enabled only the python bindings and I'm not sure what
else is still available. There's also an icon file missing, but that's
the least of our problems.
If anyone's interested in taking a look, here's a scratch build:
https://koji.fedoraproject.org/koji/taskinfo?taskID=52775710
I've also set up a copr, where things are still building, though eln
builds died almost instantly on all arches and the F32 armhfp builder
ran out of space:
https://copr.fedorainfracloud.org/coprs/alexpl/openbabel/
Going forward, there's a number of things we need to figure out, off
the top of my head:
- I suppose I could take over from Dominik (with the hope that not
many things will break down in the following year) the packages in
Fedora, but not EPEL and friends. Who wants to do that?
- Has any of the maintainers of dependent packages that are dead-ish
upstream looked at porting them to OB 3?
- Do we create a new package, openbabel3, or do we rename the existing
one openbabel2? How do we deal with the complications of having both
of them around, especially since most of the binaries have the same
name?
There were many more things in my head when I started writing this
message, but they've somehow evaporated. I'm off to bed, please feel
free to chime in.
Best regards,
A.
12:52 a.m.
On Mon, Oct 05, 2020 at 01:53:03AM +0200, Alexander Ploumistos wrote:
Hello everyone,
I've finally managed to find some time and get the latest Open Babel
snapshot to build in F32 and rawhide. The spec file is ugly with a
bunch of comments still in it and I've realized that documentation
upstream is lacking, especially concerning build options and bindings.
So far, I've enabled only the python bindings and I'm not sure what
else is still available. There's also an icon file missing, but that's
the least of our problems.
If anyone's interested in taking a look, here's a scratch build:
https://koji.fedoraproject.org/koji/taskinfo?taskID=52775710
I've also set up a copr, where things are still building, though eln
builds died almost instantly on all arches and the F32 armhfp builder
ran out of space:
https://copr.fedorainfracloud.org/coprs/alexpl/openbabel/
Going forward, there's a number of things we need to figure out, off
the top of my head:
- I suppose I could take over from Dominik (with the hope that not
many things will break down in the following year) the packages in
Fedora, but not EPEL and friends. Who wants to do that?
- Has any of the maintainers of dependent packages that are dead-ish
upstream looked at porting them to OB 3?
- Do we create a new package, openbabel3, or do we rename the existing
one openbabel2? How do we deal with the complications of having both
of them around, especially since most of the binaries have the same
name?
There were many more things in my head when I started writing this
message, but they've somehow evaporated. I'm off to bed, please feel
free to chime in.
I think it makes sense to add a new 'openbabel3' package. Like Kevin wrote
in the other mail, it seems likely that some packages will depend on
the old version for the foreseeable future. Python recently switched
to a theme where it the "main" package has a number in the version [1].
This works nicely when there are multiple incompatible versions...
(One alternative would be to rename openbabel→openbabel2, and use
openbabel for the new version. But this requires an extra rename
operation and potentially adjustments in all dependent packages. Seems
like a lot of busywork, with potential for blocking if some dependent
package FTBFS.)
How do we deal with the complications of having both
of them around, especially since most of the binaries have the same
name?
Explicit Conflicts? Unless there's a strong need to install packages
in parallel, that seems like the easiest option.
Zbyszek
[1] https://src.fedoraproject.org/rpms/python3.9
4:07 p.m.
Hi Zbigniew,
On Mon, Oct 5, 2020 at 7:53 AM Zbigniew Jędrzejewski-Szmek
<zbyszek(a)in.waw.pl> wrote:
On Mon, Oct 05, 2020 at 01:53:03AM +0200, Alexander Ploumistos wrote:
[…]
I think it makes sense to add a new 'openbabel3' package. Like Kevin wrote
in the other mail, it seems likely that some packages will depend on
the old version for the foreseeable future. Python recently switched
to a theme where it the "main" package has a number in the version [1].
This works nicely when there are multiple incompatible versions...
That might be worth discussing with upstream. In the meantime, could
the executables in /usr/bin get a "3" appended to their names or would
that just break anything that might need them?
> How do we deal with the complications of having both
> of them around, especially since most of the binaries have the same
> name?
Explicit Conflicts? Unless there's a strong need to install packages
in parallel, that seems like the easiest option.
Whatever's inside openbabel-libs and openbabel-devel can co-exist with
the files from the other version, so we're left with incompatibilities
between the binaries, the gui, docs (trivial) and python or any other
language binding I haven't discovered.
(Btw, when I run "repoquery --repo=fedora{,-source} --whatrequires
{ruby,perl,python3}-openbabel", I get no hits. Am I doing it wrong, or
could we stop caring for perl and ruby, that I'm not sure if they're
still there?)
At least packages that buildrequire openbabel or that require the
libraries are safe from breakage for now. However, our collection of
chemistry-related software is rather limited; slimming it down further
by splitting packages into mutually exclusive subgroups won't make
people's lives any easier (in our ecosystem at least).
> - I suppose I could take over from Dominik (with the hope that
not
> many things will break down in the following year) the packages in
> Fedora, but not EPEL and friends. Who wants to do that?
Dominik, if you want, you can add me (alexpl) to the repo. Is anyone
interested in maintaining the EPEL branches?
> - Has any of the maintainers of dependent packages that are
dead-ish
> upstream looked at porting them to OB 3?
Anyone?
1292
days inactive
1360
days old
8 comments
4 participants
participants (4)
-
Alexander Ploumistos -
Dominik 'Rathann' Mierzejewski -
Kevin Kofler -
Zbigniew Jędrzejewski-Szmek