GNU bug report logs - #76728
[PATCH] gnu: avogadro2: fix open babel input

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Jakob Kirsch <jakob.kirsch <at> web.de>
To: guix-patches <at> gnu.org
Subject: [PATCH] gnu: avogadro2: fix open babel input
Date: Tue, 4 Mar 2025 01:47:17 +0100

[Message part 1 (text/plain, inline)]

avogadro2 needs open babel at runtime so we should add this to the propagated inputs.

[v1-0001-gnu-avogadro2-Update-to-1.93.0.patch (text/plain, attachment)]

Message #8 received at 76728 <at> debbugs.gnu.org (full text, mbox):

From: Z572 <z572 <at> z572.online>
To: Jakob Kirsch via Guix-patches via <guix-patches <at> gnu.org>
Cc: Jakob Kirsch <jakob.kirsch <at> web.de>, 76728 <at> debbugs.gnu.org
Subject: Re: [bug#76728] [PATCH] gnu: avogadro2: fix open babel input
Date: Tue, 04 Mar 2025 11:18:34 +0800

[Message part 1 (text/plain, inline)]

Jakob Kirsch via Guix-patches via <guix-patches <at> gnu.org> writes:

> avogadro2 needs open babel at runtime so we should add this to the propagated inputs.
>
> [2. text/plain; v1-0001-gnu-avogadro2-Update-to-1.93.0.patch]...

I think wrapper might be better, if it's just an application.

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Message #14 received at 76728 <at> debbugs.gnu.org (full text, mbox):

From: Jakob Kirsch <jakob.kirsch <at> web.de>
To: 76728 <at> debbugs.gnu.org
Subject: [PATCH] v2
Date: Tue, 4 Mar 2025 20:16:26 +0100

[Message part 1 (text/plain, inline)]

This is the v2 with wrap-program instead of propagated-inputs.

[v2-0001-gnu-avogadro2-Update-to-1.93.0.patch (text/plain, attachment)]

Message #17 received at 76728 <at> debbugs.gnu.org (full text, mbox):

From: Jakob Kirsch <jakob.kirsch <at> web.de>
To: 76728 <at> debbugs.gnu.org
Subject: New patch
Date: Thu, 6 Mar 2025 15:53:25 +0100

[Message part 1 (text/plain, inline)]

Since we're rebuilding avogadro2, we might as well update it to the new version.
Btw etc/committer.scm is broken with this patch so the merger would have to properly format the commits or fix the committer.

[v1-0001-Update-avogadro2-to-1.100.patch (text/plain, attachment)]

Message #20 received at 76728 <at> debbugs.gnu.org (full text, mbox):

From: Jakob Kirsch <jakob.kirsch <at> web.de>
To: 76728 <at> debbugs.gnu.org
Date: Thu, 6 Mar 2025 15:57:54 +0100

This is still WIP as some things are broken like:
* icons don't render
* openbabel optimization is broken with DNA

Message #23 received at 76728 <at> debbugs.gnu.org (full text, mbox):

From: Jakob Kirsch <jakob.kirsch <at> web.de>
To: 76728 <at> debbugs.gnu.org
Subject: PATCH v2
Date: Fri, 7 Mar 2025 20:37:17 +0100

[Message part 1 (text/plain, inline)]

I changed some stuff (don't remember what tho). Still WIP.

[v2-0001-Update-avogadro2-to-1.100.patch (text/plain, attachment)]

Message #26 received at 76728 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Jakob Kirsch <jakob.kirsch <at> web.de>
Cc: bavier <at> posteo.net, sharlatanus <at> gmail.com, 76728 <at> debbugs.gnu.org
Subject: Re: PATCH v2
Date: Tue, 8 Apr 2025 13:09:28 +0200

Hello Jakob,

Am Fri, Mar 07, 2025 at 08:37:17PM +0100 schrieb Jakob Kirsch:
> I changed some stuff (don't remember what tho). Still WIP.

are you still progressing, or should we close this issue?

Andreas

Message #29 received at 76728 <at> debbugs.gnu.org (full text, mbox):

From: Jakob Kirsch <jakob.kirsch <at> web.de>
To: 76728 <at> debbugs.gnu.org
Date: Thu, 10 Apr 2025 18:21:39 +0200

Currently working on it, it's still broken for some reason.

Message #32 received at 76728 <at> debbugs.gnu.org (full text, mbox):

From: Jakob Kirsch <jakob.kirsch <at> web.de>
To: 76728 <at> debbugs.gnu.org
Subject: [PATCH] gnu: avogadro2: update to 1.100.0
Date: Thu, 10 Apr 2025 19:28:13 +0200

[Message part 1 (text/plain, inline)]

I fixed all the issues. It's good to merge now.

[0001-gnu-avogadro2-update-to-1.100.0.patch (text/plain, attachment)]

Message #35 received at 76728 <at> debbugs.gnu.org (full text, mbox):

From: Christopher Baines <mail <at> cbaines.net>
To: Jakob Kirsch via Guix-patches via <guix-patches <at> gnu.org>
Cc: Jakob Kirsch <jakob.kirsch <at> web.de>, 76728 <at> debbugs.gnu.org
Subject: Re: [bug#76728] [PATCH] gnu: avogadro2: update to 1.100.0
Date: Fri, 11 Apr 2025 11:59:50 +0100

[Message part 1 (text/plain, inline)]

Jakob Kirsch via Guix-patches via <guix-patches <at> gnu.org> writes:

> I fixed all the issues. It's good to merge now.
>
> [2. text/plain; 0001-gnu-avogadro2-update-to-1.100.0.patch]...

It would be clearer to add each new package in a separate commit/patch
rather than one big commit. Alternatively, I'm unsure if these new
packages should exist, why would someone install avogadro-fragments for
example? If they just exist to be symlinked in avogadrolibs, you can
directly pass the origin records you're using as sources for the new
packages as inputs.

Regarding the origin changes to spglib, doing the substitute* operations
as a package build phase is preferable if doing them on the source isn't
required since that results in one less derivation.

Thanks,

Chris

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Message #41 received at 76728 <at> debbugs.gnu.org (full text, mbox):

From: Jakob Kirsch <jakob.kirsch <at> web.de>
To: Christopher Baines <mail <at> cbaines.net>
Cc: 76728 <at> debbugs.gnu.org
Subject: Re: [bug#76728] [PATCH] gnu: avogadro2: update to 1.100.0
Date: Fri, 11 Apr 2025 14:55:55 +0200

Yeah makes sense, I'll change the things and send a patch.

Message #44 received at 76728 <at> debbugs.gnu.org (full text, mbox):

From: Jakob Kirsch <jakob.kirsch <at> web.de>
To: 76728 <at> debbugs.gnu.org
Subject: New patch series
Date: Fri, 11 Apr 2025 15:37:17 +0200

[Message part 1 (text/plain, inline)]

I've implemented the changes and split it into 3 commits (spglib, avogadrolibs, avogadro2).

[0001-gnu-spglib-Update-to-2.5.0.patch (text/plain, attachment)]

[0002-gnu-avogadrolibs-Update-to-1.100.0.patch (text/plain, attachment)]

[0003-gnu-avogadro2-Update-to-1.100.0.patch (text/plain, attachment)]

Message #47 received at 76728 <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Jakob Kirsch <jakob.kirsch <at> web.de>
Cc: bavier <at> posteo.net, sharlatanus <at> gmail.com,
 Christopher Baines <mail <at> cbaines.net>, 76728 <at> debbugs.gnu.org
Subject: Re: PATCH v2
Date: Mon, 14 Apr 2025 15:30:46 +0200

Hello,

in your spglib update, you disable the tests; this requires to add a
comment to the source. In this case it is annoying since you update a
package with tests to one without; is this on purpose or an oversight?

Andreas

Message #50 received at 76728 <at> debbugs.gnu.org (full text, mbox):

From: Jakob Kirsch <jakob.kirsch <at> web.de>
To: 76728 <at> debbugs.gnu.org
Subject: Patches with comments
Date: Tue, 15 Apr 2025 19:17:53 +0200

[Message part 1 (text/plain, inline)]

spglib wants to clone a repository using git while building the tests and that won't work so I've added a comment (spglib works with avogadro2 that is its only dependant).

[0001-gnu-spglib-Update-to-2.5.0.patch (text/plain, attachment)]

[0002-gnu-avogadrolibs-Update-to-1.100.0.patch (text/plain, attachment)]

[0003-gnu-avogadro2-Update-to-1.100.0.patch (text/plain, attachment)]

Message #53 received at 76728 <at> debbugs.gnu.org (full text, mbox):

From: Danny Milosavljevic <dannym <at> friendly-machines.com>
To: Jakob Kirsch <jakob.kirsch <at> web.de>
Cc: 76728 <at> debbugs.gnu.org
Subject: Re: [bug#76728] [PATCH] gnu: avogadro2: fix open babel input
Date: Sun, 18 May 2025 13:02:25 +0200

Hi,

As a user of the avogadro2 program, would you say that a regular user
would use openbabel as an extra program anyway? (or be aware of it)

That is, is openbabel "inside the avogadro2 black box" or "outside the
avogadro2 black box as its own black box" ?

For what it's worth, I've checked the avogadro2 source code, and they
set the variable OBABEL_EXE to where the program "obabel" is.  After
that, they set BABEL_DIR relative to that, and finally they set
ob_plugins to refer to some .so files within $BABEL_DIR/lib, and then:

install_qt5_executable(${exe} "${plugins}" "${ob_plugins}" "${dirs}" "")

So for me as not-a-user-of-avogadro2 it seems like openbabel should be
inside the black box of avogadro2?

What do you think?

Message #58 received at 76728-done <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Danny Milosavljevic <dannym <at> friendly-machines.com>
Cc: Jakob Kirsch <jakob.kirsch <at> web.de>, 76728-done <at> debbugs.gnu.org
Subject: Re: [bug#76728] [PATCH] gnu: avogadro2: fix open babel input
Date: Mon, 2 Jun 2025 14:57:34 +0200

Hello,

this somehow does not pass the hurdle of being picked up by QA, so I
ended up going through the patches manually.

I have added openbabel as an explicit input to avogadro2; I am surprised
it can be referenced without this...

Danny, I do not quite get what you mean with the "blackbox" comment.
I have pushed the patches as they are; please feel free to open a new
issue to improve the packages or correct anything I may have broken.

Thanks,

Andreas

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