[PATCH] gnu: avogadro2: fix open babel input

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2 participants
  • Jakob Kirsch
  • Z572
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unassigned
Submitted by
Jakob Kirsch
Severity
normal

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Jakob Kirsch wrote 1 weeks ago
(address . guix-patches@gnu.org)
Z8ZNlSc-d6XXvY6_@kernelpanicroom
avogadro2 needs open babel at runtime so we should add this to the propagated inputs.
From b353ae32e3b160b47ae1b34fe65e79b141caf05f Mon Sep 17 00:00:00 2001
Message-ID: <b353ae32e3b160b47ae1b34fe65e79b141caf05f.1741049088.git.jakob.kirsch@web.de>
From: Jakob Kirsch <jakob.kirsch@web.de>
Date: Tue, 4 Mar 2025 01:44:43 +0100
Subject: [PATCH v1] gnu: avogadro2: Update to 1.93.0.

* gnu/packages/chemistry.scm (avogadro2): Update to 1.93.0.
[propagated-inputs]: Add openbabel.

Change-Id: Ia7f02e66d9caced61a6a206076513806bb7b29a9
---
gnu/packages/chemistry.scm | 2 ++
1 file changed, 2 insertions(+)

Toggle diff (15 lines)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index bd27bfad7a..46728bb407 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -130,6 +130,8 @@ (define-public avogadro2
(list eigen pkg-config))
(inputs
(list avogadrolibs hdf5 molequeue qtbase-5))
+ (propagated-inputs
+ (list openbabel))
;; TODO: Enable tests with "-DENABLE_TESTING" configure flag.
(arguments
'(#:tests? #f))

base-commit: 72923a75af53a819f2be9dc4ae3c096aa3147d3f
--
2.48.1
Z572 wrote 1 weeks ago
(name . Jakob Kirsch via Guix-patches via)(address . guix-patches@gnu.org)
87wmd5jxf9.fsf@z572.online
Jakob Kirsch via Guix-patches via <guix-patches@gnu.org> writes:

Toggle quote (4 lines)
> 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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Jakob Kirsch wrote 1 weeks ago
[PATCH] v2
(address . 76728@debbugs.gnu.org)
Z8dRinHG_7y54YUj@kernelpanicroom
This is the v2 with wrap-program instead of propagated-inputs.
From 5608c37f14b7b5d46f6ac0a31b4f0c073bd186aa Mon Sep 17 00:00:00 2001
Message-ID: <5608c37f14b7b5d46f6ac0a31b4f0c073bd186aa.1741115763.git.jakob.kirsch@web.de>
From: Jakob Kirsch <jakob.kirsch@web.de>
Date: Tue, 4 Mar 2025 20:15:05 +0100
Subject: [PATCH v2] gnu: avogadro2: Update to 1.93.0.

* gnu/packages/chemistry.scm (avogadro2): Update to 1.93.0.

Change-Id: Ic133ed59aac11d9f48443c1d297d69060514d01f
---
gnu/packages/chemistry.scm | 20 +++++++++++++-------
1 file changed, 13 insertions(+), 7 deletions(-)

Toggle diff (37 lines)
diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index bd27bfad7a..78fedfd34f 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -122,17 +122,23 @@ (define-public avogadro2
(url "https://github.com/OpenChemistry/avogadroapp")
(commit version)))
(sha256
- (base32
- "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7"))
+ (base32 "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7"))
(file-name (git-file-name name version))))
(build-system cmake-build-system)
- (native-inputs
- (list eigen pkg-config))
- (inputs
- (list avogadrolibs hdf5 molequeue qtbase-5))
+ (native-inputs (list eigen pkg-config))
+ (inputs (list avogadrolibs hdf5 molequeue qtbase-5))
;; TODO: Enable tests with "-DENABLE_TESTING" configure flag.
(arguments
- '(#:tests? #f))
+ (list
+ #:tests? #f
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'install 'wrap-program
+ (lambda _
+ (wrap-program (string-append #$output "/bin/avogadro2")
+ (list "PATH"
+ 'suffix
+ (list (string-append #$openbabel "/bin")))))))))
(home-page "https://www.openchemistry.org/projects/avogadro2/")
(synopsis "Advanced molecule editor")
(description

base-commit: c1ec9e8d53da209ba1d6f8466d03180d195d7334
--
2.48.1
Jakob Kirsch wrote 6 days ago
New patch
(address . 76728@debbugs.gnu.org)
Z8m25VAAhrH0Q9wk@kernelpanicroom
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.
Attachment: v1-0001-Update-avogadro2-to-1.100.patch
Jakob Kirsch wrote 6 days ago
(no subject)
(address . 76728@debbugs.gnu.org)
Z8m38lf3HmYHkpJJ@kernelpanicroom
This is still WIP as some things are broken like:
* icons don't render
* openbabel optimization is broken with DNA
?
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