GNU bug report logs - #46107
[PATCH 1/6] gnu: Add spglib.

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

From: Kei Kebreau <kkebreau <at> posteo.net>
To: guix-patches <at> gnu.org
Cc: Kei Kebreau <kkebreau <at> posteo.net>
Subject: [PATCH 1/6] gnu: Add spglib.
Date: Mon, 25 Jan 2021 16:20:42 -0500

* gnu/packages/chemistry.scm (spglib): New variable.
---
 gnu/packages/chemistry.scm | 45 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index ddbf5ca098..7a9b3069fa 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -29,6 +29,7 @@
   #:use-module (guix git-download)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
+  #:use-module (gnu packages autotools)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
@@ -464,3 +465,47 @@ chemical data.  It's a collaborative project allowing anyone to search, convert,
 analyze, or store data from molecular modeling, chemistry, solid-state
 materials, biochemistry, or related areas.")
     (license license:gpl2)))
+
+(define-public spglib
+  (package
+    (name "spglib")
+    (version "1.16.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/spglib/spglib")
+             (commit (string-append "v" version))))
+       (sha256
+        (base32 "1kzc956m1pnazhz52vspqridlw72wd8x5l3dsilpdxl491aa2nws"))
+       (file-name (git-file-name name version))))
+    (build-system gnu-build-system)
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (arguments
+     '(#:test-target "check"
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'bootstrap
+           (lambda _
+             ;; These files are required by the Makefile, but not provided by
+             ;; the developers.
+             (for-each (lambda (file) (invoke "touch" file))
+                       '("NEWS" "README" "AUTHORS"))
+             (invoke "autoreconf" "-vi"))))))
+    (home-page "https://spglib.github.io/spglib/index.html")
+    (synopsis "Library for crystal symmetry search")
+    (description "Spglib is a library for finding and handling crystal
+symmetries written in C.  Spglib can be used to:
+
+@enumerate
+@item Find symmetry operations
+@item Identify space-group type
+@item Wyckoff position assignment
+@item Refine crystal structure
+@item Find a primitive cell
+@item Search irreducible k-points
+@end enumerate")
+    (license license:bsd-3)))
-- 
2.29.2

Message #8 received at 46107 <at> debbugs.gnu.org (full text, mbox):

From: Kei Kebreau <kkebreau <at> posteo.net>
To: 46107 <at> debbugs.gnu.org
Cc: Kei Kebreau <kkebreau <at> posteo.net>
Subject: [PATCH 2/6] gnu: Add mmtf-cpp.
Date: Mon, 25 Jan 2021 16:22:44 -0500

* gnu/packages/chemistry.scm (mmtf-cpp): New variable.
---
 gnu/packages/chemistry.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 7a9b3069fa..4ac7a90c87 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -242,6 +242,31 @@ analogy is that InChI is the bar-code for chemistry and chemical structures.")
               "file://LICENCE"
               "See LICENCE in the distribution."))))
 
+(define-public mmtf-cpp
+  (package
+    (name "mmtf-cpp")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/rcsb/mmtf-cpp")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "17ylramda69plf5w0v5hxbl4ggkdi5s15z55cv0pljl12yvyva8l"))))
+    (build-system cmake-build-system)
+    ;; Tests require the soon-to-be-deprecated version 1 of the catch-framework.
+    (arguments
+     '(#:tests? #f))
+    (home-page "https://mmtf.rcsb.org/")
+    (synopsis "C++ API for the Macromolecular Transmission Format")
+    (description "This package is a library for the
+@acronym{MMTF,macromolecular transmission format}, a binary encoding of
+biological structures.")
+    (license license:expat)))
+
 (define with-numpy-1.8
   (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
 
-- 
2.29.2

Message #11 received at 46107 <at> debbugs.gnu.org (full text, mbox):

From: Kei Kebreau <kkebreau <at> posteo.net>
To: 46107 <at> debbugs.gnu.org
Cc: Kei Kebreau <kkebreau <at> posteo.net>
Subject: [PATCH 3/6] gnu: Add molequeue.
Date: Mon, 25 Jan 2021 16:22:45 -0500

* gnu/packages/chemistry.scm (molequeue): New variable.
---
 gnu/packages/chemistry.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 4ac7a90c87..2b54df564e 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -267,6 +267,35 @@ analogy is that InChI is the bar-code for chemistry and chemical structures.")
 biological structures.")
     (license license:expat)))
 
+(define-public molequeue
+  (package
+    (name "molequeue")
+    (version "0.9.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/OpenChemistry/molequeue/"
+                           "releases/download/" version "/molequeue-"
+                           version ".tar.bz2"))
+       (sha256
+        (base32
+         "1w1fgxzqrb5yxvpmnc3c9ymnvixy0z1nfafkd9whg9zw8nbgl998"))))
+    (build-system cmake-build-system)
+    (inputs
+     `(("qtbase" ,qtbase)))
+    ;; TODO: Enable tests.
+    (arguments
+     '(#:tests? #f))
+    (home-page "https://www.openchemistry.org/projects/molequeue/")
+    (synopsis "Application for coordinating computational jobs")
+    (description "MoleQueue is a system-tray resident desktop application for
+abstracting, managing, and coordinating the execution of tasks both locally and
+ on remote computational resources.  Users can set up local and remote queues
+that describe where the task will be executed.  Each queue can have programs,
+with templates to facilitate the execution of the program.  Input files can be
+staged, and output files collected using a standard interface.")
+    (license license:bsd-3)))
+
 (define with-numpy-1.8
   (package-input-rewriting `((,python2-numpy . ,python2-numpy-1.8))))
 
-- 
2.29.2

Message #14 received at 46107 <at> debbugs.gnu.org (full text, mbox):

From: Kei Kebreau <kkebreau <at> posteo.net>
To: 46107 <at> debbugs.gnu.org
Cc: Kei Kebreau <kkebreau <at> posteo.net>
Subject: [PATCH 4/6] gnu: Add libmsym.
Date: Mon, 25 Jan 2021 16:22:46 -0500

* gnu/packages/chemistry.scm (libmsym): New variable.
---
 gnu/packages/chemistry.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 2b54df564e..73aed08d43 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -242,6 +242,30 @@ analogy is that InChI is the bar-code for chemistry and chemical structures.")
               "file://LICENCE"
               "See LICENCE in the distribution."))))
 
+(define-public libmsym
+  (package
+    (name "libmsym")
+    (version "0.2.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/mcodev31/libmsym")
+             (commit (string-append "v" version))))
+       (sha256
+        (base32
+         "0a9j28irdsr461qpzlc9z1yjyb9kp64fh5zw7ylspc9zn3189qwk"))
+       (file-name (git-file-name name version))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:configure-flags '("-DBUILD_SHARED_LIBS=ON")
+       #:tests? #f))                    ; no check target
+    (home-page "https://github.com/mcodev31/libmsym")
+    (synopsis "C library dealing with point group symmetry in molecules")
+    (description "libmsym is a C library dealing with point group symmetry in
+molecules.")
+    (license license:expat)))
+
 (define-public mmtf-cpp
   (package
     (name "mmtf-cpp")
-- 
2.29.2

Message #17 received at 46107 <at> debbugs.gnu.org (full text, mbox):

From: Kei Kebreau <kkebreau <at> posteo.net>
To: 46107 <at> debbugs.gnu.org
Cc: Kei Kebreau <kkebreau <at> posteo.net>
Subject: [PATCH 5/6] gnu: Add avogadrolibs.
Date: Mon, 25 Jan 2021 16:22:47 -0500

* gnu/packages/chemistry.scm (avogadrolibs): New variable.
---
 gnu/packages/chemistry.scm | 44 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 73aed08d43..9d4c6f07fa 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -30,6 +30,7 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages autotools)
+  #:use-module (gnu packages backup)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
@@ -44,6 +45,7 @@
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt)
+  #:use-module (gnu packages serialization)
   #:use-module (gnu packages sphinx)
   #:use-module (gnu packages xml)
   #:use-module (guix build-system cmake)
@@ -135,6 +137,48 @@ science, and related areas.  It offers flexible high quality rendering and a
 powerful plugin architecture.")
     (license license:gpl2+)))
 
+(define-public avogadrolibs
+  (package
+    (name "avogadrolibs")
+    (version "1.93.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/OpenChemistry/avogadrolibs")
+             (commit version)))
+       (sha256
+        (base32 "1xivga626n5acnmwmym8svl0pdri8hkp59czf04ri2zflnviyh39"))
+       (file-name (git-file-name name version))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("eigen" ,eigen)
+       ("mmtf-cpp" ,mmtf-cpp)
+       ("msgpack" ,msgpack)
+       ("googletest" ,googletest)
+       ("pkg-config" ,pkg-config)
+       ("pybind11" ,pybind11)))
+    (inputs
+     `(("glew" ,glew)
+       ("libarchive" ,libarchive)
+       ("libmsym" ,libmsym)
+       ("molequeue" ,molequeue)
+       ("python" ,python)
+       ("spglib" ,spglib)
+       ("qtbase" ,qtbase)))
+    (arguments
+     '(#:configure-flags (list "-DENABLE_TESTING=ON"
+                               (string-append "-DSPGLIB_INCLUDE_DIR="
+                                              (assoc-ref %build-inputs "spglib")
+                                              "/include"))))
+    (home-page "https://www.openchemistry.org/projects/avogadro2/")
+    (synopsis "Libraries for chemistry, bioinformatics, and related areas")
+    (description
+     "Avogadro libraries provide 3D rendering, visualization, analysis and data
+processing useful in computational chemistry, molecular modeling,
+bioinformatics, materials science, and related areas.")
+    (license license:bsd-3)))
+
 (define-public domainfinder
   (package
     (name "domainfinder")
-- 
2.29.2

Message #20 received at 46107 <at> debbugs.gnu.org (full text, mbox):

From: Kei Kebreau <kkebreau <at> posteo.net>
To: 46107 <at> debbugs.gnu.org
Cc: Kei Kebreau <kkebreau <at> posteo.net>
Subject: [PATCH 6/6] gnu: Add avogadro2.
Date: Mon, 25 Jan 2021 16:22:48 -0500

* gnu/packages/chemistry.scm (avogadro2): New variable.
---
 gnu/packages/chemistry.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm
index 9d4c6f07fa..8fe51d79ee 100644
--- a/gnu/packages/chemistry.scm
+++ b/gnu/packages/chemistry.scm
@@ -179,6 +179,41 @@ processing useful in computational chemistry, molecular modeling,
 bioinformatics, materials science, and related areas.")
     (license license:bsd-3)))
 
+(define-public avogadro2
+  (package
+    (name "avogadro2")
+    (version "1.93.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/OpenChemistry/avogadroapp")
+             (commit version)))
+       (sha256
+        (base32
+         "1z3pjlwja778a1dmvx9aqz2hlw5q9g3kqxhm9slz08452600jsv7"))
+       (file-name (git-file-name name version))))
+    (build-system cmake-build-system)
+    (native-inputs
+     `(("eigen" ,eigen)
+       ("pkg-config" ,pkg-config)))
+    (inputs
+     `(("avogadrolibs" ,avogadrolibs)
+       ("hdf5" ,hdf5)
+       ("molequeue" ,molequeue)
+       ("qtbase" ,qtbase)))
+    ;; TODO: Enable tests with "-DENABLE_TESTING" configure flag.
+    (arguments
+     '(#:tests? #f))
+    (home-page "https://www.openchemistry.org/projects/avogadro2/")
+    (synopsis "Advanced molecule editor")
+    (description
+     "Avogadro 2 is an advanced molecule editor and visualizer designed for use
+in computational chemistry, molecular modeling, bioinformatics, materials
+science, and related areas.  It offers flexible high quality rendering and a
+powerful plugin architecture.")
+    (license license:bsd-3)))
+
 (define-public domainfinder
   (package
     (name "domainfinder")
-- 
2.29.2

Message #23 received at 46107 <at> debbugs.gnu.org (full text, mbox):

From: Leo Famulari <leo <at> famulari.name>
To: Kei Kebreau <kkebreau <at> posteo.net>
Cc: 46107 <at> debbugs.gnu.org
Subject: Re: [bug#46107] [PATCH 1/6] gnu: Add spglib.
Date: Mon, 25 Jan 2021 17:17:55 -0500

On Mon, Jan 25, 2021 at 04:20:42PM -0500, Kei Kebreau wrote:
> * gnu/packages/chemistry.scm (spglib): New variable.

Thanks! LGTM

> +       #:phases
> +       (modify-phases %standard-phases
> +         (replace 'bootstrap
> +           (lambda _
> +             ;; These files are required by the Makefile, but not provided by
> +             ;; the developers.
> +             (for-each (lambda (file) (invoke "touch" file))
> +                       '("NEWS" "README" "AUTHORS"))
> +             (invoke "autoreconf" "-vi"))))))

Can you file a bug upstream about this?

Message #26 received at 46107 <at> debbugs.gnu.org (full text, mbox):

From: Leo Famulari <leo <at> famulari.name>
To: Kei Kebreau <kkebreau <at> posteo.net>
Cc: 46107 <at> debbugs.gnu.org
Subject: Re: [bug#46107] [PATCH 3/6] gnu: Add molequeue.
Date: Mon, 25 Jan 2021 17:18:35 -0500

On Mon, Jan 25, 2021 at 04:22:45PM -0500, Kei Kebreau wrote:
> * gnu/packages/chemistry.scm (molequeue): New variable.

> +    ;; TODO: Enable tests.
> +    (arguments
> +     '(#:tests? #f))

Can you clarify the comment? Even "It's too much work" would be helpful
for future readers.

Message #29 received at 46107 <at> debbugs.gnu.org (full text, mbox):

From: Leo Famulari <leo <at> famulari.name>
To: Kei Kebreau <kkebreau <at> posteo.net>
Cc: 46107 <at> debbugs.gnu.org
Subject: Re: [bug#46107] [PATCH 6/6] gnu: Add avogadro2.
Date: Mon, 25 Jan 2021 17:19:36 -0500

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

On Mon, Jan 25, 2021 at 04:22:48PM -0500, Kei Kebreau wrote:
> * gnu/packages/chemistry.scm (avogadro2): New variable.

Thanks a lot for taking care of this! I sent some other comments, but
they shouldn't block these patches.

LGTM

[signature.asc (application/pgp-signature, inline)]

Message #32 received at 46107 <at> debbugs.gnu.org (full text, mbox):

From: Kei <kkebreau <at> posteo.net>
To: Leo Famulari <leo <at> famulari.name>
Cc: 46107 <at> debbugs.gnu.org
Subject: Re: [bug#46107] [PATCH 1/6] gnu: Add spglib.
Date: Mon, 25 Jan 2021 22:20:19 -0500

On Mon, 2021-01-25 at 17:17 -0500, Leo Famulari wrote:
> On Mon, Jan 25, 2021 at 04:20:42PM -0500, Kei Kebreau wrote:
> > * gnu/packages/chemistry.scm (spglib): New variable.
> 
> Thanks! LGTM
> 
> > +       #:phases
> > +       (modify-phases %standard-phases
> > +         (replace 'bootstrap
> > +           (lambda _
> > +             ;; These files are required by the Makefile, but not provided
> > by
> > +             ;; the developers.
> > +             (for-each (lambda (file) (invoke "touch" file))
> > +                       '("NEWS" "README" "AUTHORS"))
> > +             (invoke "autoreconf" "-vi"))))))
> 
> Can you file a bug upstream about this?

On closer inspection, it seems that the developer is moving to make CMake the
main build system.  Using the CMake build system, I ran into a known [0]
inconsistency [1] between the GNU and CMake build systems used by spglib.  I've
patched spglib to deal with this for now, with links added in the comments.

[0]: https://github.com/spglib/spglib/issues/75
[1]: https://github.com/OpenChemistry/avogadroapp/issues/97

Message #35 received at 46107 <at> debbugs.gnu.org (full text, mbox):

From: Kei <kkebreau <at> posteo.net>
To: Leo Famulari <leo <at> famulari.name>
Cc: 46107 <at> debbugs.gnu.org
Subject: Re: [bug#46107] [PATCH 3/6] gnu: Add molequeue.
Date: Mon, 25 Jan 2021 22:21:09 -0500

On Mon, 2021-01-25 at 17:18 -0500, Leo Famulari wrote:
> On Mon, Jan 25, 2021 at 04:22:45PM -0500, Kei Kebreau wrote:
> > * gnu/packages/chemistry.scm (molequeue): New variable.
> > +    ;; TODO: Enable tests.
> > +    (arguments
> > +     '(#:tests? #f))
> 
> Can you clarify the comment? Even "It's too much work" would be helpful
> for future readers.

While I was doing this, I went ahead and enabled all but the failing tests.

Message #40 received at 46107-done <at> debbugs.gnu.org (full text, mbox):

From: Kei <kkebreau <at> posteo.net>
To: Leo Famulari <leo <at> famulari.name>
Cc: 46107-done <at> debbugs.gnu.org
Subject: Re: [bug#46107] [PATCH 6/6] gnu: Add avogadro2.
Date: Mon, 25 Jan 2021 22:24:28 -0500

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

On Mon, 2021-01-25 at 17:19 -0500, Leo Famulari wrote:
> On Mon, Jan 25, 2021 at 04:22:48PM -0500, Kei Kebreau wrote:
> > * gnu/packages/chemistry.scm (avogadro2): New variable.
> 
> Thanks a lot for taking care of this! I sent some other comments, but
> they shouldn't block these patches.
> 
> LGTM

Done and done!  Thanks for reviewing and commenting.  Avogadro is clear for
removal, especially since it doesn't seem to build anymore.

[signature.asc (application/pgp-signature, inline)]

Message #43 received at 46107-done <at> debbugs.gnu.org (full text, mbox):

From: Leo Famulari <leo <at> famulari.name>
To: Kei <kkebreau <at> posteo.net>
Cc: 46107-done <at> debbugs.gnu.org
Subject: Re: [bug#46107] [PATCH 6/6] gnu: Add avogadro2.
Date: Thu, 28 Jan 2021 20:05:28 -0500

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

On Mon, Jan 25, 2021 at 10:24:28PM -0500, Kei wrote:
> Done and done!  Thanks for reviewing and commenting.  Avogadro is clear for
> removal, especially since it doesn't seem to build anymore.

Do you know if avogradro2 is suitable as a "drop-in" replacement for
avogadro? If so, we could mark it as superseded by avogadro2, and then
it would be automatically updated in users' profiles when they do `guix
pull && guix upgrade`.

[signature.asc (application/pgp-signature, inline)]

Message #46 received at 46107-done <at> debbugs.gnu.org (full text, mbox):

From: kkebreau <at> posteo.net
To: Leo Famulari <leo <at> famulari.name>
Cc: 46107-done <at> debbugs.gnu.org
Subject: Re: [bug#46107] [PATCH 6/6] gnu: Add avogadro2.
Date: Fri, 29 Jan 2021 11:28:08 -0500

On 2021-01-28 20:05, Leo Famulari wrote:
> On Mon, Jan 25, 2021 at 10:24:28PM -0500, Kei wrote:
>> Done and done!  Thanks for reviewing and commenting.  Avogadro is 
>> clear for
>> removal, especially since it doesn't seem to build anymore.
> 
> Do you know if avogradro2 is suitable as a "drop-in" replacement for
> avogadro? If so, we could mark it as superseded by avogadro2, and then
> it would be automatically updated in users' profiles when they do `guix
> pull && guix upgrade`.

I think so. Development efforts seem to have been focused on Avogadro 2 
for
several years now, with little or no maintenance of the original 
Avogadro. This
2018 community survey [0] indicates the developers' full commitment to
Avogadro 2, so marking it as superseding avogadro is recommended.

[0]: https://avogadro.cc/news/community-survey-results/

Message #49 received at 46107-done <at> debbugs.gnu.org (full text, mbox):

From: Leo Famulari <leo <at> famulari.name>
To: kkebreau <at> posteo.net
Cc: 46107-done <at> debbugs.gnu.org
Subject: Re: [bug#46107] [PATCH 6/6] gnu: Add avogadro2.
Date: Fri, 29 Jan 2021 15:20:23 -0500

On Fri, Jan 29, 2021 at 11:28:08AM -0500, kkebreau <at> posteo.net wrote:
> I think so. Development efforts seem to have been focused on Avogadro 2 for
> several years now, with little or no maintenance of the original Avogadro.
> This
> 2018 community survey [0] indicates the developers' full commitment to
> Avogadro 2, so marking it as superseding avogadro is recommended.

Since avogadro doesn't build, I decided to remove it rather than mark it
as superseded.

Removed with commit 42008264d9fff544ee00c3c109093472b8a92bd2

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