[PATCH 1/6] gnu: Add spglib.

Done

Details

2 participants

Kei Kebreau
Leo Famulari

Owner: unassigned

Submitted by: Kei Kebreau

Severity: normal

Kei Kebreau wrote on 25 Jan 2021 22:20

Recipients:(address . guix-patches@gnu.org)(name . Kei Kebreau)(address . kkebreau@posteo.net)

Message-ID:20210125212042.4358-1-kkebreau@posteo.net

* gnu/packages/chemistry.scm (spglib): New variable.

---

gnu/packages/chemistry.scm | 45 ++++++++++++++++++++++++++++++++++++++

1 file changed, 45 insertions(+)

Toggle diff (62 lines)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

Kei Kebreau wrote on 25 Jan 2021 22:22

[PATCH 2/6] gnu: Add mmtf-cpp.

Recipients:(address . 46107@debbugs.gnu.org)(name . Kei Kebreau)(address . kkebreau@posteo.net)

Message-ID:20210125212248.4749-1-kkebreau@posteo.net

* gnu/packages/chemistry.scm (mmtf-cpp): New variable.

---

gnu/packages/chemistry.scm | 25 +++++++++++++++++++++++++

1 file changed, 25 insertions(+)

Toggle diff (38 lines)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

Kei Kebreau wrote on 25 Jan 2021 22:22

[PATCH 3/6] gnu: Add molequeue.

Recipients:(address . 46107@debbugs.gnu.org)(name . Kei Kebreau)(address . kkebreau@posteo.net)

Message-ID:20210125212248.4749-2-kkebreau@posteo.net

* gnu/packages/chemistry.scm (molequeue): New variable.

---

gnu/packages/chemistry.scm | 29 +++++++++++++++++++++++++++++

1 file changed, 29 insertions(+)

Toggle diff (42 lines)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

Kei Kebreau wrote on 25 Jan 2021 22:22

[PATCH 4/6] gnu: Add libmsym.

Recipients:(address . 46107@debbugs.gnu.org)(name . Kei Kebreau)(address . kkebreau@posteo.net)

Message-ID:20210125212248.4749-3-kkebreau@posteo.net

* gnu/packages/chemistry.scm (libmsym): New variable.

---

gnu/packages/chemistry.scm | 24 ++++++++++++++++++++++++

1 file changed, 24 insertions(+)

Toggle diff (37 lines)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

Kei Kebreau wrote on 25 Jan 2021 22:22

[PATCH 5/6] gnu: Add avogadrolibs.

Recipients:(address . 46107@debbugs.gnu.org)(name . Kei Kebreau)(address . kkebreau@posteo.net)

Message-ID:20210125212248.4749-4-kkebreau@posteo.net

* gnu/packages/chemistry.scm (avogadrolibs): New variable.

---

gnu/packages/chemistry.scm | 44 ++++++++++++++++++++++++++++++++++++++

1 file changed, 44 insertions(+)

Toggle diff (71 lines)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

Kei Kebreau wrote on 25 Jan 2021 22:22

[PATCH 6/6] gnu: Add avogadro2.

Recipients:(address . 46107@debbugs.gnu.org)(name . Kei Kebreau)(address . kkebreau@posteo.net)

Message-ID:20210125212248.4749-5-kkebreau@posteo.net

* gnu/packages/chemistry.scm (avogadro2): New variable.

---

gnu/packages/chemistry.scm | 35 +++++++++++++++++++++++++++++++++++

1 file changed, 35 insertions(+)

Toggle diff (48 lines)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

Leo Famulari wrote on 25 Jan 2021 23:17

Re: [bug#46107] [PATCH 1/6] gnu: Add spglib.

Recipients:(name . Kei Kebreau)(address . kkebreau@posteo.net)(address . 46107@debbugs.gnu.org)

Message-ID:YA9Dk9wdYLAV7OAk@jasmine.lan

On Mon, Jan 25, 2021 at 04:20:42PM -0500, Kei Kebreau wrote:

Toggle quote (2 lines)

> * gnu/packages/chemistry.scm (spglib): New variable.

Thanks! LGTM

Toggle quote (10 lines)> +       #: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?

Leo Famulari wrote on 25 Jan 2021 23:18

Re: [bug#46107] [PATCH 3/6] gnu: Add molequeue.

Recipients:(name . Kei Kebreau)(address . kkebreau@posteo.net)(address . 46107@debbugs.gnu.org)

Message-ID:YA9Du+oYqLq1o8lf@jasmine.lan

On Mon, Jan 25, 2021 at 04:22:45PM -0500, Kei Kebreau wrote:

Toggle quote (6 lines)

> * 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.

Leo Famulari wrote on 25 Jan 2021 23:19

Re: [bug#46107] [PATCH 6/6] gnu: Add avogadro2.

Recipients:(name . Kei Kebreau)(address . kkebreau@posteo.net)(address . 46107@debbugs.gnu.org)

Message-ID:YA9D+ALFzV2vqq7z@jasmine.lan

On Mon, Jan 25, 2021 at 04:22:48PM -0500, Kei Kebreau wrote:

Toggle quote (2 lines)

> * 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

Kei wrote on 26 Jan 2021 04:20

Re: [bug#46107] [PATCH 1/6] gnu: Add spglib.

Recipients:(name . Leo Famulari)(address . leo@famulari.name)(address . 46107@debbugs.gnu.org)

Message-ID:1368650a601118e624c5dec06f7c35214de3a453.camel@posteo.net

On Mon, 2021-01-25 at 17:17 -0500, Leo Famulari wrote:

Toggle quote (18 lines)> 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

Kei wrote on 26 Jan 2021 04:21

Re: [bug#46107] [PATCH 3/6] gnu: Add molequeue.

Recipients:(name . Leo Famulari)(address . leo@famulari.name)(address . 46107@debbugs.gnu.org)

Message-ID:e98c5374939d361ee3fa2d824e522345b2b98a8b.camel@posteo.net

On Mon, 2021-01-25 at 17:18 -0500, Leo Famulari wrote:

Toggle quote (9 lines)

> 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.

Kei wrote on 26 Jan 2021 04:24

Re: [bug#46107] [PATCH 6/6] gnu: Add avogadro2.

Recipients:(name . Leo Famulari)(address . leo@famulari.name)(address . 46107-done@debbugs.gnu.org)

Message-ID:a8e6d462d10b401808097c6b6c79685d8b76c340.camel@posteo.net

On Mon, 2021-01-25 at 17:19 -0500, Leo Famulari wrote:

Toggle quote (8 lines)

> 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.

Closed

Leo Famulari wrote on 29 Jan 2021 02:05

Recipients:(name . Kei)(address . kkebreau@posteo.net)(address . 46107-done@debbugs.gnu.org)

Message-ID:YBNfWJOg1qda1OsH@jasmine.lan

On Mon, Jan 25, 2021 at 10:24:28PM -0500, Kei wrote:

Toggle quote (3 lines)

> 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`.

Closed

kkebreau wrote on 29 Jan 2021 17:28

Recipients:(name . Leo Famulari)(address . leo@famulari.name)(address . 46107-done@debbugs.gnu.org)

Message-ID:5d4c2474cdc539f2792e70b0dbcf7fc4@posteo.net

On 2021-01-28 20:05, Leo Famulari wrote:

Toggle quote (10 lines)> 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/

Closed

Leo Famulari wrote on 29 Jan 2021 21:20

Recipients:(address . kkebreau@posteo.net)(address . 46107-done@debbugs.gnu.org)

Message-ID:YBRuB2sIfP090hgB@jasmine.lan

On Fri, Jan 29, 2021 at 11:28:08AM -0500, kkebreau@posteo.net wrote:

Toggle quote (6 lines)

> 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

Closed

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