GNU bug report logs - #29958
[PATCH] gnu: Add python2-mmtk.

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

From: Konrad Hinsen <konrad.hinsen <at> fastmail.net>
To: guix-patches <at> gnu.org
Subject: [PATCH] gnu: Add python2-mmtk.
Date: Tue, 2 Jan 2018 20:04:53 +0100

* gnu/packages/python.scm (python2-mmtk): New public variable.
---
 gnu/packages/python.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 875982645..eeafe159d 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -12249,3 +12249,43 @@ physical units, automatic derivatives, ...) whereas others are more
 domain-specific (e.g. netCDF and PDB support).  The library is currently
 not actively maintained and works only with Python 2 and NumPy < 1.9.")
     (license license:cecill-c)))
+
+(define-public python2-mmtk
+  (package
+    (name "python2-mmtk")
+    (version "2.7.10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://bitbucket.org/khinsen/"
+                           "mmtk/downloads/MMTK-" version ".tar.gz"))
+       (file-name (string-append "MMTK-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1k4gsd50zja89dbzgy3aji7h4zpvbvdfrds7rxr3whqrsgcffnir"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("netcdf" ,netcdf)))
+    (propagated-inputs
+     `(("python-scientific" ,python2-scientific)
+       ("python-tkinter" ,python-2 "tk")))
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'includes-from-scientific
+           (lambda* (#:key inputs #:allow-other-keys)
+             (invoke "cp" "-r"
+                     (string-append
+                      (assoc-ref inputs "python-scientific")
+                      "/include/python2.7/Scientific")
+                     "Include/"))))))
+    (home-page "http://dirac.cnrs-orleans.fr/MMTK")
+    (synopsis "Python library for molecular simulation")
+    (description "MMTK is a library for molecular simulations with an emphasis
+on biomolecules.  It provides widely used methods such as Molecular Dynamics
+and normal mode analysis, but also basic routines for implementing new methods
+for simulation and analysis.  The library is currently not actively maintained
+and works only with Python 2 and NumPy < 1.9.")
+    (license license:cecill-c)))
-- 
2.14.3 (Apple Git-98)

Message #8 received at 29958 <at> debbugs.gnu.org (full text, mbox):

From: Leo Famulari <leo <at> famulari.name>
To: Konrad Hinsen <konrad.hinsen <at> fastmail.net>
Cc: 29958 <at> debbugs.gnu.org
Subject: Re: [bug#29958] [PATCH] gnu: Add python2-mmtk.
Date: Thu, 4 Jan 2018 12:47:43 -0500

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

On Tue, Jan 02, 2018 at 08:04:53PM +0100, Konrad Hinsen wrote:
> * gnu/packages/python.scm (python2-mmtk): New public variable.

Thanks!

> +         (add-before 'build 'includes-from-scientific
> +           (lambda* (#:key inputs #:allow-other-keys)
> +             (invoke "cp" "-r"
> +                     (string-append
> +                      (assoc-ref inputs "python-scientific")
> +                      "/include/python2.7/Scientific")
> +                     "Include/"))))))

Is it possible to make this use the copy-recursively instead of `cp`? I
did try it naively and it didn't work.

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

Message #11 received at 29958 <at> debbugs.gnu.org (full text, mbox):

From: Danny Milosavljevic <dannym <at> scratchpost.org>
To: 29958 <at> debbugs.gnu.org
Cc: Konrad Hinsen <konrad.hinsen <at> fastmail.net>
Subject: [PATCH v2] gnu: Add python2-mmtk.
Date: Thu,  4 Jan 2018 23:34:12 +0100

From: Konrad Hinsen <konrad.hinsen <at> fastmail.net>

* gnu/packages/python.scm (python2-mmtk): New public variable.
---
 gnu/packages/python.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 3dde9af34..d64c9bf85 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -12249,3 +12249,44 @@ physical units, automatic derivatives, ...) whereas others are more
 domain-specific (e.g. netCDF and PDB support).  The library is currently
 not actively maintained and works only with Python 2 and NumPy < 1.9.")
     (license license:cecill-c)))
+
+(define-public python2-mmtk
+  (package
+    (name "python2-mmtk")
+    (version "2.7.10")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://bitbucket.org/khinsen/"
+                           "mmtk/downloads/MMTK-" version ".tar.gz"))
+       (file-name (string-append "MMTK-" version ".tar.gz"))
+       (sha256
+        (base32
+         "1k4gsd50zja89dbzgy3aji7h4zpvbvdfrds7rxr3whqrsgcffnir"))))
+    (build-system python-build-system)
+    (native-inputs
+     `(("netcdf" ,netcdf)))
+    (propagated-inputs
+     `(("python-scientific" ,python2-scientific)
+       ("python-tkinter" ,python-2 "tk")))
+    (arguments
+     `(#:python ,python-2
+       #:tests? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'includes-from-scientific
+           (lambda* (#:key inputs #:allow-other-keys)
+             (mkdir-p "Include/Scientific")
+             (copy-recursively
+                     (string-append
+                      (assoc-ref inputs "python-scientific")
+                      "/include/python2.7/Scientific")
+                     "Include/Scientific"))))))
+    (home-page "http://dirac.cnrs-orleans.fr/MMTK")
+    (synopsis "Python library for molecular simulation")
+    (description "MMTK is a library for molecular simulations with an emphasis
+on biomolecules.  It provides widely used methods such as Molecular Dynamics
+and normal mode analysis, but also basic routines for implementing new methods
+for simulation and analysis.  The library is currently not actively maintained
+and works only with Python 2 and NumPy < 1.9.")
+    (license license:cecill-c)))

Message #14 received at 29958 <at> debbugs.gnu.org (full text, mbox):

From: Konrad Hinsen <konrad.hinsen <at> fastmail.net>
To: <29958 <at> debbugs.gnu.org>
Subject: Re: [PATCH v2] gnu: Add python2-mmtk.
Date: Fri, 5 Jan 2018 10:24:13 +0100

Danny Milosavljevic <dannym <at> scratchpost.org> writes:

> +       (modify-phases %standard-phases
> +         (add-before 'build 'includes-from-scientific
> +           (lambda* (#:key inputs #:allow-other-keys)
> +             (mkdir-p "Include/Scientific")
> +             (copy-recursively
> +                     (string-append
> +                      (assoc-ref inputs "python-scientific")
> +                      "/include/python2.7/Scientific")
> +                     "Include/Scientific"))))))

Works fine for me!

Thanks,
  Konrad.

Message #19 received at 29958-done <at> debbugs.gnu.org (full text, mbox):

From: Danny Milosavljevic <dannym <at> scratchpost.org>
To: Konrad Hinsen <konrad.hinsen <at> fastmail.net>
Cc: 29958-done <at> debbugs.gnu.org
Subject: Re: [bug#29958] [PATCH v2] gnu: Add python2-mmtk.
Date: Fri, 5 Jan 2018 10:30:33 +0100

Pushed as 42d6bffc2ff55406e75bf2f7096d4074c18cf382 to guix master!

Thanks!

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