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authorEfraim Flashner2021-07-11 13:52:30 +0300
committerEfraim Flashner2021-07-11 14:20:07 +0300
commitac3535858a2447a92b024835415060947be83252 (patch)
tree36827dc4738c8d18cadd0b7c1cdbcaddca2f1a07 /gn/packages/python24.scm
parent8572fb7ffad93ddb880aba30ac51d3abf55a7634 (diff)
downloadguix-bioinformatics-ac3535858a2447a92b024835415060947be83252.tar.gz
gn: Add python24-direct.
* gn/packages/python24.scm (python24-direct): New variable. * gn/packages/genenetwork.scm (genenetwork1)[propagated-inputs]: Add python24-direct.
Diffstat (limited to 'gn/packages/python24.scm')
-rw-r--r--gn/packages/python24.scm71
1 files changed, 71 insertions, 0 deletions
diff --git a/gn/packages/python24.scm b/gn/packages/python24.scm
index cde8a02..b4de823 100644
--- a/gn/packages/python24.scm
+++ b/gn/packages/python24.scm
@@ -10,6 +10,7 @@
#:use-module (past packages python)
#:use-module (gnu packages compression)
#:use-module (gnu packages databases)
+ #:use-module (gnu packages gcc)
#:use-module (gnu packages maths)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages tls)
@@ -385,3 +386,73 @@ for Python. The design goals are:
@item Compatibility with MySQL-3.23 and later
@end itemize")
(license license:gpl2+)))
+
+(define-public python24-direct
+ (package
+ (name "python24-direct")
+ (version "1.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "DIRECT" version))
+ (sha256
+ (base32
+ "1d4cf9hynlr42hq0k8w7j4qi45rkrgil332sh0hymklxgmyi21h5"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Files are autogenerated using f2py.
+ (delete-file "src/direct-f2pywrappers.f")
+ (delete-file "src/directmodule.c")
+ #t))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2.4
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-source
+ (lambda _
+ (substitute* "DIRECT/__init__.py"
+ (("\\.direct") "direct"))
+ #t))
+ (replace 'check
+ (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+ (when tests?
+ (add-installed-pythonpath inputs outputs)
+ (with-directory-excursion "test"
+ (invoke "python" "test_direct.py")))
+ #t))
+ (add-after 'install 'copy-library
+ (lambda* (#:key outputs #:allow-other-keys)
+ (with-directory-excursion
+ (string-append (assoc-ref outputs "out")
+ "/lib/python2.4/site-packages")
+ (copy-file "DIRECT/direct.so" "direct.so"))
+ #t))
+ (replace 'install-license-files
+ (lambda* (#:key outputs #:allow-other-keys)
+ (install-file "COPYRIGHT"
+ (string-append (assoc-ref outputs "out")
+ "/share/doc/" ,name "-" ,version))
+ #t)))))
+ (propagated-inputs
+ `(("python24-numpy" ,python24-numpy-1.2)))
+ (inputs
+ `(("gfortran" ,gfortran)))
+ (native-inputs
+ `(("python24-nose" ,python24-nose)
+ ("python24-setuptools" ,python24-setuptools)))
+ ;; Also seems to be here: https://github.com/amitibo/pydirect
+ (home-page "http://code.google.com/p/pydirect/")
+ (synopsis "Python wrapper to the DIRECT algorithm")
+ (description
+ "DIRECT is a method to solve global bound constraint optimization problems
+and was originally developed by D. R. Jones, C. D. Perttunen and B. E. Stuckmann.
+@code{pydirect} is a python wrapper around DIRECT. It enables using DIRECT from
+the comfort of the great Python scripting language.
+The @code{pydirect} package uses the fortan implementation of DIRECT written by
+Joerg.M.Gablonsky, DIRECT Version 2.0.4. More information on the DIRECT
+algorithm can be found in Gablonsky's
+@url{http://repository.lib.ncsu.edu/ir/bitstream/1840.16/3920/1/etd.pdf,
+thesis}.")
+ (license license:expat)))