@@ 2196,6 2196,113 @@ toolkits.")
,@(alist-delete "python-numpydoc"
(package-inputs matplotlib)))))))
+;; Scipy 0.14.0 with Numpy 0.19.X fails several tests. This is known and
+;; planned to be fixed in 0.14.1. It is claimed that the failures can safely
+;; be ignored:
+;; http://mail.scipy.org/pipermail/scipy-dev/2014-September/020043.html
+;; https://github.com/scipy/scipy/issues/3853
+;;
+;; The main test suite procedure prints the summary message:
+;;
+;; Ran 16412 tests in 245.033s
+;; FAILED (KNOWNFAIL=277, SKIP=921, errors=327, failures=42)
+;;
+;; However, it still does return normally.
+(define-public python-scipy
+ (package
+ (name "python-scipy")
+ (version "0.14.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/scipy"
+ "/scipy-" version ".tar.gz"))
+ (sha256
+ (base32
+ "053bmz4qmnk4dmxvspfak8r10rpmy6mzwfzgy33z338ppzka6hab"))))
+ (build-system python-build-system)
+ (inputs
+ `(("python-numpy" ,python-numpy)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-pyparsing" ,python-pyparsing)
+ ("python-nose" ,python-nose)
+ ("python-sphinx" ,python-sphinx)
+ ("atlas" ,atlas)))
+ (native-inputs
+ `(("gfortran" ,gfortran-4.8)
+ ("texlive" ,texlive)
+ ("perl" ,perl)))
+ (outputs '("out" "doc"))
+ (arguments
+ `(#:phases
+ (alist-cons-before
+ 'build 'set-environment-variables
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let* ((atlas-threaded
+ (string-append (assoc-ref inputs "atlas")
+ "/lib/libtatlas.so"))
+ ;; On single core CPUs only the serial library is created.
+ (atlas-lib
+ (if (file-exists? atlas-threaded)
+ atlas-threaded
+ (string-append (assoc-ref inputs "atlas")
+ "/lib/libsatlas.so"))))
+ (setenv "ATLAS" atlas-lib)))
+ (alist-cons-after
+ 'install 'install-doc
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
+ (doc (string-append data "/doc/" ,name "-" ,version))
+ (html (string-append doc "/html"))
+ (pyver ,(string-append "PYVER=")))
+ (with-directory-excursion "doc"
+ ;; Without setting this variable we get an encoding error.
+ (setenv "LANG" "en_US.UTF-8")
+ ;; Fix generation of images for mathematical expressions.
+ (substitute* (find-files "source" "conf\\.py")
+ (("pngmath_use_preview = True")
+ "pngmath_use_preview = False"))
+ (mkdir-p html)
+ (system* "make" "html" pyver)
+ (system* "make" "latex" "PAPER=a4" pyver)
+ (system* "make" "-C" "build/latex" "all-pdf" "PAPER=a4" pyver)
+ (copy-file "build/latex/scipy-ref.pdf"
+ (string-append doc "/scipy-ref.pdf"))
+ (with-directory-excursion "build/html"
+ (for-each (lambda (file)
+ (let* ((dir (dirname file))
+ (tgt-dir (string-append html "/" dir)))
+ (unless (equal? "." dir)
+ (mkdir-p tgt-dir))
+ (copy-file file (string-append html "/" file))))
+ (find-files "." ".*"))))))
+ ;; Tests can only be run after the library has been installed and not
+ ;; within the source directory.
+ (alist-cons-after
+ 'install 'check
+ (lambda _
+ (with-directory-excursion "/tmp"
+ (zero? (system* "python" "-c" "import scipy; scipy.test()"))))
+ (alist-delete
+ 'check
+ %standard-phases))))))
+ (home-page "http://www.scipy.org/")
+ (synopsis "The Scipy library provides efficient numerical routines")
+ (description "The SciPy library is one of the core packages that make up
+the SciPy stack. It provides many user-friendly and efficient numerical
+routines such as routines for numerical integration and optimization.")
+ (license bsd-3)))
+
+(define-public python2-scipy
+ (let ((scipy (package-with-python2 python-scipy)))
+ (package (inherit scipy)
+ ;; Use packages customized for python-2.
+ (inputs `(("python2-matplotlib" ,python2-matplotlib)
+ ("python2-numpy" ,python2-numpy)
+ ,@(alist-delete "python-matplotlib"
+ (alist-delete "python-numpy"
+ (package-inputs scipy))))))))
+
(define-public python-sqlalchemy
(package
(name "python-sqlalchemy")
@@ 2341,3 2448,4 @@ a general image processing tool.")
(define-public python2-pillow
(package-with-python2 python-pillow))
+