gnu: Add scipy.
* gnu/packages/python.scm (python-scipy, python2-scipy): New variables.master
Federico Beffa
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65a056900f
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bb986599e6
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@ -2196,6 +2196,113 @@ toolkits.")
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,@(alist-delete "python-numpydoc"
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,@(alist-delete "python-numpydoc"
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(package-inputs matplotlib)))))))
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(package-inputs matplotlib)))))))
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;; Scipy 0.14.0 with Numpy 0.19.X fails several tests. This is known and
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;; planned to be fixed in 0.14.1. It is claimed that the failures can safely
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;; be ignored:
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;; http://mail.scipy.org/pipermail/scipy-dev/2014-September/020043.html
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;; https://github.com/scipy/scipy/issues/3853
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;;
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;; The main test suite procedure prints the summary message:
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;;
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;; Ran 16412 tests in 245.033s
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;; FAILED (KNOWNFAIL=277, SKIP=921, errors=327, failures=42)
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;;
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;; However, it still does return normally.
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(define-public python-scipy
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(package
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(name "python-scipy")
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(version "0.14.0")
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(source
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(origin
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(method url-fetch)
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(uri (string-append "mirror://sourceforge/scipy"
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"/scipy-" version ".tar.gz"))
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(sha256
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(base32
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"053bmz4qmnk4dmxvspfak8r10rpmy6mzwfzgy33z338ppzka6hab"))))
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(build-system python-build-system)
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(inputs
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`(("python-numpy" ,python-numpy)
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("python-matplotlib" ,python-matplotlib)
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("python-pyparsing" ,python-pyparsing)
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("python-nose" ,python-nose)
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("python-sphinx" ,python-sphinx)
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("atlas" ,atlas)))
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(native-inputs
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`(("gfortran" ,gfortran-4.8)
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("texlive" ,texlive)
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("perl" ,perl)))
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(outputs '("out" "doc"))
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(arguments
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`(#:phases
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(alist-cons-before
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'build 'set-environment-variables
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(lambda* (#:key inputs #:allow-other-keys)
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(let* ((atlas-threaded
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(string-append (assoc-ref inputs "atlas")
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"/lib/libtatlas.so"))
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;; On single core CPUs only the serial library is created.
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(atlas-lib
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(if (file-exists? atlas-threaded)
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atlas-threaded
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(string-append (assoc-ref inputs "atlas")
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"/lib/libsatlas.so"))))
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(setenv "ATLAS" atlas-lib)))
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(alist-cons-after
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'install 'install-doc
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((data (string-append (assoc-ref outputs "doc") "/share"))
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(doc (string-append data "/doc/" ,name "-" ,version))
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(html (string-append doc "/html"))
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(pyver ,(string-append "PYVER=")))
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(with-directory-excursion "doc"
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;; Without setting this variable we get an encoding error.
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(setenv "LANG" "en_US.UTF-8")
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;; Fix generation of images for mathematical expressions.
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(substitute* (find-files "source" "conf\\.py")
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(("pngmath_use_preview = True")
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"pngmath_use_preview = False"))
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(mkdir-p html)
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(system* "make" "html" pyver)
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(system* "make" "latex" "PAPER=a4" pyver)
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(system* "make" "-C" "build/latex" "all-pdf" "PAPER=a4" pyver)
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(copy-file "build/latex/scipy-ref.pdf"
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(string-append doc "/scipy-ref.pdf"))
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(with-directory-excursion "build/html"
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(for-each (lambda (file)
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(let* ((dir (dirname file))
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(tgt-dir (string-append html "/" dir)))
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(unless (equal? "." dir)
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(mkdir-p tgt-dir))
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(copy-file file (string-append html "/" file))))
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(find-files "." ".*"))))))
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;; Tests can only be run after the library has been installed and not
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;; within the source directory.
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(alist-cons-after
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'install 'check
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(lambda _
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(with-directory-excursion "/tmp"
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(zero? (system* "python" "-c" "import scipy; scipy.test()"))))
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(alist-delete
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'check
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%standard-phases))))))
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(home-page "http://www.scipy.org/")
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(synopsis "The Scipy library provides efficient numerical routines")
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(description "The SciPy library is one of the core packages that make up
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the SciPy stack. It provides many user-friendly and efficient numerical
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routines such as routines for numerical integration and optimization.")
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(license bsd-3)))
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(define-public python2-scipy
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(let ((scipy (package-with-python2 python-scipy)))
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(package (inherit scipy)
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;; Use packages customized for python-2.
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(inputs `(("python2-matplotlib" ,python2-matplotlib)
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("python2-numpy" ,python2-numpy)
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,@(alist-delete "python-matplotlib"
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(alist-delete "python-numpy"
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(package-inputs scipy))))))))
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(define-public python-sqlalchemy
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(define-public python-sqlalchemy
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(package
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(package
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(name "python-sqlalchemy")
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(name "python-sqlalchemy")
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@ -2341,3 +2448,4 @@ a general image processing tool.")
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(define-public python2-pillow
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(define-public python2-pillow
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(package-with-python2 python-pillow))
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(package-with-python2 python-pillow))
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