gnu: python-scipy: Move to (gnu packages python-science).
* gnu/packages/python-xyz.scm (python-scipy, python2-scipy): Move these from here... * gnu/packages/python-science.scm (python-scipy, python2-scipy): ...to here. * gnu/packages/bioinformatics.scm, gnu/packages/machine-learning.scm, gnu/packages/statistics.scm: Adjust module imports.
This commit is contained in:
Ricardo Wurmus
parent
ca7c365312
commit
ec1224a73b
5 changed files with 129 additions and 119 deletions
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@ -105,6 +105,7 @@
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#:use-module (gnu packages protobuf)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-compression)
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#:use-module (gnu packages python-science)
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#:use-module (gnu packages python-web)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages readline)
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@ -69,6 +69,7 @@
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages protobuf)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-science)
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#:use-module (gnu packages python-web)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages serialization)
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@ -24,12 +24,138 @@
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(define-module (gnu packages python-science)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (gnu packages)
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#:use-module (gnu packages base)
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#:use-module (gnu packages check)
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#:use-module (gnu packages gcc)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages sphinx)
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#:use-module (guix packages)
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#:use-module (guix download)
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#:use-module (guix utils)
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#:use-module (guix build-system python))
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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 "1.3.2")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "scipy" version))
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(sha256
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(base32 "192d8dsybvhv19igkrsafbdafx198nz7pibkjgrqjhlr66s3jfd0"))))
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(build-system python-build-system)
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(propagated-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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(inputs
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`(("lapack" ,lapack)
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("openblas" ,openblas)))
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(native-inputs
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`(("python-cython" ,python-cython)
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("python-pytest" ,python-pytest)
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("python-sphinx" ,python-sphinx)
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("python-numpydoc" ,python-numpydoc)
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("gfortran" ,gfortran)
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("perl" ,perl)
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("which" ,which)))
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(outputs '("out" "doc"))
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'disable-broken-tests
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(lambda _
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(substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py"
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(("^( +)def test_threads_parallel\\(self\\):" m indent)
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(string-append indent
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"@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
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m)))
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(substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py"
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(("^def test_parallel_threads\\(\\):" m)
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(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
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m)))
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#t))
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(add-before 'build 'configure-openblas
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(lambda* (#:key inputs #:allow-other-keys)
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(call-with-output-file "site.cfg"
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(lambda (port)
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(format port
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"[blas]
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libraries = openblas
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library_dirs = ~a/lib
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include_dirs = ~a/include
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# backslash-n to make emacs happy
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\n[atlas]
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library_dirs = ~a/lib
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atlas_libs = openblas
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"
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(assoc-ref inputs "openblas")
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(assoc-ref inputs "openblas")
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(assoc-ref inputs "openblas"))))
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#t))
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(add-after 'install 'install-doc
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(lambda* (#:key inputs 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=" (version-major+minor
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(package-version python))))
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;; By default it tries to run sphinx-build through the Python
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;; interpreter which won't work with our shell wrapper.
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(sphinxbuild "SPHINXBUILD=LANG=C sphinx-build"))
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;; Make installed package available for building the
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;; documentation
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(add-installed-pythonpath inputs outputs)
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(with-directory-excursion "doc"
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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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(invoke "make" "html" pyver sphinxbuild)
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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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(install-file file html)))
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(find-files "." ".*")))))
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#t))
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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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(delete 'check)
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(add-after 'install 'check
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(add-installed-pythonpath inputs outputs)
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(with-directory-excursion "/tmp"
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(invoke "python" "-c"
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"import scipy; scipy.test(verbose=2)")))))))
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(home-page "https://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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(properties `((python2-variant . ,(delay python2-scipy))))
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(license license:bsd-3)))
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;; Version 1.2.2 is the last version to support Python 2
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(define-public python2-scipy
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(package
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(inherit (package-with-python2
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(strip-python2-variant python-scipy)))
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(version "1.2.2")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "scipy" version))
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(sha256
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(base32
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"1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
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(define-public python-scikit-image
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(package
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(name "python-scikit-image")
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@ -4277,125 +4277,6 @@ those files. It can also efficiently manipulate ranges of integers using set
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operators such as union, intersection, and difference.")
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(license license:asl2.0)))
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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 "1.3.2")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "scipy" version))
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(sha256
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(base32 "192d8dsybvhv19igkrsafbdafx198nz7pibkjgrqjhlr66s3jfd0"))))
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(build-system python-build-system)
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(propagated-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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(inputs
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`(("lapack" ,lapack)
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("openblas" ,openblas)))
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(native-inputs
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`(("python-cython" ,python-cython)
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("python-pytest" ,python-pytest)
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("python-sphinx" ,python-sphinx)
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("python-numpydoc" ,python-numpydoc)
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("gfortran" ,gfortran)
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("perl" ,perl)
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("which" ,which)))
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(outputs '("out" "doc"))
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'disable-broken-tests
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(lambda _
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(substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py"
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(("^( +)def test_threads_parallel\\(self\\):" m indent)
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(string-append indent
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"@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
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m)))
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(substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py"
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(("^def test_parallel_threads\\(\\):" m)
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(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
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m)))
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#t))
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(add-before 'build 'configure-openblas
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(lambda* (#:key inputs #:allow-other-keys)
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(call-with-output-file "site.cfg"
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(lambda (port)
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(format port
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"[blas]
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libraries = openblas
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library_dirs = ~a/lib
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include_dirs = ~a/include
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# backslash-n to make emacs happy
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\n[atlas]
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library_dirs = ~a/lib
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atlas_libs = openblas
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"
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(assoc-ref inputs "openblas")
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(assoc-ref inputs "openblas")
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(assoc-ref inputs "openblas"))))
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#t))
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(add-after 'install 'install-doc
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(lambda* (#:key inputs 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=" (version-major+minor
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(package-version python))))
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;; By default it tries to run sphinx-build through the Python
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;; interpreter which won't work with our shell wrapper.
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(sphinxbuild "SPHINXBUILD=LANG=C sphinx-build"))
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;; Make installed package available for building the
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;; documentation
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(add-installed-pythonpath inputs outputs)
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(with-directory-excursion "doc"
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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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(invoke "make" "html" pyver sphinxbuild)
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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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(install-file file html)))
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(find-files "." ".*")))))
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#t))
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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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(delete 'check)
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(add-after 'install 'check
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(add-installed-pythonpath inputs outputs)
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(with-directory-excursion "/tmp"
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(invoke "python" "-c"
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"import scipy; scipy.test(verbose=2)")))))))
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(home-page "https://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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(properties `((python2-variant . ,(delay python2-scipy))))
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(license license:bsd-3)))
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;; Version 1.2.2 is the last version to support Python 2
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(define-public python2-scipy
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(package
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(inherit (package-with-python2
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(strip-python2-variant python-scipy)))
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(version "1.2.2")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "scipy" version))
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(sha256
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(base32
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"1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
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(define-public python-socksipy-branch
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(package
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(name "python-socksipy-branch")
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@ -66,6 +66,7 @@
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#:use-module (gnu packages perl)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-science)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages readline)
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#:use-module (gnu packages sphinx)
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