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.

1 files changed, 126 insertions, 0 deletions

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 4636180dfa..93fc63c2e7 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -24,12 +24,138 @@
 (define-module (gnu packages python-science)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages check)
+  #:use-module (gnu packages gcc)
+  #:use-module (gnu packages maths)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages sphinx)
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix utils)
   #:use-module (guix build-system python))
 
+(define-public python-scipy
+  (package
+    (name "python-scipy")
+    (version "1.3.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "scipy" version))
+       (sha256
+        (base32 "192d8dsybvhv19igkrsafbdafx198nz7pibkjgrqjhlr66s3jfd0"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-pyparsing" ,python-pyparsing)))
+    (inputs
+     `(("lapack" ,lapack)
+       ("openblas" ,openblas)))
+    (native-inputs
+     `(("python-cython" ,python-cython)
+       ("python-pytest" ,python-pytest)
+       ("python-sphinx" ,python-sphinx)
+       ("python-numpydoc" ,python-numpydoc)
+       ("gfortran" ,gfortran)
+       ("perl" ,perl)
+       ("which" ,which)))
+    (outputs '("out" "doc"))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'disable-broken-tests
+           (lambda _
+             (substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py"
+               (("^( +)def test_threads_parallel\\(self\\):" m indent)
+                (string-append indent
+                               "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
+                               m)))
+             (substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py"
+               (("^def test_parallel_threads\\(\\):" m)
+                (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
+                               m)))
+             #t))
+         (add-before 'build 'configure-openblas
+           (lambda* (#:key inputs #:allow-other-keys)
+             (call-with-output-file "site.cfg"
+               (lambda (port)
+                 (format port
+                         "[blas]
+libraries = openblas
+library_dirs = ~a/lib
+include_dirs = ~a/include
+
+# backslash-n to make emacs happy
+\n[atlas]
+library_dirs = ~a/lib
+atlas_libs = openblas
+"
+                         (assoc-ref inputs "openblas")
+                         (assoc-ref inputs "openblas")
+                         (assoc-ref inputs "openblas"))))
+             #t))
+         (add-after 'install 'install-doc
+           (lambda* (#:key inputs 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=" (version-major+minor
+                                                     (package-version python))))
+                    ;; By default it tries to run sphinx-build through the Python
+                    ;; interpreter which won't work with our shell wrapper.
+                    (sphinxbuild "SPHINXBUILD=LANG=C sphinx-build"))
+               ;; Make installed package available for building the
+               ;; documentation
+               (add-installed-pythonpath inputs outputs)
+               (with-directory-excursion "doc"
+                 ;; Fix generation of images for mathematical expressions.
+                 (substitute* (find-files "source" "conf\\.py")
+                   (("pngmath_use_preview = True")
+                    "pngmath_use_preview = False"))
+                 (mkdir-p html)
+                 (invoke "make" "html" pyver sphinxbuild)
+                 (with-directory-excursion "build/html"
+                   (for-each (lambda (file)
+                               (let* ((dir (dirname file))
+                                      (tgt-dir (string-append html "/" dir)))
+                                 (install-file file html)))
+                             (find-files "." ".*")))))
+             #t))
+         ;; Tests can only be run after the library has been installed and not
+         ;; within the source directory.
+         (delete 'check)
+         (add-after 'install 'check
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (add-installed-pythonpath inputs outputs)
+             (with-directory-excursion "/tmp"
+               (invoke "python" "-c"
+                       "import scipy; scipy.test(verbose=2)")))))))
+    (home-page "https://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.")
+    (properties `((python2-variant . ,(delay python2-scipy))))
+    (license license:bsd-3)))
+
+;; Version 1.2.2 is the last version to support Python 2
+(define-public python2-scipy
+  (package
+    (inherit (package-with-python2
+              (strip-python2-variant python-scipy)))
+    (version "1.2.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "scipy" version))
+       (sha256
+        (base32
+         "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
+
 (define-public python-scikit-image
   (package
     (name "python-scikit-image")