44/104: gnu: python-numpy-bootstrap, python-numpy: Fix build.

[Hartmut Goebel]

htgoebel pushed a commit to branch python-build-system
in repository guix.

commit 2efabc5589dc641dce75702b99253a3fb40bb2eb
Author: Hartmut Goebel <address@hidden>
Date:   Thu Oct 13 14:34:13 2016 +0200

    gnu: python-numpy-bootstrap, python-numpy: Fix build.
    
    * gnu/packages/python.scm (python-numpy-bootstrap): Correct inputs, use
      modify-phases, add dummy newlines character to string to make emacs happy,
      set PYTHONPATH prior to running tests. (python-numpy): propagate inputs, 
set
      PYTHONPATH prior to building docs.
---
 gnu/packages/python.scm |   45 ++++++++++++++++++++++++---------------------
 1 file changed, 24 insertions(+), 21 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index b160ef5..092378c 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3098,18 +3098,17 @@ between language specification and implementation 
aspects.")
         (base32
          "1bjjhvncraka5s6i4lg644jrxij6bvycxy7an20gcz3a0m11iygp"))))
     (build-system python-build-system)
-    (native-inputs
-     `(("python-nose" ,python-nose)))
     (inputs
      `(("openblas" ,openblas)
        ("lapack" ,lapack)))
     (native-inputs
-     `(("gfortran" ,gfortran)))
+     `(("python-nose" ,python-nose)
+       ("gfortran" ,gfortran)))
     (arguments
      `(#:phases
-       (alist-cons-before
-        'build 'set-environment-variables
-        (lambda* (#:key inputs #:allow-other-keys)
+       (modify-phases %standard-phases
+        (add-before 'build 'set-environment-variables
+         (lambda* (#:key inputs #:allow-other-keys)
           (call-with-output-file "site.cfg"
             (lambda (port)
               (format port
@@ -3118,7 +3117,8 @@ libraries = openblas
 library_dirs = ~a/lib
 include_dirs = ~a/include
 
-[lapack]
+# backslash-n to make emacs happy
+\n[lapack]
 lapack_libs = lapack
 library_dirs = ~a/lib
 include_dirs = ~a/include
@@ -3131,18 +3131,17 @@ include_dirs = ~a/include
           (substitute* "numpy/distutils/system_info.py"
             (("c = distutils\\.ccompiler\\.new_compiler\\(\\)")
              "c = distutils.ccompiler.new_compiler(); 
c.set_executables(compiler='gcc',compiler_so='gcc',linker_exe='gcc',linker_so='gcc
 -shared')"))
-          #t)
+          #t))
         ;; Tests can only be run after the library has been installed and not
         ;; within the source directory.
-        (alist-cons-after
-         'install 'check
-         (lambda _
+        (delete 'check)
+        (add-after 'install 'check
+         (lambda* (#:key outputs inputs #:allow-other-keys)
+           ;; Make installed package available for running the tests
+           (add-installed-pythonpath inputs outputs)
            (with-directory-excursion "/tmp"
              (zero? (system* "python" "-c"
-                             "import numpy; numpy.test(verbose=2)"))))
-         (alist-delete
-          'check
-          %standard-phases)))))
+                             "import numpy; numpy.test(verbose=2)"))))))))
     (home-page "http://www.numpy.org/";)
     (synopsis "Fundamental package for scientific computing with Python")
     (description "NumPy is the fundamental package for scientific computing
@@ -3175,10 +3174,10 @@ capabilities.")
        ("python2-matplotlib" ,python2-matplotlib)
        ("python2-pandas" ,python2-pandas)
        ("python2-scikit-learn" ,python2-scikit-learn)
-       ("python2-cython" ,python2-cython)
        ("python2-pysnptools" ,python2-pysnptools)))
     (native-inputs
      `(("unzip" ,unzip)
+       ("python2-cython" ,python2-cython)
        ("python2-mock" ,python2-mock)))
     (home-page 
"http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/";)
     (synopsis "Perform genome-wide association studies on large data sets")
@@ -3193,14 +3192,15 @@ association studies (GWAS) on extremely large data 
sets.")
     (name "python-numpy")
     (outputs '("out" "doc"))
     (inputs
-     `(("which" ,which)
-       ("python-matplotlib" ,python-matplotlib)
-       ("python-sphinx" ,python-sphinx)
+     `(("which" ,which)))
+    (propagated-inputs
+     `(("python-matplotlib" ,python-matplotlib)
        ("python-pyparsing" ,python-pyparsing)
-       ("python-numpydoc" ,python-numpydoc)
        ,@(package-inputs python-numpy-bootstrap)))
     (native-inputs
      `(("pkg-config" ,pkg-config)
+       ("python-sphinx" ,python-sphinx)
+       ("python-numpydoc" ,python-numpydoc)
        ("texlive" ,texlive)
        ("texinfo" ,texinfo)
        ("perl" ,perl)
@@ -3211,7 +3211,10 @@ association studies (GWAS) on extremely large data 
sets.")
            ((#:phases phases)
             `(alist-cons-after
               'install 'install-doc
-              (lambda* (#:key outputs #:allow-other-keys)
+              (lambda* (#:key inputs outputs #:allow-other-keys)
+                ;; Make installed package available for building the
+                ;; documentation
+                (add-installed-pythonpath inputs outputs)
                 (let* ((data (string-append (assoc-ref outputs "doc") 
"/share"))
                        (doc (string-append
                              data "/doc/" ,name "-"