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43/57: gnu: python-numpy-bootstrap, python-numpy: Fix build.
From: |
Hartmut Goebel |
Subject: |
43/57: gnu: python-numpy-bootstrap, python-numpy: Fix build. |
Date: |
Sat, 15 Oct 2016 14:08:14 +0000 (UTC) |
htgoebel pushed a commit to branch wip-python-build-system
in repository guix.
commit e7fdc6bc205c828333bd6435242a45998c4e929f
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 a79b678..4f8f6e8 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -2972,18 +2972,17 @@ writing C extensions for Python as easy as Python
itself.")
(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
@@ -2992,7 +2991,8 @@ 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
@@ -3005,18 +3005,17 @@ 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 outputs inputs)
(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
@@ -3049,10 +3048,10 @@ 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")
@@ -3067,14 +3066,15 @@ 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)
@@ -3085,7 +3085,10 @@ 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 outputs inputs)
(let* ((data (string-append (assoc-ref outputs "doc")
"/share"))
(doc (string-append
data "/doc/" ,name "-"
- 19/57: gnu: python-pytest-cov: Use upstream options for testing., (continued)
- 19/57: gnu: python-pytest-cov: Use upstream options for testing., Hartmut Goebel, 2016/10/15
- 23/57: inputs -> propagated-inputs: special, Hartmut Goebel, 2016/10/15
- 29/57: gnu: python-ccm: Update synopsis and description., Hartmut Goebel, 2016/10/15
- 22/57: gnu: Fix inputs in python.scm, part 2: native-inputs -> propagated-inputs., Hartmut Goebel, 2016/10/15
- 32/57: gnu: python-fixture: Correct inputs., Hartmut Goebel, 2016/10/15
- 38/57: gnu: python-pytest-flakes: Fix build., Hartmut Goebel, 2016/10/15
- 06/57: guix: python-build-system: Delete .egg-info file created in phase check., Hartmut Goebel, 2016/10/15
- 34/57: gnu: python-testrepositoryfixture: Correct inputs., Hartmut Goebel, 2016/10/15
- 33/57: gnu: python-fixture: Enable tests., Hartmut Goebel, 2016/10/15
- 42/57: gnu: python-fonttools: Remove intervening directory in site-packges., Hartmut Goebel, 2016/10/15
- 43/57: gnu: python-numpy-bootstrap, python-numpy: Fix build.,
Hartmut Goebel <=
- 44/57: gnu: python-matplotlib: Fix build., Hartmut Goebel, 2016/10/15
- 20/57: gnu: Fix inputs in python.scm, part 1: inputs -> propagated-inputs., Hartmut Goebel, 2016/10/15
- 30/57: gnu: python-h5py: Remove needless "python2-variant" property., Hartmut Goebel, 2016/10/15
- 24/57: gnu: python-sphinx-rtd-theme: Remove inputs., Hartmut Goebel, 2016/10/15
- 31/57: gnu: python-hdf5: Correct inputs., Hartmut Goebel, 2016/10/15
- 28/57: gnu: python-ccm: Add missing input python-psutil., Hartmut Goebel, 2016/10/15
- 57/57: Add a series of FIXME and TODO comments., Hartmut Goebel, 2016/10/15
- 10/57: gnu: Remove python-setuptools and python2-setuptools from inputs (part 1b), Hartmut Goebel, 2016/10/15
- 27/57: gnu: Ensure python-cython is a native-input., Hartmut Goebel, 2016/10/15
- 26/57: make native-inputs: simple ones: one nose, docuitls, phinx, tests, …, Hartmut Goebel, 2016/10/15