[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
02/02: gnu: python-scipy: Move to (gnu packages python-science).
|
From: |
guix-commits |
|
Subject: |
02/02: gnu: python-scipy: Move to (gnu packages python-science). |
|
Date: |
Mon, 2 Dec 2019 09:25:33 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit ec1224a73b2c0c0c15a3293261334f3927f6579d
Author: Ricardo Wurmus <address@hidden>
Date: Mon Dec 2 14:04:39 2019 +0100
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.
---
gnu/packages/bioinformatics.scm | 1 +
gnu/packages/machine-learning.scm | 1 +
gnu/packages/python-science.scm | 126 ++++++++++++++++++++++++++++++++++++++
gnu/packages/python-xyz.scm | 119 -----------------------------------
gnu/packages/statistics.scm | 1 +
5 files changed, 129 insertions(+), 119 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 616fced..b0d070b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -105,6 +105,7 @@
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages python-compression)
+ #:use-module (gnu packages python-science)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages readline)
diff --git a/gnu/packages/machine-learning.scm
b/gnu/packages/machine-learning.scm
index b83b336..ab4150c 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -69,6 +69,7 @@
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-science)
#:use-module (gnu packages python-web)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages serialization)
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 4636180..93fc63c 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")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 1d6f0a8..f52d9a4 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -4277,125 +4277,6 @@ those files. It can also efficiently manipulate ranges
of integers using set
operators such as union, intersection, and difference.")
(license license:asl2.0)))
-(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-socksipy-branch
(package
(name "python-socksipy-branch")
diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index b84b380..1d6e6aa 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -66,6 +66,7 @@
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-science)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages readline)
#:use-module (gnu packages sphinx)