Merge branch 'master' into core-updates

1 files changed, 287 insertions, 0 deletions

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
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+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
+;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
+;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
+;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018, 2019 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(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-web)
+  #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages sphinx)
+  #:use-module (gnu packages time)
+  #: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")
+    (version "0.14.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "scikit-image" version))
+       (sha256
+        (base32 "07qchljkyxvg5nrm12fvszi7pmjk4m01qp0w0z8syxzxxs20pz8s"))))
+    (build-system python-build-system)
+    (arguments
+     ;; TODO: Some tests require running X11 server. Disable them?
+     '(#:tests? #f))
+    ;; See DEPENDS.txt for the list of build and run time requiremnts
+    (propagated-inputs
+     `(("python-cloudpickle" ,python-cloudpickle)
+       ("python-dask" ,python-dask)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-networkx" ,python-networkx)
+       ("python-numpy" ,python-numpy)
+       ("python-pillow" ,python-pillow)
+       ("python-pywavelets" ,python-pywavelets)
+       ("python-scipy" ,python-scipy)
+       ("python-six" ,python-six)))
+    (native-inputs
+     `(("python-cython" ,python-cython)))
+    (home-page "http://scikit-image.org/")
+    (synopsis "Image processing in Python")
+    (description
+     "Scikit-image is a collection of algorithms for image processing.")
+    (license license:bsd-3)))
+
+(define-public python2-scikit-image
+  (package-with-python2 python-scikit-image))
+
+(define-public python-pandas
+  (package
+    (name "python-pandas")
+    (version "0.25.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pandas" version))
+       (sha256
+        (base32 "1gp2pvzdiakvgjmykdzdlzrsfbg4vjm49jjdl9s0ha0a3yfs34fa"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:modules ((guix build utils)
+                  (guix build python-build-system)
+                  (ice-9 ftw)
+                  (srfi srfi-26))
+       #:phases (modify-phases %standard-phases
+                  (add-after 'unpack 'patch-which
+                    (lambda* (#:key inputs #:allow-other-keys)
+                      (let ((which (assoc-ref inputs "which")))
+                        (substitute* "pandas/io/clipboard/__init__.py"
+                          (("^CHECK_CMD = .*")
+                           (string-append "CHECK_CMD = \"" which "\"\n"))))
+                      #t))
+                  (replace 'check
+                    (lambda _
+                      (let ((build-directory
+                             (string-append
+                              (getcwd) "/build/"
+                              (car (scandir "build"
+                                            (cut string-prefix? "lib." <>))))))
+                        ;; Disable the "strict data files" option which causes
+                        ;; the build to error out if required data files are
+                        ;; not available (as is the case with PyPI archives).
+                        (substitute* "setup.cfg"
+                          (("addopts = --strict-data-files") "addopts = "))
+                        (with-directory-excursion build-directory
+                          ;; Delete tests that require "moto" which is not yet
+                          ;; in Guix.
+                          (for-each delete-file
+                                    '("pandas/tests/io/conftest.py"
+                                      "pandas/tests/io/json/test_compression.py"
+                                      "pandas/tests/io/parser/test_network.py"
+                                      "pandas/tests/io/test_parquet.py"))
+                          (invoke "pytest" "-vv" "pandas" "--skip-slow"
+                                  "--skip-network" "-k"
+                                  ;; XXX: Due to the deleted tests above.
+                                  "not test_read_s3_jsonl"))))))))
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)
+       ("python-openpyxl" ,python-openpyxl)
+       ("python-pytz" ,python-pytz)
+       ("python-dateutil" ,python-dateutil)
+       ("python-xlrd" ,python-xlrd)))
+    (inputs
+     `(("which" ,which)))
+    (native-inputs
+     `(("python-cython" ,python-cython)
+       ("python-beautifulsoup4" ,python-beautifulsoup4)
+       ("python-lxml" ,python-lxml)
+       ("python-html5lib" ,python-html5lib)
+       ("python-nose" ,python-nose)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-mock" ,python-pytest-mock)))
+    (home-page "https://pandas.pydata.org")
+    (synopsis "Data structures for data analysis, time series, and statistics")
+    (description
+     "Pandas is a Python package providing fast, flexible, and expressive data
+structures designed to make working with structured (tabular,
+multidimensional, potentially heterogeneous) and time series data both easy
+and intuitive.  It aims to be the fundamental high-level building block for
+doing practical, real world data analysis in Python.")
+    (properties `((python2-variant . ,(delay python2-pandas))))
+    (license license:bsd-3)))
+
+;; Pandas 0.24.x are the last versions that support Python 2.
+(define-public python2-pandas
+  (let ((pandas (package-with-python2
+                 (strip-python2-variant python-pandas))))
+    (package/inherit
+     pandas
+     (version "0.24.2")
+     (source (origin
+               (method url-fetch)
+               (uri (pypi-uri "pandas" version))
+               (sha256
+                (base32
+                 "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag")))))))