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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")))))))
generated by cgit v1.2.3 (git 2.45.0) at 2024-11-20 06:36:21 +0000