gnu/packages/python-science.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
   3 ;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
   4 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
   5 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
   6 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
   7 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Marius Bakke <mbakke@fastmail.com>
   8 ;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
   9 ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
  10 ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
  11 ;;;
  12 ;;; This file is part of GNU Guix.
  13 ;;;
  14 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  15 ;;; under the terms of the GNU General Public License as published by
  16 ;;; the Free Software Foundation; either version 3 of the License, or (at
  17 ;;; your option) any later version.
  18 ;;;
  19 ;;; GNU Guix is distributed in the hope that it will be useful, but
  20 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  21 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  22 ;;; GNU General Public License for more details.
  23 ;;;
  24 ;;; You should have received a copy of the GNU General Public License
  25 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  26
  27 (define-module (gnu packages python-science)
  28   #:use-module ((guix licenses) #:prefix license:)
  29   #:use-module (gnu packages)
  30   #:use-module (gnu packages base)
  31   #:use-module (gnu packages check)
  32   #:use-module (gnu packages gcc)
  33   #:use-module (gnu packages maths)
  34   #:use-module (gnu packages perl)
  35   #:use-module (gnu packages python)
  36   #:use-module (gnu packages python-web)
  37   #:use-module (gnu packages python-xyz)
  38   #:use-module (gnu packages sphinx)
  39   #:use-module (gnu packages time)
  40   #:use-module (gnu packages xml)
  41   #:use-module (guix packages)
  42   #:use-module (guix download)
  43   #:use-module (guix utils)
  44   #:use-module (guix build-system python))
  45
  46 (define-public python-scipy
  47   (package
  48     (name "python-scipy")
  49     (version "1.3.2")
  50     (source
  51      (origin
  52        (method url-fetch)
  53        (uri (pypi-uri "scipy" version))
  54        (sha256
  55         (base32 "192d8dsybvhv19igkrsafbdafx198nz7pibkjgrqjhlr66s3jfd0"))))
  56     (build-system python-build-system)
  57     (propagated-inputs
  58      `(("python-numpy" ,python-numpy)
  59        ("python-matplotlib" ,python-matplotlib)
  60        ("python-pyparsing" ,python-pyparsing)))
  61     (inputs
  62      `(("lapack" ,lapack)
  63        ("openblas" ,openblas)))
  64     (native-inputs
  65      `(("python-cython" ,python-cython)
  66        ("python-pytest" ,python-pytest)
  67        ("python-sphinx" ,python-sphinx)
  68        ("python-numpydoc" ,python-numpydoc)
  69        ("gfortran" ,gfortran)
  70        ("perl" ,perl)
  71        ("which" ,which)))
  72     (outputs '("out" "doc"))
  73     (arguments
  74      `(#:phases
  75        (modify-phases %standard-phases
  76          (add-after 'unpack 'disable-broken-tests
  77            (lambda _
  78              (substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py"
  79                (("^( +)def test_threads_parallel\\(self\\):" m indent)
  80                 (string-append indent
  81                                "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
  82                                m)))
  83              (substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py"
  84                (("^def test_parallel_threads\\(\\):" m)
  85                 (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
  86                                m)))
  87              #t))
  88          (add-before 'build 'configure-openblas
  89            (lambda* (#:key inputs #:allow-other-keys)
  90              (call-with-output-file "site.cfg"
  91                (lambda (port)
  92                  (format port
  93                          "[blas]
  94 libraries = openblas
  95 library_dirs = ~a/lib
  96 include_dirs = ~a/include
  97
  98 # backslash-n to make emacs happy
  99 \n[atlas]
 100 library_dirs = ~a/lib
 101 atlas_libs = openblas
 102 "
 103                          (assoc-ref inputs "openblas")
 104                          (assoc-ref inputs "openblas")
 105                          (assoc-ref inputs "openblas"))))
 106              #t))
 107          (add-after 'install 'install-doc
 108            (lambda* (#:key inputs outputs #:allow-other-keys)
 109              (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
 110                     (doc (string-append data "/doc/" ,name "-" ,version))
 111                     (html (string-append doc "/html"))
 112                     (pyver ,(string-append "PYVER=" (version-major+minor
 113                                                      (package-version python))))
 114                     ;; By default it tries to run sphinx-build through the Python
 115                     ;; interpreter which won't work with our shell wrapper.
 116                     (sphinxbuild "SPHINXBUILD=LANG=C sphinx-build"))
 117                ;; Make installed package available for building the
 118                ;; documentation
 119                (add-installed-pythonpath inputs outputs)
 120                (with-directory-excursion "doc"
 121                  ;; Fix generation of images for mathematical expressions.
 122                  (substitute* (find-files "source" "conf\\.py")
 123                    (("pngmath_use_preview = True")
 124                     "pngmath_use_preview = False"))
 125                  (mkdir-p html)
 126                  (invoke "make" "html" pyver sphinxbuild)
 127                  (with-directory-excursion "build/html"
 128                    (for-each (lambda (file)
 129                                (let* ((dir (dirname file))
 130                                       (tgt-dir (string-append html "/" dir)))
 131                                  (install-file file html)))
 132                              (find-files "." ".*")))))
 133              #t))
 134          ;; Tests can only be run after the library has been installed and not
 135          ;; within the source directory.
 136          (delete 'check)
 137          (add-after 'install 'check
 138            (lambda* (#:key inputs outputs #:allow-other-keys)
 139              (add-installed-pythonpath inputs outputs)
 140              (with-directory-excursion "/tmp"
 141                (invoke "python" "-c"
 142                        "import scipy; scipy.test(verbose=2)")))))))
 143     (home-page "https://www.scipy.org/")
 144     (synopsis "The Scipy library provides efficient numerical routines")
 145     (description "The SciPy library is one of the core packages that make up
 146 the SciPy stack.  It provides many user-friendly and efficient numerical
 147 routines such as routines for numerical integration and optimization.")
 148     (properties `((python2-variant . ,(delay python2-scipy))))
 149     (license license:bsd-3)))
 150
 151 ;; Version 1.2.2 is the last version to support Python 2
 152 (define-public python2-scipy
 153   (package
 154     (inherit (package-with-python2
 155               (strip-python2-variant python-scipy)))
 156     (version "1.2.2")
 157     (source
 158      (origin
 159        (method url-fetch)
 160        (uri (pypi-uri "scipy" version))
 161        (sha256
 162         (base32
 163          "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
 164
 165 (define-public python-scikit-image
 166   (package
 167     (name "python-scikit-image")
 168     (version "0.14.2")
 169     (source
 170      (origin
 171        (method url-fetch)
 172        (uri (pypi-uri "scikit-image" version))
 173        (sha256
 174         (base32 "07qchljkyxvg5nrm12fvszi7pmjk4m01qp0w0z8syxzxxs20pz8s"))))
 175     (build-system python-build-system)
 176     (arguments
 177      ;; TODO: Some tests require running X11 server. Disable them?
 178      '(#:tests? #f))
 179     ;; See DEPENDS.txt for the list of build and run time requiremnts
 180     (propagated-inputs
 181      `(("python-cloudpickle" ,python-cloudpickle)
 182        ("python-dask" ,python-dask)
 183        ("python-matplotlib" ,python-matplotlib)
 184        ("python-networkx" ,python-networkx)
 185        ("python-numpy" ,python-numpy)
 186        ("python-pillow" ,python-pillow)
 187        ("python-pywavelets" ,python-pywavelets)
 188        ("python-scipy" ,python-scipy)
 189        ("python-six" ,python-six)))
 190     (native-inputs
 191      `(("python-cython" ,python-cython)))
 192     (home-page "https://scikit-image.org/")
 193     (synopsis "Image processing in Python")
 194     (description
 195      "Scikit-image is a collection of algorithms for image processing.")
 196     (license license:bsd-3)))
 197
 198 (define-public python-pandas
 199   (package
 200     (name "python-pandas")
 201     (version "0.25.2")
 202     (source
 203      (origin
 204        (method url-fetch)
 205        (uri (pypi-uri "pandas" version))
 206        (sha256
 207         (base32 "1gp2pvzdiakvgjmykdzdlzrsfbg4vjm49jjdl9s0ha0a3yfs34fa"))))
 208     (build-system python-build-system)
 209     (arguments
 210      `(#:modules ((guix build utils)
 211                   (guix build python-build-system)
 212                   (ice-9 ftw)
 213                   (srfi srfi-26))
 214        #:phases (modify-phases %standard-phases
 215                   (add-after 'unpack 'patch-which
 216                     (lambda* (#:key inputs #:allow-other-keys)
 217                       (let ((which (assoc-ref inputs "which")))
 218                         (substitute* "pandas/io/clipboard/__init__.py"
 219                           (("^CHECK_CMD = .*")
 220                            (string-append "CHECK_CMD = \"" which "\"\n"))))
 221                       #t))
 222                   (replace 'check
 223                     (lambda _
 224                       (let ((build-directory
 225                              (string-append
 226                               (getcwd) "/build/"
 227                               (car (scandir "build"
 228                                             (cut string-prefix? "lib." <>))))))
 229                         ;; Disable the "strict data files" option which causes
 230                         ;; the build to error out if required data files are
 231                         ;; not available (as is the case with PyPI archives).
 232                         (substitute* "setup.cfg"
 233                           (("addopts = --strict-data-files") "addopts = "))
 234                         (with-directory-excursion build-directory
 235                           ;; Delete tests that require "moto" which is not yet
 236                           ;; in Guix.
 237                           (for-each delete-file
 238                                     '("pandas/tests/io/conftest.py"
 239                                       "pandas/tests/io/json/test_compression.py"
 240                                       "pandas/tests/io/parser/test_network.py"
 241                                       "pandas/tests/io/test_parquet.py"))
 242                           (invoke "pytest" "-vv" "pandas" "--skip-slow"
 243                                   "--skip-network" "-k"
 244                                   ;; XXX: Due to the deleted tests above.
 245                                   "not test_read_s3_jsonl"))))))))
 246     (propagated-inputs
 247      `(("python-numpy" ,python-numpy)
 248        ("python-openpyxl" ,python-openpyxl)
 249        ("python-pytz" ,python-pytz)
 250        ("python-dateutil" ,python-dateutil)
 251        ("python-xlrd" ,python-xlrd)))
 252     (inputs
 253      `(("which" ,which)))
 254     (native-inputs
 255      `(("python-cython" ,python-cython)
 256        ("python-beautifulsoup4" ,python-beautifulsoup4)
 257        ("python-lxml" ,python-lxml)
 258        ("python-html5lib" ,python-html5lib)
 259        ("python-nose" ,python-nose)
 260        ("python-pytest" ,python-pytest)
 261        ("python-pytest-mock" ,python-pytest-mock)))
 262     (home-page "https://pandas.pydata.org")
 263     (synopsis "Data structures for data analysis, time series, and statistics")
 264     (description
 265      "Pandas is a Python package providing fast, flexible, and expressive data
 266 structures designed to make working with structured (tabular,
 267 multidimensional, potentially heterogeneous) and time series data both easy
 268 and intuitive.  It aims to be the fundamental high-level building block for
 269 doing practical, real world data analysis in Python.")
 270     (properties `((python2-variant . ,(delay python2-pandas))))
 271     (license license:bsd-3)))
 272
 273 ;; Pandas 0.24.x are the last versions that support Python 2.
 274 (define-public python2-pandas
 275   (let ((pandas (package-with-python2
 276                  (strip-python2-variant python-pandas))))
 277     (package
 278       (inherit pandas)
 279       (version "0.24.2")
 280       (source (origin
 281                 (method url-fetch)
 282                 (uri (pypi-uri "pandas" version))
 283                 (sha256
 284                  (base32
 285                   "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag"))
 286                 (modules '((guix build utils)))
 287                 (snippet
 288                  '(begin
 289                     ;; Adjust for renamed error message in Python 2.7.17.  Taken
 290                     ;; from <https://github.com/pandas-dev/pandas/pull/29294>.
 291                     (substitute* "pandas/io/parsers.py"
 292                       (("if 'NULL byte' in msg:")
 293                        "if 'NULL byte' in msg or 'line contains NUL' in msg:"))
 294                     #t)))))))