gnu/packages/python-science.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2015, 2016, 2020 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 ;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com>
  12 ;;;
  13 ;;; This file is part of GNU Guix.
  14 ;;;
  15 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  16 ;;; under the terms of the GNU General Public License as published by
  17 ;;; the Free Software Foundation; either version 3 of the License, or (at
  18 ;;; your option) any later version.
  19 ;;;
  20 ;;; GNU Guix is distributed in the hope that it will be useful, but
  21 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  22 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  23 ;;; GNU General Public License for more details.
  24 ;;;
  25 ;;; You should have received a copy of the GNU General Public License
  26 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  27
  28 (define-module (gnu packages python-science)
  29   #:use-module ((guix licenses) #:prefix license:)
  30   #:use-module (gnu packages)
  31   #:use-module (gnu packages base)
  32   #:use-module (gnu packages check)
  33   #:use-module (gnu packages gcc)
  34   #:use-module (gnu packages maths)
  35   #:use-module (gnu packages perl)
  36   #:use-module (gnu packages python)
  37   #:use-module (gnu packages python-web)
  38   #:use-module (gnu packages python-xyz)
  39   #:use-module (gnu packages sphinx)
  40   #:use-module (gnu packages time)
  41   #:use-module (gnu packages xdisorg)
  42   #:use-module (gnu packages xml)
  43   #:use-module (gnu packages xorg)
  44   #:use-module (guix packages)
  45   #:use-module (guix download)
  46   #:use-module (guix utils)
  47   #:use-module (guix build-system python))
  48
  49 (define-public python-scipy
  50   (package
  51     (name "python-scipy")
  52     (version "1.3.2")
  53     (source
  54      (origin
  55        (method url-fetch)
  56        (uri (pypi-uri "scipy" version))
  57        (sha256
  58         (base32 "192d8dsybvhv19igkrsafbdafx198nz7pibkjgrqjhlr66s3jfd0"))))
  59     (build-system python-build-system)
  60     (propagated-inputs
  61      `(("python-numpy" ,python-numpy)
  62        ("python-matplotlib" ,python-matplotlib)
  63        ("python-pyparsing" ,python-pyparsing)))
  64     (inputs
  65      `(("lapack" ,lapack)
  66        ("openblas" ,openblas)))
  67     (native-inputs
  68      `(("python-cython" ,python-cython)
  69        ("python-pytest" ,python-pytest)
  70        ("python-sphinx" ,python-sphinx)
  71        ("python-numpydoc" ,python-numpydoc)
  72        ("gfortran" ,gfortran)
  73        ("perl" ,perl)
  74        ("which" ,which)))
  75     (outputs '("out" "doc"))
  76     (arguments
  77      `(#:phases
  78        (modify-phases %standard-phases
  79          (add-after 'unpack 'disable-broken-tests
  80            (lambda _
  81              (substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py"
  82                (("^( +)def test_threads_parallel\\(self\\):" m indent)
  83                 (string-append indent
  84                                "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
  85                                m)))
  86              (substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py"
  87                (("^def test_parallel_threads\\(\\):" m)
  88                 (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
  89                                m)))
  90              #t))
  91          (add-before 'build 'configure-openblas
  92            (lambda* (#:key inputs #:allow-other-keys)
  93              (call-with-output-file "site.cfg"
  94                (lambda (port)
  95                  (format port
  96                          "[blas]
  97 libraries = openblas
  98 library_dirs = ~a/lib
  99 include_dirs = ~a/include
 100
 101 # backslash-n to make emacs happy
 102 \n[atlas]
 103 library_dirs = ~a/lib
 104 atlas_libs = openblas
 105 "
 106                          (assoc-ref inputs "openblas")
 107                          (assoc-ref inputs "openblas")
 108                          (assoc-ref inputs "openblas"))))
 109              #t))
 110          (add-after 'install 'install-doc
 111            (lambda* (#:key inputs outputs #:allow-other-keys)
 112              (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
 113                     (doc (string-append data "/doc/" ,name "-" ,version))
 114                     (html (string-append doc "/html"))
 115                     (pyver ,(string-append "PYVER=" (version-major+minor
 116                                                      (package-version python))))
 117                     ;; By default it tries to run sphinx-build through the Python
 118                     ;; interpreter which won't work with our shell wrapper.
 119                     (sphinxbuild "SPHINXBUILD=LANG=C sphinx-build"))
 120                ;; Make installed package available for building the
 121                ;; documentation
 122                (add-installed-pythonpath inputs outputs)
 123                (with-directory-excursion "doc"
 124                  ;; Fix generation of images for mathematical expressions.
 125                  (substitute* (find-files "source" "conf\\.py")
 126                    (("pngmath_use_preview = True")
 127                     "pngmath_use_preview = False"))
 128                  (mkdir-p html)
 129                  (invoke "make" "html" pyver sphinxbuild)
 130                  (with-directory-excursion "build/html"
 131                    (for-each (lambda (file)
 132                                (let* ((dir (dirname file))
 133                                       (tgt-dir (string-append html "/" dir)))
 134                                  (install-file file html)))
 135                              (find-files "." ".*")))))
 136              #t))
 137          ;; Tests can only be run after the library has been installed and not
 138          ;; within the source directory.
 139          (delete 'check)
 140          (add-after 'install 'check
 141            (lambda* (#:key inputs outputs #:allow-other-keys)
 142              (add-installed-pythonpath inputs outputs)
 143              (with-directory-excursion "/tmp"
 144                (invoke "python" "-c"
 145                        "import scipy; scipy.test(verbose=2)")))))))
 146     (home-page "https://www.scipy.org/")
 147     (synopsis "The Scipy library provides efficient numerical routines")
 148     (description "The SciPy library is one of the core packages that make up
 149 the SciPy stack.  It provides many user-friendly and efficient numerical
 150 routines such as routines for numerical integration and optimization.")
 151     (properties `((python2-variant . ,(delay python2-scipy))))
 152     (license license:bsd-3)))
 153
 154 ;; Version 1.2.2 is the last version to support Python 2
 155 (define-public python2-scipy
 156   (package
 157     (inherit (package-with-python2
 158               (strip-python2-variant python-scipy)))
 159     (version "1.2.2")
 160     (source
 161      (origin
 162        (method url-fetch)
 163        (uri (pypi-uri "scipy" version))
 164        (sha256
 165         (base32
 166          "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
 167
 168 (define-public python2-weave
 169   (package
 170     (name "python2-weave")
 171     (version "0.16.0")
 172     (source
 173      (origin
 174        (method url-fetch)
 175        (uri (pypi-uri "weave" version))
 176        (sha256
 177         (base32 "0jnm3584mfichgwgrd1gk5i42ll9c08nkw9716n947n4338f6ghs"))))
 178     (build-system python-build-system)
 179     (arguments
 180      `(#:python ,python-2
 181        #:phases
 182        (modify-phases %standard-phases
 183          (replace 'check
 184            (lambda _
 185              (invoke "nosetests" "-v"
 186                      "--exclude"
 187                      "test_(user|incorrect_ownership|char_fail|obj_fail)"))))))
 188     (propagated-inputs
 189      `(("python-numpy" ,python2-numpy)))
 190     (native-inputs
 191      `(("python-nose" ,python2-nose)))
 192     (home-page "https://www.scipy.org/")
 193     (synopsis "Tools for including C/C++ code within Python code")
 194     (description "Weave is the stand-alone version of the obsolete Scipy
 195 submodule @code{scipy.weave}.  It is Python 2.x only, and is provided for
 196 users that need new versions of Scipy but have existing code that still
 197 depends on @code{scipy.weave}.  For new code, users are recommended to use
 198 Cython.")
 199     (license license:bsd-3)))
 200
 201 (define-public python-scikit-image
 202   (package
 203     (name "python-scikit-image")
 204     (version "0.14.2")
 205     (source
 206      (origin
 207        (method url-fetch)
 208        (uri (pypi-uri "scikit-image" version))
 209        (sha256
 210         (base32 "07qchljkyxvg5nrm12fvszi7pmjk4m01qp0w0z8syxzxxs20pz8s"))))
 211     (build-system python-build-system)
 212     (arguments
 213      ;; TODO: Some tests require running X11 server. Disable them?
 214      '(#:tests? #f))
 215     ;; See DEPENDS.txt for the list of build and run time requiremnts
 216     (propagated-inputs
 217      `(("python-cloudpickle" ,python-cloudpickle)
 218        ("python-dask" ,python-dask)
 219        ("python-matplotlib" ,python-matplotlib)
 220        ("python-networkx" ,python-networkx)
 221        ("python-numpy" ,python-numpy)
 222        ("python-pillow" ,python-pillow)
 223        ("python-pywavelets" ,python-pywavelets)
 224        ("python-scipy" ,python-scipy)
 225        ("python-six" ,python-six)))
 226     (native-inputs
 227      `(("python-cython" ,python-cython)))
 228     (home-page "https://scikit-image.org/")
 229     (synopsis "Image processing in Python")
 230     (description
 231      "Scikit-image is a collection of algorithms for image processing.")
 232     (license license:bsd-3)))
 233
 234 (define-public python-pandas
 235   (package
 236     (name "python-pandas")
 237     (version "1.0.5")
 238     (source
 239      (origin
 240        (method url-fetch)
 241        (uri (pypi-uri "pandas" version))
 242        (sha256
 243         (base32 "1a2gv3g6jr6vb5ca43fkwjl5xf86wpfz8y3zcy787adjl0hdkib9"))))
 244     (build-system python-build-system)
 245     (arguments
 246      `(#:modules ((guix build utils)
 247                   (guix build python-build-system)
 248                   (ice-9 ftw)
 249                   (srfi srfi-26))
 250        #:phases (modify-phases %standard-phases
 251                   (add-after 'unpack 'patch-which
 252                     (lambda* (#:key inputs #:allow-other-keys)
 253                       (let ((which (assoc-ref inputs "which")))
 254                         (substitute* "pandas/io/clipboard/__init__.py"
 255                           (("^WHICH_CMD = .*")
 256                            (string-append "WHICH_CMD = \"" which "\"\n"))))
 257                       #t))
 258                   (add-before 'check 'prepare-x
 259                     (lambda _
 260                       (system "Xvfb &")
 261                       (setenv "DISPLAY" ":0")
 262                       ;; xsel needs to write a log file.
 263                       (setenv "HOME" "/tmp")
 264                       #t))
 265                   (replace 'check
 266                     (lambda _
 267                       (let ((build-directory
 268                              (string-append
 269                               (getcwd) "/build/"
 270                               (car (scandir "build"
 271                                             (cut string-prefix? "lib." <>))))))
 272                         ;; Disable the "strict data files" option which causes
 273                         ;; the build to error out if required data files are
 274                         ;; not available (as is the case with PyPI archives).
 275                         (substitute* "setup.cfg"
 276                           (("addopts = --strict-data-files") "addopts = "))
 277                         (with-directory-excursion build-directory
 278                           (invoke "pytest" "-vv" "pandas" "--skip-slow"
 279                                   "--skip-network"))))))))
 280     (propagated-inputs
 281      `(("python-jinja2" ,python-jinja2)
 282        ("python-numpy" ,python-numpy)
 283        ("python-openpyxl" ,python-openpyxl)
 284        ("python-pytz" ,python-pytz)
 285        ("python-dateutil" ,python-dateutil)
 286        ("python-xlrd" ,python-xlrd)))
 287     (inputs
 288      `(("which" ,which)
 289        ("xclip" ,xclip)
 290        ("xsel" ,xsel)))
 291     (native-inputs
 292      `(("python-cython" ,python-cython)
 293        ("python-beautifulsoup4" ,python-beautifulsoup4)
 294        ("python-lxml" ,python-lxml)
 295        ("python-html5lib" ,python-html5lib)
 296        ("python-nose" ,python-nose)
 297        ("python-pytest" ,python-pytest)
 298        ("python-pytest-mock" ,python-pytest-mock)
 299        ;; Needed to test clipboard support.
 300        ("xorg-server" ,xorg-server-for-tests)))
 301     (home-page "https://pandas.pydata.org")
 302     (synopsis "Data structures for data analysis, time series, and statistics")
 303     (description
 304      "Pandas is a Python package providing fast, flexible, and expressive data
 305 structures designed to make working with structured (tabular,
 306 multidimensional, potentially heterogeneous) and time series data both easy
 307 and intuitive.  It aims to be the fundamental high-level building block for
 308 doing practical, real world data analysis in Python.")
 309     (properties `((python2-variant . ,(delay python2-pandas))))
 310     (license license:bsd-3)))
 311
 312 (define-public python-pandas-0.25
 313   (package
 314     (inherit python-pandas)
 315     (version "0.25.3")
 316     (source (origin
 317               (method url-fetch)
 318               (uri (pypi-uri "pandas" version))
 319               (sha256
 320                (base32
 321                 "191048m6kdc6yfvqs9w412lq60cfvigrsb57y0x116lwibgp9njj"))))
 322     (arguments
 323      (substitute-keyword-arguments (package-arguments python-pandas)
 324        ((#:phases phases)
 325         `(modify-phases ,phases
 326            (replace 'patch-which
 327              (lambda* (#:key inputs #:allow-other-keys)
 328                (let ((which (assoc-ref inputs "which")))
 329                  (substitute* "pandas/io/clipboard/__init__.py"
 330                    (("^CHECK_CMD = .*")
 331                      (string-append "CHECK_CMD = \"" which "\"\n"))))
 332                #t))
 333            (delete 'prepare-x)))))))
 334
 335 ;; Pandas 0.24.x are the last versions that support Python 2.
 336 (define-public python2-pandas
 337   (let ((pandas (package-with-python2
 338                  (strip-python2-variant python-pandas-0.25))))
 339     (package
 340       (inherit pandas)
 341       (version "0.24.2")
 342       (source (origin
 343                 (method url-fetch)
 344                 (uri (pypi-uri "pandas" version))
 345                 (sha256
 346                  (base32
 347                   "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag"))
 348                 (modules '((guix build utils)))
 349                 (snippet
 350                  '(begin
 351                     ;; Adjust for renamed error message in Python 2.7.17.  Taken
 352                     ;; from <https://github.com/pandas-dev/pandas/pull/29294>.
 353                     (substitute* "pandas/io/parsers.py"
 354                       (("if 'NULL byte' in msg:")
 355                        "if 'NULL byte' in msg or 'line contains NUL' in msg:"))
 356                     #t)))))))
 357
 358 (define-public python-xarray
 359   (package
 360     (name "python-xarray")
 361     (version "0.15.1")
 362     (source (origin
 363               (method url-fetch)
 364               (uri (pypi-uri "xarray" version))
 365               (sha256
 366                (base32
 367                 "1yx8j66b7rn10m2l6gmn8yr9cn38pi5cj0x0wwpy4hdnhy6i7qv4"))))
 368     (build-system python-build-system)
 369     (native-inputs
 370      `(("python-setuptools-scm" ,python-setuptools-scm)
 371        ("python-pytest" ,python-pytest)))
 372     (propagated-inputs
 373      `(("python-numpy" ,python-numpy)
 374        ("python-pandas" ,python-pandas)))
 375     (arguments
 376      `(#:phases
 377        (modify-phases %standard-phases
 378          (replace 'check
 379            (lambda _
 380              (invoke "pytest"))))))
 381     (home-page "https://github.com/pydata/xarray")
 382     (synopsis "N-D labeled arrays and datasets")
 383     (description "Xarray (formerly xray) makes working with labelled
 384 multi-dimensional arrays simple, efficient, and fun!
 385
 386 Xarray introduces labels in the form of dimensions, coordinates and attributes
 387 on top of raw NumPy-like arrays, which allows for a more intuitive, more
 388 concise, and less error-prone developer experience.  The package includes a
 389 large and growing library of domain-agnostic functions for advanced analytics
 390 and visualization with these data structures.")
 391     (license license:asl2.0)))