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 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
  13 ;;;
  14 ;;; This file is part of GNU Guix.
  15 ;;;
  16 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  17 ;;; under the terms of the GNU General Public License as published by
  18 ;;; the Free Software Foundation; either version 3 of the License, or (at
  19 ;;; your option) any later version.
  20 ;;;
  21 ;;; GNU Guix is distributed in the hope that it will be useful, but
  22 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  23 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  24 ;;; GNU General Public License for more details.
  25 ;;;
  26 ;;; You should have received a copy of the GNU General Public License
  27 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  28
  29 (define-module (gnu packages python-science)
  30   #:use-module ((guix licenses) #:prefix license:)
  31   #:use-module (gnu packages)
  32   #:use-module (gnu packages base)
  33   #:use-module (gnu packages check)
  34   #:use-module (gnu packages gcc)
  35   #:use-module (gnu packages maths)
  36   #:use-module (gnu packages perl)
  37   #:use-module (gnu packages python)
  38   #:use-module (gnu packages python-web)
  39   #:use-module (gnu packages python-xyz)
  40   #:use-module (gnu packages sphinx)
  41   #:use-module (gnu packages time)
  42   #:use-module (gnu packages xdisorg)
  43   #:use-module (gnu packages xml)
  44   #:use-module (gnu packages xorg)
  45   #:use-module (guix packages)
  46   #:use-module (guix download)
  47   #:use-module (guix utils)
  48   #:use-module (guix build-system python))
  49
  50 (define-public python-scipy
  51   (package
  52     (name "python-scipy")
  53     (version "1.3.2")
  54     (source
  55      (origin
  56        (method url-fetch)
  57        (uri (pypi-uri "scipy" version))
  58        (sha256
  59         (base32 "192d8dsybvhv19igkrsafbdafx198nz7pibkjgrqjhlr66s3jfd0"))))
  60     (build-system python-build-system)
  61     (propagated-inputs
  62      `(("python-numpy" ,python-numpy)
  63        ("python-matplotlib" ,python-matplotlib)
  64        ("python-pyparsing" ,python-pyparsing)))
  65     (inputs
  66      `(("lapack" ,lapack)
  67        ("openblas" ,openblas)))
  68     (native-inputs
  69      `(("python-cython" ,python-cython)
  70        ("python-pytest" ,python-pytest)
  71        ("python-sphinx" ,python-sphinx)
  72        ("python-numpydoc" ,python-numpydoc)
  73        ("gfortran" ,gfortran)
  74        ("perl" ,perl)
  75        ("which" ,which)))
  76     (outputs '("out" "doc"))
  77     (arguments
  78      `(#:phases
  79        (modify-phases %standard-phases
  80          (add-after 'unpack 'disable-broken-tests
  81            (lambda _
  82              (substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py"
  83                (("^( +)def test_threads_parallel\\(self\\):" m indent)
  84                 (string-append indent
  85                                "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
  86                                m)))
  87              (substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py"
  88                (("^def test_parallel_threads\\(\\):" m)
  89                 (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
  90                                m)))
  91              #t))
  92          (add-before 'build 'configure-openblas
  93            (lambda* (#:key inputs #:allow-other-keys)
  94              (call-with-output-file "site.cfg"
  95                (lambda (port)
  96                  (format port
  97                          "[blas]
  98 libraries = openblas
  99 library_dirs = ~a/lib
 100 include_dirs = ~a/include
 101
 102 # backslash-n to make emacs happy
 103 \n[atlas]
 104 library_dirs = ~a/lib
 105 atlas_libs = openblas
 106 "
 107                          (assoc-ref inputs "openblas")
 108                          (assoc-ref inputs "openblas")
 109                          (assoc-ref inputs "openblas"))))
 110              #t))
 111          (add-after 'install 'install-doc
 112            (lambda* (#:key inputs outputs #:allow-other-keys)
 113              (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
 114                     (doc (string-append data "/doc/" ,name "-" ,version))
 115                     (html (string-append doc "/html"))
 116                     (pyver ,(string-append "PYVER=" (version-major+minor
 117                                                      (package-version python))))
 118                     ;; By default it tries to run sphinx-build through the Python
 119                     ;; interpreter which won't work with our shell wrapper.
 120                     (sphinxbuild "SPHINXBUILD=LANG=C sphinx-build"))
 121                ;; Make installed package available for building the
 122                ;; documentation
 123                (add-installed-pythonpath inputs outputs)
 124                (with-directory-excursion "doc"
 125                  ;; Fix generation of images for mathematical expressions.
 126                  (substitute* (find-files "source" "conf\\.py")
 127                    (("pngmath_use_preview = True")
 128                     "pngmath_use_preview = False"))
 129                  (mkdir-p html)
 130                  (invoke "make" "html" pyver sphinxbuild)
 131                  (with-directory-excursion "build/html"
 132                    (for-each (lambda (file)
 133                                (let* ((dir (dirname file))
 134                                       (tgt-dir (string-append html "/" dir)))
 135                                  (install-file file html)))
 136                              (find-files "." ".*")))))
 137              #t))
 138          ;; Tests can only be run after the library has been installed and not
 139          ;; within the source directory.
 140          (delete 'check)
 141          (add-after 'install 'check
 142            (lambda* (#:key inputs outputs #:allow-other-keys)
 143              (add-installed-pythonpath inputs outputs)
 144              (with-directory-excursion "/tmp"
 145                (invoke "python" "-c"
 146                        "import scipy; scipy.test(verbose=2)")))))))
 147     (home-page "https://www.scipy.org/")
 148     (synopsis "The Scipy library provides efficient numerical routines")
 149     (description "The SciPy library is one of the core packages that make up
 150 the SciPy stack.  It provides many user-friendly and efficient numerical
 151 routines such as routines for numerical integration and optimization.")
 152     (properties `((python2-variant . ,(delay python2-scipy))))
 153     (license license:bsd-3)))
 154
 155 ;; Version 1.2.2 is the last version to support Python 2
 156 (define-public python2-scipy
 157   (package
 158     (inherit (package-with-python2
 159               (strip-python2-variant python-scipy)))
 160     (version "1.2.2")
 161     (source
 162      (origin
 163        (method url-fetch)
 164        (uri (pypi-uri "scipy" version))
 165        (sha256
 166         (base32
 167          "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
 168
 169 (define-public python2-weave
 170   (package
 171     (name "python2-weave")
 172     (version "0.16.0")
 173     (source
 174      (origin
 175        (method url-fetch)
 176        (uri (pypi-uri "weave" version))
 177        (sha256
 178         (base32 "0jnm3584mfichgwgrd1gk5i42ll9c08nkw9716n947n4338f6ghs"))))
 179     (build-system python-build-system)
 180     (arguments
 181      `(#:python ,python-2
 182        #:phases
 183        (modify-phases %standard-phases
 184          (replace 'check
 185            (lambda _
 186              (invoke "nosetests" "-v"
 187                      "--exclude"
 188                      "test_(user|incorrect_ownership|char_fail|obj_fail)"))))))
 189     (propagated-inputs
 190      `(("python-numpy" ,python2-numpy)))
 191     (native-inputs
 192      `(("python-nose" ,python2-nose)))
 193     (home-page "https://www.scipy.org/")
 194     (synopsis "Tools for including C/C++ code within Python code")
 195     (description "Weave is the stand-alone version of the obsolete Scipy
 196 submodule @code{scipy.weave}.  It is Python 2.x only, and is provided for
 197 users that need new versions of Scipy but have existing code that still
 198 depends on @code{scipy.weave}.  For new code, users are recommended to use
 199 Cython.")
 200     (license license:bsd-3)))
 201
 202 (define-public python-scikit-fuzzy
 203   (package
 204     (name "python-scikit-fuzzy")
 205     (version "0.4.2")
 206     (source
 207      (origin
 208        (method url-fetch)
 209        (uri (pypi-uri "scikit-fuzzy" version))
 210        (sha256
 211         (base32 "0bp1n771fj44kdp7a00bcvfwirvv2rc803b7g6yf3va7v0j29c8s"))))
 212     (build-system python-build-system)
 213     (arguments
 214      `(#:phases
 215        (modify-phases %standard-phases
 216          (replace 'check
 217            (lambda _
 218              (invoke "nosetests" "-s" "-v" "skfuzzy")
 219              #t)))))
 220     (native-inputs
 221      `(("python-nose" ,python-nose)))
 222     (propagated-inputs
 223      `(("python-networkx" ,python-networkx)
 224        ("python-numpy" ,python-numpy)
 225        ("python-scipy" ,python-scipy)))
 226     (home-page "https://github.com/scikit-fuzzy/scikit-fuzzy")
 227     (synopsis "Fuzzy logic toolkit for SciPy")
 228     (description
 229      "This package implements many useful tools for projects involving fuzzy
 230 logic, also known as grey logic.")
 231     (license license:bsd-3)))
 232
 233 (define-public python-scikit-image
 234   (package
 235     (name "python-scikit-image")
 236     (version "0.17.2")
 237     (source
 238      (origin
 239        (method url-fetch)
 240        (uri (pypi-uri "scikit-image" version))
 241        (sha256
 242         (base32 "1cyqqbcbrg3prc36wis0sm3q5rjhd7h9bp33jwfyixzhi02lr5dx"))))
 243     (build-system python-build-system)
 244     (arguments
 245      ;; TODO: Some tests require running X11 server. Disable them?
 246      '(#:tests? #f))
 247     ;; See DEPENDS.txt for the list of build and run time requiremnts
 248     (propagated-inputs
 249      `(("python-cloudpickle" ,python-cloudpickle)
 250        ("python-dask" ,python-dask)
 251        ("python-imageio" ,python-imageio)
 252        ("python-matplotlib" ,python-matplotlib)
 253        ("python-networkx" ,python-networkx)
 254        ("python-numpy" ,python-numpy)
 255        ("python-pillow" ,python-pillow)
 256        ("python-pywavelets" ,python-pywavelets)
 257        ("python-scipy" ,python-scipy)
 258        ("python-six" ,python-six)
 259        ("python-tifffile" ,python-tifffile)))
 260     (native-inputs
 261      `(("python-cython" ,python-cython)))
 262     (home-page "https://scikit-image.org/")
 263     (synopsis "Image processing in Python")
 264     (description
 265      "Scikit-image is a collection of algorithms for image processing.")
 266     (license license:bsd-3)))
 267
 268 (define-public python-pandas
 269   (package
 270     (name "python-pandas")
 271     (version "1.0.5")
 272     (source
 273      (origin
 274        (method url-fetch)
 275        (uri (pypi-uri "pandas" version))
 276        (sha256
 277         (base32 "1a2gv3g6jr6vb5ca43fkwjl5xf86wpfz8y3zcy787adjl0hdkib9"))))
 278     (build-system python-build-system)
 279     (arguments
 280      `(#:modules ((guix build utils)
 281                   (guix build python-build-system)
 282                   (ice-9 ftw)
 283                   (srfi srfi-26))
 284        #:phases (modify-phases %standard-phases
 285                   (add-after 'unpack 'patch-which
 286                     (lambda* (#:key inputs #:allow-other-keys)
 287                       (let ((which (assoc-ref inputs "which")))
 288                         (substitute* "pandas/io/clipboard/__init__.py"
 289                           (("^WHICH_CMD = .*")
 290                            (string-append "WHICH_CMD = \"" which "\"\n"))))
 291                       #t))
 292                   (add-before 'check 'prepare-x
 293                     (lambda _
 294                       (system "Xvfb &")
 295                       (setenv "DISPLAY" ":0")
 296                       ;; xsel needs to write a log file.
 297                       (setenv "HOME" "/tmp")
 298                       #t))
 299                   (replace 'check
 300                     (lambda _
 301                       (let ((build-directory
 302                              (string-append
 303                               (getcwd) "/build/"
 304                               (car (scandir "build"
 305                                             (cut string-prefix? "lib." <>))))))
 306                         ;; Disable the "strict data files" option which causes
 307                         ;; the build to error out if required data files are
 308                         ;; not available (as is the case with PyPI archives).
 309                         (substitute* "setup.cfg"
 310                           (("addopts = --strict-data-files") "addopts = "))
 311                         (with-directory-excursion build-directory
 312                           (invoke "pytest" "-vv" "pandas" "--skip-slow"
 313                                   "--skip-network"))))))))
 314     (propagated-inputs
 315      `(("python-jinja2" ,python-jinja2)
 316        ("python-numpy" ,python-numpy)
 317        ("python-openpyxl" ,python-openpyxl)
 318        ("python-pytz" ,python-pytz)
 319        ("python-dateutil" ,python-dateutil)
 320        ("python-xlrd" ,python-xlrd)))
 321     (inputs
 322      `(("which" ,which)
 323        ("xclip" ,xclip)
 324        ("xsel" ,xsel)))
 325     (native-inputs
 326      `(("python-cython" ,python-cython)
 327        ("python-beautifulsoup4" ,python-beautifulsoup4)
 328        ("python-lxml" ,python-lxml)
 329        ("python-html5lib" ,python-html5lib)
 330        ("python-nose" ,python-nose)
 331        ("python-pytest" ,python-pytest)
 332        ("python-pytest-mock" ,python-pytest-mock)
 333        ;; Needed to test clipboard support.
 334        ("xorg-server" ,xorg-server-for-tests)))
 335     (home-page "https://pandas.pydata.org")
 336     (synopsis "Data structures for data analysis, time series, and statistics")
 337     (description
 338      "Pandas is a Python package providing fast, flexible, and expressive data
 339 structures designed to make working with structured (tabular,
 340 multidimensional, potentially heterogeneous) and time series data both easy
 341 and intuitive.  It aims to be the fundamental high-level building block for
 342 doing practical, real world data analysis in Python.")
 343     (properties `((python2-variant . ,(delay python2-pandas))))
 344     (license license:bsd-3)))
 345
 346 (define-public python-pandas-0.25
 347   (package
 348     (inherit python-pandas)
 349     (version "0.25.3")
 350     (source (origin
 351               (method url-fetch)
 352               (uri (pypi-uri "pandas" version))
 353               (sha256
 354                (base32
 355                 "191048m6kdc6yfvqs9w412lq60cfvigrsb57y0x116lwibgp9njj"))))
 356     (arguments
 357      (substitute-keyword-arguments (package-arguments python-pandas)
 358        ((#:phases phases)
 359         `(modify-phases ,phases
 360            (replace 'patch-which
 361              (lambda* (#:key inputs #:allow-other-keys)
 362                (let ((which (assoc-ref inputs "which")))
 363                  (substitute* "pandas/io/clipboard/__init__.py"
 364                    (("^CHECK_CMD = .*")
 365                      (string-append "CHECK_CMD = \"" which "\"\n"))))
 366                #t))
 367            (delete 'prepare-x)))))))
 368
 369 ;; Pandas 0.24.x are the last versions that support Python 2.
 370 (define-public python2-pandas
 371   (let ((pandas (package-with-python2
 372                  (strip-python2-variant python-pandas-0.25))))
 373     (package
 374       (inherit pandas)
 375       (version "0.24.2")
 376       (source (origin
 377                 (method url-fetch)
 378                 (uri (pypi-uri "pandas" version))
 379                 (sha256
 380                  (base32
 381                   "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag"))
 382                 (modules '((guix build utils)))
 383                 (snippet
 384                  '(begin
 385                     ;; Adjust for renamed error message in Python 2.7.17.  Taken
 386                     ;; from <https://github.com/pandas-dev/pandas/pull/29294>.
 387                     (substitute* "pandas/io/parsers.py"
 388                       (("if 'NULL byte' in msg:")
 389                        "if 'NULL byte' in msg or 'line contains NUL' in msg:"))
 390                     #t)))))))
 391
 392 (define-public python-xarray
 393   (package
 394     (name "python-xarray")
 395     (version "0.15.1")
 396     (source (origin
 397               (method url-fetch)
 398               (uri (pypi-uri "xarray" version))
 399               (sha256
 400                (base32
 401                 "1yx8j66b7rn10m2l6gmn8yr9cn38pi5cj0x0wwpy4hdnhy6i7qv4"))))
 402     (build-system python-build-system)
 403     (native-inputs
 404      `(("python-setuptools-scm" ,python-setuptools-scm)
 405        ("python-pytest" ,python-pytest)))
 406     (propagated-inputs
 407      `(("python-numpy" ,python-numpy)
 408        ("python-pandas" ,python-pandas)))
 409     (arguments
 410      `(#:phases
 411        (modify-phases %standard-phases
 412          (replace 'check
 413            (lambda _
 414              (invoke "pytest"))))))
 415     (home-page "https://github.com/pydata/xarray")
 416     (synopsis "N-D labeled arrays and datasets")
 417     (description "Xarray (formerly xray) makes working with labelled
 418 multi-dimensional arrays simple, efficient, and fun!
 419
 420 Xarray introduces labels in the form of dimensions, coordinates and attributes
 421 on top of raw NumPy-like arrays, which allows for a more intuitive, more
 422 concise, and less error-prone developer experience.  The package includes a
 423 large and growing library of domain-agnostic functions for advanced analytics
 424 and visualization with these data structures.")
 425     (license license:asl2.0)))
 426
 427 (define-public python-msgpack-numpy
 428   (package
 429     (name "python-msgpack-numpy")
 430     (version "0.4.6.post0")
 431     (source
 432      (origin
 433        (method url-fetch)
 434        (uri (pypi-uri "msgpack-numpy" version))
 435        (sha256
 436         (base32
 437          "0syzy645mwcy7lfjwz6pc8f9p2vv1qk4limc8iina3l5nnf0rjyz"))))
 438     (build-system python-build-system)
 439     (propagated-inputs
 440      `(("python-msgpack" ,python-msgpack)
 441        ("python-numpy" ,python-numpy)))
 442     (home-page "https://github.com/lebedov/msgpack-numpy")
 443     (synopsis
 444      "Numpy data serialization using msgpack")
 445     (description
 446      "This package provides encoding and decoding routines that enable the
 447 serialization and deserialization of numerical and array data types provided
 448 by numpy using the highly efficient @code{msgpack} format.  Serialization of
 449 Python's native complex data types is also supported.")
 450     (license license:bsd-3)))