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-sgp4
 269   (package
 270     (name "python-sgp4")
 271     (version "2.12")
 272     (source
 273      (origin
 274        (method url-fetch)
 275        (uri (pypi-uri "sgp4" version))
 276        (sha256
 277         (base32 "0dncp9i5b6afkg7f8mj9j0qzsp008b8v73yc0qkmizhpns7mvwvx"))))
 278     (build-system python-build-system)
 279     (propagated-inputs
 280      `(("python-numpy" ,python-numpy)))
 281     (home-page "https://github.com/brandon-rhodes/python-sgp4")
 282     (synopsis "Track earth satellite TLE orbits using SGP4")
 283     (description
 284      "This package provides a Python implementation of the most recent version
 285 of the SGP4 satellite tracking algorithm.")
 286     (license license:expat)))
 287
 288 (define-public python-pandas
 289   (package
 290     (name "python-pandas")
 291     (version "1.0.5")
 292     (source
 293      (origin
 294        (method url-fetch)
 295        (uri (pypi-uri "pandas" version))
 296        (sha256
 297         (base32 "1a2gv3g6jr6vb5ca43fkwjl5xf86wpfz8y3zcy787adjl0hdkib9"))))
 298     (build-system python-build-system)
 299     (arguments
 300      `(#:modules ((guix build utils)
 301                   (guix build python-build-system)
 302                   (ice-9 ftw)
 303                   (srfi srfi-26))
 304        #:phases (modify-phases %standard-phases
 305                   (add-after 'unpack 'patch-which
 306                     (lambda* (#:key inputs #:allow-other-keys)
 307                       (let ((which (assoc-ref inputs "which")))
 308                         (substitute* "pandas/io/clipboard/__init__.py"
 309                           (("^WHICH_CMD = .*")
 310                            (string-append "WHICH_CMD = \"" which "\"\n"))))
 311                       #t))
 312                   (add-before 'check 'prepare-x
 313                     (lambda _
 314                       (system "Xvfb &")
 315                       (setenv "DISPLAY" ":0")
 316                       ;; xsel needs to write a log file.
 317                       (setenv "HOME" "/tmp")
 318                       #t))
 319                   (replace 'check
 320                     (lambda _
 321                       (let ((build-directory
 322                              (string-append
 323                               (getcwd) "/build/"
 324                               (car (scandir "build"
 325                                             (cut string-prefix? "lib." <>))))))
 326                         ;; Disable the "strict data files" option which causes
 327                         ;; the build to error out if required data files are
 328                         ;; not available (as is the case with PyPI archives).
 329                         (substitute* "setup.cfg"
 330                           (("addopts = --strict-data-files") "addopts = "))
 331                         (with-directory-excursion build-directory
 332                           (invoke "pytest" "-vv" "pandas" "--skip-slow"
 333                                   "--skip-network"))))))))
 334     (propagated-inputs
 335      `(("python-jinja2" ,python-jinja2)
 336        ("python-numpy" ,python-numpy)
 337        ("python-openpyxl" ,python-openpyxl)
 338        ("python-pytz" ,python-pytz)
 339        ("python-dateutil" ,python-dateutil)
 340        ("python-xlrd" ,python-xlrd)))
 341     (inputs
 342      `(("which" ,which)
 343        ("xclip" ,xclip)
 344        ("xsel" ,xsel)))
 345     (native-inputs
 346      `(("python-cython" ,python-cython)
 347        ("python-beautifulsoup4" ,python-beautifulsoup4)
 348        ("python-lxml" ,python-lxml)
 349        ("python-html5lib" ,python-html5lib)
 350        ("python-nose" ,python-nose)
 351        ("python-pytest" ,python-pytest)
 352        ("python-pytest-mock" ,python-pytest-mock)
 353        ;; Needed to test clipboard support.
 354        ("xorg-server" ,xorg-server-for-tests)))
 355     (home-page "https://pandas.pydata.org")
 356     (synopsis "Data structures for data analysis, time series, and statistics")
 357     (description
 358      "Pandas is a Python package providing fast, flexible, and expressive data
 359 structures designed to make working with structured (tabular,
 360 multidimensional, potentially heterogeneous) and time series data both easy
 361 and intuitive.  It aims to be the fundamental high-level building block for
 362 doing practical, real world data analysis in Python.")
 363     (properties `((python2-variant . ,(delay python2-pandas))))
 364     (license license:bsd-3)))
 365
 366 (define-public python-pandas-0.25
 367   (package
 368     (inherit python-pandas)
 369     (version "0.25.3")
 370     (source (origin
 371               (method url-fetch)
 372               (uri (pypi-uri "pandas" version))
 373               (sha256
 374                (base32
 375                 "191048m6kdc6yfvqs9w412lq60cfvigrsb57y0x116lwibgp9njj"))))
 376     (arguments
 377      (substitute-keyword-arguments (package-arguments python-pandas)
 378        ((#:phases phases)
 379         `(modify-phases ,phases
 380            (replace 'patch-which
 381              (lambda* (#:key inputs #:allow-other-keys)
 382                (let ((which (assoc-ref inputs "which")))
 383                  (substitute* "pandas/io/clipboard/__init__.py"
 384                    (("^CHECK_CMD = .*")
 385                      (string-append "CHECK_CMD = \"" which "\"\n"))))
 386                #t))
 387            (delete 'prepare-x)))))))
 388
 389 ;; Pandas 0.24.x are the last versions that support Python 2.
 390 (define-public python2-pandas
 391   (let ((pandas (package-with-python2
 392                  (strip-python2-variant python-pandas-0.25))))
 393     (package
 394       (inherit pandas)
 395       (version "0.24.2")
 396       (source (origin
 397                 (method url-fetch)
 398                 (uri (pypi-uri "pandas" version))
 399                 (sha256
 400                  (base32
 401                   "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag"))
 402                 (modules '((guix build utils)))
 403                 (snippet
 404                  '(begin
 405                     ;; Adjust for renamed error message in Python 2.7.17.  Taken
 406                     ;; from <https://github.com/pandas-dev/pandas/pull/29294>.
 407                     (substitute* "pandas/io/parsers.py"
 408                       (("if 'NULL byte' in msg:")
 409                        "if 'NULL byte' in msg or 'line contains NUL' in msg:"))
 410                     #t)))))))
 411
 412 (define-public python-bottleneck
 413   (package
 414     (name "python-bottleneck")
 415     (version "1.3.2")
 416     (source
 417      (origin
 418        (method url-fetch)
 419        (uri (pypi-uri "Bottleneck" version))
 420        (sha256
 421         (base32 "0wz5320jx3n4q2nsvwvc7cpi66b46qbals9v53m955rmcq5ry5r0"))))
 422     (build-system python-build-system)
 423     (arguments
 424      `(#:phases
 425        (modify-phases %standard-phases
 426          (replace 'check
 427            (lambda _
 428              (invoke "python" "setup.py" "pytest"))))))
 429     (native-inputs
 430      `(("python-hypothesis" ,python-hypothesis)
 431        ("python-pytest" ,python-pytest)
 432        ("python-pytest-runner" ,python-pytest-runner)))
 433     (propagated-inputs
 434      `(("python-numpy" ,python-numpy)))
 435     (home-page "https://github.com/pydata/bottleneck")
 436     (synopsis "Fast NumPy array functions written in C")
 437     (description
 438      "Bottleneck is a collection of fast, NaN-aware NumPy array functions
 439 written in C.")
 440     (license license:bsd-2)))
 441
 442 (define-public python-xarray
 443   (package
 444     (name "python-xarray")
 445     (version "0.15.1")
 446     (source (origin
 447               (method url-fetch)
 448               (uri (pypi-uri "xarray" version))
 449               (sha256
 450                (base32
 451                 "1yx8j66b7rn10m2l6gmn8yr9cn38pi5cj0x0wwpy4hdnhy6i7qv4"))))
 452     (build-system python-build-system)
 453     (native-inputs
 454      `(("python-setuptools-scm" ,python-setuptools-scm)
 455        ("python-pytest" ,python-pytest)))
 456     (propagated-inputs
 457      `(("python-numpy" ,python-numpy)
 458        ("python-pandas" ,python-pandas)))
 459     (arguments
 460      `(#:phases
 461        (modify-phases %standard-phases
 462          (replace 'check
 463            (lambda _
 464              (invoke "pytest"))))))
 465     (home-page "https://github.com/pydata/xarray")
 466     (synopsis "N-D labeled arrays and datasets")
 467     (description "Xarray (formerly xray) makes working with labelled
 468 multi-dimensional arrays simple, efficient, and fun!
 469
 470 Xarray introduces labels in the form of dimensions, coordinates and attributes
 471 on top of raw NumPy-like arrays, which allows for a more intuitive, more
 472 concise, and less error-prone developer experience.  The package includes a
 473 large and growing library of domain-agnostic functions for advanced analytics
 474 and visualization with these data structures.")
 475     (license license:asl2.0)))
 476
 477 (define-public python-msgpack-numpy
 478   (package
 479     (name "python-msgpack-numpy")
 480     (version "0.4.6.post0")
 481     (source
 482      (origin
 483        (method url-fetch)
 484        (uri (pypi-uri "msgpack-numpy" version))
 485        (sha256
 486         (base32
 487          "0syzy645mwcy7lfjwz6pc8f9p2vv1qk4limc8iina3l5nnf0rjyz"))))
 488     (build-system python-build-system)
 489     (propagated-inputs
 490      `(("python-msgpack" ,python-msgpack)
 491        ("python-numpy" ,python-numpy)))
 492     (home-page "https://github.com/lebedov/msgpack-numpy")
 493     (synopsis
 494      "Numpy data serialization using msgpack")
 495     (description
 496      "This package provides encoding and decoding routines that enable the
 497 serialization and deserialization of numerical and array data types provided
 498 by numpy using the highly efficient @code{msgpack} format.  Serialization of
 499 Python's native complex data types is also supported.")
 500     (license license:bsd-3)))