gnu/packages/python-science.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2015, 2016, 2020, 2021 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, 2021 Vinicius Monego <monego@posteo.net>
  13 ;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
  14 ;;; Copyright © 2021 Roel Janssen <roel@gnu.org>
  15 ;;; Copyright © 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
  16 ;;;
  17 ;;; This file is part of GNU Guix.
  18 ;;;
  19 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  20 ;;; under the terms of the GNU General Public License as published by
  21 ;;; the Free Software Foundation; either version 3 of the License, or (at
  22 ;;; your option) any later version.
  23 ;;;
  24 ;;; GNU Guix is distributed in the hope that it will be useful, but
  25 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  26 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  27 ;;; GNU General Public License for more details.
  28 ;;;
  29 ;;; You should have received a copy of the GNU General Public License
  30 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  31
  32 (define-module (gnu packages python-science)
  33   #:use-module ((guix licenses) #:prefix license:)
  34   #:use-module (gnu packages)
  35   #:use-module (gnu packages base)
  36   #:use-module (gnu packages check)
  37   #:use-module (gnu packages gcc)
  38   #:use-module (gnu packages image-processing)
  39   #:use-module (gnu packages maths)
  40   #:use-module (gnu packages mpi)
  41   #:use-module (gnu packages perl)
  42   #:use-module (gnu packages pkg-config)
  43   #:use-module (gnu packages python)
  44   #:use-module (gnu packages python-build)
  45   #:use-module (gnu packages python-check)
  46   #:use-module (gnu packages python-web)
  47   #:use-module (gnu packages python-xyz)
  48   #:use-module (gnu packages simulation)
  49   #:use-module (gnu packages sphinx)
  50   #:use-module (gnu packages time)
  51   #:use-module (gnu packages xdisorg)
  52   #:use-module (gnu packages xml)
  53   #:use-module (gnu packages xorg)
  54   #:use-module (guix packages)
  55   #:use-module (guix download)
  56   #:use-module (guix git-download)
  57   #:use-module (guix utils)
  58   #:use-module (guix build-system python))
  59
  60 (define-public python-scipy
  61   (package
  62     (name "python-scipy")
  63     (version "1.6.0")
  64     (source
  65      (origin
  66        (method url-fetch)
  67        (uri (pypi-uri "scipy" version))
  68        (sha256
  69         (base32 "0rh5b1rwdcvvagld8vpxnpaibszy1skpx39a0fwzd5gx5pwcjvfb"))))
  70     (build-system python-build-system)
  71     (propagated-inputs
  72      `(("python-numpy" ,python-numpy)
  73        ("python-matplotlib" ,python-matplotlib)
  74        ("python-pyparsing" ,python-pyparsing)))
  75     (inputs
  76      `(("openblas" ,openblas)
  77        ("pybind11" ,pybind11)))
  78     (native-inputs
  79      `(("python-cython" ,python-cython)
  80        ("python-pytest" ,python-pytest)
  81        ("python-sphinx" ,python-sphinx)
  82        ("python-numpydoc" ,python-numpydoc)
  83        ("gfortran" ,gfortran)
  84        ("perl" ,perl)
  85        ("which" ,which)))
  86     (outputs '("out" "doc"))
  87     (arguments
  88      `(#:phases
  89        (modify-phases %standard-phases
  90          (add-before 'build 'change-home-dir
  91            (lambda _
  92              ;; Change from /homeless-shelter to /tmp for write permission.
  93              (setenv "HOME" "/tmp")
  94              #t))
  95          (add-after 'unpack 'disable-broken-tests
  96            (lambda _
  97              (substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py"
  98                (("^( +)def test_threads_parallel\\(self\\):" m indent)
  99                 (string-append indent
 100                                "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
 101                                m)))
 102              (substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py"
 103                (("^def test_parallel_threads\\(\\):" m)
 104                 (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
 105                                m)))
 106              #t))
 107          (add-before 'build 'configure-openblas
 108            (lambda* (#:key inputs #:allow-other-keys)
 109              (call-with-output-file "site.cfg"
 110                (lambda (port)
 111                  (format port
 112                          "[blas]
 113 libraries = openblas
 114 library_dirs = ~a/lib
 115 include_dirs = ~a/include
 116
 117 # backslash-n to make emacs happy
 118 \n[atlas]
 119 library_dirs = ~a/lib
 120 atlas_libs = openblas
 121 "
 122                          (assoc-ref inputs "openblas")
 123                          (assoc-ref inputs "openblas")
 124                          (assoc-ref inputs "openblas"))))
 125              #t))
 126          (add-after 'install 'install-doc
 127            (lambda* (#:key inputs outputs #:allow-other-keys)
 128              (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
 129                     (doc (string-append data "/doc/" ,name "-" ,version))
 130                     (html (string-append doc "/html"))
 131                     (pyver ,(string-append "PYVER=" (version-major+minor
 132                                                      (package-version python))))
 133                     ;; By default it tries to run sphinx-build through the Python
 134                     ;; interpreter which won't work with our shell wrapper.
 135                     (sphinxbuild "SPHINXBUILD=LANG=C sphinx-build"))
 136                ;; Make installed package available for building the
 137                ;; documentation
 138                (add-installed-pythonpath inputs outputs)
 139                (with-directory-excursion "doc"
 140                  ;; Fix generation of images for mathematical expressions.
 141                  (substitute* (find-files "source" "conf\\.py")
 142                    (("pngmath_use_preview = True")
 143                     "pngmath_use_preview = False"))
 144                  (mkdir-p html)
 145                  (invoke "make" "html" pyver sphinxbuild)
 146                  (with-directory-excursion "build/html"
 147                    (for-each (lambda (file)
 148                                (let* ((dir (dirname file))
 149                                       (tgt-dir (string-append html "/" dir)))
 150                                  (install-file file html)))
 151                              (find-files "." ".*")))))
 152              #t))
 153          ;; Tests can only be run after the library has been installed and not
 154          ;; within the source directory.
 155          (delete 'check)
 156          (add-after 'install 'check
 157            (lambda* (#:key inputs outputs #:allow-other-keys)
 158              (add-installed-pythonpath inputs outputs)
 159              (with-directory-excursion "/tmp"
 160                (invoke "python" "-c"
 161                        "import scipy; scipy.test(verbose=2)")))))))
 162     (home-page "https://www.scipy.org/")
 163     (synopsis "The Scipy library provides efficient numerical routines")
 164     (description "The SciPy library is one of the core packages that make up
 165 the SciPy stack.  It provides many user-friendly and efficient numerical
 166 routines such as routines for numerical integration and optimization.")
 167     (properties `((python2-variant . ,(delay python2-scipy))))
 168     (license license:bsd-3)))
 169
 170 ;; Version 1.2.2 is the last version to support Python 2
 171 (define-public python2-scipy
 172   (package
 173     (inherit (package-with-python2
 174               (strip-python2-variant python-scipy)))
 175     (version "1.2.2")
 176     (source
 177      (origin
 178        (method url-fetch)
 179        (uri (pypi-uri "scipy" version))
 180        (sha256
 181         (base32
 182          "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
 183
 184 (define-public python2-weave
 185   (package
 186     (name "python2-weave")
 187     (version "0.16.0")
 188     (source
 189      (origin
 190        (method url-fetch)
 191        (uri (pypi-uri "weave" version))
 192        (sha256
 193         (base32 "0jnm3584mfichgwgrd1gk5i42ll9c08nkw9716n947n4338f6ghs"))))
 194     (build-system python-build-system)
 195     (arguments
 196      `(#:python ,python-2
 197        #:phases
 198        (modify-phases %standard-phases
 199          (replace 'check
 200            (lambda _
 201              (invoke "nosetests" "-v"
 202                      "--exclude"
 203                      "test_(user|incorrect_ownership|char_fail|obj_fail)"))))))
 204     (propagated-inputs
 205      `(("python-numpy" ,python2-numpy)))
 206     (native-inputs
 207      `(("python-nose" ,python2-nose)))
 208     (home-page "https://www.scipy.org/")
 209     (synopsis "Tools for including C/C++ code within Python code")
 210     (description "Weave is the stand-alone version of the obsolete Scipy
 211 submodule @code{scipy.weave}.  It is Python 2.x only, and is provided for
 212 users that need new versions of Scipy but have existing code that still
 213 depends on @code{scipy.weave}.  For new code, users are recommended to use
 214 Cython.")
 215     (license license:bsd-3)))
 216
 217 (define-public python-scikit-fuzzy
 218   (package
 219     (name "python-scikit-fuzzy")
 220     (version "0.4.2")
 221     (source
 222      (origin
 223        (method url-fetch)
 224        (uri (pypi-uri "scikit-fuzzy" version))
 225        (sha256
 226         (base32 "0bp1n771fj44kdp7a00bcvfwirvv2rc803b7g6yf3va7v0j29c8s"))))
 227     (build-system python-build-system)
 228     (arguments
 229      `(#:phases
 230        (modify-phases %standard-phases
 231          (replace 'check
 232            (lambda _
 233              (invoke "nosetests" "-s" "-v" "skfuzzy")
 234              #t)))))
 235     (native-inputs
 236      `(("python-nose" ,python-nose)))
 237     (propagated-inputs
 238      `(("python-networkx" ,python-networkx)
 239        ("python-numpy" ,python-numpy)
 240        ("python-scipy" ,python-scipy)))
 241     (home-page "https://github.com/scikit-fuzzy/scikit-fuzzy")
 242     (synopsis "Fuzzy logic toolkit for SciPy")
 243     (description
 244      "This package implements many useful tools for projects involving fuzzy
 245 logic, also known as grey logic.")
 246     (license license:bsd-3)))
 247
 248 (define-public python-scikit-image
 249   (package
 250     (name "python-scikit-image")
 251     (version "0.18.1")
 252     (source
 253      (origin
 254        (method url-fetch)
 255        (uri (pypi-uri "scikit-image" version))
 256        (sha256
 257         (base32 "0wgisa03smhrphcjnhq7waa5vyyd32b67hblapjbqrqqj751idpv"))))
 258     (build-system python-build-system)
 259     (arguments
 260      `(#:phases
 261        (modify-phases %standard-phases
 262          (add-before 'build 'change-home-dir
 263            (lambda _
 264              ;; Change from /homeless-shelter to /tmp for write permission.
 265              (setenv "HOME" "/tmp")
 266              #t))
 267          (replace 'build
 268            (lambda _
 269              (invoke "make")))
 270          (replace 'check
 271            (lambda _
 272              ;; The following tests require online data.
 273              (invoke "python" "-m" "pytest" "skimage" "--doctest-modules" "-k"
 274                      (string-append "not test_ndim"
 275                                     " and not test_skin")))))))
 276     ;; See requirements/ for the list of build and run time requirements.
 277     ;; NOTE: scikit-image has an optional dependency on python-pooch, however
 278     ;; propagating it would enable many more tests that require online data.
 279     (propagated-inputs
 280      `(("python-cloudpickle" ,python-cloudpickle)
 281        ("python-dask" ,python-dask)
 282        ("python-imageio" ,python-imageio)
 283        ("python-matplotlib" ,python-matplotlib)
 284        ("python-networkx" ,python-networkx)
 285        ("python-numpy" ,python-numpy)
 286        ("python-pillow" ,python-pillow)
 287        ("python-pywavelets" ,python-pywavelets)
 288        ("python-scipy" ,python-scipy)
 289        ("python-tifffile" ,python-tifffile)))
 290     (native-inputs
 291      `(("python-codecov" ,python-codecov)
 292        ("python-cython" ,python-cython)
 293        ("python-flake8" ,python-flake8)
 294        ("python-pytest" ,python-pytest)
 295        ("python-pytest-cov" ,python-pytest-cov)
 296        ("python-pytest-localserver" ,python-pytest-localserver)
 297        ("python-wheel" ,python-wheel)))
 298     (home-page "https://scikit-image.org/")
 299     (synopsis "Image processing in Python")
 300     (description
 301      "Scikit-image is a collection of algorithms for image processing.")
 302     (license license:bsd-3)))
 303
 304 (define-public python-sgp4
 305   (package
 306     (name "python-sgp4")
 307     (version "2.12")
 308     (source
 309      (origin
 310        (method url-fetch)
 311        (uri (pypi-uri "sgp4" version))
 312        (sha256
 313         (base32 "0dncp9i5b6afkg7f8mj9j0qzsp008b8v73yc0qkmizhpns7mvwvx"))))
 314     (build-system python-build-system)
 315     (propagated-inputs
 316      `(("python-numpy" ,python-numpy)))
 317     (home-page "https://github.com/brandon-rhodes/python-sgp4")
 318     (synopsis "Track earth satellite TLE orbits using SGP4")
 319     (description
 320      "This package provides a Python implementation of the most recent version
 321 of the SGP4 satellite tracking algorithm.")
 322     (license license:expat)))
 323
 324 (define-public python-pandas
 325   (package
 326     (name "python-pandas")
 327     (version "1.0.5")
 328     (source
 329      (origin
 330        (method url-fetch)
 331        (uri (pypi-uri "pandas" version))
 332        (sha256
 333         (base32 "1a2gv3g6jr6vb5ca43fkwjl5xf86wpfz8y3zcy787adjl0hdkib9"))))
 334     (build-system python-build-system)
 335     (arguments
 336      `(#:modules ((guix build utils)
 337                   (guix build python-build-system)
 338                   (ice-9 ftw)
 339                   (srfi srfi-26))
 340        #:phases (modify-phases %standard-phases
 341                   (add-after 'unpack 'patch-which
 342                     (lambda* (#:key inputs #:allow-other-keys)
 343                       (let ((which (assoc-ref inputs "which")))
 344                         (substitute* "pandas/io/clipboard/__init__.py"
 345                           (("^WHICH_CMD = .*")
 346                            (string-append "WHICH_CMD = \"" which "\"\n"))))
 347                       #t))
 348                   (add-before 'check 'prepare-x
 349                     (lambda _
 350                       (system "Xvfb &")
 351                       (setenv "DISPLAY" ":0")
 352                       ;; xsel needs to write a log file.
 353                       (setenv "HOME" "/tmp")
 354                       #t))
 355                   (replace 'check
 356                     (lambda _
 357                       (let ((build-directory
 358                              (string-append
 359                               (getcwd) "/build/"
 360                               (car (scandir "build"
 361                                             (cut string-prefix? "lib." <>))))))
 362                         ;; Disable the "strict data files" option which causes
 363                         ;; the build to error out if required data files are
 364                         ;; not available (as is the case with PyPI archives).
 365                         (substitute* "setup.cfg"
 366                           (("addopts = --strict-data-files") "addopts = "))
 367                         (with-directory-excursion build-directory
 368                           (invoke "pytest" "-vv" "pandas" "--skip-slow"
 369                                   "--skip-network"))))))))
 370     (propagated-inputs
 371      `(("python-jinja2" ,python-jinja2)
 372        ("python-numpy" ,python-numpy)
 373        ("python-openpyxl" ,python-openpyxl)
 374        ("python-pytz" ,python-pytz)
 375        ("python-dateutil" ,python-dateutil)
 376        ("python-xlrd" ,python-xlrd)))
 377     (inputs
 378      `(("which" ,which)
 379        ("xclip" ,xclip)
 380        ("xsel" ,xsel)))
 381     (native-inputs
 382      `(("python-cython" ,python-cython)
 383        ("python-beautifulsoup4" ,python-beautifulsoup4)
 384        ("python-lxml" ,python-lxml)
 385        ("python-html5lib" ,python-html5lib)
 386        ("python-nose" ,python-nose)
 387        ("python-pytest" ,python-pytest)
 388        ("python-pytest-mock" ,python-pytest-mock)
 389        ;; Needed to test clipboard support.
 390        ("xorg-server" ,xorg-server-for-tests)))
 391     (home-page "https://pandas.pydata.org")
 392     (synopsis "Data structures for data analysis, time series, and statistics")
 393     (description
 394      "Pandas is a Python package providing fast, flexible, and expressive data
 395 structures designed to make working with structured (tabular,
 396 multidimensional, potentially heterogeneous) and time series data both easy
 397 and intuitive.  It aims to be the fundamental high-level building block for
 398 doing practical, real world data analysis in Python.")
 399     (properties `((python2-variant . ,(delay python2-pandas))))
 400     (license license:bsd-3)))
 401
 402 (define-public python-pandas-0.25
 403   (package
 404     (inherit python-pandas)
 405     (version "0.25.3")
 406     (source (origin
 407               (method url-fetch)
 408               (uri (pypi-uri "pandas" version))
 409               (sha256
 410                (base32
 411                 "191048m6kdc6yfvqs9w412lq60cfvigrsb57y0x116lwibgp9njj"))))
 412     (arguments
 413      (substitute-keyword-arguments (package-arguments python-pandas)
 414        ((#:phases phases)
 415         `(modify-phases ,phases
 416            (replace 'patch-which
 417              (lambda* (#:key inputs #:allow-other-keys)
 418                (let ((which (assoc-ref inputs "which")))
 419                  (substitute* "pandas/io/clipboard/__init__.py"
 420                    (("^CHECK_CMD = .*")
 421                      (string-append "CHECK_CMD = \"" which "\"\n"))))
 422                #t))
 423            (delete 'prepare-x)))))))
 424
 425 ;; Pandas 0.24.x are the last versions that support Python 2.
 426 (define-public python2-pandas
 427   (let ((pandas (package-with-python2
 428                  (strip-python2-variant python-pandas-0.25))))
 429     (package
 430       (inherit pandas)
 431       (version "0.24.2")
 432       (source (origin
 433                 (method url-fetch)
 434                 (uri (pypi-uri "pandas" version))
 435                 (sha256
 436                  (base32
 437                   "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag"))
 438                 (modules '((guix build utils)))
 439                 (snippet
 440                  '(begin
 441                     ;; Adjust for renamed error message in Python 2.7.17.  Taken
 442                     ;; from <https://github.com/pandas-dev/pandas/pull/29294>.
 443                     (substitute* "pandas/io/parsers.py"
 444                       (("if 'NULL byte' in msg:")
 445                        "if 'NULL byte' in msg or 'line contains NUL' in msg:"))
 446                     #t)))))))
 447
 448 (define-public python-pyflow
 449   (package
 450     (name "python-pyflow")
 451     (version "1.1.20")
 452     (source (origin
 453               (method url-fetch)
 454               (uri (string-append
 455                     "https://github.com/Illumina/pyflow/releases/download/v"
 456                     version "/pyflow-" version ".tar.gz"))
 457               (sha256
 458                (base32
 459                 "1bvfvviw58cndyn862qnv9nj3d9cd3a0dm4vc4sd9vwq8a6z1riv"))))
 460     (build-system python-build-system)
 461     (arguments
 462      `(#:tests? #f)) ; There is no test suite.
 463     (home-page "https://illumina.github.io/pyflow/")
 464     (synopsis "Tool to manage tasks in a task dependency graph")
 465     (description "This package is a Python module to manage tasks in the
 466 context of a task dependency graph.  It has some similarities to make.")
 467     (license license:bsd-2)))
 468
 469 (define-public python-bottleneck
 470   (package
 471     (name "python-bottleneck")
 472     (version "1.3.2")
 473     (source
 474      (origin
 475        (method url-fetch)
 476        (uri (pypi-uri "Bottleneck" version))
 477        (sha256
 478         (base32 "0wz5320jx3n4q2nsvwvc7cpi66b46qbals9v53m955rmcq5ry5r0"))))
 479     (build-system python-build-system)
 480     (arguments
 481      `(#:phases
 482        (modify-phases %standard-phases
 483          (replace 'check
 484            (lambda _
 485              (invoke "python" "setup.py" "pytest"))))))
 486     (native-inputs
 487      `(("python-hypothesis" ,python-hypothesis)
 488        ("python-pytest" ,python-pytest)
 489        ("python-pytest-runner" ,python-pytest-runner)))
 490     (propagated-inputs
 491      `(("python-numpy" ,python-numpy)))
 492     (home-page "https://github.com/pydata/bottleneck")
 493     (synopsis "Fast NumPy array functions written in C")
 494     (description
 495      "Bottleneck is a collection of fast, NaN-aware NumPy array functions
 496 written in C.")
 497     (license license:bsd-2)))
 498
 499 (define-public python-baycomp
 500   (package
 501     (name "python-baycomp")
 502     (version "1.0.2")
 503     (source
 504      (origin
 505        (method url-fetch)
 506        (uri (pypi-uri "baycomp" version))
 507        (sha256
 508         (base32 "1c1354a7b3g8slychjgyjxqdm8z40z9kviyl9n4g9kfpdg0p4d64"))))
 509     (build-system python-build-system)
 510     (propagated-inputs
 511      `(("python-matplotlib" ,python-matplotlib)
 512        ("python-numpy" ,python-numpy)
 513        ("python-scipy" ,python-scipy)))
 514     (home-page "https://github.com/janezd/baycomp")
 515     (synopsis "Library for comparison of Bayesian classifiers")
 516     (description
 517      "Baycomp is a library for Bayesian comparison of classifiers.  Functions
 518 in the library compare two classifiers on one or on multiple data sets.  They
 519 compute three probabilities: the probability that the first classifier has
 520 higher scores than the second, the probability that differences are within the
 521 region of practical equivalence (rope), or that the second classifier has
 522 higher scores.")
 523     (license license:expat)))
 524
 525 (define-public python-xarray
 526   (package
 527     (name "python-xarray")
 528     (version "0.15.1")
 529     (source (origin
 530               (method url-fetch)
 531               (uri (pypi-uri "xarray" version))
 532               (sha256
 533                (base32
 534                 "1yx8j66b7rn10m2l6gmn8yr9cn38pi5cj0x0wwpy4hdnhy6i7qv4"))))
 535     (build-system python-build-system)
 536     (native-inputs
 537      `(("python-setuptools-scm" ,python-setuptools-scm)
 538        ("python-pytest" ,python-pytest)))
 539     (propagated-inputs
 540      `(("python-numpy" ,python-numpy)
 541        ("python-pandas" ,python-pandas)))
 542     (arguments
 543      `(#:phases
 544        (modify-phases %standard-phases
 545          (replace 'check
 546            (lambda _
 547              (invoke "pytest"))))))
 548     (home-page "https://github.com/pydata/xarray")
 549     (synopsis "N-D labeled arrays and datasets")
 550     (description "Xarray (formerly xray) makes working with labelled
 551 multi-dimensional arrays simple, efficient, and fun!
 552
 553 Xarray introduces labels in the form of dimensions, coordinates and attributes
 554 on top of raw NumPy-like arrays, which allows for a more intuitive, more
 555 concise, and less error-prone developer experience.  The package includes a
 556 large and growing library of domain-agnostic functions for advanced analytics
 557 and visualization with these data structures.")
 558     (license license:asl2.0)))
 559
 560 (define-public python-msgpack-numpy
 561   (package
 562     (name "python-msgpack-numpy")
 563     (version "0.4.6.post0")
 564     (source
 565      (origin
 566        (method url-fetch)
 567        (uri (pypi-uri "msgpack-numpy" version))
 568        (sha256
 569         (base32
 570          "0syzy645mwcy7lfjwz6pc8f9p2vv1qk4limc8iina3l5nnf0rjyz"))))
 571     (build-system python-build-system)
 572     (propagated-inputs
 573      `(("python-msgpack" ,python-msgpack)
 574        ("python-numpy" ,python-numpy)))
 575     (home-page "https://github.com/lebedov/msgpack-numpy")
 576     (synopsis
 577      "Numpy data serialization using msgpack")
 578     (description
 579      "This package provides encoding and decoding routines that enable the
 580 serialization and deserialization of numerical and array data types provided
 581 by numpy using the highly efficient @code{msgpack} format.  Serialization of
 582 Python's native complex data types is also supported.")
 583     (license license:bsd-3)))
 584
 585 (define-public python-ruffus
 586   (package
 587     (name "python-ruffus")
 588     (version "2.8.4")
 589     (source
 590      (origin
 591        (method url-fetch)
 592        (uri (pypi-uri "ruffus" version))
 593        (sha256
 594         (base32
 595          "1ai673k1s94s8b6pyxai8mk17p6zvvyi87rl236fs6ls8mpdklvc"))))
 596     (build-system python-build-system)
 597     (arguments
 598      `(#:phases
 599        (modify-phases %standard-phases
 600          (delete 'check)
 601          (add-after 'install 'check
 602            (lambda* (#:key tests? inputs outputs #:allow-other-keys)
 603              (when tests?
 604                (add-installed-pythonpath inputs outputs)
 605                (with-directory-excursion "ruffus/test"
 606                  (invoke "bash" "run_all_unit_tests3.cmd"))))))))
 607     (native-inputs
 608      `(("python-pytest" ,python-pytest)))
 609     (home-page "http://www.ruffus.org.uk")
 610     (synopsis "Light-weight computational pipeline management")
 611     (description
 612      "Ruffus is designed to allow scientific and other analyses to be
 613 automated with the minimum of fuss and the least effort.")
 614     (license license:expat)))
 615
 616 (define-public python-statannot
 617   (package
 618     (name "python-statannot")
 619     (version "0.2.3")
 620     (source
 621      (origin
 622        (method url-fetch)
 623        (uri (pypi-uri "statannot" version))
 624        (sha256
 625         (base32
 626          "1f8c2sylzr7lpjbyqxsqlp9xi8rj3d8c9hfh98x4jbb83zxc4026"))))
 627     (build-system python-build-system)
 628     (propagated-inputs
 629      `(("python-numpy" ,python-numpy)
 630        ("python-seaborn" ,python-seaborn)
 631        ("python-matplotlib" ,python-matplotlib)
 632        ("python-pandas" ,python-pandas)
 633        ("python-scipy" ,python-scipy)))
 634     (home-page
 635      "https://github.com/webermarcolivier/statannot")
 636     (synopsis "Add annotations to existing plots generated by seaborn")
 637     (description
 638      "This is a Python package to compute statistical test and add statistical
 639 annotations on an existing boxplots and barplots generated by seaborn.")
 640     (license license:expat)))
 641
 642 (define-public python-upsetplot
 643   (package
 644     (name "python-upsetplot")
 645     (version "0.4.1")
 646     (source
 647      (origin
 648        (method url-fetch)
 649        (uri (pypi-uri "UpSetPlot" version))
 650        (sha256
 651         (base32
 652          "0kwljcmsvrxm33y3ssham2bwv4a5m31mv96y9h18va0cv7s3mqn1"))))
 653     (build-system python-build-system)
 654     (arguments
 655      `(#:phases
 656        (modify-phases %standard-phases
 657          (add-after 'unpack 'fix-versioning
 658            (lambda _
 659              (substitute* "setup.py"
 660                (("pytest-cov<2.6") "pytest-cov"))))
 661          (replace 'check
 662            (lambda* (#:key inputs outputs #:allow-other-keys)
 663              (add-installed-pythonpath inputs outputs)
 664              (invoke "pytest" "-v" "--doctest-modules"))))))
 665     (propagated-inputs
 666      `(("python-matplotlib" ,python-matplotlib)
 667        ("python-pandas" ,python-pandas)))
 668     (native-inputs
 669      `(("python-pytest-runner" ,python-pytest-runner)
 670        ("python-pytest-cov" ,python-pytest-cov)))
 671     (home-page "https://upsetplot.readthedocs.io")
 672     (synopsis "Draw UpSet plots with Pandas and Matplotlib")
 673     (description
 674      "This is a Python implementation of UpSet plots by Lex et al.
 675 UpSet plots are used to visualize set overlaps; like Venn diagrams but more
 676 readable.")
 677     (license license:bsd-3)))
 678
 679 (define-public python-vedo
 680   (package
 681     (name "python-vedo")
 682     (version "2021.0.3")
 683     (source
 684      (origin
 685        (method git-fetch)
 686        (uri (git-reference
 687              (url "https://github.com/marcomusy/vedo")
 688              (commit version)))
 689        (file-name (git-file-name name version))
 690        (sha256
 691         (base32
 692          "18i3ajh5jzhpc86di15lwh4jv97jhm627ii877sa4yhv6abzjfpn"))))
 693     (build-system python-build-system)
 694     (arguments
 695      `(#:phases
 696        (modify-phases %standard-phases
 697          (add-after 'build 'mpi-setup
 698            ,%openmpi-setup)
 699          (replace 'check
 700            (lambda* (#:key inputs outputs #:allow-other-keys)
 701              (setenv "HOME" (getcwd))
 702              (add-installed-pythonpath inputs outputs)
 703              (with-directory-excursion "tests"
 704                (for-each (lambda (dir)
 705                            (with-directory-excursion dir
 706                              (invoke "./run_all.sh")))
 707                          '("common" "dolfin")))
 708              #t)))))
 709     (inputs        ; for the check phase
 710      `(("dolfin" ,fenics)
 711        ("pkgconfig" ,python-pkgconfig)
 712        ("matplotlib" ,python-matplotlib)))
 713     (native-inputs ; for python-pkgconfig
 714      `(("pkg-config" ,pkg-config)))
 715     (propagated-inputs
 716      `(("numpy" ,python-numpy)
 717        ("vtk" ,vtk)))
 718     (home-page "https://github.com/marcomusy/vedo")
 719     (synopsis
 720      "Analysis and visualization of 3D objects and point clouds")
 721     (description
 722      "@code{vedo} is a fast and lightweight python module for
 723 scientific analysis and visualization.  The package provides a wide
 724 range of functionalities for working with three-dimensional meshes and
 725 point clouds.  It can also be used to generate high quality
 726 two-dimensional renderings such as scatter plots and histograms.
 727 @code{vedo} is based on @code{vtk} and @code{numpy}, with no other
 728 dependencies.")
 729     ;; vedo is released under the Expat license.  Included fonts are
 730     ;; covered by the OFL license and textures by the CC0 license.
 731     ;; The earth images are in the public domain.
 732     (license (list license:expat
 733                    license:silofl1.1
 734                    license:cc0
 735                    license:public-domain))))