guix/gnu/packages/python-science.scm

;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016, 2017, 2018, 2019, 2020 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
;;; Copyright © 2020 Pierre Langlois <pierre.langlois@gmx.com>
;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net>
;;; Copyright © 2021 Greg Hogan <code@greghogan.com>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages python-science)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (gnu packages)
  #:use-module (gnu packages base)
  #:use-module (gnu packages check)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-check)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages sphinx)
  #:use-module (gnu packages time)
  #:use-module (gnu packages xdisorg)
  #:use-module (gnu packages xml)
  #:use-module (gnu packages xorg)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix utils)
  #:use-module (guix build-system python))

(define-public python-scipy
  (package
    (name "python-scipy")
    (version "1.6.0")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "scipy" version))
       (sha256
        (base32 "0rh5b1rwdcvvagld8vpxnpaibszy1skpx39a0fwzd5gx5pwcjvfb"))))
    (build-system python-build-system)
    (propagated-inputs
     `(("python-numpy" ,python-numpy)
       ("python-matplotlib" ,python-matplotlib)
       ("python-pyparsing" ,python-pyparsing)))
    (inputs
     `(("lapack" ,lapack)
       ("openblas" ,openblas)
       ("pybind11" ,pybind11)))
    (native-inputs
     `(("python-cython" ,python-cython)
       ("python-pytest" ,python-pytest)
       ("python-sphinx" ,python-sphinx)
       ("python-numpydoc" ,python-numpydoc)
       ("gfortran" ,gfortran)
       ("perl" ,perl)
       ("which" ,which)))
    (outputs '("out" "doc"))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-before 'build 'change-home-dir
           (lambda _
             ;; Change from /homeless-shelter to /tmp for write permission.
             (setenv "HOME" "/tmp")
             #t))
         (add-after 'unpack 'disable-broken-tests
           (lambda _
             (substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py"
               (("^( +)def test_threads_parallel\\(self\\):" m indent)
                (string-append indent
                               "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
                               m)))
             (substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py"
               (("^def test_parallel_threads\\(\\):" m)
                (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
                               m)))
             #t))
         (add-before 'build 'configure-openblas
           (lambda* (#:key inputs #:allow-other-keys)
             (call-with-output-file "site.cfg"
               (lambda (port)
                 (format port
                         "[blas]
libraries = openblas
library_dirs = ~a/lib
include_dirs = ~a/include

# backslash-n to make emacs happy
\n[atlas]
library_dirs = ~a/lib
atlas_libs = openblas
"
                         (assoc-ref inputs "openblas")
                         (assoc-ref inputs "openblas")
                         (assoc-ref inputs "openblas"))))
             #t))
         (add-after 'install 'install-doc
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (let* ((data (string-append (assoc-ref outputs "doc") "/share"))
                    (doc (string-append data "/doc/" ,name "-" ,version))
                    (html (string-append doc "/html"))
                    (pyver ,(string-append "PYVER=" (version-major+minor
                                                     (package-version python))))
                    ;; By default it tries to run sphinx-build through the Python
                    ;; interpreter which won't work with our shell wrapper.
                    (sphinxbuild "SPHINXBUILD=LANG=C sphinx-build"))
               ;; Make installed package available for building the
               ;; documentation
               (add-installed-pythonpath inputs outputs)
               (with-directory-excursion "doc"
                 ;; Fix generation of images for mathematical expressions.
                 (substitute* (find-files "source" "conf\\.py")
                   (("pngmath_use_preview = True")
                    "pngmath_use_preview = False"))
                 (mkdir-p html)
                 (invoke "make" "html" pyver sphinxbuild)
                 (with-directory-excursion "build/html"
                   (for-each (lambda (file)
                               (let* ((dir (dirname file))
                                      (tgt-dir (string-append html "/" dir)))
                                 (install-file file html)))
                             (find-files "." ".*")))))
             #t))
         ;; Tests can only be run after the library has been installed and not
         ;; within the source directory.
         (delete 'check)
         (add-after 'install 'check
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (add-installed-pythonpath inputs outputs)
             (with-directory-excursion "/tmp"
               (invoke "python" "-c"
                       "import scipy; scipy.test(verbose=2)")))))))
    (home-page "https://www.scipy.org/")
    (synopsis "The Scipy library provides efficient numerical routines")
    (description "The SciPy library is one of the core packages that make up
the SciPy stack.  It provides many user-friendly and efficient numerical
routines such as routines for numerical integration and optimization.")
    (properties `((python2-variant . ,(delay python2-scipy))))
    (license license:bsd-3)))

;; Version 1.2.2 is the last version to support Python 2
(define-public python2-scipy
  (package
    (inherit (package-with-python2
              (strip-python2-variant python-scipy)))
    (version "1.2.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "scipy" version))
       (sha256
        (base32
         "1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))

(define-public python2-weave
  (package
    (name "python2-weave")
    (version "0.16.0")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "weave" version))
       (sha256
        (base32 "0jnm3584mfichgwgrd1gk5i42ll9c08nkw9716n947n4338f6ghs"))))
    (build-system python-build-system)
    (arguments
     `(#:python ,python-2
       #:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda _
             (invoke "nosetests" "-v"
                     "--exclude"
                     "test_(user|incorrect_ownership|char_fail|obj_fail)"))))))
    (propagated-inputs
     `(("python-numpy" ,python2-numpy)))
    (native-inputs
     `(("python-nose" ,python2-nose)))
    (home-page "https://www.scipy.org/")
    (synopsis "Tools for including C/C++ code within Python code")
    (description "Weave is the stand-alone version of the obsolete Scipy
submodule @code{scipy.weave}.  It is Python 2.x only, and is provided for
users that need new versions of Scipy but have existing code that still
depends on @code{scipy.weave}.  For new code, users are recommended to use
Cython.")
    (license license:bsd-3)))

(define-public python-scikit-fuzzy
  (package
    (name "python-scikit-fuzzy")
    (version "0.4.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "scikit-fuzzy" version))
       (sha256
        (base32 "0bp1n771fj44kdp7a00bcvfwirvv2rc803b7g6yf3va7v0j29c8s"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda _
             (invoke "nosetests" "-s" "-v" "skfuzzy")
             #t)))))
    (native-inputs
     `(("python-nose" ,python-nose)))
    (propagated-inputs
     `(("python-networkx" ,python-networkx)
       ("python-numpy" ,python-numpy)
       ("python-scipy" ,python-scipy)))
    (home-page "https://github.com/scikit-fuzzy/scikit-fuzzy")
    (synopsis "Fuzzy logic toolkit for SciPy")
    (description
     "This package implements many useful tools for projects involving fuzzy
logic, also known as grey logic.")
    (license license:bsd-3)))

(define-public python-scikit-image
  (package
    (name "python-scikit-image")
    (version "0.18.1")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "scikit-image" version))
       (sha256
        (base32 "0wgisa03smhrphcjnhq7waa5vyyd32b67hblapjbqrqqj751idpv"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-before 'build 'change-home-dir
           (lambda _
             ;; Change from /homeless-shelter to /tmp for write permission.
             (setenv "HOME" "/tmp")
             #t))
         (replace 'build
           (lambda _
             (invoke "make")))
         (replace 'check
           (lambda _
             ;; The following tests require online data.
             (invoke "python" "-m" "pytest" "skimage" "--doctest-modules" "-k"
                     (string-append "not test_ndim"
                                    " and not test_skin")))))))
    ;; See requirements/ for the list of build and run time requirements.
    ;; NOTE: scikit-image has an optional dependency on python-pooch, however
    ;; propagating it would enable many more tests that require online data.
    (propagated-inputs
     `(("python-cloudpickle" ,python-cloudpickle)
       ("python-dask" ,python-dask)
       ("python-imageio" ,python-imageio)
       ("python-matplotlib" ,python-matplotlib)
       ("python-networkx" ,python-networkx)
       ("python-numpy" ,python-numpy)
       ("python-pillow" ,python-pillow)
       ("python-pywavelets" ,python-pywavelets)
       ("python-scipy" ,python-scipy)
       ("python-tifffile" ,python-tifffile)))
    (native-inputs
     `(("python-codecov" ,python-codecov)
       ("python-cython" ,python-cython)
       ("python-flake8" ,python-flake8)
       ("python-pytest" ,python-pytest)
       ("python-pytest-cov" ,python-pytest-cov)
       ("python-pytest-localserver" ,python-pytest-localserver)
       ("python-wheel" ,python-wheel)))
    (home-page "https://scikit-image.org/")
    (synopsis "Image processing in Python")
    (description
     "Scikit-image is a collection of algorithms for image processing.")
    (license license:bsd-3)))

(define-public python-sgp4
  (package
    (name "python-sgp4")
    (version "2.12")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "sgp4" version))
       (sha256
        (base32 "0dncp9i5b6afkg7f8mj9j0qzsp008b8v73yc0qkmizhpns7mvwvx"))))
    (build-system python-build-system)
    (propagated-inputs
     `(("python-numpy" ,python-numpy)))
    (home-page "https://github.com/brandon-rhodes/python-sgp4")
    (synopsis "Track earth satellite TLE orbits using SGP4")
    (description
     "This package provides a Python implementation of the most recent version
of the SGP4 satellite tracking algorithm.")
    (license license:expat)))

(define-public python-pandas
  (package
    (name "python-pandas")
    (version "1.0.5")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "pandas" version))
       (sha256
        (base32 "1a2gv3g6jr6vb5ca43fkwjl5xf86wpfz8y3zcy787adjl0hdkib9"))))
    (build-system python-build-system)
    (arguments
     `(#:modules ((guix build utils)
                  (guix build python-build-system)
                  (ice-9 ftw)
                  (srfi srfi-26))
       #:phases (modify-phases %standard-phases
                  (add-after 'unpack 'patch-which
                    (lambda* (#:key inputs #:allow-other-keys)
                      (let ((which (assoc-ref inputs "which")))
                        (substitute* "pandas/io/clipboard/__init__.py"
                          (("^WHICH_CMD = .*")
                           (string-append "WHICH_CMD = \"" which "\"\n"))))
                      #t))
                  (add-before 'check 'prepare-x
                    (lambda _
                      (system "Xvfb &")
                      (setenv "DISPLAY" ":0")
                      ;; xsel needs to write a log file.
                      (setenv "HOME" "/tmp")
                      #t))
                  (replace 'check
                    (lambda _
                      (let ((build-directory
                             (string-append
                              (getcwd) "/build/"
                              (car (scandir "build"
                                            (cut string-prefix? "lib." <>))))))
                        ;; Disable the "strict data files" option which causes
                        ;; the build to error out if required data files are
                        ;; not available (as is the case with PyPI archives).
                        (substitute* "setup.cfg"
                          (("addopts = --strict-data-files") "addopts = "))
                        (with-directory-excursion build-directory
                          (invoke "pytest" "-vv" "pandas" "--skip-slow"
                                  "--skip-network"))))))))
    (propagated-inputs
     `(("python-jinja2" ,python-jinja2)
       ("python-numpy" ,python-numpy)
       ("python-openpyxl" ,python-openpyxl)
       ("python-pytz" ,python-pytz)
       ("python-dateutil" ,python-dateutil)
       ("python-xlrd" ,python-xlrd)))
    (inputs
     `(("which" ,which)
       ("xclip" ,xclip)
       ("xsel" ,xsel)))
    (native-inputs
     `(("python-cython" ,python-cython)
       ("python-beautifulsoup4" ,python-beautifulsoup4)
       ("python-lxml" ,python-lxml)
       ("python-html5lib" ,python-html5lib)
       ("python-nose" ,python-nose)
       ("python-pytest" ,python-pytest)
       ("python-pytest-mock" ,python-pytest-mock)
       ;; Needed to test clipboard support.
       ("xorg-server" ,xorg-server-for-tests)))
    (home-page "https://pandas.pydata.org")
    (synopsis "Data structures for data analysis, time series, and statistics")
    (description
     "Pandas is a Python package providing fast, flexible, and expressive data
structures designed to make working with structured (tabular,
multidimensional, potentially heterogeneous) and time series data both easy
and intuitive.  It aims to be the fundamental high-level building block for
doing practical, real world data analysis in Python.")
    (properties `((python2-variant . ,(delay python2-pandas))))
    (license license:bsd-3)))

(define-public python-pandas-0.25
  (package
    (inherit python-pandas)
    (version "0.25.3")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "pandas" version))
              (sha256
               (base32
                "191048m6kdc6yfvqs9w412lq60cfvigrsb57y0x116lwibgp9njj"))))
    (arguments
     (substitute-keyword-arguments (package-arguments python-pandas)
       ((#:phases phases)
        `(modify-phases ,phases
           (replace 'patch-which
             (lambda* (#:key inputs #:allow-other-keys)
               (let ((which (assoc-ref inputs "which")))
                 (substitute* "pandas/io/clipboard/__init__.py"
                   (("^CHECK_CMD = .*")
                     (string-append "CHECK_CMD = \"" which "\"\n"))))
               #t))
           (delete 'prepare-x)))))))

;; Pandas 0.24.x are the last versions that support Python 2.
(define-public python2-pandas
  (let ((pandas (package-with-python2
                 (strip-python2-variant python-pandas-0.25))))
    (package
      (inherit pandas)
      (version "0.24.2")
      (source (origin
                (method url-fetch)
                (uri (pypi-uri "pandas" version))
                (sha256
                 (base32
                  "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag"))
                (modules '((guix build utils)))
                (snippet
                 '(begin
                    ;; Adjust for renamed error message in Python 2.7.17.  Taken
                    ;; from <https://github.com/pandas-dev/pandas/pull/29294>.
                    (substitute* "pandas/io/parsers.py"
                      (("if 'NULL byte' in msg:")
                       "if 'NULL byte' in msg or 'line contains NUL' in msg:"))
                    #t)))))))

(define-public python-bottleneck
  (package
    (name "python-bottleneck")
    (version "1.3.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "Bottleneck" version))
       (sha256
        (base32 "0wz5320jx3n4q2nsvwvc7cpi66b46qbals9v53m955rmcq5ry5r0"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda _
             (invoke "python" "setup.py" "pytest"))))))
    (native-inputs
     `(("python-hypothesis" ,python-hypothesis)
       ("python-pytest" ,python-pytest)
       ("python-pytest-runner" ,python-pytest-runner)))
    (propagated-inputs
     `(("python-numpy" ,python-numpy)))
    (home-page "https://github.com/pydata/bottleneck")
    (synopsis "Fast NumPy array functions written in C")
    (description
     "Bottleneck is a collection of fast, NaN-aware NumPy array functions
written in C.")
    (license license:bsd-2)))

(define-public python-baycomp
  (package
    (name "python-baycomp")
    (version "1.0.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "baycomp" version))
       (sha256
        (base32 "1c1354a7b3g8slychjgyjxqdm8z40z9kviyl9n4g9kfpdg0p4d64"))))
    (build-system python-build-system)
    (propagated-inputs
     `(("python-matplotlib" ,python-matplotlib)
       ("python-numpy" ,python-numpy)
       ("python-scipy" ,python-scipy)))
    (home-page "https://github.com/janezd/baycomp")
    (synopsis "Library for comparison of Bayesian classifiers")
    (description
     "Baycomp is a library for Bayesian comparison of classifiers.  Functions
in the library compare two classifiers on one or on multiple data sets.  They
compute three probabilities: the probability that the first classifier has
higher scores than the second, the probability that differences are within the
region of practical equivalence (rope), or that the second classifier has
higher scores.")
    (license license:expat)))

(define-public python-xarray
  (package
    (name "python-xarray")
    (version "0.15.1")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "xarray" version))
              (sha256
               (base32
                "1yx8j66b7rn10m2l6gmn8yr9cn38pi5cj0x0wwpy4hdnhy6i7qv4"))))
    (build-system python-build-system)
    (native-inputs
     `(("python-setuptools-scm" ,python-setuptools-scm)
       ("python-pytest" ,python-pytest)))
    (propagated-inputs
     `(("python-numpy" ,python-numpy)
       ("python-pandas" ,python-pandas)))
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda _
             (invoke "pytest"))))))
    (home-page "https://github.com/pydata/xarray")
    (synopsis "N-D labeled arrays and datasets")
    (description "Xarray (formerly xray) makes working with labelled
multi-dimensional arrays simple, efficient, and fun!

Xarray introduces labels in the form of dimensions, coordinates and attributes
on top of raw NumPy-like arrays, which allows for a more intuitive, more
concise, and less error-prone developer experience.  The package includes a
large and growing library of domain-agnostic functions for advanced analytics
and visualization with these data structures.")
    (license license:asl2.0)))

(define-public python-msgpack-numpy
  (package
    (name "python-msgpack-numpy")
    (version "0.4.6.post0")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "msgpack-numpy" version))
       (sha256
        (base32
         "0syzy645mwcy7lfjwz6pc8f9p2vv1qk4limc8iina3l5nnf0rjyz"))))
    (build-system python-build-system)
    (propagated-inputs
     `(("python-msgpack" ,python-msgpack)
       ("python-numpy" ,python-numpy)))
    (home-page "https://github.com/lebedov/msgpack-numpy")
    (synopsis
     "Numpy data serialization using msgpack")
    (description
     "This package provides encoding and decoding routines that enable the
serialization and deserialization of numerical and array data types provided
by numpy using the highly efficient @code{msgpack} format.  Serialization of
Python's native complex data types is also supported.")
    (license license:bsd-3)))

(define-public python-statannot
  (package
    (name "python-statannot")
    (version "0.2.3")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "statannot" version))
       (sha256
        (base32
         "1f8c2sylzr7lpjbyqxsqlp9xi8rj3d8c9hfh98x4jbb83zxc4026"))))
    (build-system python-build-system)
    (propagated-inputs
     `(("python-numpy" ,python-numpy)
       ("python-seaborn" ,python-seaborn)
       ("python-matplotlib" ,python-matplotlib)
       ("python-pandas" ,python-pandas)
       ("python-scipy" ,python-scipy)))
    (home-page
     "https://github.com/webermarcolivier/statannot")
    (synopsis "Add annotations to existing plots generated by seaborn")
    (description
     "This is a Python package to compute statistical test and add statistical
annotations on an existing boxplots and barplots generated by seaborn.")
    (license license:expat)))

(define-public python-upsetplot
  (package
    (name "python-upsetplot")
    (version "0.4.1")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "UpSetPlot" version))
       (sha256
        (base32
         "0kwljcmsvrxm33y3ssham2bwv4a5m31mv96y9h18va0cv7s3mqn1"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'fix-versioning
           (lambda _
             (substitute* "setup.py"
               (("pytest-cov<2.6") "pytest-cov"))))
         (replace 'check
           (lambda* (#:key inputs outputs #:allow-other-keys)
             (add-installed-pythonpath inputs outputs)
             (invoke "pytest" "-v" "--doctest-modules"))))))
    (propagated-inputs
     `(("python-matplotlib" ,python-matplotlib)
       ("python-pandas" ,python-pandas)))
    (native-inputs
     `(("python-pytest-runner" ,python-pytest-runner)
       ("python-pytest-cov" ,python-pytest-cov)))
    (home-page "https://upsetplot.readthedocs.io")
    (synopsis "Draw UpSet plots with Pandas and Matplotlib")
    (description
     "This is a Python implementation of UpSet plots by Lex et al.
UpSet plots are used to visualize set overlaps; like Venn diagrams but more
readable.")
    (license license:bsd-3)))