[jackhill/guix/guix.git] / gnu / packages / python-science.scm

;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016 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 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>
;;;
;;; 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-web)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages sphinx)
  #:use-module (gnu packages time)
  #: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 "1.3.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "scipy" version))
       (sha256
        (base32 "192d8dsybvhv19igkrsafbdafx198nz7pibkjgrqjhlr66s3jfd0"))))
    (build-system python-build-system)
    (propagated-inputs
     `(("python-numpy" ,python-numpy)
       ("python-matplotlib" ,python-matplotlib)
       ("python-pyparsing" ,python-pyparsing)))
    (inputs
     `(("lapack" ,lapack)
       ("openblas" ,openblas)))
    (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-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 python-scikit-image
  (package
    (name "python-scikit-image")
    (version "0.14.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "scikit-image" version))
       (sha256
        (base32 "07qchljkyxvg5nrm12fvszi7pmjk4m01qp0w0z8syxzxxs20pz8s"))))
    (build-system python-build-system)
    (arguments
     ;; TODO: Some tests require running X11 server. Disable them?
     '(#:tests? #f))
    ;; See DEPENDS.txt for the list of build and run time requiremnts
    (propagated-inputs
     `(("python-cloudpickle" ,python-cloudpickle)
       ("python-dask" ,python-dask)
       ("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-six" ,python-six)))
    (native-inputs
     `(("python-cython" ,python-cython)))
    (home-page "http://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 python2-scikit-image
  (package-with-python2 python-scikit-image))

(define-public python-pandas
  (package
    (name "python-pandas")
    (version "0.25.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "pandas" version))
       (sha256
        (base32 "1gp2pvzdiakvgjmykdzdlzrsfbg4vjm49jjdl9s0ha0a3yfs34fa"))))
    (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"
                          (("^CHECK_CMD = .*")
                           (string-append "CHECK_CMD = \"" which "\"\n"))))
                      #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
                          ;; Delete tests that require "moto" which is not yet
                          ;; in Guix.
                          (for-each delete-file
                                    '("pandas/tests/io/conftest.py"
                                      "pandas/tests/io/json/test_compression.py"
                                      "pandas/tests/io/parser/test_network.py"
                                      "pandas/tests/io/test_parquet.py"))
                          (invoke "pytest" "-vv" "pandas" "--skip-slow"
                                  "--skip-network" "-k"
                                  ;; XXX: Due to the deleted tests above.
                                  "not test_read_s3_jsonl"))))))))
    (propagated-inputs
     `(("python-numpy" ,python-numpy)
       ("python-openpyxl" ,python-openpyxl)
       ("python-pytz" ,python-pytz)
       ("python-dateutil" ,python-dateutil)
       ("python-xlrd" ,python-xlrd)))
    (inputs
     `(("which" ,which)))
    (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)))
    (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)))

;; 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))))
    (package/inherit
     pandas
     (version "0.24.2")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "pandas" version))
               (sha256
                (base32
                 "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag")))))))
Commit	Line	Data
ca7c3653	1	;;; GNU Guix --- Functional package management for GNU
312ec128	2	;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net>
ca7c3653	3	;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
312ec128	4	;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
ca7c3653 RW	5	;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
ca7c3653 RW	6	;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
312ec128	7	;;; Copyright © 2016, 2017, 2018, 2019 Marius Bakke <mbakke@fastmail.com>
ca7c3653	8	;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
312ec128 RW	9	;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com>
312ec128 RW	10	;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
ca7c3653 RW	11	;;;
	12	;;; This file is part of GNU Guix.
	13	;;;
	14	;;; GNU Guix is free software; you can redistribute it and/or modify it
	15	;;; under the terms of the GNU General Public License as published by
	16	;;; the Free Software Foundation; either version 3 of the License, or (at
	17	;;; your option) any later version.
	18	;;;
	19	;;; GNU Guix is distributed in the hope that it will be useful, but
	20	;;; WITHOUT ANY WARRANTY; without even the implied warranty of
	21	;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
	22	;;; GNU General Public License for more details.
	23	;;;
	24	;;; You should have received a copy of the GNU General Public License
	25	;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
	26
	27	(define-module (gnu packages python-science)
	28	#:use-module ((guix licenses) #:prefix license:)
	29	#:use-module (gnu packages)
ec1224a7 RW	30	#:use-module (gnu packages base)
	31	#:use-module (gnu packages check)
	32	#:use-module (gnu packages gcc)
	33	#:use-module (gnu packages maths)
	34	#:use-module (gnu packages perl)
	35	#:use-module (gnu packages python)
312ec128	36	#:use-module (gnu packages python-web)
ca7c3653	37	#:use-module (gnu packages python-xyz)
ec1224a7	38	#:use-module (gnu packages sphinx)
312ec128	39	#:use-module (gnu packages time)
ca7c3653 RW	40	#:use-module (guix packages)
	41	#:use-module (guix download)
	42	#:use-module (guix utils)
	43	#:use-module (guix build-system python))
	44
ec1224a7 RW	45	(define-public python-scipy
	46	(package
	47	(name "python-scipy")
	48	(version "1.3.2")
	49	(source
	50	(origin
	51	(method url-fetch)
	52	(uri (pypi-uri "scipy" version))
	53	(sha256
	54	(base32 "192d8dsybvhv19igkrsafbdafx198nz7pibkjgrqjhlr66s3jfd0"))))
	55	(build-system python-build-system)
	56	(propagated-inputs
	57	`(("python-numpy" ,python-numpy)
	58	("python-matplotlib" ,python-matplotlib)
	59	("python-pyparsing" ,python-pyparsing)))
	60	(inputs
	61	`(("lapack" ,lapack)
	62	("openblas" ,openblas)))
	63	(native-inputs
	64	`(("python-cython" ,python-cython)
	65	("python-pytest" ,python-pytest)
	66	("python-sphinx" ,python-sphinx)
	67	("python-numpydoc" ,python-numpydoc)
	68	("gfortran" ,gfortran)
	69	("perl" ,perl)
	70	("which" ,which)))
	71	(outputs '("out" "doc"))
	72	(arguments
	73	`(#:phases
	74	(modify-phases %standard-phases
	75	(add-after 'unpack 'disable-broken-tests
	76	(lambda _
	77	(substitute* "scipy/sparse/linalg/dsolve/tests/test_linsolve.py"
	78	(("^( +)def test_threads_parallel\\(self\\):" m indent)
	79	(string-append indent
	80	"@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
	81	m)))
	82	(substitute* "scipy/sparse/linalg/eigen/arpack/tests/test_arpack.py"
	83	(("^def test_parallel_threads\\(\\):" m)
	84	(string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
	85	m)))
	86	#t))
	87	(add-before 'build 'configure-openblas
	88	(lambda* (#:key inputs #:allow-other-keys)
	89	(call-with-output-file "site.cfg"
	90	(lambda (port)
	91	(format port
	92	"[blas]
	93	libraries = openblas
	94	library_dirs = ~a/lib
	95	include_dirs = ~a/include
	96
	97	# backslash-n to make emacs happy
	98	\n[atlas]
	99	library_dirs = ~a/lib
	100	atlas_libs = openblas
	101	"
	102	(assoc-ref inputs "openblas")
	103	(assoc-ref inputs "openblas")
	104	(assoc-ref inputs "openblas"))))
	105	#t))
	106	(add-after 'install 'install-doc
	107	(lambda* (#:key inputs outputs #:allow-other-keys)
	108	(let* ((data (string-append (assoc-ref outputs "doc") "/share"))
109	(doc (string-append data "/doc/" ,name "-" ,version))
110	(html (string-append doc "/html"))
111	(pyver ,(string-append "PYVER=" (version-major+minor
112	(package-version python))))
113	;; By default it tries to run sphinx-build through the Python
114	;; interpreter which won't work with our shell wrapper.
115	(sphinxbuild "SPHINXBUILD=LANG=C sphinx-build"))
116	;; Make installed package available for building the
117	;; documentation
118	(add-installed-pythonpath inputs outputs)
119	(with-directory-excursion "doc"
120	;; Fix generation of images for mathematical expressions.
121	(substitute* (find-files "source" "conf\\.py")
122	(("pngmath_use_preview = True")
123	"pngmath_use_preview = False"))
124	(mkdir-p html)
125	(invoke "make" "html" pyver sphinxbuild)
126	(with-directory-excursion "build/html"
127	(for-each (lambda (file)
128	(let* ((dir (dirname file))
129	(tgt-dir (string-append html "/" dir)))
130	(install-file file html)))
131	(find-files "." ".*")))))
132	#t))
133	;; Tests can only be run after the library has been installed and not
134	;; within the source directory.
135	(delete 'check)
136	(add-after 'install 'check
137	(lambda* (#:key inputs outputs #:allow-other-keys)
138	(add-installed-pythonpath inputs outputs)
139	(with-directory-excursion "/tmp"
140	(invoke "python" "-c"
141	"import scipy; scipy.test(verbose=2)")))))))
142	(home-page "https://www.scipy.org/")
143	(synopsis "The Scipy library provides efficient numerical routines")
144	(description "The SciPy library is one of the core packages that make up
145	the SciPy stack. It provides many user-friendly and efficient numerical
146	routines such as routines for numerical integration and optimization.")
147	(properties `((python2-variant . ,(delay python2-scipy))))
148	(license license:bsd-3)))
149
150	;; Version 1.2.2 is the last version to support Python 2
151	(define-public python2-scipy
152	(package
153	(inherit (package-with-python2
154	(strip-python2-variant python-scipy)))
155	(version "1.2.2")
156	(source
157	(origin
158	(method url-fetch)
159	(uri (pypi-uri "scipy" version))
160	(sha256
161	(base32
162	"1cgvgin8fvckv96hjh3ikmwkra5rif51bdb75ifzf7xbil5iwcx4"))))))
163
ca7c3653 RW	164	(define-public python-scikit-image
	165	(package
	166	(name "python-scikit-image")
	167	(version "0.14.2")
	168	(source
	169	(origin
	170	(method url-fetch)
	171	(uri (pypi-uri "scikit-image" version))
	172	(sha256
	173	(base32 "07qchljkyxvg5nrm12fvszi7pmjk4m01qp0w0z8syxzxxs20pz8s"))))
	174	(build-system python-build-system)
	175	(arguments
	176	;; TODO: Some tests require running X11 server. Disable them?
	177	'(#:tests? #f))
	178	;; See DEPENDS.txt for the list of build and run time requiremnts
	179	(propagated-inputs
	180	`(("python-cloudpickle" ,python-cloudpickle)
	181	("python-dask" ,python-dask)
	182	("python-matplotlib" ,python-matplotlib)
	183	("python-networkx" ,python-networkx)
	184	("python-numpy" ,python-numpy)
	185	("python-pillow" ,python-pillow)
	186	("python-pywavelets" ,python-pywavelets)
	187	("python-scipy" ,python-scipy)
	188	("python-six" ,python-six)))
	189	(native-inputs
	190	`(("python-cython" ,python-cython)))
	191	(home-page "http://scikit-image.org/")
	192	(synopsis "Image processing in Python")
	193	(description
	194	"Scikit-image is a collection of algorithms for image processing.")
	195	(license license:bsd-3)))
	196
	197	(define-public python2-scikit-image
	198	(package-with-python2 python-scikit-image))
312ec128 RW	199
	200	(define-public python-pandas
	201	(package
	202	(name "python-pandas")
	203	(version "0.25.2")
	204	(source
	205	(origin
	206	(method url-fetch)
	207	(uri (pypi-uri "pandas" version))
	208	(sha256
	209	(base32 "1gp2pvzdiakvgjmykdzdlzrsfbg4vjm49jjdl9s0ha0a3yfs34fa"))))
	210	(build-system python-build-system)
	211	(arguments
	212	`(#:modules ((guix build utils)
	213	(guix build python-build-system)
	214	(ice-9 ftw)
	215	(srfi srfi-26))
	216	#:phases (modify-phases %standard-phases
	217	(add-after 'unpack 'patch-which
	218	(lambda* (#:key inputs #:allow-other-keys)
	219	(let ((which (assoc-ref inputs "which")))
	220	(substitute* "pandas/io/clipboard/__init__.py"
	221	(("^CHECK_CMD = .*")
	222	(string-append "CHECK_CMD = \"" which "\"\n"))))
	223	#t))
	224	(replace 'check
	225	(lambda _
	226	(let ((build-directory
	227	(string-append
	228	(getcwd) "/build/"
	229	(car (scandir "build"
	230	(cut string-prefix? "lib." <>))))))
	231	;; Disable the "strict data files" option which causes
	232	;; the build to error out if required data files are
	233	;; not available (as is the case with PyPI archives).
	234	(substitute* "setup.cfg"
	235	(("addopts = --strict-data-files") "addopts = "))
	236	(with-directory-excursion build-directory
	237	;; Delete tests that require "moto" which is not yet
	238	;; in Guix.
	239	(for-each delete-file
	240	'("pandas/tests/io/conftest.py"
	241	"pandas/tests/io/json/test_compression.py"
	242	"pandas/tests/io/parser/test_network.py"
	243	"pandas/tests/io/test_parquet.py"))
	244	(invoke "pytest" "-vv" "pandas" "--skip-slow"
	245	"--skip-network" "-k"
	246	;; XXX: Due to the deleted tests above.
	247	"not test_read_s3_jsonl"))))))))
	248	(propagated-inputs
	249	`(("python-numpy" ,python-numpy)
	250	("python-openpyxl" ,python-openpyxl)
	251	("python-pytz" ,python-pytz)
	252	("python-dateutil" ,python-dateutil)
	253	("python-xlrd" ,python-xlrd)))
	254	(inputs
	255	`(("which" ,which)))
	256	(native-inputs
	257	`(("python-cython" ,python-cython)
	258	("python-beautifulsoup4" ,python-beautifulsoup4)
	259	("python-lxml" ,python-lxml)
	260	("python-html5lib" ,python-html5lib)
	261	("python-nose" ,python-nose)
	262	("python-pytest" ,python-pytest)
263	("python-pytest-mock" ,python-pytest-mock)))
264	(home-page "https://pandas.pydata.org")
265	(synopsis "Data structures for data analysis, time series, and statistics")
266	(description
267	"Pandas is a Python package providing fast, flexible, and expressive data
268	structures designed to make working with structured (tabular,
269	multidimensional, potentially heterogeneous) and time series data both easy
270	and intuitive. It aims to be the fundamental high-level building block for
271	doing practical, real world data analysis in Python.")
272	(properties `((python2-variant . ,(delay python2-pandas))))
273	(license license:bsd-3)))
274
275	;; Pandas 0.24.x are the last versions that support Python 2.
276	(define-public python2-pandas
277	(let ((pandas (package-with-python2
278	(strip-python2-variant python-pandas))))
279	(package/inherit
280	pandas
281	(version "0.24.2")
282	(source (origin
283	(method url-fetch)
284	(uri (pypi-uri "pandas" version))
285	(sha256
286	(base32
287	"18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag")))))))