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Diffstat (limited to 'gnu/packages/python-science.scm')
| -rw-r--r-- | gnu/packages/python-science.scm | 287 |
1 files changed, 287 insertions, 0 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm new file mode 100644 index 0000000000..4a262ec793 --- /dev/null +++ b/gnu/packages/python-science.scm @@ -0,0 +1,287 @@ +;;; 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"))))))) |