diff options
Diffstat (limited to 'gnu/packages/python.scm')
| -rw-r--r-- | gnu/packages/python.scm | 272 |
1 files changed, 225 insertions, 47 deletions
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm index b2a2d84d00..34f40f0c72 100644 --- a/gnu/packages/python.scm +++ b/gnu/packages/python.scm @@ -974,7 +974,7 @@ from the Python interpreter, or as a small part of a larger application.") (native-inputs `(("python-py" ,python-py) ("python-pytest" ,python-pytest-bootstrap))) - (home-page "http://pypi.python.org/pypi/six/") + (home-page "https://pypi.python.org/pypi/six/") (synopsis "Python 2 and 3 compatibility utilities") (description "Six is a Python 2 and 3 compatibility library. It provides utility @@ -2681,12 +2681,12 @@ between language specification and implementation aspects.") (arguments `(#:phases (modify-phases %standard-phases - (add-before 'build 'set-environment-variables - (lambda* (#:key inputs #:allow-other-keys) - (call-with-output-file "site.cfg" - (lambda (port) - (format port - "[openblas] + (add-before 'build 'configure-blas-lapack + (lambda* (#:key inputs #:allow-other-keys) + (call-with-output-file "site.cfg" + (lambda (port) + (format port + "[openblas] libraries = openblas library_dirs = ~a/lib include_dirs = ~a/include @@ -2697,30 +2697,33 @@ lapack_libs = lapack library_dirs = ~a/lib include_dirs = ~a/include " - (assoc-ref inputs "openblas") - (assoc-ref inputs "openblas") - (assoc-ref inputs "lapack") - (assoc-ref inputs "lapack")))) - ;; Make /gnu/store/...-bash-.../bin/sh the default shell, instead of - ;; /bin/sh. - (substitute* "numpy/distutils/exec_command.py" - (("(os.environ.get\\('SHELL', ')(/bin/sh'\\))" match match-start match-end) - (string-append match-start (assoc-ref inputs "bash") match-end))) - ;; Use "gcc" executable, not "cc". - (substitute* "numpy/distutils/system_info.py" - (("c = distutils\\.ccompiler\\.new_compiler\\(\\)") - "c = distutils.ccompiler.new_compiler(); c.set_executables(compiler='gcc',compiler_so='gcc',linker_exe='gcc',linker_so='gcc -shared')")) - #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 outputs inputs #:allow-other-keys) - ;; Make installed package available for running the tests - (add-installed-pythonpath inputs outputs) - (with-directory-excursion "/tmp" - (zero? (system* "python" "-c" - "import numpy; numpy.test(verbose=2)")))))))) + (assoc-ref inputs "openblas") + (assoc-ref inputs "openblas") + (assoc-ref inputs "lapack") + (assoc-ref inputs "lapack")))) + #t)) + (add-before 'build 'fix-executable-paths + (lambda* (#:key inputs #:allow-other-keys) + ;; Make /gnu/store/...-bash-.../bin/sh the default shell, + ;; instead of /bin/sh. + (substitute* "numpy/distutils/exec_command.py" + (("(os.environ.get\\('SHELL', ')(/bin/sh'\\))" match match-start match-end) + (string-append match-start (assoc-ref inputs "bash") match-end))) + ;; Use "gcc" executable, not "cc". + (substitute* "numpy/distutils/system_info.py" + (("c = distutils\\.ccompiler\\.new_compiler\\(\\)") + "c = distutils.ccompiler.new_compiler(); c.set_executables(compiler='gcc',compiler_so='gcc',linker_exe='gcc',linker_so='gcc -shared')")) + #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 outputs inputs #:allow-other-keys) + ;; Make installed package available for running the tests + (add-installed-pythonpath inputs outputs) + (with-directory-excursion "/tmp" + (zero? (system* "python" "-c" + "import numpy; numpy.test(verbose=2)")))))))) (home-page "http://www.numpy.org/") (synopsis "Fundamental package for scientific computing with Python") (description "NumPy is the fundamental package for scientific computing @@ -2753,6 +2756,49 @@ capabilities.") (define-public python2-numpy-next (package-with-python2 python-numpy-next)) +;; NOTE: NumPy 1.8 is packaged only for Python 2 because it is of +;; interest only for legacy code going back to NumPy's predecessor +;; Numeric. +(define-public python2-numpy-1.8 + (package (inherit python2-numpy) + (version "1.8.2") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/numpy/numpy/archive/v" version ".tar.gz")) + (file-name (string-append "python2-numpy-" version ".tar.gz")) + (sha256 + (base32 + "0sc20gz1b17xnyrkp5frca3ql5qfalpv916hfg2kqxpwr6jg0f1g")))) + (arguments + (substitute-keyword-arguments (package-arguments python2-numpy) + ((#:phases phases) + `(modify-phases ,phases + (replace 'configure-blas-lapack + (lambda* (#:key inputs #:allow-other-keys) + (call-with-output-file "site.cfg" + (lambda (port) + (format port + "[openblas] +libraries = openblas,lapack +library_dirs = ~a/lib:~a/lib +include_dirs = ~a/include:~a/include +" + (assoc-ref inputs "openblas") + (assoc-ref inputs "lapack") + (assoc-ref inputs "openblas") + (assoc-ref inputs "lapack")))) + #t)))))) + (description "NumPy is the fundamental package for scientific computing +with Python. It contains among other things: a powerful N-dimensional array +object, sophisticated (broadcasting) functions, tools for integrating C/C++ +and Fortran code, useful linear algebra, Fourier transform, and random number +capabilities. Version 1.8 is the last one to contain the numpy.oldnumeric API +that includes the compatibility layer numpy.oldnumeric with NumPy's predecessor +Numeric.") + (license license:bsd-3))) + (define-public python-munch (package (name "python-munch") @@ -2820,7 +2866,7 @@ objects.") `(("python-colormath" ,python-colormath))) (native-inputs `(("python-nose" ,python-nose))) - (home-page "http://github.com/jsvine/spectra") + (home-page "https://github.com/jsvine/spectra") (synopsis "Color scales and color conversion") (description "This package provides a Python library intended to make color math, @@ -3541,7 +3587,7 @@ atlas_libs = openblas (zero? (system* "python" "-c" "import scipy; scipy.test('full')"))) #t))))) - (home-page "http://www.scipy.org/") + (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 @@ -3719,18 +3765,45 @@ Python's distutils.") services for your Python modules and applications.") (license license:lgpl3+))) +(define-public python-olefile + (package + (name "python-olefile") + (version "0.44") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/decalage2/olefile/archive/v" + version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1wmxbrhyqjry2000zx0zdhqdqxhgi06nz7sbzjlh222q2zjv1gpj")))) + (build-system python-build-system) + (home-page + "https://www.decalage.info/python/olefileio") + (synopsis "Read and write Microsoft OLE2 files.") + (description + "@code{olefile} can parse, read and write Microsoft OLE2 files (Structured +Storage or Compound Document, Microsoft Office). It is an improved version of +the OleFileIO module from PIL, the Python Image Library.") + (license license:bsd-3))) + +(define-public python2-olefile + (package-with-python2 python-olefile)) + (define-public python-pillow (package (name "python-pillow") - (version "3.3.3") + (version "4.3.0") (source (origin (method url-fetch) (uri (pypi-uri "Pillow" version)) - (patches (search-patches "python-pillow-freetype-2.7-test-failure.patch")) (sha256 (base32 - "0xkv0p1d73gz0a1qaasf0ai4262g8f334j07vd60bjrxs2wr3nmj")))) + "09xmn7rl6840sli2iz1k3fgxfgmri2nqz6vkinmb9mgg8ifp2z59")) + (patch-flags '("-p1" "--binary")) + (patches (search-patches "python-pillow-fix-failing-tests.patch")))) (build-system python-build-system) (native-inputs `(("python-nose" ,python-nose))) @@ -3742,6 +3815,8 @@ services for your Python modules and applications.") ("openjpeg" ,openjpeg) ("libtiff" ,libtiff) ("libwebp" ,libwebp))) + (propagated-inputs + `(("python-olefile" ,python-olefile))) (arguments `(#:phases (modify-phases %standard-phases (add-after @@ -4709,7 +4784,7 @@ libxml2 and libxslt.") (replace 'check (lambda _ (zero? (system* "./convert-py3k"))))))) (home-page - "http://www.crummy.com/software/BeautifulSoup/bs4/") + "https://www.crummy.com/software/BeautifulSoup/bs4/") (synopsis "Python screen-scraping library") (description @@ -6101,7 +6176,7 @@ a hash value.") (arguments ;; There are no tests. `(#:tests? #f)) - (home-page "http://pypi.python.org/pypi/termcolor") + (home-page "https://pypi.python.org/pypi/termcolor") (synopsis "ANSII Color formatting for terminal output") (description "This package provides ANSII Color formatting for output in terminals.") @@ -7231,7 +7306,7 @@ text.") encryption and decryption, signing and verifying signatures, and key generation according to PKCS#1 version 1.5. It can be used as a Python library as well as on the command line.") - (home-page "http://stuvel.eu/rsa") + (home-page "https://stuvel.eu/rsa") (license license:asl2.0))) (define-public python2-rsa @@ -7490,7 +7565,7 @@ fast xml and html manipulation.") ;; but it could be annoying/difficult. ;; We can enable tests for the Python 2 version, though, and do below. #:tests? #f)) - (home-page "http://bitbucket.org/runeh/anyjson/") + (home-page "https://bitbucket.org/runeh/anyjson/") (synopsis "Wraps best available JSON implementation in a common interface") (description @@ -7835,7 +7910,7 @@ useful for solving the Assignment Problem.") (build-system python-build-system) (native-inputs `(("python-pytest" ,python-pytest))) - (home-page "http://bitbucket.org/mchaput/whoosh") + (home-page "https://bitbucket.org/mchaput/whoosh") (synopsis "Full text indexing, search, and spell checking library") (description "Whoosh is a fast, pure-Python full text indexing, search, and spell @@ -7905,7 +7980,7 @@ anymore.") `(#:python ,python-2)) (native-inputs `(("python2-six" ,python2-six))) - (home-page "http://pypi.python.org/pypi/pathlib2/") + (home-page "https://pypi.python.org/pypi/pathlib2/") (synopsis "Object-oriented file system paths - backport of standard pathlib module") (description "The goal of pathlib2 is to provide a backport of standard @@ -10035,7 +10110,7 @@ protocols written in pure Python.") (zero? (system* "python" "test/test_pbkdf2.py"))))))) (propagated-inputs `(("python-pycrypto" ,python-pycrypto))) ; optional - (home-page "http://www.dlitz.net/software/python-pbkdf2/") + (home-page "https://www.dlitz.net/software/python-pbkdf2/") (synopsis "Password-based key derivation") (description "This module implements the password-based key derivation function, PBKDF2, specified in RSA PKCS#5 v2.0. @@ -10121,7 +10196,7 @@ to ansi-escaped strings suitable for display in a terminal.") ("python-nose" ,python-nose))) (propagated-inputs `(("python-six" ,python-six))) - (home-page "http://github.com/ralphbean/ansi2html") + (home-page "https://github.com/ralphbean/ansi2html") (synopsis "Convert ANSI-decorated console output to HTML") (description "@command{ansi2html} is a Python library and command line utility for @@ -11292,7 +11367,7 @@ applying JSON Patches according to RFC 6902.") (base32 "192pclzs2y0yaywqkrlvd0x73740q310kvqvm6jldhi619mq59wi")))) (build-system python-build-system) - (home-page "http://pypi.python.org/pypi/rfc3987") + (home-page "https://pypi.python.org/pypi/rfc3987") (synopsis "Parsing and validation of URIs (RFC 3986) and IRIs (RFC 3987)") (description "@code{rfc3987} provides routines for parsing and validation of URIs (see RFC 3986) and IRIs (see RFC 3987).") @@ -11313,7 +11388,7 @@ validation of URIs (see RFC 3986) and IRIs (see RFC 3987).") (base32 "1bxffaf5yz2cph8ki55vdvdypbwkvn2xr1firlcy62vqbzf1jivq")))) (build-system python-build-system) - (home-page "http://github.com/syrusakbary/validate_email") + (home-page "https://github.com/syrusakbary/validate_email") (synopsis "Verifies if an email address is valid and really exists") (description "@code{validate_email} can be used to verify if an email address is valid and really exists.") @@ -11476,7 +11551,7 @@ from your Flask project. It is a fork of Flask-Swagger.") `(("python-jsonschema" ,python-jsonschema) ("python-six" ,python-six))) (home-page - "http://github.com/Yelp/swagger_spec_validator") + "https://github.com/Yelp/swagger_spec_validator") (synopsis "Validation of Swagger specifications") (description "@code{swagger_spec_validator} provides a library for validating Swagger API specifications.") @@ -12072,3 +12147,106 @@ particularly convenient for use in tests.") (define-public python2-tempdir (package-with-python2 python-tempdir)) +(define-public python-activepapers + (package + (name "python-activepapers") + (version "0.2.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ActivePapers.Py" version)) + (sha256 + (base32 + "12wkhjh90ffipjzv10swndp2xv9hd7xrxvg6v0n4n3i411pj4xb8")))) + (build-system python-build-system) + (arguments + `(#:modules ((ice-9 ftw) + (srfi srfi-1) + (guix build utils) + (guix build python-build-system)) + + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'delete-python2-code + (lambda _ + (for-each delete-file + '("lib/activepapers/builtins2.py" + "lib/activepapers/standardlib2.py" + "lib/activepapers/utility2.py")))) + (replace 'check + (lambda _ + ;; Deactivate the test cases that download files + (setenv "NO_NETWORK_ACCESS" "1") + ;; For some strange reason, some tests fail if nosetests runs all + ;; test modules in a single execution. They pass if each test + ;; module is run individually. + (for-each (lambda (filename) + (invoke "nosetests" + (string-append "tests/" filename))) + (scandir "tests" + (lambda (filename) + (string-suffix? ".py" filename))))))))) + (native-inputs + `(("python-tempdir" ,python-tempdir) + ("python-nose" ,python-nose))) + (propagated-inputs + `(("python-h5py" ,python-h5py))) + (home-page "http://www.activepapers.org/") + (synopsis "Executable papers for scientific computing") + (description + "ActivePapers is a tool for working with executable papers, which +combine data, code, and documentation in single-file packages, +suitable for publication as supplementary material or on repositories +such as figshare or Zenodo.") + (properties `((python2-variant . ,(delay python2-activepapers)))) + (license license:bsd-3))) + +(define-public python2-activepapers + (let ((base (package-with-python2 + (strip-python2-variant python-activepapers)))) + (package + (inherit base) + (arguments + (substitute-keyword-arguments (package-arguments base) + ((#:phases phases) + `(modify-phases ,phases + (delete 'delete-python2-code) + (add-after 'unpack 'delete-python3-code + (lambda _ + (for-each delete-file + '("lib/activepapers/builtins3.py" + "lib/activepapers/standardlib3.py" + "lib/activepapers/utility3.py"))))))))))) + +(define-public python-semver + (package + (name "python-semver") + (version "2.7.9") + (source + (origin + (method url-fetch) + (uri (pypi-uri "semver" version)) + (sha256 + (base32 + "0hhgqppchv59rqj0yzi1prdg2nfsywqmjsqy2rycyxm0hvxmbyqz")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-test-requirements + (lambda _ + (substitute* "setup.py" + ;; Our Python is new enough. + (("'virtualenv<14\\.0\\.0'") "'virtualenv'")) + #t))))) + (native-inputs + `(("python-tox" ,python-tox) + ("python-virtualenv" ,python-virtualenv))) + (home-page "https://github.com/k-bx/python-semver") + (synopsis "Python helper for Semantic Versioning") + (description "This package provides a Python library for +@url{Semantic Versioning, http://semver.org/}.") + (license license:bsd-3))) + +(define-public python2-semver + (package-with-python2 python-semver)) |