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-rw-r--r--gnu/packages/python.scm272
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))