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-rw-r--r--gnu/packages/python.scm445
1 files changed, 324 insertions, 121 deletions
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 2308ece4e0..c2685f6055 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1029,44 +1029,6 @@ get the local timezone information, unless you know the zoneinfo name, and
under several distributions that's hard or impossible to figure out.")
(license cc0)))
-(define-public python-pysam
- (package
- (name "python-pysam")
- (version "0.8.1")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "https://pypi.python.org/packages/source/p/pysam/pysam-"
- version ".tar.gz"))
- (sha256
- (base32
- "1fb6i6hbpzxaxb62kyyp5alaidwhj40f7c6gwbhr6njzlqd5l459"))))
- (build-system python-build-system)
- (arguments
- `(#:tests? #f ; tests are excluded in the manifest
- #:phases
- (alist-cons-before
- 'build 'set-flags
- (lambda _
- (setenv "LDFLAGS" "-lncurses")
- (setenv "CFLAGS" "-D_CURSES_LIB=1"))
- %standard-phases)))
- (inputs
- `(("python-cython" ,python-cython)
- ("python-setuptools" ,python-setuptools)
- ("ncurses" ,ncurses)
- ("zlib" ,zlib)))
- (home-page "https://github.com/pysam-developers/pysam")
- (synopsis "Python bindings to the SAMtools C API")
- (description
- "Pysam is a Python module for reading and manipulating files in the
-SAM/BAM format. Pysam is a lightweight wrapper of the SAMtools C API. It
-also includes an interface for tabix.")
- (license license:expat)))
-
-(define-public python2-pysam
- (package-with-python2 python-pysam))
-
(define-public python2-pysqlite
(package
(name "python2-pysqlite")
@@ -1160,10 +1122,10 @@ Python 3.3+.")
(package-with-python2 python-simplejson))
-(define-public python2-pyicu
+(define-public python-pyicu
(package
- (name "python2-pyicu")
- (version "1.8")
+ (name "python-pyicu")
+ (version "1.9.2")
(source
(origin
(method url-fetch)
@@ -1171,19 +1133,22 @@ Python 3.3+.")
version ".tar.gz"))
(sha256
(base32
- "1y361x82lnh9k9srmdx3q92z5iag112z7r5fxm0n1sfwb349yjdw"))))
+ "1diba0g8md614fvm9yf50paiwdkhj6rd7xwf1rg9mc0pxc0hhn4v"))))
(build-system python-build-system)
(inputs
`(("icu4c" ,icu4c)))
- (arguments
- `(#:python ,python-2 ; Python 3 works also, but needs special care for
- ; linking with libpython3.3m
- #:tests? #f)) ; no check target
(home-page "http://pyicu.osafoundation.org/")
(synopsis "Python extension wrapping the ICU C++ API")
(description
"PyICU is a python extension wrapping the ICU C++ API.")
- (license x11)))
+ (license x11)
+ (properties `((python2-variant . ,(delay python2-pyicu))))))
+
+(define-public python2-pyicu
+ (package
+ (inherit (package-with-python2
+ (strip-python2-variant python-pyicu)))
+ (native-inputs `(("python2-setuptools" ,python2-setuptools)))))
(define-public python2-dogtail
;; Python 2 only, as it leads to "TabError: inconsistent use of tabs and
@@ -4585,67 +4550,6 @@ converts incoming documents to Unicode and outgoing documents to UTF-8.")
(strip-python2-variant python-beautifulsoup4)))
(native-inputs `(("python2-setuptools" ,python2-setuptools)))))
-(define-public python2-pil
- (package
- (name "python2-pil")
- (version "1.1.7")
- (source
- (origin
- (method url-fetch)
- (uri (string-append
- "http://effbot.org/downloads/Imaging-"
- version ".tar.gz"))
- (sha256
- (base32
- "04aj80jhfbmxqzvmq40zfi4z3cw6vi01m3wkk6diz3lc971cfnw9"))
- (modules '((guix build utils)))
- (snippet
- ;; Adapt to newer freetype. As the package is unmaintained upstream,
- ;; there is no use in creating a patch and reporting it.
- '(substitute* "_imagingft.c"
- (("freetype/")
- "freetype2/")))))
- (build-system python-build-system)
- (inputs
- `(("freetype" ,freetype)
- ("libjpeg" ,libjpeg)
- ("libtiff" ,libtiff)
- ("python-setuptools" ,python-setuptools)
- ("zlib" ,zlib)))
- (arguments
- ;; Only the fork python-pillow works with Python 3.
- `(#:python ,python-2
- #:tests? #f ; no check target
- #:phases
- (alist-cons-before
- 'build 'configure
- ;; According to README and setup.py, manual configuration is
- ;; the preferred way of "searching" for inputs.
- ;; lcms is not found, TCL_ROOT refers to the unavailable tkinter.
- (lambda* (#:key inputs #:allow-other-keys)
- (let ((jpeg (assoc-ref inputs "libjpeg"))
- (zlib (assoc-ref inputs "zlib"))
- (tiff (assoc-ref inputs "libtiff"))
- (freetype (assoc-ref inputs "freetype")))
- (substitute* "setup.py"
- (("JPEG_ROOT = None")
- (string-append "JPEG_ROOT = libinclude(\"" jpeg "\")"))
- (("ZLIB_ROOT = None")
- (string-append "ZLIB_ROOT = libinclude(\"" zlib "\")"))
- (("TIFF_ROOT = None")
- (string-append "TIFF_ROOT = libinclude(\"" tiff "\")"))
- (("FREETYPE_ROOT = None")
- (string-append "FREETYPE_ROOT = libinclude(\""
- freetype "\")")))))
- %standard-phases)))
- (home-page "http://www.pythonware.com/products/pil/")
- (synopsis "Python Imaging Library")
- (description "The Python Imaging Library (PIL) adds image processing
-capabilities to the Python interpreter.")
- (license (x11-style
- "file://README"
- "See 'README' in the distribution."))))
-
(define-public python2-cssutils
(package
(name "python2-cssutils")
@@ -4947,20 +4851,19 @@ It is written entirely in Python.")
(define-public python-tornado
(package
(name "python-tornado")
- (version "4.1")
+ (version "4.3")
(source
(origin
(method url-fetch)
- (uri (string-append
- "https://pypi.python.org/packages/source/t/tornado/"
- "tornado-" version ".tar.gz"))
+ (uri (pypi-uri "tornado" version))
(sha256
- (base32 "0a12f00h277zbifibnj46wf14801f573irvf6hwkgja5vspd7awr"))))
+ (base32 "1gzgwayl6hmc9jfcl88bni4jcsk2jcca9dn1rvrfsvnijcjx7hn9"))))
(build-system python-build-system)
(inputs
`(("python-certifi" ,python-certifi)))
(native-inputs
- `(("python-setuptools" ,python-setuptools)))
+ `(("python-backports-abc" ,python-backports-abc)
+ ("python-setuptools" ,python-setuptools)))
(home-page "http://www.tornadoweb.org/")
(synopsis "Python web framework and asynchronous networking library")
(description
@@ -4977,8 +4880,34 @@ connection to each user.")
(inputs
`(("python2-backport-ssl-match-hostname"
,python2-backport-ssl-match-hostname)
+ ("python2-singledispatch", python2-singledispatch)
,@(package-inputs tornado))))))
+;; the python- version can be removed with python-3.5
+(define-public python-backports-abc
+ (package
+ (name "python-backports-abc")
+ (version "0.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "backports_abc" version))
+ (sha256
+ (base32
+ "19fh75lni9pb673n2fn505m1rckm0af0szcv5xx1qm1xpa940glb"))))
+ (build-system python-build-system)
+ (inputs
+ `(("python-setuptools" ,python-setuptools)))
+ (home-page "https://github.com/cython/backports_abc")
+ (synopsis "Backport of additions to the 'collections.abc' module.")
+ (description
+ "Python-backports-abc provides a backport of additions to the
+'collections.abc' module in Python-3.5.")
+ (license psfl)))
+
+(define-public python2-backports-abc
+ (package-with-python2 python-backports-abc))
+
(define-public python-waf
(package
(name "python-waf")
@@ -5831,7 +5760,7 @@ responses, rather than doing any computation.")
(define-public python-cryptography-vectors
(package
(name "python-cryptography-vectors")
- (version "1.2.2")
+ (version "1.2.3")
(source
(origin
(method url-fetch)
@@ -5840,7 +5769,7 @@ responses, rather than doing any computation.")
version ".tar.gz"))
(sha256
(base32
- "1zg47fzzn30mgkkbwrxqqcfq9crgabcmxyiy106n9404wbhfjkkl"))))
+ "0shawgpax79gvjrj0a313sll9gaqys7q1hxngn6j4k24lmz7bwki"))))
(build-system python-build-system)
(native-inputs
`(("python-setuptools" ,python-setuptools)))
@@ -5857,14 +5786,14 @@ responses, rather than doing any computation.")
(define-public python-cryptography
(package
(name "python-cryptography")
- (version "1.2.2")
+ (version "1.2.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cryptography" version))
(sha256
(base32
- "0rvaha7ymgbqkzbxk7xmj67k5b3hbp8w8cn3m5z776vd22wrq89z"))))
+ "0kj511z4g21fhcr649pyzpl0zzkkc7hsgxxjys6z8wwfvmvirccf"))))
(build-system python-build-system)
(inputs
`(("openssl" ,openssl)))
@@ -6819,7 +6748,14 @@ WebSocket usage in Python programs.")
(description "Library for atomic file writes using platform dependent tools
for atomic filesystem operations.")
(home-page "https://github.com/untitaker/python-atomicwrites")
- (license license:expat)))
+ (license license:expat)
+ (properties `((python2-variant . ,(delay python2-atomicwrites))))))
+
+(define-public python2-atomicwrites
+ (package (inherit (package-with-python2
+ (strip-python2-variant python-atomicwrites)))
+ (native-inputs
+ `(("python2-setuptools" ,python2-setuptools)))))
(define-public python-requests-toolbelt
(package
@@ -7520,13 +7456,13 @@ Amazon Web Services (AWS) API.")
(define-public python-hypothesis
(package
(name "python-hypothesis")
- (version "3.0.4")
+ (version "3.1.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "hypothesis" version))
(sha256
(base32
- "0bh6pqyc56cqlbpg0ffzjs6466blyylix4nsw11qrqwf01cg9gdq"))))
+ "0qyqq9akm4vshhn8cngjc1qykcvsn7cz6dlm6njfsgpbraqrmbbw"))))
(build-system python-build-system)
(propagated-inputs
`(("python-flake8" ,python-flake8)
@@ -8256,3 +8192,270 @@ introspection of @code{zope.interface} instances in code.")
(inherit (package-with-python2
(strip-python2-variant python-psycopg2)))
(native-inputs `(("python2-setuptools" ,python2-setuptools)))))
+
+(define-public python-vobject
+ (package
+ (name "python-vobject")
+ (version "0.9.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "vobject" version))
+ (sha256
+ (base32
+ "1cwzjnrdr9yg2x21wbf3kf59ibnchvj33mygd69yzi178a9gs9gz"))))
+ (build-system python-build-system)
+ (inputs
+ `(("python-dateutil-2" ,python-dateutil-2)
+ ("python-pyicu" ,python-pyicu)))
+ (synopsis "Parse and generate vCard and vCalendar files")
+ (description "Vobject is intended to be a full featured Python package for
+parsing and generating vCard and vCalendar files. Currently, iCalendar files
+are supported and well tested. vCard 3.0 files are supported, and all data
+should be imported, but only a few components are understood in a sophisticated
+way.")
+ (home-page "http://eventable.github.io/vobject/")
+ (license asl2.0)
+ (properties `((python2-variant . ,(delay python2-vobject))))))
+
+(define-public python2-vobject
+ (package
+ (inherit (package-with-python2
+ (strip-python2-variant python-vobject)))
+ (native-inputs `(("python2-setuptools" ,python2-setuptools)))))
+
+(define-public python-munkres
+ (package
+ (name "python-munkres")
+ (version "1.0.7")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "munkres" version))
+ (sha256
+ (base32
+ "1i6nf45i0kkzdx6k70giybsqxz4dxsjbrkrfqgjd7znfkf25sjik"))))
+ (build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ; no test suite
+ (home-page "http://software.clapper.org/munkres/")
+ (synopsis "Implementation of the Munkres algorithm")
+ (description "The Munkres module provides an implementation of the Munkres
+algorithm (also called the Hungarian algorithm or the Kuhn-Munkres algorithm),
+useful for solving the Assignment Problem.")
+ (license bsd-3)))
+
+(define-public python2-munkres
+ (package-with-python2 python-munkres))
+
+(define-public python-flask
+ (package
+ (name "python-flask")
+ (version "0.10.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "Flask" version))
+ (sha256
+ (base32
+ "0wrkavjdjndknhp8ya8j850jq7a1cli4g5a93mg8nh1xz2gq50sc"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-itsdangerous" ,python-itsdangerous)
+ ("python-jinja2" ,python-jinja2)
+ ("python-werkzeug" ,python-werkzeug)))
+ (home-page "https://github.com/mitsuhiko/flask/")
+ (synopsis "Microframework based on Werkzeug, Jinja2 and good intentions")
+ (description "Flask is a micro web framework based on the Werkzeug toolkit
+and Jinja2 template engine. It is called a micro framework because it does not
+presume or force a developer to use a particular tool or library.")
+ (license bsd-3)
+ (properties `((python2-variant . ,(delay python2-flask))))))
+
+(define-public python2-flask
+ (package (inherit (package-with-python2
+ (strip-python2-variant python-flask)))
+ (native-inputs `(("python2-setuptools" ,python2-setuptools)))))
+
+(define-public python-cookies
+ (package
+ (name "python-cookies")
+ (version "2.2.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "cookies" version))
+ (sha256
+ (base32
+ "13pfndz8vbk4p2a44cfbjsypjarkrall71pgc97glk5fiiw9idnn"))))
+ (build-system python-build-system)
+ (arguments
+ `(;; test are broken: https://gitlab.com/sashahart/cookies/issues/3
+ #:tests? #f))
+ (native-inputs
+ `(("python-pytest" ,python2-pytest)))
+ (synopsis "HTTP cookie parser and renderer")
+ (description "A RFC 6265-compliant HTTP cookie parser and renderer in
+Python.")
+ (home-page "https://gitlab.com/sashahart/cookies")
+ (license license:expat)
+ (properties `((python2-variant . ,(delay python2-cookies))))))
+
+(define-public python2-cookies
+ (let ((cookies (package-with-python2
+ (strip-python2-variant python-cookies))))
+ (package (inherit cookies)
+ (native-inputs `(("python2-setuptools" ,python2-setuptools)
+ ,@(package-native-inputs cookies))))))
+
+(define-public python-responses
+ (package
+ (name "python-responses")
+ (version "0.5.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "responses" version))
+ (sha256
+ (base32
+ "1spcfxixyk9k7pk82jm6zqkwk031s95lh8q0mz7539jrb7269bcc"))))
+ (build-system python-build-system)
+ (arguments
+ `(;; Test suite is not distributed:
+ ;; https://github.com/getsentry/responses/issues/38
+ #:tests? #f))
+ (native-inputs
+ `(("python-cookies" ,python-cookies)
+ ("python-mock" ,python-mock)))
+ (propagated-inputs
+ `(("python-requests" ,python-requests)
+ ("python-six" ,python-six)))
+ (home-page "https://github.com/getsentry/responses")
+ (synopsis "Utility for mocking out the `requests` Python library")
+ (description "A utility library for mocking out the `requests` Python
+library.")
+ (license asl2.0)
+ (properties `((python2-variant . ,(delay python2-responses))))))
+
+(define-public python2-responses
+ (let ((responses (package-with-python2
+ (strip-python2-variant python-responses))))
+ (package (inherit responses)
+ (native-inputs `(("python2-setuptools" ,python2-setuptools)
+ ,@(package-native-inputs responses))))))
+
+(define-public python-pathlib
+ (package
+ (name "python-pathlib")
+ (version "1.0.1")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "pathlib" version))
+ (sha256
+ (base32
+ "17zajiw4mjbkkv6ahp3xf025qglkj0805m9s41c45zryzj6p2h39"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _ (zero? (system* "python" "./test_pathlib.py")))))))
+ (home-page "https://pathlib.readthedocs.org/")
+ (synopsis "Object-oriented filesystem paths")
+ (description "Pathlib offers a set of classes to handle filesystem paths.
+It offers the following advantages over using string objects:
+
+@enumerate
+@item No more cumbersome use of os and os.path functions. Everything can
+be done easily through operators, attribute accesses, and method calls.
+@item Embodies the semantics of different path types. For example,
+comparing Windows paths ignores casing.
+@item Well-defined semantics, eliminating any inconsistencies or
+ambiguities (forward vs. backward slashes, etc.).
+@end enumerate\n")
+ (license license:expat)))
+
+(define-public python2-pathlib
+ (package-with-python2 python-pathlib))
+
+(define-public python-jellyfish
+ (package
+ (name "python-jellyfish")
+ (version "0.5.3")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "jellyfish" version))
+ (sha256
+ (base32
+ "12bxh8cy9xmvyrjz7aw159nd5pyvb645rkvw4r6bvm4xbvs8gd07"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://github.com/jamesturk/jellyfish")
+ (synopsis "Approximate and phonetic matching of strings")
+ (description "Jellyfish uses a variety of string comparison and phonetic
+encoding algorithms to do fuzzy string matching.")
+ (license bsd-2)
+ (properties `((python2-variant . ,(delay python2-jellyfish))))))
+
+(define-public python2-jellyfish
+ (let ((jellyfish (package-with-python2
+ (strip-python2-variant python-jellyfish))))
+ (package (inherit jellyfish)
+ (native-inputs `(("python2-setuptools" ,python2-setuptools)
+ ("python2-unicodecsv" ,python2-unicodecsv)
+ ,@(package-native-inputs jellyfish))))))
+
+(define-public python2-unicodecsv
+ (package
+ (name "python2-unicodecsv")
+ (version "0.14.1")
+ (source (origin
+ (method url-fetch)
+ ;; The test suite is not included in the PyPi release.
+ ;; https://github.com/jdunck/python-unicodecsv/issues/19
+ (uri (string-append "https://github.com/jdunck/python-unicodecsv/"
+ "archive/" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "087nqanfcyp6mlfbbr5lva5f3w6iz1bybls9xlrb8icmc474wh4w"))))
+ (build-system python-build-system)
+ (arguments
+ `(;; It supports Python 3, but Python 3 can already do Unicode CSV.
+ #:python ,python-2))
+ (native-inputs
+ `(("python2-setuptools" ,python2-setuptools)
+ ("python2-unittest2" ,python2-unittest2)))
+ (home-page "https://github.com/jdunck/python-unicodecsv")
+ (synopsis "Unicode CSV module for Python 2")
+ (description "Unicodecsv is a drop-in replacement for Python 2.7's CSV
+module, adding support for Unicode strings.")
+ (license bsd-2)))
+
+(define-public python-rarfile
+ (package
+ (name "python-rarfile")
+ (version "2.7")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "rarfile" version))
+ (sha256
+ (base32
+ "0d8n1dlpiz7av8dmbp0vclrwl9cnxizr4f2c9xvj1h5nvn480527"))
+ ;; https://github.com/markokr/rarfile/pull/17/
+ (patches (list (search-patch "python-rarfile-fix-tests.patch")))))
+ (build-system python-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ ;; Many tests fail, but the installation proceeds.
+ (lambda _ (zero? (system* "make" "-C" "test" "test")))))))
+ (native-inputs
+ `(("which" ,which))) ; required for tests
+ (propagated-inputs
+ `(("libarchive" ,libarchive)))
+ (home-page "https://github.com/markokr/rarfile")
+ (synopsis "RAR archive reader for Python")
+ (description "This is Python module for RAR archive reading. The interface
+is made as zipfile like as possible.")
+ (license isc)))
+
+(define-public python2-rarfile
+ (package-with-python2 python-rarfile))