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-rw-r--r--gnu/packages/python.scm389
1 files changed, 364 insertions, 25 deletions
diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 5a1f3ed229..96a0e81a2c 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -54,6 +54,7 @@
;;; Copyright © 2018 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2018 Oleg Pykhalov <go.wigust@gmail.com>
;;; Copyright © 2018 Clément Lassieur <clement@lassieur.org>
+;;; Copyright © 2018 Maxim Cournoyer <maxim.cournoyer@gmail.com>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -1519,14 +1520,14 @@ backported for previous versions of Python from 2.4 to 3.3.")
(define-public python-parse
(package
(name "python-parse")
- (version "1.8.2")
+ (version "1.8.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "parse" version))
(sha256
(base32
- "1lj9v1q4imszyhvipb6drsm3xdl35nan011mqxxas1yaypixsj40"))))
+ "0f8997xr8nq2nq35iiviq8ningd1zvy59fg503xfpbi2dwhgdkf3"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -1536,7 +1537,7 @@ backported for previous versions of Python from 2.4 to 3.3.")
(home-page "https://github.com/r1chardj0n3s/parse")
(synopsis "Parse strings")
(description
- "Parse strings using a specification based on the Python format()
+ "Parse strings using a specification based on the Python @code{format()}
syntax.")
(license license:x11)))
@@ -2627,6 +2628,62 @@ which can produce feeds in RSS 2.0, RSS 0.91, and Atom formats.")
(define-public python2-feedgenerator
(package-with-python2 python-feedgenerator))
+(define-public python-toml
+ (package
+ (name "python-toml")
+ (version "0.9.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "toml" version))
+ (sha256
+ (base32
+ "0bdbpbip67wdm6c7xwc6mmbmskyradj4cdxn1iibj4fcx1nbv1lf"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f)) ;no tests suite in release
+ (home-page "https://github.com/uiri/toml")
+ (synopsis "Library for TOML")
+ (description
+ "@code{toml} is a library for parsing and creating Tom's Obvious, Minimal
+Language (TOML) configuration files.")
+ (license license:expat)))
+
+(define-public python-black
+ (package
+ (name "python-black")
+ (version "18.6b4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "black" version))
+ (sha256
+ (base32
+ "0i4sfqgz6w15vd50kbhi7g7rifgqlf8yfr8y78rypd56q64qn592"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'patch-source-shebangs 'patch-extra-shebangs
+ (lambda _
+ (let ((python3 (which "python3")))
+ (substitute* '("tests/data/fmtonoff.py"
+ "tests/data/string_prefixes.py"
+ "tests/data/function.py")
+ (("#!/usr/bin/env python3(\\.[0-9]+)?" _ minor-version)
+ (string-append "#!" python3 (if (string? minor-version)
+ minor-version
+ ""))))))))))
+ (propagated-inputs
+ `(("python-click" ,python-click)
+ ("python-attrs" ,python-attrs)
+ ("python-appdirs" ,python-appdirs)
+ ("python-toml" ,python-toml)))
+ (home-page "https://github.com/ambv/black")
+ (synopsis "The uncompromising code formatter")
+ (description "Black is the uncompromising Python code formatter.")
+ (license license:expat)))
+
(define-public python-blinker
(package
(name "python-blinker")
@@ -5061,13 +5118,13 @@ Python.")
(define-public snakemake
(package
(name "snakemake")
- (version "5.2.0")
+ (version "5.2.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "snakemake" version))
(sha256
- (base32 "0a1i5v5qxbmmpznp7my9nva8y7pxp8pjrwk2gxgisdskg35sq8s1"))))
+ (base32 "18x36n78ph5v1fxk54gvdbc3d8nfncha78phifg3lqaa9gifgzxd"))))
(build-system python-build-system)
(arguments
;; TODO: Package missing test dependencies.
@@ -5096,7 +5153,7 @@ Python.")
("python-networkx" ,python-networkx)
("python-pyyaml" ,python-pyyaml)
("python-ratelimiter" ,python-ratelimiter)))
- (home-page "https://bitbucket.org/snakemake/snakemake/wiki/Home")
+ (home-page "https://snakemake.readthedocs.io")
(synopsis "Python-based execution environment for make-like workflows")
(description
"Snakemake aims to reduce the complexity of creating workflows by
@@ -6455,7 +6512,7 @@ Python Package Index (PyPI).")
(define-public python-tlsh
(package
(name "python-tlsh")
- (version "3.4.4")
+ (version "3.4.5")
(home-page "https://github.com/trendmicro/tlsh")
(source (origin
(method url-fetch)
@@ -6463,7 +6520,7 @@ Python Package Index (PyPI).")
version ".tar.gz"))
(sha256
(base32
- "00bhzjqrlh7v538kbkbn8lgx976j1138al3sdhklaizqjvpwyk4r"))
+ "1x1vahd4zg5kpyr9h9hs3fvh460p25rjy4cclwdnbbw8x3vc30q3"))
(file-name (string-append name "-" version ".tar.gz"))))
(build-system cmake-build-system)
(arguments
@@ -6524,13 +6581,13 @@ a hash value.")
(define-public python-libarchive-c
(package
(name "python-libarchive-c")
- (version "2.2")
+ (version "2.8")
(source (origin
(method url-fetch)
(uri (pypi-uri "libarchive-c" version))
(sha256
(base32
- "0z4r7v3dhd6b3120mav05ff08srih176r2rg5k8kn7mjd9pslm2x"))))
+ "0qg0v1s9c1xdk9philhnv8k6c6nicvnvfwlc0j9srg90jmdlvm06"))))
(build-system python-build-system)
(arguments
'(#:phases (modify-phases %standard-phases
@@ -6542,7 +6599,12 @@ a hash value.")
(substitute* "libarchive/ffi.py"
(("find_library\\('archive'\\)")
(string-append "'" libarchive
- "/lib/libarchive.so'")))))))))
+ "/lib/libarchive.so'"))))))
+ (replace 'check
+ (lambda _ (invoke "pytest" "-vv"))))))
+ (native-inputs
+ `(("python-mock" ,python-mock)
+ ("python-pytest" ,python-pytest)))
(inputs
`(("libarchive" ,libarchive)))
(home-page "https://github.com/Changaco/python-libarchive-c")
@@ -6589,6 +6651,7 @@ serve the same purpose: provide Python bindings for libmagic.")))
(define-public python-debian
(package
(name "python-debian")
+ (home-page "https://salsa.debian.org/python-debian-team/python-debian")
(version "0.1.28")
(source
(origin
@@ -6600,7 +6663,6 @@ serve the same purpose: provide Python bindings for libmagic.")))
(build-system python-build-system)
(propagated-inputs
`(("python-six" ,python-six)))
- (home-page "http://packages.debian.org/sid/python-debian")
(synopsis "Debian package related modules")
(description
;; XXX: Use @enumerate instead of @itemize to work around
@@ -9543,14 +9605,14 @@ characters, mouse support, and auto suggestions.")
(define-public python-jedi
(package
(name "python-jedi")
- (version "0.12.0")
+ (version "0.12.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "jedi" version))
(sha256
(base32
- "1bcr7csx4xil1iwmk03d79jis0bkmgi9k0kir3xa4rmwqsagcwhr"))))
+ "1h8ypnjisn57kiv1zqrkj1im6sbfnhxllqaa8znh39qkd47ys2dl"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -9559,14 +9621,18 @@ characters, mouse support, and auto suggestions.")
(invoke "py.test" "-vv"))))))
(native-inputs
`(("python-pytest" ,python-pytest)
- ("python-parso" ,python-parso)
("python-docopt" ,python-docopt)))
+ (propagated-inputs
+ `(("python-parso" ,python-parso)))
(home-page "https://github.com/davidhalter/jedi")
- (synopsis
- "Autocompletion for Python that can be used for text editors")
+ (synopsis "Autocompletion and static analysis library for Python")
(description
- "Jedi is an autocompletion tool for Python that can be used for text
- editors.")
+ "Jedi is a static analysis tool for Python that can be used in Integrated
+Development Environments (@dfn{IDE}s) and text editors. It understands Python
+on a deeper level than many other static analysis frameworks for Python.
+
+Jedi understands docstrings and you can use Jedi autocompletion in your REPL as
+well.")
(license license:expat)))
(define-public python2-jedi
@@ -9745,13 +9811,13 @@ hardware-accelerated multitouch applications.")
(define-public python-binaryornot
(package
(name "python-binaryornot")
- (version "0.4.0")
+ (version "0.4.4")
(source (origin
(method url-fetch)
(uri (pypi-uri "binaryornot" version))
(sha256
(base32
- "1j4f51dxic39mdwf6alj7gd769wy6mhk916v031wjali51xkh3xb"))))
+ "0qc006986rb6bcbmiymwgcl1mns2jphr1j7sr7nk41nlr7gh359m"))))
(build-system python-build-system)
(propagated-inputs
`(("python-chardet" ,python-chardet)
@@ -13169,14 +13235,14 @@ source bytes using the UTF-8 encoding and then rewrites Python 3.6 style
(define-public python-typing
(package
(name "python-typing")
- (version "3.6.4")
+ (version "3.6.6")
(source
(origin
(method url-fetch)
(uri (pypi-uri "typing" version))
(sha256
(base32
- "1wmk9nkh30n37cbrqwkbggmj2390lhrlagjkd0ikm02l88saj06l"))))
+ "0ba9acs4awx15bf9v3nrs781msbd2nx826906nj6fqks2bvca9s0"))))
(build-system python-build-system)
(home-page "https://docs.python.org/3/library/typing.html")
(synopsis "Type hints for Python")
@@ -13449,14 +13515,14 @@ time-based (TOTP) passwords.")
(define-public python-parso
(package
(name "python-parso")
- (version "0.2.1")
+ (version "0.3.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "parso" version))
(sha256
(base32
- "0zvh4rdhv2wkglkgh0h9kn9ndpsw5p639wcwv47jn1kfp504lq7h"))))
+ "18p89iwcm8mnf380f92g9w0bhx5km8wxp392vvjcq4y1ld1llw1m"))))
(native-inputs
`(("python-pytest" ,python-pytest)))
(build-system python-build-system)
@@ -13953,3 +14019,276 @@ scalable way of keeping track of data together with learned annotations and
reduces the code overhead typically encountered when using a mostly
object-oriented library such as @code{scikit-learn}.")
(license license:bsd-3)))
+
+(define-public python-dill
+ (package
+ (name "python-dill")
+ (version "0.2.8.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "dill" version))
+ (sha256
+ (base32
+ "1cymzn9fxwdy33h21zkk4gqgzvd25110hh3zdqnvnwa3p52c4kb2"))))
+ (build-system python-build-system)
+ ;; FIXME: The check phase fails with "don't know how to make test".
+ (arguments '(#:tests? #f))
+ (home-page "https://pypi.org/project/dill")
+ (synopsis "Serialize all of Python")
+ (description "Dill extends Python's @code{pickle} module for serializing
+and de-serializing Python objects to the majority of the built-in Python
+types. Dill provides the user the same interface as the @code{pickle} module,
+and also includes some additional features. In addition to pickling Python
+objects, @code{dill} provides the ability to save the state of an interpreter
+session in a single command. Hence, it would be feasable to save a
+interpreter session, close the interpreter, ship the pickled file to another
+computer, open a new interpreter, unpickle the session and thus continue from
+the saved state of the original interpreter session.")
+ (license license:bsd-3)))
+
+(define-public python-multiprocess
+ (package
+ (name "python-multiprocess")
+ (version "0.70.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "multiprocess" version))
+ (sha256
+ (base32
+ "1ip5caz67b3q0553mr8gm8xwsb8x500jn8ml0gihgyfy52m2ypcq"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-dill" ,python-dill)))
+ (home-page "https://pypi.org/project/multiprocess")
+ (synopsis "Multiprocessing and multithreading in Python")
+ (description
+ "This package is a fork of the multiprocessing Python package, a package
+which supports the spawning of processes using the API of the standard
+library's @code{threading} module.")
+ (license license:bsd-3)))
+
+(define-public python-toolz
+ (package
+ (name "python-toolz")
+ (version "0.9.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "toolz" version))
+ (sha256
+ (base32
+ "1j9i7fdjnx9dz35fdj5gvgxx6585ja9sxgaiv65if77nlxz0m7wj"))))
+ (build-system python-build-system)
+ ;; FIXME: tests cannot be computed: "Can't perform this operation for
+ ;; unregistered loader type"
+ (arguments '(#:tests? #f))
+ (home-page "https://github.com/pytoolz/toolz/")
+ (synopsis "List processing tools and functional utilities")
+ (description
+ "This package provides a set of utility functions for iterators,
+functions, and dictionaries.")
+ (license license:bsd-3)))
+
+(define-public python-cytoolz
+ (package
+ (name "python-cytoolz")
+ (version "0.9.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "cytoolz" version))
+ (sha256
+ (base32
+ "1r80p88hm3f3r4zpixzr047y5hw4bzy41m4xywnhycda83x0dk44"))))
+ (build-system python-build-system)
+ ;; FIXME: tests fail with "module 'cytoolz.curried' has no attribute
+ ;; 'exceptions'"
+ (arguments '(#:tests? #f))
+ (propagated-inputs
+ `(("python-toolz" ,python-toolz)))
+ (native-inputs
+ `(("python-cython" ,python-cython)))
+ (home-page "https://github.com/pytoolz/cytoolz")
+ (synopsis "High performance functional utilities")
+ (description
+ "The cytoolz package implements the same API as provided by toolz. The
+main differences are that @code{cytoolz} is faster and cytoolz offers a C API
+that is accessible to other projects developed in Cython.")
+ (license license:bsd-3)))
+
+(define-public python-sortedcontainers
+ (package
+ (name "python-sortedcontainers")
+ (version "2.0.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "sortedcontainers" version))
+ (sha256
+ (base32
+ "10hrk2k0hbf9x78vd3f0lj277m1yzfhzzxr0hja718liwb398wk0"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-tox" ,python-tox)))
+ (home-page "http://www.grantjenks.com/docs/sortedcontainers/")
+ (synopsis "Sorted List, Sorted Dict, Sorted Set")
+ (description
+ "This package provides a sorted collections library, written in
+pure-Python.")
+ (license license:asl2.0)))
+
+(define-public python-cloudpickle
+ (package
+ (name "python-cloudpickle")
+ (version "0.5.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "cloudpickle" version))
+ (sha256
+ (base32
+ "0gdg5n025v4wqmdg65rm0n6fvp6731ip30ji0rmn2kqsyr4bb93f"))))
+ (build-system python-build-system)
+ ;; FIXME: there are 5 errors in 122 tests:
+ ;; ERROR: test_function_pickle_compat_0_4_0 (tests.cloudpickle_test.CloudPickleTest)
+ ;; ERROR: test_function_pickle_compat_0_4_1 (tests.cloudpickle_test.CloudPickleTest)
+ ;; ERROR: test_function_pickle_compat_0_4_0 (tests.cloudpickle_test.Protocol2CloudPickleTest)
+ ;; ERROR: test_function_pickle_compat_0_4_1 (tests.cloudpickle_test.Protocol2CloudPickleTest)
+ ;; ERROR: test_temp_file (tests.cloudpickle_file_test.CloudPickleFileTests)
+ ;; TypeError: cannot serialize '_io.BufferedRandom' object
+ (arguments '(#:tests? #f))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)
+ ("python-mock" ,python-mock)
+ ("python-tornado" ,python-tornado)))
+ (home-page "https://github.com/cloudpipe/cloudpickle")
+ (synopsis "Extended pickling support for Python objects")
+ (description
+ "Cloudpickle makes it possible to serialize Python constructs not
+supported by the default pickle module from the Python standard library. It
+is especially useful for cluster computing where Python expressions are
+shipped over the network to execute on remote hosts, possibly close to the
+data.")
+ (license license:bsd-3)))
+
+(define-public python-locket
+ (package
+ (name "python-locket")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "locket" version))
+ (sha256
+ (base32
+ "1d4z2zngrpqkrfhnd4yhysh66kjn4mblys2l06sh5dix2p0n7vhz"))))
+ (build-system python-build-system)
+ (home-page "https://github.com/mwilliamson/locket.py")
+ (synopsis "File-based locks for Python")
+ (description
+ "Locket implements a lock that can be used by multiple processes provided
+they use the same path.")
+ (license license:bsd-2)))
+
+(define-public python-blosc
+ (package
+ (name "python-blosc")
+ (version "1.5.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "blosc" version))
+ (sha256
+ (base32
+ "1cm91c6r431yla2mbs4895bgiianjf30dfz14vvv99dslygd65jw"))))
+ (build-system python-build-system)
+ ;; FIXME: all tests pass, but then this error is printed:
+ ;; TypeError: calling <function run at 0x7ffff2568d90> returned None, not a test
+ (arguments '(#:tests? #f))
+ (propagated-inputs
+ `(("python-numpy" ,python-numpy)))
+ (home-page "https://github.com/blosc/python-blosc")
+ (synopsis "Python wrapper for the Blosc data compressor library")
+ (description "Blosc is a high performance compressor optimized for binary
+data. It has been designed to transmit data to the processor cache faster
+than the traditional, non-compressed, direct memory fetch approach via a
+@code{memcpy()} system call.
+
+Blosc works well for compressing numerical arrays that contains data with
+relatively low entropy, like sparse data, time series, grids with
+regular-spaced values, etc.
+
+This Python package wraps the Blosc library.")
+ (license license:bsd-3)))
+
+(define-public python-partd
+ (package
+ (name "python-partd")
+ (version "0.3.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "partd" version))
+ (sha256
+ (base32
+ "03s0i5qfgkx6y24bmfgyd5hnsjznkbbfafwb2khf7k9790f1yab7"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-blosc" ,python-blosc)
+ ("python-locket" ,python-locket)
+ ("python-numpy" ,python-numpy)
+ ("python-pandas" ,python-pandas)
+ ("python-pyzmq" ,python-pyzmq)
+ ("python-toolz" ,python-toolz)))
+ (home-page "https://github.com/dask/partd/")
+ (synopsis "Appendable key-value storage")
+ (description "Partd stores key-value pairs. Values are raw bytes. We
+append on old values. Partd excels at shuffling operations.")
+ (license license:bsd-3)))
+
+(define-public python-dask
+ (package
+ (name "python-dask")
+ (version "0.19.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "dask" version))
+ (sha256
+ (base32
+ "1pm1163qb6s22p8fnvj0zlfazihvs7hxjn8l2n52bzs7shw6kdz3"))))
+ (build-system python-build-system)
+ ;; A single test out of 5000+ fails. This test is marked as xfail when
+ ;; pytest-xdist is used.
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'disable-broken-test
+ (lambda _
+ (substitute* "dask/tests/test_threaded.py"
+ (("def test_interrupt\\(\\)" m)
+ (string-append "@pytest.mark.skip(reason=\"Disabled by Guix\")\n"
+ m)))
+ #t)))))
+ (propagated-inputs
+ `(("python-cloudpickle" ,python-cloudpickle)
+ ("python-numpy" ,python-numpy)
+ ("python-pandas" ,python-pandas)
+ ("python-partd" ,python-partd)
+ ("python-toolz" ,python-toolz)
+ ("python-pyyaml" ,python-pyyaml)))
+ (native-inputs
+ `(("python-pytest" ,python-pytest)
+ ("python-pytest-runner" ,python-pytest-runner)))
+ (home-page "https://github.com/dask/dask/")
+ (synopsis "Parallel computing with task scheduling")
+ (description
+ "Dask is a flexible parallel computing library for analytics. It
+consists of two components: dynamic task scheduling optimized for computation,
+and large data collections like parallel arrays, dataframes, and lists that
+extend common interfaces like NumPy, Pandas, or Python iterators to
+larger-than-memory or distributed environments. These parallel collections
+run on top of the dynamic task schedulers. ")
+ (license license:bsd-3)))
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