diff options
Diffstat (limited to 'gnu/packages/python.scm')
| -rw-r--r-- | gnu/packages/python.scm | 389 |
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))) |