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-rw-r--r--gnu/packages/python-xyz.scm704
1 files changed, 550 insertions, 154 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 8137d665fd..d2786e4826 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -38,7 +38,7 @@
;;; Copyright © 2017 Frederick M. Muriithi <fredmanglis@gmail.com>
;;; Copyright © 2017, 2018 Adriano Peluso <catonano@gmail.com>
;;; Copyright © 2017 Ben Sturmfels <ben@sturm.com.au>
-;;; Copyright © 2017, 2018 Mathieu Othacehe <m.othacehe@gmail.com>
+;;; Copyright © 2017, 2018, 2019 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2017 José Miguel Sánchez García <jmi2k@openmailbox.org>
;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
;;; Copyright © 2017, 2018 Kei Kebreau <kkebreau@posteo.net>
@@ -66,6 +66,7 @@
;;; Copyright © 2019 Jacob MacDonald <jaccarmac@gmail.com>
;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
+;;; Copyright © 2019 Tanguy Le Carrour <tanguy@bioneland.org>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -165,14 +166,13 @@
(define-public python-psutil
(package
(name "python-psutil")
- (version "5.6.2")
+ (version "5.6.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "psutil" version))
(sha256
- (base32
- "1v95vb5385qscfdvphv8l2w22bmir3d7yhpi02n58v3mlqy1r3l2"))))
+ (base32 "0isil5jxwwd8awz54qk28rpgjg43i5l6yl70g40vxwa4r4m56lfh"))))
(build-system python-build-system)
(arguments
;; FIXME: some tests does not return and times out.
@@ -548,14 +548,13 @@ concepts.")
(define-public python-cftime
(package
(name "python-cftime")
- (version "1.0.3.4")
+ (version "1.0.4.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cftime" version))
(sha256
- (base32
- "0362dhxbzk593walyjz30dll6y2y79wialik647cbwdsf3ad0x6x"))))
+ (base32 "0w0gi6jnch38hiygl62j4xkcirv4y3dcwrvxl9p7bsk6j27lzihs"))))
(build-system python-build-system)
(propagated-inputs
`(("python-numpy" ,python-numpy)))
@@ -909,10 +908,18 @@ some helpful Python 2 compatibility convenience methods.")
(base32
"09z4d1jiasn7k1hs5af2ckmnrd0i1d1m04bhfjhv7z6svzfdwgg3"))))
(build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ ;; Do not run pylint plugin test, as astroid is an old
+ ;; unsupported version.
+ (invoke "pytest" "-v" "-k" "not test_pylint_plugin"
+ "verboselogs/tests.py"))))))
(native-inputs
`(("python-mock" ,python-mock)
- ("python-astroid" ,python-astroid)
- ("python-pylint" ,python-pylint)))
+ ("python-pytest" ,python-pytest)))
(home-page "https://verboselogs.readthedocs.io")
(synopsis "Verbose logging level for Python's logging module")
(description
@@ -926,14 +933,14 @@ add the log levels NOTICE, SPAM, SUCCESS and VERBOSE.")
(define-public python-coloredlogs
(package
(name "python-coloredlogs")
- (version "7.3")
+ (version "10.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "coloredlogs" version))
(sha256
(base32
- "1blcann6dyg5dhps9pg12rn0q0rjrlajpmmil0gy0j4cbvnl2il9"))))
+ "0dkw6xp0r1dwgz4s2f58npx5nxfq51wf4l6qkm5ib27slgfs4sdq"))))
(build-system python-build-system)
(arguments
`(;Tests require some updated modules
@@ -1150,13 +1157,13 @@ human-friendly syntax.")
(define-public python-pandas
(package
(name "python-pandas")
- (version "0.24.2")
+ (version "0.25.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pandas" version))
(sha256
- (base32 "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag"))))
+ (base32 "1gp2pvzdiakvgjmykdzdlzrsfbg4vjm49jjdl9s0ha0a3yfs34fa"))))
(build-system python-build-system)
(arguments
`(#:modules ((guix build utils)
@@ -1219,10 +1226,22 @@ structures designed to make working with structured (tabular,
multidimensional, potentially heterogeneous) and time series data both easy
and intuitive. It aims to be the fundamental high-level building block for
doing practical, real world data analysis in Python.")
+ (properties `((python2-variant . ,(delay python2-pandas))))
(license license:bsd-3)))
+;; Pandas 0.24.x are the last versions that support Python 2.
(define-public python2-pandas
- (package-with-python2 python-pandas))
+ (let ((pandas (package-with-python2
+ (strip-python2-variant python-pandas))))
+ (package/inherit
+ pandas
+ (version "0.24.2")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "pandas" version))
+ (sha256
+ (base32
+ "18imlm8xbhcbwy4wa957a1fkamrcb0z988z006jpfda3ki09z4ag")))))))
(define-public python2-mechanize
(package
@@ -1571,6 +1590,27 @@ existing ones.")
;; Tests don't work with python2.
#:tests? #f)))))
+(define-public python-poyo
+ (package
+ (name "python-poyo")
+ (version "0.5.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "poyo" version))
+ (sha256
+ (base32
+ "1pflivs6j22frz0v3dqxnvc8yb8fb52g11lqr88z0i8cg2m5csg2"))))
+ (build-system python-build-system)
+ (home-page "https://github.com/hackebrot/poyo")
+ (synopsis "Lightweight YAML Parser for Python")
+ (description
+ "This package provides a lightweight YAML Parser for Python. It supports
+only a chosen subset of the YAML format that is required to parse cookiecutter
+user configuration files. It does not have support for serializing into YAML
+and is not compatible with JSON.")
+ (license license:expat)))
+
(define-public scons
(package
(name "scons")
@@ -1894,13 +1934,13 @@ files.")
(define-public python-pyld
(package
(name "python-pyld")
- (version "1.0.3")
+ (version "1.0.5")
(source (origin
(method url-fetch)
(uri (pypi-uri "PyLD" version))
(sha256
(base32
- "12i2g6xdj30k7xxcibg3sc5y76snwq8l6n8fy9lyi577kgy0h2pm"))))
+ "1ywbdbsrkg533qh8xn9ifjh2mvam6v5msrjyqq73jfpvcp89qvff"))))
(build-system python-build-system)
(home-page "https://github.com/digitalbazaar/pyld")
(synopsis "Python implementation of the JSON-LD specification")
@@ -2173,13 +2213,13 @@ cutting and pasting that code over and over.")
(define-public python-unidecode
(package
(name "python-unidecode")
- (version "1.1.0")
+ (version "1.1.1")
(source (origin
(method url-fetch)
(uri (pypi-uri "Unidecode" version))
(sha256
(base32
- "00pi0czzwvbf7djhkkjyvimj60wqdx0llbddzfnax650g9b8yscc"))))
+ "1s6cp2lv4m0f00hjckjz8p6m7d3n3v16jvg353llf5ia1iqsnsib"))))
(build-system python-build-system)
(home-page "https://pypi.python.org/pypi/Unidecode")
(synopsis "ASCII transliterations of Unicode text")
@@ -2495,6 +2535,30 @@ written in pure Python.")
(define-public python2-jinja2
(package-with-python2 python-jinja2))
+(define-public python-jinja2-time
+ (package
+ (name "python-jinja2-time")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "jinja2-time" version))
+ (sha256
+ (base32
+ "0h0dr7cfpjnjj8bgl2vk9063a53649pn37wnlkd8hxjy656slkni"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-arrow" ,python-arrow)
+ ("python-jinja2" ,python-jinja2)))
+ (home-page
+ "https://github.com/hackebrot/jinja2-time")
+ (synopsis "Jinja2 Extension for Dates and Times")
+ (description
+ "This package provides an extension for the template engine Jinja2. It
+adds a 'now' tag providing a convenient access to the arrow.now() API from
+templates. A format string can be provided to control the output.")
+ (license license:expat)))
+
(define-public python-pystache
(package
(name "python-pystache")
@@ -2714,7 +2778,7 @@ to deprecate classes, functions or methods.")
(define-public python-pygithub
(package
(name "python-pygithub")
- (version "1.43.7")
+ (version "1.43.8")
(source
;; We fetch from the Git repo because there are no tests in the PyPI
;; archive.
@@ -2725,8 +2789,7 @@ to deprecate classes, functions or methods.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32
- "0ww92zz0ja9w6rw83vphmn8rwmcn6abg16j4q7zxjc0rrg2cfj9i"))))
+ (base32 "1625v558xga5mwhl9jqmibywy5qafmg1vqrirqz6zfq1la1d22mw"))))
(build-system python-build-system)
(arguments
`(#:phases (modify-phases %standard-phases
@@ -2947,14 +3010,13 @@ receive files via the SCP1 protocol, as implemented by the OpenSSH
(define-public python-rst.linker
(package
(name "python-rst.linker")
- (version "1.10")
+ (version "1.11")
(source
(origin
(method url-fetch)
(uri (pypi-uri "rst.linker" version))
(sha256
- (base32
- "0iqaacp7pj1s8avs4kc0qg0r7dscywaq37y6l9j14glqdikk0wdj"))))
+ (base32 "0pqsfqqx8h0pq21k8l3k62kznrgaj2ala93c64s4d9rpbr4mgkd2"))))
(build-system python-build-system)
(propagated-inputs
`(("python-dateutil" ,python-dateutil)
@@ -3075,44 +3137,39 @@ Language (TOML) configuration files.")
Server (PLS).")
(license license:expat)))
-;; XXX: We must use a non-release version since the latest release version
-;; requires python-jedi version < 0.15.
(define-public python-language-server
- (let ((commit "c3cab77a85b1de4af1aec1bafea6a7320d6baec5")
- (revision "1"))
- (package
- (name "python-language-server")
- (version (git-version "0.28.3" revision commit))
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/palantir/python-language-server.git")
- (commit commit)))
- (sha256
- (base32
- "1q0xdwgln09sh58j0ryygj92hfgdhwcs57zjvqihya23jr5v0bz4"))))
- (build-system python-build-system)
- (propagated-inputs
- `(("python-pluggy" ,python-pluggy)
- ("python-jsonrpc-server" ,python-jsonrpc-server)
- ("python-jedi" ,python-jedi)
- ("python-yapf" ,python-yapf)
- ("python-pyflakes" ,python-pyflakes)
- ("python-pydocstyle" ,python-pydocstyle)
- ("python-pycodestyle" ,python-pycodestyle)
- ("python-mccabe" ,python-mccabe)
- ("python-rope" ,python-rope)
- ("python-autopep8" ,python-autopep8)
- ("python-pylint" ,python-pylint)))
- (home-page "https://github.com/palantir/python-language-server")
- (synopsis "Python implementation of the Language Server Protocol")
- (description
- "The Python Language Server (pyls) is an implementation of the Python 3
+ (package
+ (name "python-language-server")
+ (version "0.29.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "python-language-server" version))
+ (sha256
+ (base32
+ "1f8qlflh6j3s7qfmzhirpl8fgidl6f0qbakdmiml96wdxzvka0s3"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-pluggy" ,python-pluggy)
+ ("python-jsonrpc-server" ,python-jsonrpc-server)
+ ("python-jedi" ,python-jedi)
+ ("python-yapf" ,python-yapf)
+ ("python-pyflakes" ,python-pyflakes)
+ ("python-pydocstyle" ,python-pydocstyle)
+ ("python-pycodestyle" ,python-pycodestyle)
+ ("python-mccabe" ,python-mccabe)
+ ("python-rope" ,python-rope)
+ ("python-autopep8" ,python-autopep8)
+ ("python-flake8" ,python-flake8)
+ ("python-pylint" ,python-pylint)))
+ (home-page "https://github.com/palantir/python-language-server")
+ (synopsis "Python implementation of the Language Server Protocol")
+ (description
+ "The Python Language Server (pyls) is an implementation of the Python 3
language specification for the Language Server Protocol (LSP). This tool is
used in text editing environments to provide a complete and integrated
feature-set for programming Python effectively.")
- (license license:expat))))
+ (license license:expat)))
(define-public python-black
(package
@@ -3405,7 +3462,7 @@ between language specification and implementation aspects.")
(define-public python-numpy
(package
(name "python-numpy")
- (version "1.15.4")
+ (version "1.17.3")
(source
(origin
(method url-fetch)
@@ -3414,7 +3471,7 @@ between language specification and implementation aspects.")
version "/numpy-" version ".tar.gz"))
(sha256
(base32
- "102vcl2qq4pjbm7a3d67vkkvn4466ngia1d8wi5avqwqh8j0jvkn"))))
+ "1ak9dmjja0q90a7fsxli51ypcwssh8c4pb6f8wkrsnf2xgdk6dy9"))))
(build-system python-build-system)
(inputs
`(("openblas" ,openblas)
@@ -3479,10 +3536,24 @@ 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.")
+ (properties `((python2-variant . ,(delay python2-numpy))))
(license license:bsd-3)))
+;; Numpy 1.16.x are the last versions that support Python 2.
(define-public python2-numpy
- (package-with-python2 python-numpy))
+ (let ((numpy (package-with-python2
+ (strip-python2-variant python-numpy))))
+ (package/inherit
+ numpy
+ (version "1.16.5")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/numpy/numpy/releases/download/v"
+ version "/numpy-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0lg1cycxzi4rvvrd5zxinpdz0ni792fpx6xjd75z1923zcac8qrb")))))))
;; 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
@@ -3892,7 +3963,7 @@ To address this and enable easy cycling over arbitrary @code{kwargs}, the
(define-public python-colorspacious
(package
(name "python-colorspacious")
- (version "1.1.0")
+ (version "1.1.2")
(source
(origin
(method git-fetch)
@@ -3901,7 +3972,7 @@ To address this and enable easy cycling over arbitrary @code{kwargs}, the
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0g0lxqiscy5g5rq9421vv7abg0c90jzy0zmas2z3hya6k2dr5aid"))))
+ (base32 "0x7nkphr6g5ql5fvgss8l56rgiyjgh6fm8zzs73i94ci9wzlm63w"))))
(build-system python-build-system)
(propagated-inputs
`(("python-numpy" ,python-numpy)))
@@ -4238,14 +4309,13 @@ operators such as union, intersection, and difference.")
(define-public python-scipy
(package
(name "python-scipy")
- (version "1.3.1")
+ (version "1.3.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "scipy" version))
(sha256
- (base32
- "1df113c9i6vazsn6y3n9wc22jh737z1g7dmx3mypkdwpdnscyhr6"))))
+ (base32 "192d8dsybvhv19igkrsafbdafx198nz7pibkjgrqjhlr66s3jfd0"))))
(build-system python-build-system)
(propagated-inputs
`(("python-numpy" ,python-numpy)
@@ -4383,6 +4453,35 @@ as the original project seems to have been abandoned circa 2007.")
(define-public python2-socksipy-branch
(package-with-python2 python-socksipy-branch))
+(define-public python-socksipychain
+ (package
+ (name "python-socksipychain")
+ (version "2.0.15")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pagekite/PySocksipyChain.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1pkljnh9hfwla8sg7mil4f9zrnsqj0dbhr3crxjw3k8dnjz70dvk"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f)) ; Tests try to access the network.
+ (home-page "http://pagekite.net/wiki/Floss/PySocksipyChain/")
+ (synopsis "Python SOCKS module with chained proxies support")
+ (description
+ "SocksiPyChain is a modified version of the SocksiPy SOCKS module, which
+adds support for arbitrary chaining of proxy servers and various modes of
+TLS/SSL encryption. It was developed for use in PageKite, and also includes
+a simple netcat replacement with chaining support.")
+ (license license:bsd-3)))
+
+(define-public python2-socksipychain
+ (package-with-python2 python-socksipychain))
+
(define-public python-pycodestyle
(package
(name "python-pycodestyle")
@@ -5071,6 +5170,18 @@ child application and control it as if a human were typing commands.")
them as the version argument or in a SCM managed file.")
(license license:expat)))
+;; Needed by python-lazy-object-proxy, remove on next update cycle.
+(define-public python-setuptools-scm-3.3
+ (package
+ (inherit python-setuptools-scm)
+ (version "3.3.3")
+ (source (origin
+ (method url-fetch)
+ (uri (pypi-uri "setuptools_scm" version))
+ (sha256
+ (base32
+ "19cyndx23xmpbhz4qrwmfwsmnnaczd0dw7qg977ksq2dbvxy29dx"))))))
+
(define-public python2-setuptools-scm
(package-with-python2 python-setuptools-scm))
@@ -5160,13 +5271,13 @@ releases.")
(define-public python-pathpy
(package
(name "python-pathpy")
- (version "11.5.0")
+ (version "11.5.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "path.py" version))
(sha256
- (base32 "1jxkf91syzxlpiwgm83fjfz1m5xh3jrvv4iyl5wjsnkk599pls5n"))))
+ (base32 "0ir9j1haq2jbi7aip6k2fa9l7q1l03k4hp1awxhjhcwzsnwp3ll8"))))
(outputs '("out" "doc"))
(build-system python-build-system)
(propagated-inputs
@@ -5380,13 +5491,13 @@ installing @code{kernelspec}s for use with Jupyter frontends.")
(define-public python-ipykernel
(package
(name "python-ipykernel")
- (version "5.1.1")
+ (version "5.1.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ipykernel" version))
(sha256
- (base32 "173nm29g85w8cac3fg40b27qaq26g41wgg6qn79ql1hq4w2n5sgh"))))
+ (base32 "1a08y677lpn80qzvv7z0smgggmr5m5ayf0bs6vds47xpxl9sss5k"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -5411,8 +5522,9 @@ installing @code{kernelspec}s for use with Jupyter frontends.")
;; imported at runtime during connect
("python-jupyter-client" ,python-jupyter-client)))
(native-inputs
- `(("python-pytest" ,python-pytest)
- ("python-nose" ,python-nose)))
+ `(("python-flaky" ,python-flaky)
+ ("python-nose" ,python-nose)
+ ("python-pytest" ,python-pytest)))
(home-page "https://ipython.org")
(synopsis "IPython Kernel for Jupyter")
(description
@@ -5566,13 +5678,13 @@ computing.")
(define-public python-ipython
(package
(name "python-ipython")
- (version "7.5.0")
+ (version "7.9.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "ipython" version ".tar.gz"))
(sha256
- (base32 "09mbxq37mfn88xjnib7qfzaq9krr7gf1jxwy1p6mcjr254082h78"))))
+ (base32 "103jkw18z7fnwdal1mdbijjxi1fndzn31g887lmj7ddpf2r07lyz"))))
(build-system python-build-system)
(propagated-inputs
`(("python-backcall" ,python-backcall)
@@ -5832,27 +5944,15 @@ parsing (browser/HTTP) user agent strings.")
(define-public python-dbus
(package
(name "python-dbus")
- (version "1.2.8")
+ (version "1.2.10")
(source
(origin
(method url-fetch)
(uri (string-append "https://dbus.freedesktop.org/releases/dbus-python/"
"dbus-python-" version ".tar.gz"))
(sha256
- (base32
- "0vvvjmiwnc9cjlks3gcdk43ap7llhlpz7cm1wbw0nc2yfsxjpwdb"))))
+ (base32 "11nqk01iq5bx2llgb3ksknyinijdp29w4ndj210glm009ayjncyl"))))
(build-system gnu-build-system)
- (arguments
- '(#:phases
- (modify-phases %standard-phases
- (add-before
- 'check 'pre-check
- (lambda _
- ;; XXX: For the missing '/etc/machine-id'.
- (substitute* "test/run-test.sh"
- (("DBUS_FATAL_WARNINGS=1")
- "DBUS_FATAL_WARNINGS=0"))
- #t)))))
(native-inputs
`(("pkg-config" ,pkg-config)))
(inputs
@@ -5905,15 +6005,20 @@ the GObject Introspection bindings to libnotify for non-GTK applications.")
(define-public python-lxml
(package
(name "python-lxml")
- (version "4.2.5")
+ (version "4.4.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "lxml" version))
(sha256
(base32
- "0zw0y9hs0nflxhl9cs6ipwwh53szi3w2x06wl0k9cylyqac0cwin"))))
+ "14jnpfcpgqr9sx8ppd286jzcbk0b36hbqsvd8jkvffipzw5v8768"))))
(build-system python-build-system)
+ (arguments
+ `(#:phases (modify-phases %standard-phases
+ (replace 'check
+ (lambda _
+ (invoke "make" "test"))))))
(inputs
`(("libxml2" ,libxml2)
("libxslt" ,libxslt)))
@@ -5976,14 +6081,14 @@ converts incoming documents to Unicode and outgoing documents to UTF-8.")
(define-public python-soupsieve
(package
(name "python-soupsieve")
- (version "1.9.2")
+ (version "1.9.5")
(source
(origin
(method url-fetch)
(uri (pypi-uri "soupsieve" version))
(sha256
(base32
- "0in9rc9q3h8w5b4qf7kvl3qxcvw6vrz35ckblchgf70hm6pg3dbj"))))
+ "1nhd0q0ifwva9wn645s6pn74p1rd97asn3qfg75nphx1wkgcbhg2"))))
(build-system python-build-system)
(arguments `(#:tests? #f))
;;XXX: 2 tests fail currently despite claming they were to be
@@ -6086,13 +6191,13 @@ Python.")
(define-public snakemake
(package
(name "snakemake")
- (version "5.2.4")
+ (version "5.7.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "snakemake" version))
(sha256
- (base32 "0gj0xxgiq3mp9qyyrbfzldiaq1giliqw0in64nqiz7vx49myqj7z"))))
+ (base32 "1pnpvvn8n2a78cg360wz3ldmpqrsm2wzi0c0dmvki9fnsw6fxdas"))))
(build-system python-build-system)
(arguments
;; TODO: Package missing test dependencies.
@@ -6110,18 +6215,19 @@ Python.")
"/bin/snakemake")))
#t)))))
(propagated-inputs
- `(("python-gitpython" ,python-gitpython)
- ("python-wrapt" ,python-wrapt)
- ("python-requests" ,python-requests)
- ("python-appdirs" ,python-appdirs)
+ `(("python-appdirs" ,python-appdirs)
("python-configargparse" ,python-configargparse)
("python-datrie" ,python-datrie)
("python-docutils" ,python-docutils)
+ ("python-gitpython" ,python-gitpython)
("python-jinja2" ,python-jinja2)
("python-jsonschema" ,python-jsonschema)
("python-networkx" ,python-networkx)
+ ("python-psutil" ,python-psutil)
("python-pyyaml" ,python-pyyaml)
- ("python-ratelimiter" ,python-ratelimiter)))
+ ("python-ratelimiter" ,python-ratelimiter)
+ ("python-requests" ,python-requests)
+ ("python-wrapt" ,python-wrapt)))
(home-page "https://snakemake.readthedocs.io")
(synopsis "Python-based execution environment for make-like workflows")
(description
@@ -6130,24 +6236,6 @@ providing a clean and modern domain specific specification language (DSL) in
Python style, together with a fast and comfortable execution environment.")
(license license:expat)))
-;; This is currently needed for the pigx-* packages.
-(define-public snakemake-4
- (package (inherit snakemake)
- (version "4.4.0")
- (source
- (origin
- (method url-fetch)
- (uri (pypi-uri "snakemake" version))
- (sha256
- (base32 "0g0paia4z7w3srnqdmavq3hrb2x7qnpf81jx50njl0p7y4y0j8jv"))))
- (propagated-inputs
- `(("python-wrapt" ,python-wrapt)
- ("python-requests" ,python-requests)
- ("python-appdirs" ,python-appdirs)
- ("python-configargparse" ,python-configargparse)
- ("python-pyyaml" ,python-pyyaml)
- ("python-ratelimiter" ,python-ratelimiter)))))
-
(define-public python-pyqrcode
(package
(name "python-pyqrcode")
@@ -7201,21 +7289,23 @@ Supported netlink families and protocols include:
(define-public python-xlrd
(package
(name "python-xlrd")
- (version "1.0.0")
+ (version "1.2.0")
(source (origin
(method url-fetch)
(uri (pypi-uri "xlrd" version))
(sha256
(base32
- "0s8hjiz01vbhy85xalrz0qlsmd9ypf36zjqrf97hh984spapvy0g"))))
+ "1ci93fda4n67qhdvfl16zasyxrpygzk53hs6m8z0rd4dxrnb6vjl"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
- ;; Current test in setup.py does not work as of 1.0.0, so use nose to
- ;; run tests instead for now.
- (replace 'check (lambda _ (invoke "nosetests"))))))
- (native-inputs `(("python-nose" ,python-nose)))
+ ;; Some tests depend on writing a temporary file to the user's home
+ ;; directory.
+ (add-after 'unpack 'fix-tests
+ (lambda _
+ (delete-file "tests/test_open_workbook.py")
+ #t)))))
(home-page "http://www.python-excel.org/")
(synopsis "Library for extracting data from Excel files")
(description "This package provides a library to extract data from
@@ -8930,14 +9020,14 @@ servers.")
(define-public python-jmespath
(package
(name "python-jmespath")
- (version "0.9.3")
+ (version "0.9.4")
(source
(origin
(method url-fetch)
(uri (pypi-uri "jmespath" version))
(sha256
(base32
- "0r7wc7fsxmlwzxx9j1j7rms06c6xs6d4sysirdhz1jk2mb4x90ba"))))
+ "0k0765x1mybcrzajh3hiqkl8sy9hs0bmn4900frxy0j3ykvaxqmx"))))
(build-system python-build-system)
(native-inputs
`(("python-nose" ,python-nose)))
@@ -9081,6 +9171,63 @@ server with very acceptable performance.")
(define-public python2-waitress
(package-with-python2 python-waitress))
+(define-public python-whichcraft
+ (package
+ (name "python-whichcraft")
+ (version "0.6.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "whichcraft" version))
+ (sha256
+ (base32
+ "11yfkzyplizdgndy34vyd5qlmr1n5mxis3a3svxmx8fnccdvknxc"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page "https://github.com/pydanny/whichcraft")
+ (synopsis "Cross-platform cross-python shutil.which functionality")
+ (description
+ "This package provides a shim of the shutil.which function that's
+designed to work across multiple versions of Python.")
+ (license license:bsd-3)))
+
+(define-public python-cookiecutter
+ (package
+ (name "python-cookiecutter")
+ (version "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "cookiecutter" version))
+ (sha256
+ (base32
+ "0glsvaz8igi2wy1hsnhm9fkn6560vdvdixzvkq6dn20z3hpaa5hk"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-freezegun" ,python-freezegun)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-catchlog" ,python-pytest-catchlog)
+ ("python-pytest-cov" ,python-pytest-cov)
+ ("python-pytest-mock" ,python-pytest-mock)))
+ (propagated-inputs
+ `(("python-binaryornot" ,python-binaryornot)
+ ("python-click" ,python-click)
+ ("python-future" ,python-future)
+ ("python-jinja2" ,python-jinja2)
+ ("python-jinja2-time" ,python-jinja2-time)
+ ("python-poyo" ,python-poyo)
+ ("python-requests" ,python-requests)
+ ("python-whichcraft" ,python-whichcraft)))
+ (home-page "https://github.com/audreyr/cookiecutter")
+ (synopsis
+ "Command-line utility that creates projects from project templates")
+ (description
+ "This package provides a command-line utility that creates projects from
+project templates, e.g. creating a Python package project from a Python package
+project template.")
+ (license license:bsd-3)))
+
(define-public python-pyquery
(package
(name "python-pyquery")
@@ -9459,6 +9606,7 @@ useful for solving the Assignment Problem.")
(base32
"10qsqdjpbc85fykc1vgcs8xwbgn4l2l52c8d83xf1q59pwyn79bw"))))
(build-system python-build-system)
+ (arguments '(#:tests? #f)) ; Test invocation is no longer supported by Python.
(native-inputs
`(("python-pytest" ,python-pytest)))
(home-page "https://bitbucket.org/mchaput/whoosh")
@@ -9962,14 +10110,13 @@ to occurrences in strings and comments.")
(define-public python-py3status
(package
(name "python-py3status")
- (version "3.16")
+ (version "3.21")
(source
(origin
(method url-fetch)
(uri (pypi-uri "py3status" version))
(sha256
- (base32
- "1xrfph277bgjln3jbpzpgkhxad04fjvj7s3xfil42q1sxi4s3q3g"))))
+ (base32 "16z8zq83hxy48g6hh4xczbdz50qvxv9k1aahr4fqq7jis60cc262"))))
(build-system python-build-system)
(inputs
`(("file" ,file)))
@@ -10490,16 +10637,16 @@ Wikipedia code samples at
(define-public python-cleo
(package
(name "python-cleo")
- (version "0.6.1")
+ (version "0.6.8")
(source (origin
(method url-fetch)
(uri (pypi-uri "cleo" version))
(sha256
(base32
- "0q1cf0szr0d54am4pypzwdnm74zpladdsinad94c2fz5i06fdpf7"))))
+ "06zp695hq835rkaq6irr1ds1dp2qfzyf32v60vxpd8rcnxv319l5"))))
(build-system python-build-system)
(native-inputs
- `(;; For testing
+ `( ;; For testing
("python-mock" ,python-mock)
("python-pytest-mock" ,python-pytest-mock)
("python-pytest" ,python-pytest)))
@@ -10517,16 +10664,203 @@ docstring and colored output.")
(define-public python2-cleo
(package-with-python2 python-cleo))
+(define-public python-tomlkit
+ (package
+ (name "python-tomlkit")
+ (version "0.5.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "tomlkit" version))
+ (sha256
+ (base32
+ "18820ga5z3if1w8dvykxrfm000akracq01ic402xrbljgbn5grn4"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-pytest" ,python-pytest)))
+ (home-page
+ "https://github.com/sdispater/tomlkit")
+ (synopsis "Style preserving TOML library")
+ (description
+ "TOML Kit is a 0.5.0-compliant TOML library. It includes a parser that
+preserves all comments, indentations, whitespace and internal element ordering,
+and makes them accessible and editable via an intuitive API. It can also
+create new TOML documents from scratch using the provided helpers. Part of the
+implementation as been adapted, improved and fixed from Molten.")
+ (license license:expat)))
+
+(define-public python-shellingham
+ (package
+ (name "python-shellingham")
+ (version "1.3.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "shellingham" version))
+ (sha256
+ (base32
+ "1q7kws7w4x2hji3g7y0ni9ddk4sd676ylrb3db54gbpys6xj6nwq"))))
+ (build-system python-build-system)
+ (home-page
+ "https://github.com/sarugaku/shellingham")
+ (synopsis "Tool to detect surrounding shell")
+ (description
+ "Shellingham detects what shell the current Python executable is
+running in.")
+ (license license:isc)))
+
+(define-public python-memcached
+ (package
+ (name "python-memcached")
+ (version "1.59")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "python-memcached" version))
+ (sha256
+ (base32
+ "0kvyapavbirk2x3n1jx4yb9nyigrj1s3x15nm3qhpvhkpqvqdqm2"))))
+ (build-system python-build-system)
+ (propagated-inputs `(("python-six" ,python-six)))
+ (home-page
+ "https://github.com/linsomniac/python-memcached")
+ (synopsis "Pure python memcached client")
+ (description
+ "This software is a pure Python interface to the memcached memory cache
+daemon. It is the client side software which allows storing values in one or
+more, possibly remote, memcached servers.")
+ (license license:psfl)))
+
+(define-public python-clikit
+ (package
+ (name "python-clikit")
+ (version "0.2.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "clikit" version))
+ (sha256
+ (base32
+ "0dc8czib5f4j9px1ivcpqnmivnx2zjpc0xb00ldrhsqylks7r06n"))))
+ (build-system python-build-system)
+ (propagated-inputs
+ `(("python-pastel" ,python-pastel)
+ ("python-pylev" ,python-pylev)))
+ (home-page "https://github.com/sdispater/clikit")
+ (synopsis "Group of utilities to build command line interfaces")
+ (description
+ "CliKit is a group of utilities to build testable command line
+interfaces.")
+ (license license:expat)))
+
+(define-public python-msgpack-python
+ (package
+ (name "python-msgpack-python")
+ (version "0.5.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "msgpack-python" version))
+ (sha256
+ (base32
+ "16wh8qgybmfh4pjp8vfv78mdlkxfmcasg78lzlnm6nslsfkci31p"))))
+ (build-system python-build-system)
+ (home-page "http://msgpack.org/")
+ (synopsis "Package to deserialize messages in MessagePack binary format")
+ (description
+ "MessagePack is an efficient binary serialization format. It lets you
+exchange data among multiple languages like JSON. But it's faster and
+smaller. Small integers are encoded into a single byte, and typical short
+strings require only one extra byte in addition to the strings themselves.")
+ (license license:asl2.0)))
+
+(define-public python-cachy
+ (package
+ (name "python-cachy")
+ (version "0.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "cachy" version))
+ (sha256
+ (base32
+ "0v6mjyhgx6j7ya20bk69cr3gdzdkdf6psay0h090rscclgji65dp"))))
+ (build-system python-build-system)
+ (native-inputs
+ `(("python-fakeredis" ,python-fakeredis)
+ ("python-flexmock" ,python-flexmock)
+ ("python-pytest" ,python-pytest)))
+ (propagated-inputs
+ `(("python-memcached" ,python-memcached)
+ ("python-msgpack-python" ,python-msgpack-python)
+ ("python-redis" ,python-redis)))
+ (home-page "https://github.com/sdispater/cachy")
+ (synopsis "Simple yet effective caching library")
+ (description
+ "Cachy provides a simple yet effective caching library. A simple but
+powerful API: thread-safety; decorator syntax; support for memcached, redis,
+database, file, dict stores. Cachy supports python versions 2.7+ and 3.2+.")
+ (license license:expat)))
+
+(define-public poetry
+ (package
+ (name "poetry")
+ (version "0.12.17")
+ ;; Poetry can only be built from source with poetry.
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "poetry" version))
+ (sha256
+ (base32
+ "0gxwcd65qjmzqzppf53x51sic1rbcd9py6cdzx3aprppipimslvf"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:tests? #f ;; Pypi does not have tests.
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'build
+ (lambda _
+ ;; Bug in poetry https://github.com/sdispater/poetry/issues/866.
+ (invoke "sed" "-i" "-e" "s/from distutils.core/from setuptools/"
+ "setup.py")
+ #t)))))
+ (propagated-inputs
+ `(("python-cachecontrol" ,python-cachecontrol)
+ ("python-cachy" ,python-cachy)
+ ("python-cleo" ,python-cleo)
+ ("python-glob2" ,python-glob2)
+ ("python-html5lib" ,python-html5lib)
+ ("python-jsonschema" ,python-jsonschema)
+ ("python-msgpack" ,python-msgpack)
+ ("python-pathlib2" ,python-pathlib2)
+ ("python-pkginfo" ,python-pkginfo)
+ ("python-pyparsing" ,python-pyparsing)
+ ("python-pyrsistent" ,python-pyrsistent)
+ ("python-requests" ,python-requests)
+ ("python-requests-toolbelt" ,python-requests-toolbelt)
+ ("python-shellingham" ,python-shellingham)
+ ("python-tomlkit" ,python-tomlkit)
+ ("python-virtualenv" ,python-virtualenv)))
+ (home-page "https://poetry.eustace.io/")
+ (synopsis "Python dependency management and packaging made easy")
+ (description "Poetry is a tool for dependency management and packaging
+in Python. It allows you to declare the libraries your project depends on and
+it will manage (install/update) them for you.")
+ (license license:expat)))
+
(define-public python-lazy-object-proxy
(package
(name "python-lazy-object-proxy")
- (version "1.3.1")
+ (version "1.4.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "lazy-object-proxy" version))
(sha256
(base32
- "0yha7q9bhw857fwaby785d63mffhngl9npwzlk9i0pwlkwvbx4gb"))))
+ "1wgl0fmddi0ind78a74yyk2qrr9pb5llvj1892cdpp6z6n6mn4zx"))))
+ (native-inputs
+ `(("python-setuptools-scm" ,python-setuptools-scm-3.3)))
(build-system python-build-system)
(home-page "https://github.com/ionelmc/python-lazy-object-proxy")
(synopsis "Lazy object proxy for python")
@@ -12428,18 +12762,18 @@ clone, while other processes access the original tree.")
(define-public python-astroid
(package
(name "python-astroid")
- (version "2.1.0")
+ (version "2.3.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "astroid" version))
(sha256
- (base32
- "08hz675knh4294bancdapql392fmbjyimhbyrmfkz1ka7l035c1m"))))
+ (base32 "0fnibsl2cb5mvzbfm7sycj85smx48f8w8m7ks1sqlmpr9ps0gski"))))
(build-system python-build-system)
(propagated-inputs
`(("python-lazy-object-proxy" ,python-lazy-object-proxy)
("python-six" ,python-six)
+ ("python-typed-ast" ,python-typed-ast)
("python-wrapt" ,python-wrapt)))
(native-inputs
`(("python-dateutil" ,python-dateutil)
@@ -12506,7 +12840,8 @@ builds partial trees by inspecting living objects.")
,python2-backports-functools-lru-cache)
("python2-enum34" ,python2-enum34)
("python2-singledispatch" ,python2-singledispatch)
- ,@(package-propagated-inputs base))))))
+ ,@(alist-delete "python-typed-ast"
+ (package-propagated-inputs base)))))))
(define-public python-isort
(package
@@ -14223,14 +14558,20 @@ such as figshare or Zenodo.")
(define-public python-pyro4
(package
(name "python-pyro4")
- (version "4.75")
+ (version "4.77")
(source
(origin
(method url-fetch)
(uri (pypi-uri "Pyro4" version))
(sha256
- (base32 "1dfpp36imddx19yv0kd28gk1l71ckhpqy6jd590wpm2680jw15rq"))))
+ (base32 "0gsjg869y4gpy265s1gj1f2qy6jn5iz8r2bwwnq78r1r5yi15zib"))))
(build-system python-build-system)
+ (arguments
+ '(#:tests? #f)) ;FIXME: Some tests require network access.
+ (native-inputs
+ `(("python-cloudpickle" ,python-cloudpickle)
+ ("python-dill" ,python-dill)
+ ("python-msgpack" ,python-msgpack)))
(propagated-inputs
`(("python-serpent" ,python-serpent)))
(home-page "https://pyro4.readthedocs.io")
@@ -14625,14 +14966,16 @@ source bytes using the UTF-8 encoding and then rewrites Python 3.6 style
(define-public python-typed-ast
(package
(name "python-typed-ast")
- (version "1.3.5")
+ (version "1.4.0")
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "typed-ast" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/python/typed_ast.git")
+ (commit version)))
(sha256
- (base32
- "1m7pr6qpana3cvqwiw7mlvrgvmw27ch5mx1592572xhlki8g85ak"))))
+ (base32 "0l0hz809f7i356kmqkvfsaswiidb98j9hs9rrjnfawzqcbffzgyb"))
+ (file-name (git-file-name name version))))
(build-system python-build-system)
(arguments
`(#:modules ((guix build utils)
@@ -14732,14 +15075,13 @@ Included are implementations of:
(define-public bpython
(package
(name "bpython")
- (version "0.17.1")
+ (version "0.18")
(source
(origin
(method url-fetch)
(uri (pypi-uri "bpython" version))
(sha256
- (base32
- "0bxhxi5zxdkrf8b4gwn0d363kdz3qnypjwhm1aydki53ph8ca1w9"))))
+ (base32 "1hl6frgvr2lqaxqczl8amg9xih32b3gzv429vs0qrjb8wpdj1k2n"))))
(build-system python-build-system)
(arguments
`(#:phases
@@ -14762,10 +15104,10 @@ Included are implementations of:
(propagated-inputs
`(("python-pygments" ,python-pygments)
("python-requests" ,python-requests)
- ("python-babel" ,python-babel) ; optional, for internationalization
+ ("python-babel" ,python-babel) ; optional, for internationalization
("python-curtsies" ,python-curtsies) ; >= 0.1.18
("python-greenlet" ,python-greenlet)
- ("python-urwid" ,python-urwid) ; for bpython-urwid only
+ ("python-urwid" ,python-urwid) ; for bpython-urwid only
("python-six" ,python-six)))
(native-inputs
`(("python-sphinx" ,python-sphinx)
@@ -14937,13 +15279,13 @@ working with iterables.")
(define-public python-latexcodec
(package
(name "python-latexcodec")
- (version "1.0.6")
+ (version "1.0.7")
(source
(origin
(method url-fetch)
(uri (pypi-uri "latexcodec" version))
(sha256
- (base32 "0s4wdbg0w2l8pj3i0y4510i0s04p8nhxcsa2z41bjsv0k66npb81"))))
+ (base32 "0wnp3yqcgx0rpy8dz51vh75lbp2qif67da19zi7m3ca98n887hgb"))))
(build-system python-build-system)
(inputs
`(("python-six" ,python-six)))
@@ -15065,16 +15407,16 @@ manager compatible with @code{asyncio}.")
(define-public python-glob2
(package
(name "python-glob2")
- (version "0.6")
+ (version "0.7")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/miracle2k/python-glob2.git")
- (commit version)))
+ (commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1lm1xz3k3l0k1c5bcp9hlzmi3gp5j8dl1k3xhpiq5mnm0xq6n163"))))
+ (base32 "160nh2ay9lw2hi0rixpzb2k87r6ql56k0j2cm87lqz8xc8zbw919"))))
(build-system python-build-system)
(home-page "https://github.com/miracle2k/python-glob2/")
(synopsis "Extended Version of the python buildin glob module")
@@ -16488,3 +16830,57 @@ It is the recommended replacement for Python's original
@code{distro} also provides a command-line interface to output the platform
information in various formats.")
(license license:asl2.0)))
+
+(define-public python-cairosvg
+ (package
+ (name "python-cairosvg")
+ (version "2.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "CairoSVG" version))
+ (sha256
+ (base32 "1bb7irxbaxxb9ahm3z5wsx1q96mm5gzskc7b6q07h9ikcnb8yrjf"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda _ (invoke "pytest"))))))
+ (propagated-inputs
+ `(("python-cairocffi" ,python-cairocffi)
+ ("python-cssselect2" ,python-cssselect2)
+ ("python-defusedxml" ,python-defusedxml)
+ ("python-pillow" ,python-pillow)
+ ("python-tinycss2" ,python-tinycss2)))
+ (native-inputs
+ `(("python-pytest-flake8" ,python-pytest-flake8)
+ ("python-pytest-isort" ,python-pytest-isort)
+ ("python-pytest-runner" ,python-pytest-runner)))
+ (home-page "https://cairosvg.org/")
+ (synopsis "SVG to PDF/PS/PNG converter based on Cairo")
+ (description "CairoSVG is a SVG converter based on Cairo. It can export
+SVG files to PDF, PostScript and PNG files. The main part of CairoSVG is a
+SVG parser, trying to follow the SVG 1.1 recommendation from the W3C. Once
+parsed, the result is drawn to a Cairo surface that can be exported to
+qvarious formats: PDF, PostScript, PNG and even SVG.")
+ (license license:lgpl3+)))
+
+(define-public python-pyphen
+ (package
+ (name "python-pyphen")
+ (version "0.9.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "Pyphen" version))
+ (sha256
+ (base32 "08c9y69ry9d6m4zalhnalg86lsp9v2j5n1ziw5vxfmiihx83lqrv"))))
+ (build-system python-build-system)
+ ;; TODO: Use the Guix system hyphenation packages hyphen-* rather than the
+ ;; embedded set provided by upstream - like Debian does.
+ (home-page "https://github.com/Kozea/Pyphen")
+ (synopsis "Pure Python module to hyphenate text")
+ (description "Pyphen is a pure Python module to hyphenate text using
+existing Hunspell hyphenation dictionaries.")
+ (license (list license:gpl2 license:lgpl2.1 license:mpl1.1))))
generated by cgit v1.2.3 (git 2.45.2) at 2024-07-13 08:01:52 +0000