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Merge branch 'master' into core-updates

Browse source 
Note: this merge actually changes the 'curl' and 'python-attrs' derivations,
as part of solving caf4a7a277 and
12964df69a respectively.

4604d43c0e (gnu: gnutls@3.6.16: Fix cross-compilation.) was ignored because it
cannot currently be tested.

 Conflicts:
	gnu/local.mk
	gnu/packages/aidc.scm
	gnu/packages/boost.scm
	gnu/packages/curl.scm
	gnu/packages/nettle.scm
	gnu/packages/networking.scm
	gnu/packages/python-xyz.scm
	gnu/packages/tls.scm
This commit is contained in:
Marius Bakke 2021-06-19 17:38:47 +02:00
commit 6f9a80b331
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217 changed files with 13322 additions and 4178 deletions
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gnu/packages/python-xyz.scm
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@ -29,7 +29,7 @@
;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Marius Bakke <marius@gnu.org>
;;; Copyright © 2016, 2017, 2021 Stefan Reichör <stefan@xsteve.at>
;;; Copyright © 2016, 2017, 2019 Alex Vong <alexvong1995@gmail.com>
;;; Copyright © 2016, 2017, 2018 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2016, 2017, 2018, 2021 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2016, 2017, 2018, 2020, 2021 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2016–2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
@ -1103,9 +1103,6 @@ NetCDF files can also be read and modified. Python-HDF4 is a fork of
@url{http://hdfeos.org/software/pyhdf.php,pyhdf}.")
(license license:expat)))
(define-public python2-hdf4
(package-with-python2 python-hdf4))
(define-public python-h5py
(package
(name "python-h5py")
@ -2284,28 +2281,6 @@ information created by most SVG editors. Optimization options are typically
lossless but can be tweaked for more aggressive cleaning.")
(license license:asl2.0)))
(define-public python-mappy
(package
(name "python-mappy")
(version "2.18")
(source (origin
(method url-fetch)
(uri (pypi-uri "mappy" version))
(sha256
(base32
"1a05p7rkmxa6qhm108na8flzj2v45jab06drk59kzk1ip2sgvzqq"))))
(build-system python-build-system)
(native-inputs
`(("python-cython" ,python-cython)))
(inputs
`(("zlib" ,zlib)))
(home-page "https://github.com/lh3/minimap2")
(synopsis "Python binding for minimap2")
(description "This package provides a convenient interface to minimap2,
a fast and accurate C program to align genomic and transcribe nucleotide
sequences.")
(license license:expat)))
(define-public python-mechanize
(package
(name "python-mechanize")
@ -2825,14 +2800,14 @@ matching them against a list of media-ranges.")
(define-public python-miniboa
(package
(name "python-miniboa")
(version "1.0.7")
(version "1.0.8")
(source
(origin
(method url-fetch)
(uri (pypi-uri "miniboa" version))
(sha256
(base32
"09jh3pn4rh7kh7jayanf8jzy6gp03791b5a193w6148cf3i6k9m3"))))
"002c1aki9hsrwj5plrwdrf3sk8rn95fqylqyjx2arrjfpsih4dgs"))))
(build-system python-build-system)
(home-page "https://github.com/shmup/miniboa")
(synopsis "Simple, single-threaded Telnet server")
@ -5310,23 +5285,16 @@ color scales, and color space conversion easy. It has support for:
(description (package-description python-numpy))
(license (package-license python-numpy))))
(define-public python2-numpy-documentation
(let ((numpy-documentation (package-with-python2 python-numpy-documentation)))
(package
(inherit numpy-documentation)
(native-inputs `(("python2-functools32" ,python2-functools32)
,@(package-native-inputs numpy-documentation))))))
(define-public python-pygit2
(package
(name "python-pygit2")
(version "1.4.0")
(version "1.6.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pygit2" version))
(sha256
(base32 "1j71iskvirkm8jzfmwdm79v69878m9iix8a8cn4xidgr3nmkisyb"))))
(base32 "0qjd5aqpmla64da4pb47vdnrmnqdbn7248a4fzs7f5q1ax7fmb3s"))))
(build-system python-build-system)
(arguments
'(#:tests? #f)) ; tests don't run correctly in our environment
@ -6236,13 +6204,13 @@ the OleFileIO module from PIL, the Python Image Library.")
(define-public python-pikepdf
(package
(name "python-pikepdf")
(version "2.12.1")
(version "2.12.2")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pikepdf" version))
(sha256
(base32 "1si1x4dc4i4ghyirjfws1zkgiwk8kypnpp4gf68haascrdy7znqw"))))
(base32 "1r68zh8whp8wg4brjf5vha8h1ly8pjqyb37pfw91hyxfn6cm9wsz"))))
(build-system python-build-system)
(arguments
`(#:tests? #false)) ;require python-xmp-toolkit
@ -7054,9 +7022,6 @@ cluster directly from Python. You can directly map Python functions onto the
cluster without needing to write any wrapper code yourself.")
(license license:gpl3+)))
(define-public python2-gridmap
(package-with-python2 python-gridmap))
(define-public python-honcho
(package
(name "python-honcho")
@ -8844,9 +8809,6 @@ more advanced mathematics.")
multiprecision arithmetic.")
(license license:lgpl3+)))
(define-public python2-bigfloat
(package-with-python2 python-bigfloat))
(define-public python-sympy
(package
(name "python-sympy")
@ -9100,25 +9062,29 @@ applications.")
(define-public python-pyzmq
(package
(name "python-pyzmq")
(version "22.0.3")
(version "22.1.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "pyzmq" version))
(sha256
(base32 "0bgrn65cxfz1c1sjrgyq5dy1mkhppxxbizd5wvrl03cq4zhkrxpp"))))
(base32 "0pa1y97z75xqyca9xfp9zrzksydbgzsxf8yh0hwp0rgahpfxch3h"))))
(build-system python-build-system)
(arguments
`(#:configure-flags
(list (string-append "--zmq=" (assoc-ref %build-inputs "zeromq")))
;; FIXME: You must build pyzmq with 'python setup.py build_ext
;; --inplace' for 'python setup.py test' to work.
#:tests? #f))
#:phases
(modify-phases %standard-phases
(add-before 'check 'build-extensions
(lambda _
;; Cython extensions have to be built before running the tests.
(invoke "python" "setup.py" "build_ext" "--inplace"))))))
(inputs
`(("zeromq" ,zeromq)))
(native-inputs
`(("pkg-config" ,pkg-config)
("python-nose" ,python-nose)))
("python-cython" ,python-cython)
("python-pytest" ,python-pytest)))
(home-page "https://github.com/zeromq/pyzmq")
(synopsis "Python bindings for 0MQ")
(description
@ -13292,7 +13258,7 @@ ISO 8859, etc.).")
("python-pytest-cov" ,python-pytest-cov)
("python-pytest-xdist" ,python-pytest-xdist)))
(inputs
`(("qtbase" ,qtbase)))
`(("qtbase" ,qtbase-5)))
(propagated-inputs
`(("python-h5py" ,python-h5py)
("python-numpy" ,python-numpy)
@ -13687,6 +13653,56 @@ is made as zipfile like as possible.")
(define-public python2-rarfile
(package-with-python2 python-rarfile))
(define-public python-rich
(package
(name "python-rich")
(version "10.2.2")
(source (origin
(method url-fetch)
(uri (pypi-uri "rich" version))
(sha256
(base32
"1z5m5brcdf3vndpavcqj5nl35xby4x5rfj48klhwqycfqf3g9cqp"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key inputs tests? #:allow-other-keys)
(when tests?
(copy-recursively (string-append
(assoc-ref inputs "tests") "/tests")
"tests")
(invoke "python" "-m" "pytest" "-vv")))))))
(propagated-inputs
`(("python-attrs" ,python-attrs)
("python-colorama" ,python-colorama)
("python-commonmark" ,python-commonmark)
("python-ipywidgets" ,python-ipywidgets)
("python-pygments" ,python-pygments)
("python-typing-extensions" ,python-typing-extensions)))
(native-inputs
`(("python-pytest" ,python-pytest)
("tests"
;; The release on pypi comes without tests. We can't build from this
;; checkout, though, because installation requires an invocation of
;; poetry.
,(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/willmcgugan/rich")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"19f4svb363sn5708qkpa6lakmiwzyb25h8kmh7bqrsbbrvi9hr70"))))))
(home-page "https://github.com/willmcgugan/rich")
(synopsis "Render rich text and more to the terminal")
(description
"This is a Python package for rendering rich text, tables, progress bars,
syntax highlighting, markdown and more to the terminal.")
(license license:expat)))
(define-public python-magic
(package
(name "python-magic")
@ -14266,9 +14282,6 @@ graphviz.")
format.")
(license license:gpl2+)))
(define-public python2-fastimport
(package-with-python2 python-fastimport))
(define-public python-twisted
(package
(name "python-twisted")
@ -15147,13 +15160,13 @@ collections of data.")
(define-public python-prompt-toolkit
(package
(name "python-prompt-toolkit")
(version "3.0.9")
(version "3.0.18")
(source
(origin
(method url-fetch)
(uri (pypi-uri "prompt_toolkit" version))
(sha256
(base32 "0bvjp62cs6aj9lrh7njzxdjgg8pjfw3qgmr551243d9ivmcapvn5"))))
(base32 "1g1kq1aimhm23k2dmlmnznfzc83l6ly65g0h32hqz8injcdz3d71"))))
(build-system python-build-system)
(arguments
`(#:phases
@ -15257,18 +15270,19 @@ well.")
(define-public ptpython
(package
(name "ptpython")
(version "3.0.5")
(version "3.0.17")
(source (origin
(method url-fetch)
(uri (pypi-uri "ptpython" version))
(sha256
(base32
"0c2ry5gwi2v99slna62j8r2bwq0hpzmvgdryqg9m6x57vbjfg52h"))))
"1phk1grcvn456igjg8gwjjg8bf4kszddq5nd5sdlz3hslg62a7ci"))))
(build-system python-build-system)
(arguments
'(#:tests? #f)) ; FIXME: No tests in pypi tarball.
`(#:tests? #f)) ;there are no tests
(propagated-inputs
`(("python-appdirs" ,python-appdirs)
("python-black" ,python-black)
("python-jedi" ,python-jedi)
("python-prompt-toolkit" ,python-prompt-toolkit)
("python-pygments" ,python-pygments)))
@ -16867,8 +16881,9 @@ and bit flag values.")
(arguments
`(#:phases (modify-phases %standard-phases
(replace 'check
(lambda _
(invoke "pytest"))))))
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "pytest")))))))
(native-inputs
`(("python-coverage" ,python-coverage)
("python-hypothesis" ,python-hypothesis)
@ -21160,18 +21175,26 @@ library's @code{threading} module.")
(define-public python-toolz
(package
(name "python-toolz")
(version "0.9.0")
(version "0.11.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "toolz" version))
(sha256
(base32
"1j9i7fdjnx9dz35fdj5gvgxx6585ja9sxgaiv65if77nlxz0m7wj"))))
"1grz3zvw5ixwqqlbv0n7j11mlcxb66cirh5i9x9zw8kqy0hpk967"))))
(build-system python-build-system)
;; FIXME: tests cannot be computed: "Can't perform this operation for
;; unregistered loader type"
(arguments '(#:tests? #f))
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda* (#:key inputs outputs tests? #:allow-other-keys)
(when tests?
(add-installed-pythonpath inputs outputs)
(invoke "python" "-m" "pytest" "--doctest-modules"
"--pyargs" "toolz")))))))
(native-inputs
`(("python-pytest" ,python-pytest)))
(home-page "https://github.com/pytoolz/toolz/")
(synopsis "List processing tools and functional utilities")
(description
@ -21386,9 +21409,6 @@ This Python package wraps the Blosc library.")
append on old values. Partd excels at shuffling operations.")
(license license:bsd-3)))
(define-public python2-partd
(package-with-python2 python-partd))
(define-public python-fsspec
(package
(name "python-fsspec")
@ -25204,14 +25224,14 @@ disk files in asyncio applications.")
(define-public python-dataclasses
(package
(name "python-dataclasses")
(version "0.7")
(version "0.8")
(source
(origin
(method url-fetch)
(uri (pypi-uri "dataclasses" version))
(sha256
(base32
"1rh8111fbws2vxyf2qy2zw3x6p6cq1jfz8pf904gig5qwg56sjj9"))))
"15sc12nrc7gxwb30vfa6frzdnpmbap9ibi1fr1yrbkra6izhcyc4"))))
(build-system python-build-system)
(home-page
"https://github.com/ericvsmith/dataclasses")
@ -25499,7 +25519,7 @@ implementations.")
("swig" ,swig)))
(inputs
`(("python-wrapper" ,python-wrapper)
("qtbase" ,qtbase)
("qtbase" ,qtbase-5)
("libxi" ,libxi)
("libice" ,libice)
("soqt" ,soqt)