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authorMarius Bakke <marius@gnu.org>2021-06-19 17:38:47 +0200
committerMarius Bakke <marius@gnu.org>2021-06-19 17:38:47 +0200
commit6f9a80b331ae41d142a49fbeb94b90ee587b6155 (patch)
tree2da042a6ccf5368c73d6e3d54c2ee02a62d284e4 /gnu/packages/python-xyz.scm
parent6500c9a5b364616e38a7e03aa4516fc2d7cee876 (diff)
parentdece03e2b98fc1c2428c2448ce5792f813eb79bf (diff)
Merge branch 'master' into core-updates
Note: this merge actually changes the 'curl' and 'python-attrs' derivations, as part of solving caf4a7a2770ef4d05a6e18f40d602e51da749ddc and 12964df69a99de6190422c752fef65ef813f3b6b 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
Diffstat (limited to 'gnu/packages/python-xyz.scm')
-rw-r--r--gnu/packages/python-xyz.scm166
1 files changed, 93 insertions, 73 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 56c2732018..bbc51590b6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -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)