(define-public python-psutil
(package
(name "python-psutil")
- (version "5.6.2")
+ (version "5.6.3")
(source
(origin
(method url-fetch)
(uri (pypi-uri "psutil" version))
(sha256
- (base32
- "1v95vb5385qscfdvphv8l2w22bmir3d7yhpi02n58v3mlqy1r3l2"))))
+ (base32 "1wv31zly44qj0rp2acg58xbnc7bf6ffyadasq093l455q30qafl6"))))
(build-system python-build-system)
(arguments
;; FIXME: some tests does not return and times out.
(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)))
(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
(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
(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")
(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)
(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
(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
;; 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
(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)
(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)))
(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.
"/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
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")
,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
(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")
(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
(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)
@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))))