diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 627 |
1 files changed, 430 insertions, 197 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 789e83728f..92ac335272 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2013, 2014, 2015, 2016, 2019 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org> -;;; Copyright © 2014, 2017 Eric Bavier <bavier@member.fsf.org> +;;; Copyright © 2014, 2017, 2021 Eric Bavier <bavier@posteo.net> ;;; Copyright © 2014, 2015 Federico Beffa <beffa@fbengineering.ch> ;;; Copyright © 2015 Omar Radwan <toxemicsquire4@gmail.com> ;;; Copyright © 2015 Pierre-Antoine Rault <par@rigelk.eu> @@ -27,7 +27,7 @@ ;;; Copyright © 2016 Dylan Jeffers <sapientech@sapientech@openmailbox.org> ;;; Copyright © 2016 David Craven <david@craven.ch> ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Marius Bakke <marius@gnu.org> -;;; Copyright © 2016, 2017 Stefan Reichör <stefan@xsteve.at> +;;; 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, 2020, 2021 Julien Lepiller <julien@lepiller.eu> @@ -98,6 +98,7 @@ ;;; Copyright © 2020 EuAndreh <eu@euandre.org> ;;; Copyright © 2021 Sharlatan Hellseher <sharlatanus@gmail.com> ;;; Copyright © 2021 Ellis Kenyő <me@elken.dev> +;;; Copyright © 2021 LibreMiami <packaging-guix@libremiami.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -569,8 +570,7 @@ iotop, uptime, pidof, tty, taskset, pmap.") (define-public python2-psutil (let ((base (package-with-python2 (strip-python2-variant python-psutil)))) - (package - (inherit base) + (package/inherit base (propagated-inputs `(("python2-enum34" ,python2-enum34) ;optional ,@(package-propagated-inputs base)))))) @@ -652,25 +652,31 @@ module and then similar looking characters are removed.") (define-public python-logwrap (package (name "python-logwrap") - (version "3.2.1") + (version "8.2.0.post0") (source (origin (method url-fetch) - (uri (pypi-uri "logwrap" version ".zip")) + (uri (pypi-uri "logwrap" version)) (sha256 (base32 - "1d2k0hvpbi51vl410y8fbs5m0nxnlh2k7gr2nrh3k81ibhzscsra")))) + "1dv7gny3rfci5cal2ipr6d0pcz3yhka7af96dfsd3ir1mxy8p1j9")))) (build-system python-build-system) - (propagated-inputs - `(("python-six" ,python-six) - ("python-typing" ,python-typing))) + (arguments + `(#:tests? #f ; Tests not included in pypi release. + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest")) + #t))))) (native-inputs - `(("unzip" ,unzip) - ("python-cython" ,python-cython) + `(("python-cython" ,python-cython) ("python-pytest" ,python-pytest) - ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-runner" ,python-pytest-runner))) - (home-page "https://github.com/penguinolog/logwrap") + ("python-setuptools-scm" ,python-setuptools-scm) + ("python-toml" ,python-toml) + ("python-wheel" ,python-wheel))) + (home-page "https://github.com/python-useful-helpers/logwrap") (synopsis "Decorator for logging function arguments") (description "This package provides a decorator to log function arguments and function call return values in a human-readable way.") @@ -763,6 +769,47 @@ certificate returned by the server to which a connection has been established, and verifies that it matches the intended target hostname.") (license license:psfl))) +(define-public python-bidict + (package + (name "python-bidict") + (version "0.21.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "bidict" version)) + (sha256 + (base32 + "02dy0b1k7qlhn7ajyzkrvxhyhjj0hzcq6ws3zjml9hkdz5znz92g")))) + (build-system python-build-system) + (native-inputs + `(("python-coverage" ,python-coverage) + ("python-hypothesis" ,python-hypothesis) + ("python-pre-commit" ,python-pre-commit) + ("python-py" ,python-py) + ("python-pytest" ,python-pytest) + ("python-pytest-benchmark" ,python-pytest-benchmark) + ("python-pytest-cov" ,python-pytest-cov) + ("python-setuptools-scm" ,python-setuptools-scm) + ("python-sortedcollections" ,python-sortedcollections) + ("python-sortedcontainers" ,python-sortedcontainers) + ("python-sphinx" ,python-sphinx) + ("python-sphinx-autodoc-typehints" ,python-sphinx-autodoc-typehints) + ("python-tox" ,python-tox))) + (arguments + `(#:phases (modify-phases %standard-phases + (add-after 'unpack 'relax-reqs + (lambda _ + (substitute* "setup.py" + (("sortedcollections < 2") "sortedcollections")) + #t)) + (replace 'check + (lambda _ (invoke "./run_tests.py")))))) + (home-page "https://bidict.readthedocs.io") + (synopsis "Bidirectional mapping library") + (description "The @code{bidict} library provides several data structures +for working with bidirectional mappings in Python.") + (license license:mpl2.0))) + (define-public python-bitarray (package (name "python-bitarray") @@ -928,9 +975,6 @@ concepts.") @code{subprocess} feature.") (license license:expat))) -(define-public python2-sh - (package-with-python2 python-sh)) - (define-public python-cftime (package (name "python-cftime") @@ -1118,8 +1162,7 @@ other machines, such as over the network.") (define-public python2-serpent (let ((base (package-with-python2 (strip-python2-variant python-serpent)))) - (package - (inherit base) + (package/inherit base (propagated-inputs `(("python-enum34" ,python2-enum34) ,@(package-propagated-inputs base)))))) @@ -1292,7 +1335,7 @@ helpers.") (define-public python2-humanfriendly (let ((base (package-with-python2 (strip-python2-variant python-humanfriendly)))) - (package (inherit base) + (package/inherit base (propagated-inputs `(("python2-monotonic" ,python2-monotonic) ,@(package-propagated-inputs base)))))) @@ -1814,7 +1857,9 @@ standard.") "1hgz8jq19wlz8vwqj900ry8cjv578nz4scc91mlc8944yid6573c")))) (build-system python-build-system) (propagated-inputs - `(("python-greenlet" ,python-greenlet))) + `(("python-dnspython" ,python-dnspython) + ("python-greenlet" ,python-greenlet) + ("python-monotonic" ,python-monotonic))) (arguments ;; TODO: Requires unpackaged 'enum-compat'. '(#:tests? #f)) @@ -2116,8 +2161,7 @@ commands.") (define-public python2-empy (let ((base (package-with-python2 (strip-python2-variant python-empy)))) - (package - (inherit base) + (package/inherit base (arguments `(,@(package-arguments base) #:tests? #t))))) @@ -2246,7 +2290,7 @@ backported for previous versions of Python from 2.4 to 3.3.") (define-public python2-parse-type (let ((base (package-with-python2 (strip-python2-variant python-parse-type)))) - (package (inherit base) + (package/inherit base (propagated-inputs `(("python2-enum34" ,python2-enum34) ,@(package-propagated-inputs base)))))) @@ -2295,8 +2339,7 @@ existing ones.") (define-public python2-polib (let ((base (package-with-python2 (strip-python2-variant python-polib)))) - (package - (inherit base) + (package/inherit base (arguments `(,@(package-arguments base) ;; Tests don't work with python2. #:tests? #f))))) @@ -2878,7 +2921,7 @@ compare, diff, and patch JSON and JSON-like structures in Python.") (define-public python2-jsonschema (let ((jsonschema (package-with-python2 (strip-python2-variant python-jsonschema)))) - (package (inherit jsonschema) + (package/inherit jsonschema (propagated-inputs `(("python2-functools32" ,python2-functools32) ,@(package-propagated-inputs jsonschema)))))) @@ -3381,15 +3424,16 @@ logic-free templating system Mustache.") (properties `((python2-variant . ,(delay python2-pystache)))))) (define-public python2-pystache - (package (inherit (package-with-python2 - (strip-python2-variant python-pystache))) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ - (invoke "python" "test_pystache.py")))))))) + (let ((base (package-with-python2 + (strip-python2-variant python-pystache)))) + (package/inherit base + (arguments + `(#:python ,python-2 + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + (invoke "python" "test_pystache.py"))))))))) (define-public python-joblib (package @@ -3728,7 +3772,7 @@ to deprecate classes, functions or methods.") (define-public python-pygithub (package (name "python-pygithub") - (version "1.43.8") + (version "1.54.1") (source ;; We fetch from the Git repo because there are no tests in the PyPI ;; archive. @@ -3739,27 +3783,24 @@ to deprecate classes, functions or methods.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1625v558xga5mwhl9jqmibywy5qafmg1vqrirqz6zfq1la1d22mw")))) + (base32 "1nl74bp5ikdnrc8xq0qr25ryl1mvarf0xi43k8w5jzlrllhq0nkq")))) (build-system python-build-system) (arguments - `(#:phases (modify-phases %standard-phases - ;; Some tests rely on the network. - (add-after 'unpack 'disable-failing-tests - (lambda _ - (substitute* "tests/Issue142.py" - (("testDecodeJson") - "disabled_testDecodeJson")))) - (add-before 'check 'prepare-for-tests - (lambda _ - (for-each (lambda (f) - (chmod f #o666)) - (find-files "./tests")) - (system* "python" "-m" "lib2to3" "-w" "-n" "tests")))))) + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest")) + #t))))) (propagated-inputs - `(("python-deprecated" ,python-deprecated) + `(("python-cryptography" ,python-cryptography) + ("python-deprecated" ,python-deprecated) ("python-pyjwt" ,python-pyjwt) ("python-requests" ,python-requests))) - (native-inputs `(("python-httpretty" ,python-httpretty))) + (native-inputs + `(("python-httpretty" ,python-httpretty) + ("python-pytest" ,python-pytest))) (home-page "https://pygithub.readthedocs.io/en/latest/") (synopsis "Python library for the GitHub API") (description "This library allows managing GitHub resources such as @@ -4450,8 +4491,7 @@ writing C extensions for Python as easy as Python itself.") (define-public python2-cython (let ((base (package-with-python2 (strip-python2-variant python-cython)))) - (package - (inherit base) + (package/inherit base (name "python2-cython") (inputs `(("python-2" ,python-2))) ;this is not automatically changed @@ -5001,8 +5041,7 @@ that client code uses to construct the grammar directly in Python code.") (define-public python2-numpydoc (let ((base (package-with-python2 (strip-python2-variant python-numpydoc)))) - (package - (inherit base) + (package/inherit base (propagated-inputs `(("python2-jinja2" ,python2-jinja2) ,@(package-propagated-inputs base)))))) @@ -5769,13 +5808,13 @@ the OleFileIO module from PIL, the Python Image Library.") (define-public python-pikepdf (package (name "python-pikepdf") - (version "2.8.0") + (version "2.9.1") (source (origin (method url-fetch) (uri (pypi-uri "pikepdf" version)) (sha256 - (base32 "1dfc8a7gp6ib6a2gdx6fz2zvvk4yx8vr2m7b6044rk91vpyrdzvl")))) + (base32 "1n53fhdgnq9yxvm2m039vl8l2kg3fkln3pm0wv4rzj0gvpq9rhcr")))) (build-system python-build-system) (arguments `(#:tests? #false)) ;require python-xmp-toolkit @@ -6335,9 +6374,6 @@ graphics library with support for multiple backends including image buffers, PNG, PostScript, PDF, and SVG file output.") (license license:bsd-3))) -(define-public python2-cairocffi - (package-with-python2 python-cairocffi)) - (define-public python-decorator (package (name "python-decorator") @@ -7031,8 +7067,7 @@ CLI scripts: (define-public python2-ipyparallel (let ((ipyparallel (package-with-python2 python-ipyparallel))) - (package - (inherit ipyparallel) + (package/inherit ipyparallel (propagated-inputs `(("python2-futures" ,python2-futures) ,@(package-propagated-inputs ipyparallel)))))) @@ -7121,8 +7156,7 @@ without using the configuration machinery.") (define-public python2-traitlets (let ((traitlets (package-with-python2 (strip-python2-variant python-traitlets)))) - (package - (inherit traitlets) + (package/inherit traitlets (propagated-inputs `(("python2-enum34" ,python2-enum34) ,@(package-propagated-inputs traitlets)))))) @@ -7674,7 +7708,7 @@ implementation of D-Bus.") (license license:expat))) (define-public python2-dbus - (package (inherit python-dbus) + (package/inherit python-dbus (name "python2-dbus") (inputs `(("python" ,python-2) ,@(alist-delete "python" @@ -7748,10 +7782,10 @@ converts incoming documents to Unicode and outgoing documents to UTF-8.") (properties `((python2-variant . ,(delay python2-beautifulsoup4)))))) (define-public python2-beautifulsoup4 - (package - (inherit (package-with-python2 - (strip-python2-variant python-beautifulsoup4))) - (arguments `(#:python ,python-2)))) + (let ((base (package-with-python2 + (strip-python2-variant python-beautifulsoup4)))) + (package/inherit base + (arguments `(#:python ,python-2))))) (define-public python-soupsieve (package @@ -7895,16 +7929,81 @@ of the structure, dynamics, and functions of complex networks.") Python.") (license license:lgpl2.1+))) +(define-public python-amply + (package + (name "python-amply") + (version "0.1.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "amply" version)) + (sha256 + (base32 + "0f1db9zp0rsfzxvaz55xwh8h5rfdgr9a2a715g06ic8nknsdq4nb")))) + (build-system python-build-system) + (propagated-inputs + `(("python-docutils" ,python-docutils) + ("python-pyparsing" ,python-pyparsing))) + (native-inputs + `(("python-setuptools-scm" ,python-setuptools-scm))) + (home-page "https://github.com/willu47/amply") + (synopsis "Load and manipulate AMPL/GLPK data as Python data structures") + (description + "Amply allows you to load and manipulate AMPL/GLPK data as Python data +structures.") + (license license:epl1.0))) + +(define-public python-pulp + (package + (name "python-pulp") + (version "2.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "PuLP" version)) + (sha256 + (base32 + "1dammrg0f1v0r028i3rpxbf2bsyxmjq0q6ihb4x2wsdki44z3bxj")))) + (build-system python-build-system) + (propagated-inputs + `(("python-amply" ,python-amply))) + (home-page "https://github.com/coin-or/pulp") + (synopsis "Linear Programming modeler") + (description + "PuLP is a Linear Programming modeler written in Python. PuLP can +generate MPS or LP files and call GLPK, COIN CLP/CBC, CPLEX, and GUROBI to +solve linear problems.") + (license license:expat))) + +(define-public python-toposort + (package + (name "python-toposort") + (version "1.6") + (source + (origin + (method url-fetch) + (uri (pypi-uri "toposort" version)) + (sha256 + (base32 + "1b2hppzjg3p006qya3yfdnp76dwq8frl97lypdam0kw4xxb8yhm7")))) + (build-system python-build-system) + (home-page "https://gitlab.com/ericvsmith/toposort") + (synopsis "Topological sort algorithm") + (description + "This package provides an implementation of a topological sort +algorithm.") + (license license:asl2.0))) + (define-public snakemake (package (name "snakemake") - (version "5.7.1") + (version "5.32.2") (source (origin (method url-fetch) (uri (pypi-uri "snakemake" version)) (sha256 - (base32 "1pnpvvn8n2a78cg360wz3ldmpqrsm2wzi0c0dmvki9fnsw6fxdas")))) + (base32 "13013gdavwvyj1qr9xfi9fpwhb3km8c3z53bja5b7ic3sb2z6dgz")))) (build-system python-build-system) (arguments ;; TODO: Package missing test dependencies. @@ -7916,7 +8015,7 @@ Python.") ;; this by calling the snakemake wrapper instead. (add-after 'unpack 'call-wrapper-not-wrapped-snakemake (lambda* (#:key outputs #:allow-other-keys) - (substitute* "snakemake/executors.py" + (substitute* "snakemake/executors/__init__.py" (("\\{sys.executable\\} -m snakemake") (string-append (assoc-ref outputs "out") "/bin/snakemake"))) @@ -7929,11 +8028,14 @@ Python.") ("python-gitpython" ,python-gitpython) ("python-jinja2" ,python-jinja2) ("python-jsonschema" ,python-jsonschema) + ("python-nbformat" ,python-nbformat) ("python-networkx" ,python-networkx) ("python-psutil" ,python-psutil) + ("python-pulp" ,python-pulp) ("python-pyyaml" ,python-pyyaml) ("python-ratelimiter" ,python-ratelimiter) ("python-requests" ,python-requests) + ("python-toposort" ,python-toposort) ("python-wrapt" ,python-wrapt))) (home-page "https://snakemake.readthedocs.io") (synopsis "Python-based execution environment for make-like workflows") @@ -8403,8 +8505,7 @@ PEP 8.") (define-public python2-pep517 (let ((base (package-with-python2 (strip-python2-variant python-pep517)))) - (package - (inherit base) + (package/inherit base (name "python2-pep517") (arguments `(#:tests? #f @@ -8496,7 +8597,7 @@ cyclomatic complexity of Python source code.") (define-public python2-flake8 (let ((base (package-with-python2 (strip-python2-variant python-flake8)))) - (package (inherit base) + (package/inherit base (propagated-inputs `(("python2-configparser" ,python2-configparser) ("python2-enum34" ,python2-enum34) @@ -9019,9 +9120,10 @@ third-party code.") (properties `((python2-variant . ,(delay python2-llfuse)))))) (define-public python2-llfuse - (package (inherit (package-with-python2 - (strip-python2-variant python-llfuse))) - (propagated-inputs `(("python2-contextlib2" ,python2-contextlib2))))) + (let ((base (package-with-python2 + (strip-python2-variant python-llfuse)))) + (package/inherit base + (propagated-inputs `(("python2-contextlib2" ,python2-contextlib2)))))) (define-public python-msgpack (package @@ -9367,9 +9469,6 @@ tasks, sockets, files, locks, and queues.") designed to efficiently cope with extremely large amounts of data.") (license license:bsd-3))) -(define-public python2-tables - (package-with-python2 python-tables)) - (define-public python-sniffio (package (name "python-sniffio") @@ -9763,8 +9862,7 @@ a hash value.") (license license:asl2.0))) (define-public python2-tlsh - (package - (inherit python-tlsh) + (package/inherit python-tlsh (name "python2-tlsh") (inputs `(("python" ,python-2))))) @@ -9853,8 +9951,7 @@ Python's @code{ctypes} foreign function interface (FFI).") (package-with-python2 python-libarchive-c)) (define-public python-file - (package - (inherit file) + (package/inherit file (name "python-file") (build-system python-build-system) (arguments @@ -10212,7 +10309,7 @@ interactive computing.") (define-public python2-notebook (let ((base (package-with-python2 (strip-python2-variant python-notebook)))) - (package (inherit base) + (package/inherit base (native-inputs `(("python2-mock" ,python2-mock) ,@(package-native-inputs base))) @@ -10253,9 +10350,6 @@ interactive computing.") notebooks.") (license license:bsd-3))) -(define-public python2-widgetsnbextension - (package-with-python2 python-widgetsnbextension)) - (define-public python-ipywidgets (package (name "python-ipywidgets") @@ -10283,9 +10377,6 @@ widgets are used. Users gain control of their data and can visualize changes in the data.") (license license:bsd-3))) -(define-public python2-ipywidgets - (package-with-python2 python-ipywidgets)) - (define-public python-jupyter-console (package (name "python-jupyter-console") @@ -10346,8 +10437,7 @@ Jupyter kernels such as IJulia and IRKernel.") ;; the functionality in both packages working, strip down the ;; python-jupyter-console package when using it as an input to python-ipython. (define python-jupyter-console-minimal - (package - (inherit python-jupyter-console) + (package/inherit python-jupyter-console (name "python-jupyter-console-minimal") (arguments (substitute-keyword-arguments @@ -10687,8 +10777,7 @@ the standard library.") (define-public python2-contextlib2 (let ((base (package-with-python2 (strip-python2-variant python-contextlib2)))) - (package - (inherit base) + (package/inherit base (arguments (substitute-keyword-arguments (package-arguments base) ((#:phases phases) @@ -10797,6 +10886,27 @@ applications.") (home-page "https://github.com/click-contrib/click-log") (license license:expat))) +(define-public python-click-default-group + (package + (name "python-click-default-group") + (version "1.2.2") + (source (origin + (method url-fetch) + (uri (pypi-uri "click-default-group" version)) + (sha256 + (base32 + "015r78jk8gznfw0dphpwaqcx5mhg5822b55w5xbb6i7sin70wmnr")))) + (build-system python-build-system) + (arguments + `(#:tests? #f)) ; no target + (propagated-inputs + `(("python-click" ,python-click))) + (synopsis "Extends click.Group") + (description "This package extends click.Group to invoke a command without +explicit subcommand name.") + (home-page "https://github.com/click-contrib/click-default-group") + (license license:bsd-3))) + (define-public python-structlog (package (name "python-structlog") @@ -11138,7 +11248,7 @@ concurrent.futures package from Python 3.2") (define-public python2-promise (let ((promise (package-with-python2 (strip-python2-variant python-promise)))) - (package (inherit promise) + (package/inherit promise (arguments (substitute-keyword-arguments (package-arguments promise) ((#:tests? _) #t))) (native-inputs @@ -11437,6 +11547,85 @@ document.") manipulation library.") (license license:expat))) +(define-public python-uncertainties + (package + (name "python-uncertainties") + (version "3.1.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "uncertainties" version)) + (sha256 + (base32 + "00z9xl40czmqk0vmxjvmjvwb41r893l4dad7nj1nh6blw3kw28li")))) + (build-system python-build-system) + ;; While there are test files, there is no "tests" directory, so the tests + ;; fail. + (arguments '(#:tests? #false)) + (propagated-inputs + `(("python-future" ,python-future))) + (native-inputs + `(("python-nose" ,python-nose) + ("python-numpy" ,python-numpy))) + (home-page "https://uncertainties-python-package.readthedocs.io/") + (synopsis "Calculations with uncertainties") + (description + "The uncertainties package transparently handles calculations with +numbers with uncertainties. It can also yield the derivatives of any +expression.") + (license license:bsd-3))) + +(define-public python-asteval + (package + (name "python-asteval") + (version "0.9.23") + (source + (origin + (method url-fetch) + (uri (pypi-uri "asteval" version)) + (sha256 + (base32 + "0f54sd4w1a72ij1bcxs2x7dk9xf8bzclawijf1z18bqx9f96l2gm")))) + (build-system python-build-system) + (native-inputs + `(("python-pytest" ,python-pytest))) + (home-page "https://github.com/newville/asteval") + (synopsis "Minimalistic evaluator of Python expressions") + (description + "This package provides a minimalistic evaluator of Python expression +using the @code{ast} module") + (license license:expat))) + +(define-public python-lmfit + (package + (name "python-lmfit") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "lmfit" version)) + (sha256 + (base32 + "0iab33jjb60f8kn0k0cqb0vjp1mdskks2n3kpn97zkw5cvjhq2b7")))) + (build-system python-build-system) + (propagated-inputs + `(("python-asteval" ,python-asteval) + ("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy) + ("python-uncertainties" ,python-uncertainties))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (home-page "https://lmfit.github.io/lmfit-py/") + (synopsis "Least-Squares minimization with bounds and constraints") + (description + "Lmfit provides a high-level interface to non-linear optimization and +curve fitting problems for Python. It builds on and extends many of the +optimization methods of @code{scipy.optimize}. Initially inspired by (and +named for) extending the Levenberg-Marquardt method from +@code{scipy.optimize.leastsq}, lmfit now provides a number of useful +enhancements to optimization and data fitting problems.") + (license license:bsd-3))) + (define-public python-boto (package (name "python-boto") @@ -11761,8 +11950,7 @@ and provides a uniform API regardless of which JSON implementation is used.") (define-public python2-anyjson (let ((anyjson (package-with-python2 (strip-python2-variant python-anyjson)))) - (package - (inherit anyjson) + (package/inherit anyjson (arguments `(;; Unlike the python 3 variant, we do run tests. See above! #:tests? #t ,@(package-arguments anyjson))) @@ -11799,8 +11987,7 @@ alternative when librabbitmq is not available.") (define-public python2-amqp (let ((amqp (package-with-python2 (strip-python2-variant python-amqp)))) - (package - (inherit amqp) + (package/inherit amqp (arguments `(;; Tries to run coverage tests with nose-cover3, which seems ;; unmaintained. Weirdly, does not do this on the python 3 ;; version? @@ -11872,8 +12059,7 @@ RabbitMQ messaging server is the most popular implementation.") (define-public python2-kombu (let ((kombu (package-with-python2 (strip-python2-variant python-kombu)))) - (package - (inherit kombu) + (package/inherit kombu (arguments `(;; FIXME: 'TestTransport.test_del_sync' fails on python2. ;; It works fine on the python3 variant. #:tests? #f @@ -11910,8 +12096,7 @@ Python 2.4 and 2.5, and will draw its fixes/improvements from python-trunk.") (define-public python2-billiard (let ((billiard (package-with-python2 (strip-python2-variant python-billiard)))) - (package - (inherit billiard) + (package/inherit billiard (native-inputs `(("python2-unittest2" ,python2-unittest2) ("python2-mock" ,python2-mock) ,@(package-native-inputs billiard)))))) @@ -11961,8 +12146,7 @@ synchronously (wait until ready).") (define-public python2-celery (let ((celery (package-with-python2 (strip-python2-variant python-celery)))) - (package - (inherit celery) + (package/inherit celery (native-inputs `(("python2-unittest2" ,python2-unittest2) ("python2-mock" ,python2-mock) ,@(package-native-inputs celery)))))) @@ -12116,7 +12300,7 @@ checking library.") (define-public python2-whoosh (let ((whoosh (package-with-python2 (strip-python2-variant python-whoosh)))) - (package (inherit whoosh) + (package/inherit whoosh (propagated-inputs `(("python2-backport-ssl-match-hostname" ,python2-backport-ssl-match-hostname) @@ -12230,7 +12414,7 @@ encoding algorithms to do fuzzy string matching.") (define-public python2-jellyfish (let ((jellyfish (package-with-python2 (strip-python2-variant python-jellyfish)))) - (package (inherit jellyfish) + (package/inherit jellyfish (native-inputs `(("python2-unicodecsv" ,python2-unicodecsv) ,@(package-native-inputs jellyfish)))))) @@ -12645,8 +12829,7 @@ to occurrences in strings and comments.") (license license:gpl2))) (define-public python-rope - (package - (inherit python2-rope) + (package/inherit python2-rope (name "python-rope") (arguments `(#:python ,python-wrapper ;; XXX: Only partial python3 support, results in some failing @@ -13408,7 +13591,7 @@ database, file, dict stores. Cachy supports python versions 2.7+ and 3.2+.") (define-public poetry (package (name "poetry") - (version "1.1.4") + (version "1.1.5") ;; Poetry can only be built from source with Poetry. (source (origin @@ -13416,7 +13599,7 @@ database, file, dict stores. Cachy supports python versions 2.7+ and 3.2+.") (uri (pypi-uri "poetry" version)) (sha256 (base32 - "1a2kgfiw66fvxhlqk5qc83s6l38czfh5hcsrbiy7qq5yfc8mlsll")))) + "1dvx08ksv5wnsj45db23921rj136akmcnxa0kmlsddf3wbh6wcka")))) (build-system python-build-system) (arguments `(#:tests? #f ;; Pypi does not have tests. @@ -13951,8 +14134,7 @@ etc.") (define-public ptpython-2 (let ((base (package-with-python2 (strip-python2-variant ptpython)))) - (package - (inherit base) + (package/inherit base (name "ptpython2")))) (define-public python-stem @@ -13987,9 +14169,6 @@ control protocol to script against the Tor process and read descriptor data relays publish about themselves.") (license license:lgpl3))) -(define-public python2-stem - (package-with-python2 python-stem)) - (define-public python-pyserial (package (name "python-pyserial") @@ -14095,7 +14274,7 @@ binary or text.") (define-public python2-binaryornot (let ((base (package-with-python2 (strip-python2-variant python-binaryornot)))) - (package (inherit base) + (package/inherit base (propagated-inputs `(("python2-enum34" ,python2-enum34) ,@(package-propagated-inputs base)))))) @@ -14324,13 +14503,13 @@ command @command{natsort} that exposes this functionality in the command line.") (define-public glances (package (name "glances") - (version "3.1.4") + (version "3.1.6") (source (origin (method url-fetch) (uri (pypi-uri "Glances" version)) (sha256 - (base32 "0dc47gbvp9a3wxppdqihxpglxxaxbj3hcvzgcxxq8zcsciah3plq")) + (base32 "11xbm8jgcxha191ly7q76nab1ilabiz14mqf6i3y6aw5xvgg017c")) (modules '((guix build utils))) (snippet '(begin @@ -14394,9 +14573,6 @@ This library is a port of @url{https://github.com/graphql/graphql-js,graphql-js} to Python.") (license license:expat))) -(define-public python2-graphql-core - (package-with-python2 python-graphql-core)) - (define-public python-graphql-relay (package (name "python-graphql-relay") @@ -14592,8 +14768,7 @@ is used by PostgreSQL and the OpenSSH Server for example.") (define-public python2-setproctitle (let ((base (package-with-python2 (strip-python2-variant python-setproctitle)))) - (package - (inherit base) + (package/inherit base (native-inputs `(("python2-nose" ,python2-nose) ,@(package-native-inputs base)))))) @@ -14770,8 +14945,7 @@ network.") (define-public python2-argcomplete (let ((variant (package-with-python2 (strip-python2-variant python-argcomplete)))) - (package - (inherit variant) + (package/inherit variant (arguments (substitute-keyword-arguments (package-arguments variant) ((#:phases phases '%standard-phases) @@ -14895,8 +15069,7 @@ possible on all supported Python versions.") (define-public python2-xopen (let ((base (package-with-python2 (strip-python2-variant python-xopen)))) - (package - (inherit base) + (package/inherit base (propagated-inputs `(("python2-bz2file" ,python2-bz2file) ,@(package-propagated-inputs base)))))) @@ -15010,9 +15183,6 @@ protocols written in pure Python.") ;; Can be used with either license. (license (list license:asl2.0 license:gpl2+)))) -(define-public python2-dulwich - (package-with-python2 python-dulwich)) - (define-public python-pbkdf2 (package (name "python-pbkdf2") @@ -15782,7 +15952,16 @@ version, is suitable to be include as a dependency in other projects.") imports alphabetically, and automatically separated into sections. It provides a command line utility, a python library and plugins for various editors.") - (license license:expat))) + (license license:expat) + (properties `((python2-variant . ,(delay python2-isort)))))) + +(define-public python2-isort + (let ((base (package-with-python2 + (strip-python2-variant python-isort)))) + (package/inherit base + (native-inputs + `(("python2-futures" ,python2-futures) + ,@(package-native-inputs base)))))) (define-public python2-backports-functools-lru-cache (package @@ -16018,9 +16197,6 @@ exception message with a traceback that points to the culprit.") make common patterns shorter and easier.") (license license:bsd-2))) -(define-public python2-utils - (package-with-python2 python-utils)) - (define-public python-diff-match-patch (package (name "python-diff-match-patch") @@ -16362,8 +16538,7 @@ Supported metrics are: (define-public python2-radon (let ((base (package-with-python2 (strip-python2-variant python-radon)))) - (package - (inherit base) + (package/inherit base (propagated-inputs `(("python-configparser" ,python2-configparser) ("python-future" ,python2-future) @@ -16650,8 +16825,7 @@ and integration into other projects.") (define-public python2-rfc6555 (let ((base (package-with-python2 (strip-python2-variant python-rfc6555)))) - (package - (inherit base) + (package/inherit base (propagated-inputs `(("python2-selectors2" ,python2-selectors2)))))) @@ -17768,8 +17942,7 @@ such as figshare or Zenodo.") (define-public python2-activepapers (let ((base (package-with-python2 (strip-python2-variant python-activepapers)))) - (package - (inherit base) + (package/inherit base (arguments (substitute-keyword-arguments (package-arguments base) ((#:phases phases) @@ -18003,7 +18176,18 @@ user's @file{~/Trash} directory.") (license license:bsd-3))) (define-public python2-send2trash - (package-with-python2 (strip-python2-variant python-send2trash))) + (let ((base (package-with-python2 + (strip-python2-variant python-send2trash)))) + (package/inherit base + (arguments + (substitute-keyword-arguments (package-arguments python-send2trash) + ((#:phases phases) + `(modify-phases ,phases + (add-before 'check 'setenv + (lambda _ + (setenv "PYTHONPATH" + (string-append (getcwd) ":" (getenv "PYTHONPATH"))) + #t))))))))) (define-public python-pyfavicon (package @@ -19148,6 +19332,31 @@ library: to minimize boilerplate code in traditional extension modules by inferring type information using compile-time introspection.") (license license:bsd-3))) +(define-public python-pooch + (package + (name "python-pooch") + (version "1.3.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pooch" version)) + (sha256 + (base32 "1618adsg9r8fsv422sv35z1i723q3a1iir5v7dv2sklh4pl4im1h")))) + (build-system python-build-system) + (arguments + `(#:tests? #f)) ;requires online data + (propagated-inputs + `(("python-appdirs" ,python-appdirs) + ("python-packaging" ,python-packaging) + ("python-requests" ,python-requests))) + (home-page "https://github.com/fatiando/pooch") + (synopsis "Manage your Python library's sample data files") + (description + "Pooch manages your Python library's sample data files: it automatically +downloads and stores them in a local directory, with support for versioning +and corruption checks.") + (license license:bsd-3))) + (define-public python-fasteners (package (name "python-fasteners") @@ -19724,6 +19933,26 @@ 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-sortedcollections + (package + (name "python-sortedcollections") + (version "2.1.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sortedcollections" version)) + (sha256 + (base32 + "1kfabpnjyjm5ml2zspry9jy3xq49aybchgaa4ahic2jqdjfn1sfq")))) + (build-system python-build-system) + (propagated-inputs + `(("python-sortedcontainers" ,python-sortedcontainers))) + (arguments '(#:tests? #f)) ; Tests not included in release tarball. + (home-page "http://www.grantjenks.com/docs/sortedcollections/") + (synopsis "Python Sorted Collections") + (description "Sorted Collections is a Python sorted collections library.") + (license license:asl2.0))) + (define-public python-sortedcontainers (package (name "python-sortedcontainers") @@ -19792,8 +20021,7 @@ data.") (define-public python2-cloudpickle (let ((base (package-with-python2 (strip-python2-variant python-cloudpickle)))) - (package - (inherit base) + (package/inherit base (native-inputs `(("python-mock" ,python2-mock) ,@(package-native-inputs base))) @@ -20033,7 +20261,7 @@ on regular expressions.") (define-public python2-reparser (let ((reparser (package-with-python2 (strip-python2-variant python-reparser)))) - (package (inherit reparser) + (package/inherit reparser (propagated-inputs `(("python2-enum34" ,python2-enum34) ,@(package-propagated-inputs reparser)))))) @@ -20994,14 +21222,14 @@ register custom encoders and decoders.") (define-public python-ujson (package (name "python-ujson") - (version "4.0.1") + (version "4.0.2") (source (origin (method url-fetch) (uri (pypi-uri "ujson" version)) (sha256 (base32 - "1lr9lbm76y3ah1463jggwg2hjcb709mpns5f752wxxbgnd0n5kr6")) + "0k9w0kypy7vlskzzp2vsjswaw8lbqdrplzkbflxki9vqwglsj5f6")) (modules '((guix build utils))) (snippet '(begin (delete-file-recursively "deps") #t)))) @@ -21439,29 +21667,6 @@ and cuts down boilerplate code when testing libraries for asyncio.") (description "This project allows Python code to extend built-in types.") (license (list license:gpl3+ license:expat)))) -(define-public python-shouldbe - (package - (name "python-shouldbe") - (version "0.1.2") - (source - (origin - (method url-fetch) - (uri (pypi-uri "shouldbe" version)) - (sha256 - (base32 - "16zbvjxf71dl4yfbgcr6idyim3mdrfvix1dv8b95p0s9z07372pj")) - (patches (search-patches "python-shouldbe-0.1.2-cpy3.8.patch")))) - (build-system python-build-system) - (propagated-inputs - `(("python-forbiddenfruit" ,python-forbiddenfruit))) - (native-inputs - `(("python-nose" ,python-nose))) - (home-page "https://github.com/directxman12/should_be") - (synopsis "Python Assertion Helpers inspired by Shouldly") - (description - "Python Assertion Helpers inspired by Shouldly.") - (license license:isc))) - (define-public python-k5test (package (name "python-k5test") @@ -21499,31 +21704,15 @@ tests.") (define-public python-gssapi (package (name "python-gssapi") - (version "1.6.9") + (version "1.6.12") (source (origin (method url-fetch) (uri (pypi-uri "gssapi" version)) (sha256 (base32 - "1fa78pn5jzfbwf3y6mj4fc8sh11wjf1hwh5qv39cdlxb71qsq2hb")))) + "1j2idrbrbczykzlb56q1bn0ivc9c0rjjljpk4yz86xn3gxfkpv8n")))) (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; Work around - ;; https://github.com/pythongssapi/python-gssapi/issues/220. - (add-before 'check 'disable-failing-tests - (lambda _ - (let ((reason "Disabled failing test (see: \ -https://github.com/pythongssapi/python-gssapi/issues/220).")) - (substitute* "gssapi/tests/test_high_level.py" - ((".*def test_add_with_impersonate.*" all) - (string-append all " self.skipTest('" reason "')\n"))) - (substitute* "gssapi/tests/test_raw.py" - ((".*def test_.*impersonate_name.*" all) - (string-append all " self.skipTest('" reason "')\n"))) - #t)))))) (propagated-inputs `(("python-decorator" ,python-decorator) ("python-six" ,python-six))) @@ -21531,8 +21720,7 @@ https://github.com/pythongssapi/python-gssapi/issues/220).")) `(("mit-krb5" ,mit-krb5))) ;; for tests (native-inputs - `(("python-shouldbe" ,python-shouldbe) - ("python-parameterized" ,python-parameterized) + `(("python-parameterized" ,python-parameterized) ("python-k5test" ,python-k5test) ("python-nose" ,python-nose))) (home-page "https://github.com/pythongssapi/python-gssapi") @@ -23515,14 +23703,14 @@ process.") (define-public python-aiofiles (package (name "python-aiofiles") - (version "0.5.0") + (version "0.6.0") (source (origin (method url-fetch) (uri (pypi-uri "aiofiles" version)) (sha256 (base32 - "1bqmv019x16qa3zah0z915cw6z4va3fjs60fk2s7vyah3gyvrrlq")))) + "14m01kjxm2j7zyljjj6xlhlgygcsriymbx730gc5jp9xglaina70")))) (build-system python-build-system) (home-page "https://github.com/Tinche/aiofiles") (synopsis "File support for @code{asyncio}") @@ -23903,3 +24091,48 @@ and frame grabber interface.") "This package provides a command-line interface (CLI) to the Jinja2 template engine.") (license license:bsd-3))) + +(define-public python-readability + (package + (name "python-readability") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "readability" version)) + (sha256 + (base32 + "1b8gq3g2zwvx0aivvdg56cc0bn7xw6f2v6psmxdx9aiipkw0s0zr")))) + (build-system python-build-system) + (home-page + "https://github.com/andreasvc/readability/") + (synopsis + "Measure the readability of a given text using surface +characteristics") + (description + "This package provides a Python library that is an implementation of +traditional readability measures based on simple surface +characteristics. These measures are basically linear regressions based on the +number of words, syllables, and sentences.") + (license license:asl2.0))) + +(define-public python-listparser + (package + (name "python-listparser") + (version "0.18") + (source + (origin + (method url-fetch) + (uri (pypi-uri "listparser" version)) + (sha256 + (base32 + "0hdqs1mmayw1r8yla43hgb4d9y3zqs5483vgf8j9ygczkd2wrq2b")))) + (build-system python-build-system) + (home-page + "https://github.com/kurtmckee/listparser") + (synopsis + "Parse subscription lists in Python") + (description + "This package provides a Python library that can parse OPML, FOAF, and +iGoogle subscription lists.") + (license license:expat))) |