mirror of
https://git.in.rschanz.org/ryan77627/guix.git
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439f7c6887
* gnu/packages/jupyter.scm (python-jupyter-server)[native-inputs]: Replace python-pytest-6 with python-pytest.
576 lines
23 KiB
Scheme
576 lines
23 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
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;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2021 Hugo Lecomte <hugo.lecomte@inria.fr>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (gnu packages jupyter)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix packages)
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#:use-module (guix download)
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#:use-module (guix git-download)
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#:use-module (guix build-system cmake)
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#:use-module (guix build-system python)
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#:use-module (gnu packages bash)
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#:use-module (gnu packages check)
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#:use-module (gnu packages cpp)
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#:use-module (gnu packages linux)
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#:use-module (gnu packages monitoring)
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#:use-module (gnu packages networking)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-build)
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#:use-module (gnu packages python-check)
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#:use-module (gnu packages python-crypto)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages python-web)
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#:use-module (gnu packages rdf)
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#:use-module (gnu packages time)
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#:use-module (gnu packages xml)
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#:use-module (gnu packages tls)
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#:use-module (gnu packages sphinx)
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#:use-module (gnu packages serialization)
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#:use-module (gnu packages docker))
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(define-public python-jupyter-protocol
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(package
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(name "python-jupyter-protocol")
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(version "0.1.1")
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(source (origin
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(method url-fetch)
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(uri (pypi-uri "jupyter_protocol" version))
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(sha256
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(base32
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"1bk3as5yw9y5nmq6l15nr46aby34phmvsx9kxgqnm5pd5q2b5h57"))))
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(build-system python-build-system)
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(propagated-inputs
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`(("python-dateutil" ,python-dateutil)
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("python-jupyter-core" ,python-jupyter-core)
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("python-pyzmq" ,python-pyzmq)
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("python-traitlets" ,python-traitlets)))
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(native-inputs
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`(("python-ipykernel" ,python-ipykernel)
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("python-ipython" ,python-ipython)
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("python-mock" ,python-mock)
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("python-pytest" ,python-pytest)))
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(home-page "https://jupyter.org")
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(synopsis "Jupyter protocol implementation")
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(description
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"This Python library is an experimental implementation of the
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@uref{https://jupyter-client.readthedocs.io/en/latest/messaging.html, Jupyter
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protocol} to be used by both clients and kernels.")
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(license license:bsd-3)
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(properties '((upstream-name . "jupyter_protocol")))))
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(define-public python-jupyter-kernel-mgmt
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(package
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(name "python-jupyter-kernel-mgmt")
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(version "0.4.0")
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(source (origin
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(method url-fetch)
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(uri (pypi-uri "jupyter_kernel_mgmt" version))
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(sha256
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(base32
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"0i7a78dn89ca8h0a42giyxwcmk6y4wrdr7q8h2ax9vybb84c795q"))))
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(build-system python-build-system)
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(propagated-inputs
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`(("python-dateutil" ,python-dateutil)
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("python-entrypoints" ,python-entrypoints)
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("python-jupyter-core" ,python-jupyter-core)
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("python-jupyter-protocol" ,python-jupyter-protocol)
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("python-pyzmq" ,python-pyzmq)
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("python-traitlets" ,python-traitlets)))
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(native-inputs
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`(("python-ipykernel" ,python-ipykernel)
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("python-ipython" ,python-ipython)
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("python-mock" ,python-mock)
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("python-pytest" ,python-pytest)))
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(home-page "https://jupyter.org")
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(synopsis "Discover, launch, and communicate with Jupyter kernels")
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(description
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"This package is an experimental refactoring of the machinery for
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launching and using Jupyter kernels.")
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(license license:bsd-3)
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(properties '((upstream-name . "jupyter_kernel_mgmt")))))
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(define-public python-jupyter-kernel-test
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(package
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(name "python-jupyter-kernel-test")
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(version "0.3")
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(home-page "https://github.com/jupyter/jupyter_kernel_test")
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(source (origin
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;; PyPI has a ".whl" file but not a proper source release.
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;; Thus, fetch code from Git.
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(method git-fetch)
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(uri (git-reference (url home-page) (commit version)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"00iy74i4i8is6axb9vlsm0b9wxkvyyxnbl8r0i4gaj3xd788jm83"))))
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(build-system python-build-system)
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(arguments
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;; The repo doesn't contain a "setup.py" file so install files manually.
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'(#:phases (modify-phases %standard-phases
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(delete 'build)
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(delete 'check)
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(replace 'install
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(version (python-version (assoc-ref inputs "python")))
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(pydir (string-append out "/lib/python"
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version "/site-packages/"
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"jupyter_kernel_test")))
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(for-each (lambda (file)
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(install-file file pydir))
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(find-files "jupyter_kernel_test"
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"\\.py$"))
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#t))))))
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(propagated-inputs
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`(("python-jupyter-kernel-mgmt" ,python-jupyter-kernel-mgmt)
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("python-jupyter-protocol" ,python-jupyter-protocol)
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("python-jsonschema" ,python-jsonschema)))
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(synopsis "Test Jupyter kernels")
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(description
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"@code{jupyter_kernel_test} is a tool for testing Jupyter kernels. It
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tests kernels for successful code execution and conformance with the
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@uref{https://jupyter-client.readthedocs.io/en/latest/messaging.html, Jupyter
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Messaging Protocol}.")
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(license license:bsd-3)))
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(define-public xeus
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(package
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(name "xeus")
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(version "0.23.2")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/QuantStack/xeus")
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(commit version)))
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(sha256
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(base32
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"1m1b6z1538r7mv2ggn7bdbd9570ja7cadplq64zl8rgl2c8vdi2a"))
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(file-name (git-file-name name version))))
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(build-system cmake-build-system)
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(arguments
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'(#:configure-flags '("-DBUILD_STATIC_LIBS=OFF"
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"-DDISABLE_ARCH_NATIVE=ON" ;no '-march=native'
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"-DBUILD_TESTING=ON")))
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(native-inputs
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`(("pkg-config" ,pkg-config)
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;; The following inputs are used by the test suite.
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("googletest" ,googletest)
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("python-pytest" ,python-pytest)
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("python" ,python-3)
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("python-jupyter-kernel-test" ,python-jupyter-kernel-test)
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("python-jupyter-client" ,python-jupyter-client)))
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(inputs
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`(("xtl" ,xtl)
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("json-modern-cxx" ,json-modern-cxx)
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("cppzmq" ,cppzmq)
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("zeromq" ,zeromq)
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("openssl" ,openssl)
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("util-linux" ,util-linux "lib"))) ;libuuid
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(home-page "https://quantstack.net/xeus")
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(synopsis "C++ implementation of the Jupyter Kernel protocol")
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(description
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"@code{xeus} is a library meant to facilitate the implementation of
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kernels for Jupyter. It takes the burden of implementing the Jupyter Kernel
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protocol so developers can focus on implementing the interpreter part of the
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kernel.
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Several Jupyter kernels are built upon @code{xeus}, such as @code{xeus-cling},
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a kernel for the C++ programming language, and @code{xeus-python}, an
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alternative Python kernel for Jupyter.")
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(license license:bsd-3)))
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(define-public python-jupyterlab-pygments
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(package
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(name "python-jupyterlab-pygments")
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(version "0.1.2")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "jupyterlab_pygments" version))
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(sha256
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(base32
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"0ij14mmnc39nmf84i0av6j9glazjic7wzv1qyhr0j5966s3s1kfg"))))
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(build-system python-build-system)
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(arguments '(#:tests? #false)) ; there are no tests
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(propagated-inputs
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`(("python-pygments" ,python-pygments)))
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(home-page "https://jupyter.org")
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(synopsis "Pygments theme using JupyterLab CSS variables")
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(description
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"This package contains a syntax coloring theme for pygments making use of
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the JupyterLab CSS variables.")
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(license license:bsd-3)))
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(define-public python-jupyter-packaging
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(package
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(name "python-jupyter-packaging")
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(version "0.9.1")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "jupyter_packaging" version))
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(sha256
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(base32
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"0r015c0m713d19asmpimsw6bk2sqv2lpd2nccgjzjdj5h1crg0bg"))))
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(build-system python-build-system)
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(propagated-inputs
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`(("python-deprecation" ,python-deprecation)
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("python-packaging" ,python-packaging)
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("python-setuptools" ,python-setuptools)
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("python-tomlkit" ,python-tomlkit)
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("python-wheel" ,python-wheel)))
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(native-inputs
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`(("python-pypa-build" ,python-pypa-build)
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("python-coverage" ,python-coverage)
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("python-pytest" ,python-pytest)
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("python-pytest-cov" ,python-pytest-cov)
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("python-pytest-mock" ,python-pytest-mock)))
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(home-page "https://jupyter.org")
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(synopsis "Jupyter packaging utilities")
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(description "This package provides tools to help build and install
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Jupyter Python packages that require a pre-build step that may include
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JavaScript build steps.")
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(license license:bsd-3)))
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(define-public python-jupyter-server
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(package
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(name "python-jupyter-server")
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(version "1.10.2")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "jupyter_server" version))
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(sha256
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(base32
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"1gvjbsw5nl94hz02rnkr4g4kkvh9fz7i45vz17hzwyvdpj7bd8yk"))))
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(build-system python-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(replace 'check
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(lambda* (#:key inputs outputs tests? #:allow-other-keys)
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(when tests?
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(add-installed-pythonpath inputs outputs)
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(let ((home (string-append (getcwd) "/guix-home")))
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(setenv "HOME" home))
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;; Add jupyter-server executable to PATH.
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(setenv "PATH"
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(string-append (assoc-ref outputs "out") "/bin:"
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(getenv "PATH")))
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(with-directory-excursion "jupyter_server"
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;; The pytest fixtures are only loaded when the file is
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;; called conftest.py.
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(rename-file "pytest_plugin.py" "conftest.py")
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(invoke "pytest" "-vv"
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;; Fails with internal server error
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"-k" "not test_list_formats"
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;; Integration tests require a server.
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"-m" "not integration_test"))))))))
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(propagated-inputs
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`(("python-anyio" ,python-anyio)
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("python-argon2-cffi" ,python-argon2-cffi)
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("python-ipython-genutils" ,python-ipython-genutils)
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("python-jinja2" ,python-jinja2)
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("python-jupyter-client" ,python-jupyter-client)
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("python-jupyter-core" ,python-jupyter-core)
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("python-nbconvert" ,python-nbconvert)
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("python-nbformat" ,python-nbformat)
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("python-prometheus-client" ,python-prometheus-client)
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("python-pyzmq" ,python-pyzmq)
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("python-requests-unixsocket" ,python-requests-unixsocket)
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("python-send2trash" ,python-send2trash)
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("python-terminado" ,python-terminado)
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("python-tornado" ,python-tornado-6)
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("python-traitlets" ,python-traitlets)
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("python-websocket-client" ,python-websocket-client)))
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(native-inputs
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`(("python-coverage" ,python-coverage)
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("python-ipykernel" ,python-ipykernel)
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("python-pytest" ,python-pytest)
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("python-pytest-console-scripts" ,python-pytest-console-scripts)
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("python-pytest-cov" ,python-pytest-cov)
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("python-pytest-mock" ,python-pytest-mock)
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("python-pytest-tornasync" ,python-pytest-tornasync)
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("python-requests" ,python-requests)))
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(home-page "https://jupyter.org")
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(synopsis "Core services, APIs, and REST endpoints for Jupyter web applications")
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(description
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"This package provides the backend—i.e. core services, APIs, and REST
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endpoints—to Jupyter web applications.")
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(license license:expat)))
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(define-public python-jupyterlab-widgets
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(package
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(name "python-jupyterlab-widgets")
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(version "1.0.0")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "jupyterlab_widgets" version))
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(sha256
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(base32
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"0y7vhhas3qndiypcpcfnhrj9n92v2w4hdc86nn620s9h9nl2j6jw"))))
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(build-system python-build-system)
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(native-inputs
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`(("python-jupyter-packaging" ,python-jupyter-packaging)
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("python-setuptools" ,python-setuptools)))
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(home-page "https://github.com/jupyter-widgets/ipywidgets")
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(synopsis "Interactive widgets for Jupyter Notebooks")
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(description "ipywidgets, also known as jupyter-widgets or simply widgets,
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are interactive HTML widgets for Jupyter notebooks and the IPython kernel.")
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(license license:bsd-3)))
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(define-public python-nbclient
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(package
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(name "python-nbclient")
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(version "0.5.3")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "nbclient" version))
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(sha256
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(base32
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"172q4r6mq0lg394di0pc6ipvniy14jg38wkdsj48r366609jf5yv"))))
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(build-system python-build-system)
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;; Tests require a kernel via python-ipykernel, and also tools from
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;; nbconvert.
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(arguments '(#:tests? #false))
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(propagated-inputs
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`(("python-async-generator" ,python-async-generator)
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("python-jupyter-client" ,python-jupyter-client)
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("python-nbformat" ,python-nbformat)
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("python-nest-asyncio" ,python-nest-asyncio)
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("python-traitlets" ,python-traitlets)))
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(native-inputs
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`(("python-black" ,python-black)
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("python-bumpversion" ,python-bumpversion)
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("python-check-manifest" ,python-check-manifest)
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("python-codecov" ,python-codecov)
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("python-coverage" ,python-coverage)
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("python-flake8" ,python-flake8)
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;; ("python-ipykernel" ,python-ipykernel)
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;; ("python-ipython" ,python-ipython)
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;; ("python-ipywidgets" ,python-ipywidgets)
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("python-mypy" ,python-mypy)
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("python-pip" ,python-pip)
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("python-pytest" ,python-pytest)
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("python-pytest-cov" ,python-pytest-cov)
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("python-setuptools" ,python-setuptools)
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("python-testpath" ,python-testpath)
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("python-tox" ,python-tox)
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("python-twine" ,python-twine)
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("python-wheel" ,python-wheel)
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("python-xmltodict" ,python-xmltodict)))
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(home-page "https://jupyter.org")
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(synopsis "Client library for executing notebooks")
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(description
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"This package provides a client library for executing notebooks. Formerly
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nbconvert's @code{ExecutePreprocessor.}")
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(license license:bsd-3)))
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(define-public repo2docker
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(package
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(name "repo2docker")
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(version "2021.03.0")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/jupyterhub/repo2docker/")
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(commit "2021.03.0")))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"18w8rgf7fpf79kx36y2c3xi3d52i41z112l3sz719d8kg0bir16m"))))
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(outputs '("out" "doc"))
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(build-system python-build-system)
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(arguments
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`(#:phases (modify-phases %standard-phases
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(add-after 'patch-shebangs 'fix-install-miniforge
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out")))
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(substitute* (find-files
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out "^(install-miniforge|install-nix|\
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nix-shell-wrapper|repo2docker-entrypoint)")
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(("^#!(.*)/bin/bash")
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"#!/bin/bash"))
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(substitute* (find-files out "^freeze\\.py$")
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(("^#!(.*)/bin/python3")
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"#!/bin/python3\n")))))
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(add-after 'install 'make-doc
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(lambda* (#:key outputs #:allow-other-keys)
|
|
(let* ((out (assoc-ref outputs "doc"))
|
|
(doc (string-append out "/share/doc/"
|
|
,name)))
|
|
(setenv "PYTHONPATH"
|
|
(string-append (getcwd) ":"
|
|
(getenv "PYTHONPATH")))
|
|
(with-directory-excursion "docs"
|
|
(invoke "make" "html")
|
|
(copy-recursively "build/html"
|
|
(string-append doc "/html")))))))))
|
|
(inputs
|
|
`(("python-traitlets" ,python-traitlets)
|
|
("python-toml" ,python-toml)
|
|
("python-semver" ,python-semver)
|
|
("python-ruamel.yaml" ,python-ruamel.yaml)
|
|
("python-requests" ,python-requests)
|
|
("python-json-logger" ,python-json-logger)
|
|
("python-jinja2" ,python-jinja2)
|
|
("python-escapism" ,python-escapism)
|
|
("python-docker" ,python-docker)))
|
|
(native-inputs
|
|
`(("python-sphinx" ,python-sphinx)
|
|
("python-recommonmark" ,python-recommonmark)
|
|
("python-sphinxcontrib-autoprogram" ,python-sphinxcontrib-autoprogram)
|
|
("python-pydata-sphinx-theme" ,python-pydata-sphinx-theme)))
|
|
(home-page "https://repo2docker.readthedocs.io/en/latest/index.html#")
|
|
(synopsis "Generate docker images from repositories")
|
|
(description
|
|
"repo2docker fetches a repository (from GitHub, GitLab, Zenodo, Figshare,
|
|
Dataverse installations, a Git repository or a local directory) and builds a
|
|
container image in which the code can be executed. The image build process is
|
|
based on the configuration files found in the repository. repo2docker can be
|
|
used to explore a repository locally by building and executing the constructed
|
|
image of the repository, or as a means of building images that are pushed to a
|
|
Docker registry.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-bash-kernel
|
|
(package
|
|
(name "python-bash-kernel")
|
|
(version "0.7.2")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "bash_kernel" version))
|
|
(sha256
|
|
(base32
|
|
"0w0nbr3iqqsgpk83rgd0f5b02462bkyj2n0h6i9dwyc1vpnq9350"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:tests? #f
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'bash-references
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(substitute* "bash_kernel/kernel.py"
|
|
(("\"bash\"")
|
|
(string-append "\"" (assoc-ref inputs "bash") "/bin/bash\""))
|
|
(("\\['bash', ")
|
|
(string-append "['" (assoc-ref inputs "bash") "/bin/bash', ")))
|
|
#t))
|
|
(add-after 'install 'install-kernelspec
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let ((out (assoc-ref outputs "out")))
|
|
(setenv "HOME" "/tmp")
|
|
(invoke "python" "-m" "bash_kernel.install" "--prefix" out)
|
|
#t))))))
|
|
(inputs
|
|
`(("bash" ,bash)))
|
|
(propagated-inputs
|
|
`(("python-pexpect" ,python-pexpect)
|
|
("python-ipykernel" ,python-ipykernel)
|
|
("python-jupyter-client" ,python-jupyter-client)))
|
|
(home-page "https://github.com/takluyver/bash_kernel")
|
|
(synopsis "Jupyter kernel for Bash")
|
|
(description "A bash shell kernel for Jupyter.")
|
|
(license license:expat)))
|
|
|
|
(define-public python-sparqlkernel
|
|
(package
|
|
(name "python-sparqlkernel")
|
|
(version "1.3.0")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "sparqlkernel" version))
|
|
(sha256
|
|
(base32
|
|
"004v22nyi5cnpxq4fiws89p7i5wcnzv45n3n70axdd6prh6rkapx"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:tests? #f
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'no-custom-css
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(substitute* "sparqlkernel/install.py"
|
|
(("install_custom_css\\( destd, PKGNAME \\)") ""))
|
|
#t))
|
|
(add-after 'install 'install-kernelspec
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(let ((out (assoc-ref outputs "out")))
|
|
(setenv "HOME" "/tmp")
|
|
(add-installed-pythonpath inputs outputs)
|
|
(invoke
|
|
(string-append out "/bin/jupyter-sparqlkernel")
|
|
"install"
|
|
(string-append "--InstallKernelSpec.prefix=" out))
|
|
#t))))))
|
|
(native-inputs
|
|
`(("python-traitlets" ,python-traitlets)
|
|
("python-jupyter-client" ,python-jupyter-client)
|
|
("python-notebook" ,python-notebook)
|
|
("python-ipykernel" ,python-ipykernel)
|
|
("python-html5lib" ,python-html5lib-0.9)))
|
|
(propagated-inputs
|
|
`(("python-sparqlwrapper" ,python-sparqlwrapper)
|
|
("python-pygments" ,python-pygments)))
|
|
(home-page "https://github.com/paulovn/sparql-kernel")
|
|
(synopsis "Jupyter kernel for SPARQL")
|
|
(description "This module installs a Jupyter kernel for SPARQL. It allows
|
|
sending queries to an SPARQL endpoint and fetching & presenting the results in
|
|
a notebook.")
|
|
(license license:bsd-3)))
|
|
|
|
(define-public python-voila
|
|
(package
|
|
(name "python-voila")
|
|
(version "0.2.10")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (pypi-uri "voila" version))
|
|
(sha256
|
|
(base32
|
|
"0krfc95yjlhjdmrsladhy6lpf4xs1zw49nmkyl4pkykndglvwa1m"))))
|
|
(build-system python-build-system)
|
|
(propagated-inputs
|
|
`(("python-jupyter-client" ,python-jupyter-client)
|
|
("python-jupyter-server" ,python-jupyter-server)
|
|
("python-nbclient" ,python-nbclient)
|
|
("python-nbconvert" ,python-nbconvert)))
|
|
(native-inputs
|
|
`(("python-ipywidgets" ,python-ipywidgets)
|
|
("python-jupyter-packaging" ,python-jupyter-packaging)
|
|
("python-matplotlib" ,python-matplotlib)
|
|
("python-mock" ,python-mock)
|
|
("python-pytest" ,python-pytest)
|
|
("python-pytest-tornasync" ,python-pytest-tornasync)
|
|
("python-setuptools" ,python-setuptools)
|
|
("python-tornado" ,python-tornado-6)))
|
|
(home-page "https://github.com/voila-dashboards/voila")
|
|
(synopsis "Render live Jupyter notebooks with interactive widgets")
|
|
(description
|
|
"Voilà turns Jupyter notebooks into standalone web applications. Unlike
|
|
the usual HTML-converted notebooks, each user connecting to the Voilà tornado
|
|
application gets a dedicated Jupyter kernel which can execute the callbacks to
|
|
changes in Jupyter interactive widgets.")
|
|
(license license:bsd-3)))
|