c157ed08c7
* gnu/packages/jupyter.scm (repo2docker): Update to 2021.08.0. [arguments]: Disable Sphinx warnings, set PYTHONPATH, and refer to THIS-PACKAGE instead of the "name" variable directly. [native-inputs]: Add PYTHON-ENTRYPOINTS.
551 lines
21 KiB
Scheme
551 lines
21 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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;;; Copyright © 2022 Marius Bakke <marius@gnu.org>
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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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(list python-dateutil python-jupyter-core python-pyzmq
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python-traitlets))
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(native-inputs
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(list python-ipykernel python-ipython python-mock 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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(list python-dateutil
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python-entrypoints
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python-jupyter-core
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python-jupyter-protocol
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python-pyzmq
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python-traitlets))
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(native-inputs
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(list python-ipykernel python-ipython python-mock 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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(list python-jupyter-kernel-mgmt python-jupyter-protocol
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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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(list pkg-config
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;; The following inputs are used by the test suite.
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googletest
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python-pytest
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python-3
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python-jupyter-kernel-test
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python-jupyter-client))
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(inputs
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(list xtl
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json-modern-cxx
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cppzmq
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zeromq
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openssl
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`(,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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(list 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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(list python-deprecation python-packaging python-setuptools
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python-tomlkit python-wheel))
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(native-inputs
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(list python-pypa-build python-coverage python-pytest
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python-pytest-cov 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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(list python-anyio
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python-argon2-cffi
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python-ipython-genutils
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python-jinja2
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python-jupyter-client
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python-jupyter-core
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python-nbconvert
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python-nbformat
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python-prometheus-client
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python-pyzmq
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python-requests-unixsocket
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python-send2trash
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python-terminado
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python-tornado-6
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python-traitlets
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python-websocket-client))
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(native-inputs
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(list python-coverage
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python-ipykernel
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python-pytest
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python-pytest-console-scripts
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python-pytest-cov
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python-pytest-mock
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python-pytest-tornasync
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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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(list python-jupyter-packaging 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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(list python-async-generator python-jupyter-client python-nbformat
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python-nest-asyncio python-traitlets))
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(native-inputs
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(list python-black
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python-bumpversion
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python-check-manifest
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python-codecov
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python-coverage
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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
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python-pip
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python-pytest
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python-pytest-cov
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python-setuptools
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python-testpath
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python-tox
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python-twine
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python-wheel
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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 "2021.08.0")
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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 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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"111irpghzys0s5ixs8paskz7465cls1sm9d5bg45a15jklcw84a9"))))
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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)
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(let* ((out (assoc-ref outputs "doc"))
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(doc (string-append out "/share/doc/"
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,(package-name this-package))))
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(setenv "PYTHONPATH"
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(string-append (getcwd) ":"
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(getenv "GUIX_PYTHONPATH")))
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;; Don't treat warnings as errors.
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(substitute* "docs/Makefile"
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(("(SPHINXOPTS[[:blank:]]+= )-W" _ group)
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group))
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(with-directory-excursion "docs"
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(invoke "make" "html")
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(copy-recursively "build/html"
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(string-append doc "/html")))))))))
|
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(inputs
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(list python-traitlets
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python-toml
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python-semver
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python-ruamel.yaml
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python-requests
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python-json-logger
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python-jinja2
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python-escapism
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python-docker))
|
|
(native-inputs
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(list python-sphinx python-entrypoints python-recommonmark
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python-sphinxcontrib-autoprogram python-pydata-sphinx-theme))
|
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(home-page "https://repo2docker.readthedocs.io/en/latest/index.html#")
|
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(synopsis "Generate docker images from repositories")
|
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(description
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"repo2docker fetches a repository (from GitHub, GitLab, Zenodo, Figshare,
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Dataverse installations, a Git repository or a local directory) and builds a
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container image in which the code can be executed. The image build process is
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based on the configuration files found in the repository. repo2docker can be
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used to explore a repository locally by building and executing the constructed
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image of the repository, or as a means of building images that are pushed to a
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Docker registry.")
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(license license:bsd-3)))
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(define-public python-bash-kernel
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(package
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(name "python-bash-kernel")
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(version "0.7.2")
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(source (origin
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(method url-fetch)
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(uri (pypi-uri "bash_kernel" version))
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(sha256
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(base32
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"0w0nbr3iqqsgpk83rgd0f5b02462bkyj2n0h6i9dwyc1vpnq9350"))))
|
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(build-system python-build-system)
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(arguments
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`(#:tests? #f
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#:phases
|
|
(modify-phases %standard-phases
|
|
(add-after 'unpack 'bash-references
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|
(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
|
|
(list bash))
|
|
(propagated-inputs
|
|
(list python-pexpect python-ipykernel 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
|
|
(list python-traitlets python-jupyter-client python-notebook
|
|
python-ipykernel python-html5lib-0.9))
|
|
(propagated-inputs
|
|
(list python-sparqlwrapper 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
|
|
(list python-jupyter-client python-jupyter-server python-nbclient
|
|
python-nbconvert))
|
|
(native-inputs
|
|
(list python-ipywidgets
|
|
python-jupyter-packaging
|
|
python-matplotlib
|
|
python-mock
|
|
python-pytest
|
|
python-pytest-tornasync
|
|
python-setuptools
|
|
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)))
|