guix/gnu/packages/jupyter.scm

;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2021 Hugo Lecomte <hugo.lecomte@inria.fr>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages jupyter)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system python)
  #:use-module (gnu packages bash)
  #:use-module (gnu packages check)
  #:use-module (gnu packages cpp)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages monitoring)
  #:use-module (gnu packages networking)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-check)
  #:use-module (gnu packages python-crypto)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages rdf)
  #:use-module (gnu packages time)
  #:use-module (gnu packages xml)
  #:use-module (gnu packages tls)
  #:use-module (gnu packages sphinx)
  #:use-module (gnu packages serialization)
  #:use-module (gnu packages docker))

(define-public python-jupyter-protocol
  (package
    (name "python-jupyter-protocol")
    (version "0.1.1")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "jupyter_protocol" version))
              (sha256
               (base32
                "1bk3as5yw9y5nmq6l15nr46aby34phmvsx9kxgqnm5pd5q2b5h57"))))
    (build-system python-build-system)
    (propagated-inputs
     `(("python-dateutil" ,python-dateutil)
       ("python-jupyter-core" ,python-jupyter-core)
       ("python-pyzmq" ,python-pyzmq)
       ("python-traitlets" ,python-traitlets)))
    (native-inputs
     `(("python-ipykernel" ,python-ipykernel)
       ("python-ipython" ,python-ipython)
       ("python-mock" ,python-mock)
       ("python-pytest" ,python-pytest)))
    (home-page "https://jupyter.org")
    (synopsis "Jupyter protocol implementation")
    (description
     "This Python library is an experimental implementation of the
@uref{https://jupyter-client.readthedocs.io/en/latest/messaging.html, Jupyter
protocol} to be used by both clients and kernels.")
    (license license:bsd-3)
    (properties '((upstream-name . "jupyter_protocol")))))

(define-public python-jupyter-kernel-mgmt
  (package
    (name "python-jupyter-kernel-mgmt")
    (version "0.4.0")
    (source (origin
              (method url-fetch)
              (uri (pypi-uri "jupyter_kernel_mgmt" version))
              (sha256
               (base32
                "0i7a78dn89ca8h0a42giyxwcmk6y4wrdr7q8h2ax9vybb84c795q"))))
    (build-system python-build-system)
    (propagated-inputs
     `(("python-dateutil" ,python-dateutil)
       ("python-entrypoints" ,python-entrypoints)
       ("python-jupyter-core" ,python-jupyter-core)
       ("python-jupyter-protocol" ,python-jupyter-protocol)
       ("python-pyzmq" ,python-pyzmq)
       ("python-traitlets" ,python-traitlets)))
    (native-inputs
     `(("python-ipykernel" ,python-ipykernel)
       ("python-ipython" ,python-ipython)
       ("python-mock" ,python-mock)
       ("python-pytest" ,python-pytest)))
    (home-page "https://jupyter.org")
    (synopsis "Discover, launch, and communicate with Jupyter kernels")
    (description
     "This package is an experimental refactoring of the machinery for
launching and using Jupyter kernels.")
    (license license:bsd-3)
    (properties '((upstream-name . "jupyter_kernel_mgmt")))))

(define-public python-jupyter-kernel-test
  (package
    (name "python-jupyter-kernel-test")
    (version "0.3")
    (home-page "https://github.com/jupyter/jupyter_kernel_test")
    (source (origin
              ;; PyPI has a ".whl" file but not a proper source release.
              ;; Thus, fetch code from Git.
              (method git-fetch)
              (uri (git-reference (url home-page) (commit version)))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "00iy74i4i8is6axb9vlsm0b9wxkvyyxnbl8r0i4gaj3xd788jm83"))))
    (build-system python-build-system)
    (arguments
     ;; The repo doesn't contain a "setup.py" file so install files manually.
     '(#:phases (modify-phases %standard-phases
                  (delete 'build)
                  (delete 'check)
                  (replace 'install
                    (lambda* (#:key inputs outputs #:allow-other-keys)
                      (let* ((out (assoc-ref outputs "out"))
                             (version (python-version (assoc-ref inputs "python")))
                             (pydir (string-append out "/lib/python"
                                                   version "/site-packages/"
                                                   "jupyter_kernel_test")))
                        (for-each (lambda (file)
                                    (install-file file pydir))
                                  (find-files "jupyter_kernel_test"
                                              "\\.py$"))
                        #t))))))
    (propagated-inputs
     `(("python-jupyter-kernel-mgmt" ,python-jupyter-kernel-mgmt)
       ("python-jupyter-protocol" ,python-jupyter-protocol)
       ("python-jsonschema" ,python-jsonschema)))
    (synopsis "Test Jupyter kernels")
    (description
     "@code{jupyter_kernel_test} is a tool for testing Jupyter kernels.  It
tests kernels for successful code execution and conformance with the
@uref{https://jupyter-client.readthedocs.io/en/latest/messaging.html, Jupyter
Messaging Protocol}.")
    (license license:bsd-3)))

(define-public xeus
  (package
    (name "xeus")
    (version "0.23.2")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/QuantStack/xeus")
                    (commit version)))
              (sha256
               (base32
                "1m1b6z1538r7mv2ggn7bdbd9570ja7cadplq64zl8rgl2c8vdi2a"))
              (file-name (git-file-name name version))))
    (build-system cmake-build-system)
    (arguments
     '(#:configure-flags '("-DBUILD_STATIC_LIBS=OFF"
                           "-DDISABLE_ARCH_NATIVE=ON" ;no '-march=native'
                           "-DBUILD_TESTING=ON")))
    (native-inputs
     `(("pkg-config" ,pkg-config)

       ;; The following inputs are used by the test suite.
       ("googletest" ,googletest)
       ("python-pytest" ,python-pytest)
       ("python" ,python-3)
       ("python-jupyter-kernel-test" ,python-jupyter-kernel-test)
       ("python-jupyter-client" ,python-jupyter-client)))
    (inputs
     `(("xtl" ,xtl)
       ("json-modern-cxx" ,json-modern-cxx)
       ("cppzmq" ,cppzmq)
       ("zeromq" ,zeromq)
       ("openssl" ,openssl)
       ("util-linux" ,util-linux "lib")))         ;libuuid
    (home-page "https://quantstack.net/xeus")
    (synopsis "C++ implementation of the Jupyter Kernel protocol")
    (description
     "@code{xeus} is a library meant to facilitate the implementation of
kernels for Jupyter.  It takes the burden of implementing the Jupyter Kernel
protocol so developers can focus on implementing the interpreter part of the
kernel.

Several Jupyter kernels are built upon @code{xeus}, such as @code{xeus-cling},
a kernel for the C++ programming language, and @code{xeus-python}, an
alternative Python kernel for Jupyter.")
    (license license:bsd-3)))

(define-public python-jupyterlab-pygments
  (package
    (name "python-jupyterlab-pygments")
    (version "0.1.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "jupyterlab_pygments" version))
       (sha256
        (base32
         "0ij14mmnc39nmf84i0av6j9glazjic7wzv1qyhr0j5966s3s1kfg"))))
    (build-system python-build-system)
    (arguments '(#:tests? #false)) ; there are no tests
    (propagated-inputs
     `(("python-pygments" ,python-pygments)))
    (home-page "https://jupyter.org")
    (synopsis "Pygments theme using JupyterLab CSS variables")
    (description
     "This package contains a syntax coloring theme for pygments making use of
the JupyterLab CSS variables.")
    (license license:bsd-3)))

(define-public python-jupyter-packaging
  (package
    (name "python-jupyter-packaging")
    (version "0.9.1")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "jupyter_packaging" version))
       (sha256
        (base32
         "0r015c0m713d19asmpimsw6bk2sqv2lpd2nccgjzjdj5h1crg0bg"))))
    (build-system python-build-system)
    (propagated-inputs
     `(("python-deprecation" ,python-deprecation)
       ("python-packaging" ,python-packaging)
       ("python-setuptools" ,python-setuptools)
       ("python-tomlkit" ,python-tomlkit)
       ("python-wheel" ,python-wheel)))
    (native-inputs
     `(("python-pypa-build" ,python-pypa-build)
       ("python-coverage" ,python-coverage)
       ("python-pytest" ,python-pytest)
       ("python-pytest-cov" ,python-pytest-cov)
       ("python-pytest-mock" ,python-pytest-mock)))
    (home-page "https://jupyter.org")
    (synopsis "Jupyter packaging utilities")
    (description "This package provides tools to help build and install
Jupyter Python packages that require a pre-build step that may include
JavaScript build steps.")
    (license license:bsd-3)))

(define-public python-jupyter-server
  (package
    (name "python-jupyter-server")
    (version "1.10.2")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "jupyter_server" version))
       (sha256
        (base32
         "1gvjbsw5nl94hz02rnkr4g4kkvh9fz7i45vz17hzwyvdpj7bd8yk"))))
    (build-system python-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (replace 'check
           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
             (when tests?
               (add-installed-pythonpath inputs outputs)
               (let ((home (string-append (getcwd) "/guix-home")))
                 (setenv "HOME" home))
               ;; Add jupyter-server executable to PATH.
               (setenv "PATH"
                       (string-append (assoc-ref outputs "out") "/bin:"
                                      (getenv "PATH")))
               (with-directory-excursion "jupyter_server"
                 ;; The pytest fixtures are only loaded when the file is
                 ;; called conftest.py.
                 (rename-file "pytest_plugin.py" "conftest.py")
                 (invoke "pytest" "-vv"
                         ;; Fails with internal server error
                         "-k" "not test_list_formats"
                         ;; Integration tests require a server.
                         "-m" "not integration_test"))))))))
    (propagated-inputs
     `(("python-anyio" ,python-anyio)
       ("python-argon2-cffi" ,python-argon2-cffi)
       ("python-ipython-genutils" ,python-ipython-genutils)
       ("python-jinja2" ,python-jinja2)
       ("python-jupyter-client" ,python-jupyter-client)
       ("python-jupyter-core" ,python-jupyter-core)
       ("python-nbconvert" ,python-nbconvert)
       ("python-nbformat" ,python-nbformat)
       ("python-prometheus-client" ,python-prometheus-client)
       ("python-pyzmq" ,python-pyzmq)
       ("python-requests-unixsocket" ,python-requests-unixsocket)
       ("python-send2trash" ,python-send2trash)
       ("python-terminado" ,python-terminado)
       ("python-tornado" ,python-tornado-6)
       ("python-traitlets" ,python-traitlets)
       ("python-websocket-client" ,python-websocket-client)))
    (native-inputs
     `(("python-coverage" ,python-coverage)
       ("python-ipykernel" ,python-ipykernel)
       ("python-pytest" ,python-pytest)
       ("python-pytest-console-scripts" ,python-pytest-console-scripts)
       ("python-pytest-cov" ,python-pytest-cov)
       ("python-pytest-mock" ,python-pytest-mock)
       ("python-pytest-tornasync" ,python-pytest-tornasync)
       ("python-requests" ,python-requests)))
    (home-page "https://jupyter.org")
    (synopsis "Core services, APIs, and REST endpoints for Jupyter web applications")
    (description
     "This package provides the backend—i.e. core services, APIs, and REST
endpoints—to Jupyter web applications.")
    (license license:expat)))

(define-public python-jupyterlab-widgets
  (package
    (name "python-jupyterlab-widgets")
    (version "1.0.0")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "jupyterlab_widgets" version))
       (sha256
        (base32
         "0y7vhhas3qndiypcpcfnhrj9n92v2w4hdc86nn620s9h9nl2j6jw"))))
    (build-system python-build-system)
    (native-inputs
     `(("python-jupyter-packaging" ,python-jupyter-packaging)
       ("python-setuptools" ,python-setuptools)))
    (home-page "https://github.com/jupyter-widgets/ipywidgets")
    (synopsis "Interactive widgets for Jupyter Notebooks")
    (description "ipywidgets, also known as jupyter-widgets or simply widgets,
are interactive HTML widgets for Jupyter notebooks and the IPython kernel.")
    (license license:bsd-3)))

(define-public python-nbclient
  (package
    (name "python-nbclient")
    (version "0.5.3")
    (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "nbclient" version))
       (sha256
        (base32
         "172q4r6mq0lg394di0pc6ipvniy14jg38wkdsj48r366609jf5yv"))))
    (build-system python-build-system)
    ;; Tests require a kernel via python-ipykernel, and also tools from
    ;; nbconvert.
    (arguments '(#:tests? #false))
    (propagated-inputs
     `(("python-async-generator" ,python-async-generator)
       ("python-jupyter-client" ,python-jupyter-client)
       ("python-nbformat" ,python-nbformat)
       ("python-nest-asyncio" ,python-nest-asyncio)
       ("python-traitlets" ,python-traitlets)))
    (native-inputs
     `(("python-black" ,python-black)
       ("python-bumpversion" ,python-bumpversion)
       ("python-check-manifest" ,python-check-manifest)
       ("python-codecov" ,python-codecov)
       ("python-coverage" ,python-coverage)
       ("python-flake8" ,python-flake8)
       ;; ("python-ipykernel" ,python-ipykernel)
       ;; ("python-ipython" ,python-ipython)
       ;; ("python-ipywidgets" ,python-ipywidgets)
       ("python-mypy" ,python-mypy)
       ("python-pip" ,python-pip)
       ("python-pytest" ,python-pytest)
       ("python-pytest-cov" ,python-pytest-cov)
       ("python-setuptools" ,python-setuptools)
       ("python-testpath" ,python-testpath)
       ("python-tox" ,python-tox)
       ("python-twine" ,python-twine)
       ("python-wheel" ,python-wheel)
       ("python-xmltodict" ,python-xmltodict)))
    (home-page "https://jupyter.org")
    (synopsis "Client library for executing notebooks")
    (description
     "This package provides a client library for executing notebooks. Formerly
nbconvert's @code{ExecutePreprocessor.}")
    (license license:bsd-3)))

(define-public repo2docker
  (package
    (name "repo2docker")
    (version "2021.03.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/jupyterhub/repo2docker/")
                    (commit "2021.03.0")))
              (file-name (git-file-name name version))
              (sha256
               (base32
                "18w8rgf7fpf79kx36y2c3xi3d52i41z112l3sz719d8kg0bir16m"))))
    (outputs '("out" "doc"))
    (build-system python-build-system)
    (arguments
     `(#:phases (modify-phases %standard-phases
                  (add-after 'patch-shebangs 'fix-install-miniforge
                    (lambda* (#:key outputs #:allow-other-keys)
                      (let* ((out (assoc-ref outputs "out")))
                        (substitute* (find-files
                                      out "^(install-miniforge|install-nix|\
nix-shell-wrapper|repo2docker-entrypoint)")
                          (("^#!(.*)/bin/bash")
                           "#!/bin/bash"))
                        (substitute* (find-files out "^freeze\\.py$")
                          (("^#!(.*)/bin/python3")
                           "#!/bin/python3\n")))))
                  (add-after 'install 'make-doc
                    (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)))