gnu/packages/jupyter.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org>
   3 ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
   4 ;;; Copyright © 2021 Hugo Lecomte <hugo.lecomte@inria.fr>
   5 ;;; Copyright © 2022 Marius Bakke <marius@gnu.org>
   6 ;;;
   7 ;;; This file is part of GNU Guix.
   8 ;;;
   9 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  10 ;;; under the terms of the GNU General Public License as published by
  11 ;;; the Free Software Foundation; either version 3 of the License, or (at
  12 ;;; your option) any later version.
  13 ;;;
  14 ;;; GNU Guix is distributed in the hope that it will be useful, but
  15 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  16 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  17 ;;; GNU General Public License for more details.
  18 ;;;
  19 ;;; You should have received a copy of the GNU General Public License
  20 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  21
  22 (define-module (gnu packages jupyter)
  23   #:use-module ((guix licenses) #:prefix license:)
  24   #:use-module (guix packages)
  25   #:use-module (guix download)
  26   #:use-module (guix git-download)
  27   #:use-module (guix build-system cmake)
  28   #:use-module (guix build-system python)
  29   #:use-module (gnu packages bash)
  30   #:use-module (gnu packages check)
  31   #:use-module (gnu packages cpp)
  32   #:use-module (gnu packages linux)
  33   #:use-module (gnu packages monitoring)
  34   #:use-module (gnu packages networking)
  35   #:use-module (gnu packages pkg-config)
  36   #:use-module (gnu packages python)
  37   #:use-module (gnu packages python-build)
  38   #:use-module (gnu packages python-check)
  39   #:use-module (gnu packages python-crypto)
  40   #:use-module (gnu packages python-xyz)
  41   #:use-module (gnu packages python-web)
  42   #:use-module (gnu packages rdf)
  43   #:use-module (gnu packages time)
  44   #:use-module (gnu packages xml)
  45   #:use-module (gnu packages tls)
  46   #:use-module (gnu packages sphinx)
  47   #:use-module (gnu packages serialization)
  48   #:use-module (gnu packages docker))
  49
  50 (define-public python-jupyter-protocol
  51   (package
  52     (name "python-jupyter-protocol")
  53     (version "0.1.1")
  54     (source (origin
  55               (method url-fetch)
  56               (uri (pypi-uri "jupyter_protocol" version))
  57               (sha256
  58                (base32
  59                 "1bk3as5yw9y5nmq6l15nr46aby34phmvsx9kxgqnm5pd5q2b5h57"))))
  60     (build-system python-build-system)
  61     (propagated-inputs
  62      (list python-dateutil python-jupyter-core python-pyzmq
  63            python-traitlets))
  64     (native-inputs
  65      (list python-ipykernel python-ipython python-mock python-pytest))
  66     (home-page "https://jupyter.org")
  67     (synopsis "Jupyter protocol implementation")
  68     (description
  69      "This Python library is an experimental implementation of the
  70 @uref{https://jupyter-client.readthedocs.io/en/latest/messaging.html, Jupyter
  71 protocol} to be used by both clients and kernels.")
  72     (license license:bsd-3)
  73     (properties '((upstream-name . "jupyter_protocol")))))
  74
  75 (define-public python-jupyter-kernel-mgmt
  76   (package
  77     (name "python-jupyter-kernel-mgmt")
  78     (version "0.4.0")
  79     (source (origin
  80               (method url-fetch)
  81               (uri (pypi-uri "jupyter_kernel_mgmt" version))
  82               (sha256
  83                (base32
  84                 "0i7a78dn89ca8h0a42giyxwcmk6y4wrdr7q8h2ax9vybb84c795q"))))
  85     (build-system python-build-system)
  86     (propagated-inputs
  87      (list python-dateutil
  88            python-entrypoints
  89            python-jupyter-core
  90            python-jupyter-protocol
  91            python-pyzmq
  92            python-traitlets))
  93     (native-inputs
  94      (list python-ipykernel python-ipython python-mock python-pytest))
  95     (home-page "https://jupyter.org")
  96     (synopsis "Discover, launch, and communicate with Jupyter kernels")
  97     (description
  98      "This package is an experimental refactoring of the machinery for
  99 launching and using Jupyter kernels.")
 100     (license license:bsd-3)
 101     (properties '((upstream-name . "jupyter_kernel_mgmt")))))
 102
 103 (define-public python-jupyter-kernel-test
 104   (package
 105     (name "python-jupyter-kernel-test")
 106     (version "0.3")
 107     (home-page "https://github.com/jupyter/jupyter_kernel_test")
 108     (source (origin
 109               ;; PyPI has a ".whl" file but not a proper source release.
 110               ;; Thus, fetch code from Git.
 111               (method git-fetch)
 112               (uri (git-reference (url home-page) (commit version)))
 113               (file-name (git-file-name name version))
 114               (sha256
 115                (base32
 116                 "00iy74i4i8is6axb9vlsm0b9wxkvyyxnbl8r0i4gaj3xd788jm83"))))
 117     (build-system python-build-system)
 118     (arguments
 119      ;; The repo doesn't contain a "setup.py" file so install files manually.
 120      '(#:phases (modify-phases %standard-phases
 121                   (delete 'build)
 122                   (delete 'check)
 123                   (replace 'install
 124                     (lambda* (#:key inputs outputs #:allow-other-keys)
 125                       (let* ((out (assoc-ref outputs "out"))
 126                              (version (python-version (assoc-ref inputs "python")))
 127                              (pydir (string-append out "/lib/python"
 128                                                    version "/site-packages/"
 129                                                    "jupyter_kernel_test")))
 130                         (for-each (lambda (file)
 131                                     (install-file file pydir))
 132                                   (find-files "jupyter_kernel_test"
 133                                               "\\.py$"))
 134                         #t))))))
 135     (propagated-inputs
 136      (list python-jupyter-kernel-mgmt python-jupyter-protocol
 137            python-jsonschema))
 138     (synopsis "Test Jupyter kernels")
 139     (description
 140      "@code{jupyter_kernel_test} is a tool for testing Jupyter kernels.  It
 141 tests kernels for successful code execution and conformance with the
 142 @uref{https://jupyter-client.readthedocs.io/en/latest/messaging.html, Jupyter
 143 Messaging Protocol}.")
 144     (license license:bsd-3)))
 145
 146 (define-public xeus
 147   (package
 148     (name "xeus")
 149     (version "0.23.2")
 150     (source (origin
 151               (method git-fetch)
 152               (uri (git-reference
 153                     (url "https://github.com/QuantStack/xeus")
 154                     (commit version)))
 155               (sha256
 156                (base32
 157                 "1m1b6z1538r7mv2ggn7bdbd9570ja7cadplq64zl8rgl2c8vdi2a"))
 158               (file-name (git-file-name name version))))
 159     (build-system cmake-build-system)
 160     (arguments
 161      '(#:configure-flags '("-DBUILD_STATIC_LIBS=OFF"
 162                            "-DDISABLE_ARCH_NATIVE=ON" ;no '-march=native'
 163                            "-DBUILD_TESTING=ON")))
 164     (native-inputs
 165      (list pkg-config
 166            ;; The following inputs are used by the test suite.
 167            googletest
 168            python-pytest
 169            python-3
 170            python-jupyter-kernel-test
 171            python-jupyter-client))
 172     (inputs
 173      (list xtl
 174            json-modern-cxx
 175            cppzmq
 176            zeromq
 177            openssl
 178            `(,util-linux "lib")))         ;libuuid
 179     (home-page "https://quantstack.net/xeus")
 180     (synopsis "C++ implementation of the Jupyter Kernel protocol")
 181     (description
 182      "@code{xeus} is a library meant to facilitate the implementation of
 183 kernels for Jupyter.  It takes the burden of implementing the Jupyter Kernel
 184 protocol so developers can focus on implementing the interpreter part of the
 185 kernel.
 186
 187 Several Jupyter kernels are built upon @code{xeus}, such as @code{xeus-cling},
 188 a kernel for the C++ programming language, and @code{xeus-python}, an
 189 alternative Python kernel for Jupyter.")
 190     (license license:bsd-3)))
 191
 192 (define-public python-jupyterlab-pygments
 193   (package
 194     (name "python-jupyterlab-pygments")
 195     (version "0.1.2")
 196     (source
 197      (origin
 198        (method url-fetch)
 199        (uri (pypi-uri "jupyterlab_pygments" version))
 200        (sha256
 201         (base32
 202          "0ij14mmnc39nmf84i0av6j9glazjic7wzv1qyhr0j5966s3s1kfg"))))
 203     (build-system python-build-system)
 204     (arguments '(#:tests? #false)) ; there are no tests
 205     (propagated-inputs
 206      (list python-pygments))
 207     (home-page "https://jupyter.org")
 208     (synopsis "Pygments theme using JupyterLab CSS variables")
 209     (description
 210      "This package contains a syntax coloring theme for pygments making use of
 211 the JupyterLab CSS variables.")
 212     (license license:bsd-3)))
 213
 214 (define-public python-jupyter-packaging
 215   (package
 216     (name "python-jupyter-packaging")
 217     (version "0.9.1")
 218     (source
 219      (origin
 220        (method url-fetch)
 221        (uri (pypi-uri "jupyter_packaging" version))
 222        (sha256
 223         (base32
 224          "0r015c0m713d19asmpimsw6bk2sqv2lpd2nccgjzjdj5h1crg0bg"))))
 225     (build-system python-build-system)
 226     (propagated-inputs
 227      (list python-deprecation python-packaging python-setuptools
 228            python-tomlkit python-wheel))
 229     (native-inputs
 230      (list python-pypa-build python-coverage python-pytest
 231            python-pytest-cov python-pytest-mock))
 232     (home-page "https://jupyter.org")
 233     (synopsis "Jupyter packaging utilities")
 234     (description "This package provides tools to help build and install
 235 Jupyter Python packages that require a pre-build step that may include
 236 JavaScript build steps.")
 237     (license license:bsd-3)))
 238
 239 (define-public python-jupyter-server
 240   (package
 241     (name "python-jupyter-server")
 242     (version "1.10.2")
 243     (source
 244      (origin
 245        (method url-fetch)
 246        (uri (pypi-uri "jupyter_server" version))
 247        (sha256
 248         (base32
 249          "1gvjbsw5nl94hz02rnkr4g4kkvh9fz7i45vz17hzwyvdpj7bd8yk"))))
 250     (build-system python-build-system)
 251     (arguments
 252      `(#:phases
 253        (modify-phases %standard-phases
 254          (replace 'check
 255            (lambda* (#:key inputs outputs tests? #:allow-other-keys)
 256              (when tests?
 257                (add-installed-pythonpath inputs outputs)
 258                (let ((home (string-append (getcwd) "/guix-home")))
 259                  (setenv "HOME" home))
 260                ;; Add jupyter-server executable to PATH.
 261                (setenv "PATH"
 262                        (string-append (assoc-ref outputs "out") "/bin:"
 263                                       (getenv "PATH")))
 264                (with-directory-excursion "jupyter_server"
 265                  ;; The pytest fixtures are only loaded when the file is
 266                  ;; called conftest.py.
 267                  (rename-file "pytest_plugin.py" "conftest.py")
 268                  (invoke "pytest" "-vv"
 269                          ;; Fails with internal server error
 270                          "-k" "not test_list_formats"
 271                          ;; Integration tests require a server.
 272                          "-m" "not integration_test"))))))))
 273     (propagated-inputs
 274      (list python-anyio
 275            python-argon2-cffi
 276            python-ipython-genutils
 277            python-jinja2
 278            python-jupyter-client
 279            python-jupyter-core
 280            python-nbconvert
 281            python-nbformat
 282            python-prometheus-client
 283            python-pyzmq
 284            python-requests-unixsocket
 285            python-send2trash
 286            python-terminado
 287            python-tornado-6
 288            python-traitlets
 289            python-websocket-client))
 290     (native-inputs
 291      (list python-coverage
 292            python-ipykernel
 293            python-pytest
 294            python-pytest-console-scripts
 295            python-pytest-cov
 296            python-pytest-mock
 297            python-pytest-tornasync
 298            python-requests))
 299     (home-page "https://jupyter.org")
 300     (synopsis "Core services, APIs, and REST endpoints for Jupyter web applications")
 301     (description
 302      "This package provides the backend—i.e. core services, APIs, and REST
 303 endpoints—to Jupyter web applications.")
 304     (license license:expat)))
 305
 306 (define-public python-jupyterlab-widgets
 307   (package
 308     (name "python-jupyterlab-widgets")
 309     (version "1.0.0")
 310     (source
 311      (origin
 312        (method url-fetch)
 313        (uri (pypi-uri "jupyterlab_widgets" version))
 314        (sha256
 315         (base32
 316          "0y7vhhas3qndiypcpcfnhrj9n92v2w4hdc86nn620s9h9nl2j6jw"))))
 317     (build-system python-build-system)
 318     (native-inputs
 319      (list python-jupyter-packaging python-setuptools))
 320     (home-page "https://github.com/jupyter-widgets/ipywidgets")
 321     (synopsis "Interactive widgets for Jupyter Notebooks")
 322     (description "ipywidgets, also known as jupyter-widgets or simply widgets,
 323 are interactive HTML widgets for Jupyter notebooks and the IPython kernel.")
 324     (license license:bsd-3)))
 325
 326 (define-public python-nbclient
 327   (package
 328     (name "python-nbclient")
 329     (version "0.5.3")
 330     (source
 331      (origin
 332        (method url-fetch)
 333        (uri (pypi-uri "nbclient" version))
 334        (sha256
 335         (base32
 336          "172q4r6mq0lg394di0pc6ipvniy14jg38wkdsj48r366609jf5yv"))))
 337     (build-system python-build-system)
 338     ;; Tests require a kernel via python-ipykernel, and also tools from
 339     ;; nbconvert.
 340     (arguments '(#:tests? #false))
 341     (propagated-inputs
 342      (list python-async-generator python-jupyter-client python-nbformat
 343            python-nest-asyncio python-traitlets))
 344     (native-inputs
 345      (list python-black
 346            python-bumpversion
 347            python-check-manifest
 348            python-codecov
 349            python-coverage
 350            python-flake8
 351            ;; ("python-ipykernel" ,python-ipykernel)
 352            ;; ("python-ipython" ,python-ipython)
 353            ;; ("python-ipywidgets" ,python-ipywidgets)
 354            python-mypy
 355            python-pip
 356            python-pytest
 357            python-pytest-cov
 358            python-setuptools
 359            python-testpath
 360            python-tox
 361            python-twine
 362            python-wheel
 363            python-xmltodict))
 364     (home-page "https://jupyter.org")
 365     (synopsis "Client library for executing notebooks")
 366     (description
 367      "This package provides a client library for executing notebooks. Formerly
 368 nbconvert's @code{ExecutePreprocessor.}")
 369     (license license:bsd-3)))
 370
 371 (define-public repo2docker
 372   (package
 373     (name "repo2docker")
 374     (version "2021.08.0")
 375     (source (origin
 376               (method git-fetch)
 377               (uri (git-reference
 378                     (url "https://github.com/jupyterhub/repo2docker/")
 379                     (commit version)))
 380               (file-name (git-file-name name version))
 381               (sha256
 382                (base32
 383                 "111irpghzys0s5ixs8paskz7465cls1sm9d5bg45a15jklcw84a9"))))
 384     (outputs '("out" "doc"))
 385     (build-system python-build-system)
 386     (arguments
 387      `(#:phases (modify-phases %standard-phases
 388                   (add-after 'patch-shebangs 'fix-install-miniforge
 389                     (lambda* (#:key outputs #:allow-other-keys)
 390                       (let* ((out (assoc-ref outputs "out")))
 391                         (substitute* (find-files
 392                                       out "^(install-miniforge|install-nix|\
 393 nix-shell-wrapper|repo2docker-entrypoint)")
 394                           (("^#!(.*)/bin/bash")
 395                            "#!/bin/bash"))
 396                         (substitute* (find-files out "^freeze\\.py$")
 397                           (("^#!(.*)/bin/python3")
 398                            "#!/bin/python3\n")))))
 399                   (add-after 'install 'make-doc
 400                     (lambda* (#:key outputs #:allow-other-keys)
 401                       (let* ((out (assoc-ref outputs "doc"))
 402                              (doc (string-append out "/share/doc/"
 403                                                  ,(package-name this-package))))
 404                         (setenv "PYTHONPATH"
 405                                 (string-append (getcwd) ":"
 406                                                (getenv "GUIX_PYTHONPATH")))
 407                         ;; Don't treat warnings as errors.
 408                         (substitute* "docs/Makefile"
 409                           (("(SPHINXOPTS[[:blank:]]+= )-W" _ group)
 410                            group))
 411                         (with-directory-excursion "docs"
 412                           (invoke  "make" "html")
 413                           (copy-recursively "build/html"
 414                                             (string-append doc "/html")))))))))
 415     (inputs
 416      (list python-traitlets
 417            python-toml
 418            python-semver
 419            python-ruamel.yaml
 420            python-requests
 421            python-json-logger
 422            python-jinja2
 423            python-escapism
 424            python-docker))
 425     (native-inputs
 426      (list python-sphinx python-entrypoints python-recommonmark
 427            python-sphinxcontrib-autoprogram python-pydata-sphinx-theme))
 428     (home-page "https://repo2docker.readthedocs.io/en/latest/index.html#")
 429     (synopsis "Generate docker images from repositories")
 430     (description
 431      "repo2docker fetches a repository (from GitHub, GitLab, Zenodo, Figshare,
 432 Dataverse installations, a Git repository or a local directory) and builds a
 433 container image in which the code can be executed.  The image build process is
 434 based on the configuration files found in the repository.  repo2docker can be
 435 used to explore a repository locally by building and executing the constructed
 436 image of the repository, or as a means of building images that are pushed to a
 437 Docker registry.")
 438     (license license:bsd-3)))
 439
 440 (define-public python-bash-kernel
 441   (package
 442    (name "python-bash-kernel")
 443    (version "0.7.2")
 444    (source (origin
 445             (method url-fetch)
 446             (uri (pypi-uri "bash_kernel" version))
 447             (sha256
 448              (base32
 449               "0w0nbr3iqqsgpk83rgd0f5b02462bkyj2n0h6i9dwyc1vpnq9350"))))
 450    (build-system python-build-system)
 451    (arguments
 452     `(#:tests? #f
 453       #:phases
 454       (modify-phases %standard-phases
 455         (add-after 'unpack 'bash-references
 456           (lambda* (#:key inputs #:allow-other-keys)
 457              (substitute* "bash_kernel/kernel.py"
 458                (("\"bash\"")
 459                 (string-append "\"" (assoc-ref inputs "bash") "/bin/bash\""))
 460                (("\\['bash', ")
 461                 (string-append "['" (assoc-ref inputs "bash") "/bin/bash', ")))
 462              #t))
 463         (add-after 'install 'install-kernelspec
 464           (lambda* (#:key outputs #:allow-other-keys)
 465             (let ((out (assoc-ref outputs "out")))
 466               (setenv "HOME" "/tmp")
 467               (invoke "python" "-m" "bash_kernel.install" "--prefix" out)
 468               #t))))))
 469    (inputs
 470      (list bash))
 471    (propagated-inputs
 472      (list python-pexpect python-ipykernel python-jupyter-client))
 473    (home-page "https://github.com/takluyver/bash_kernel")
 474    (synopsis "Jupyter kernel for Bash")
 475    (description "A bash shell kernel for Jupyter.")
 476    (license license:expat)))
 477
 478 (define-public python-sparqlkernel
 479   (package
 480     (name "python-sparqlkernel")
 481     (version "1.3.0")
 482     (source (origin
 483               (method url-fetch)
 484               (uri (pypi-uri "sparqlkernel" version))
 485               (sha256
 486                (base32
 487                 "004v22nyi5cnpxq4fiws89p7i5wcnzv45n3n70axdd6prh6rkapx"))))
 488     (build-system python-build-system)
 489     (arguments
 490      `(#:tests? #f
 491        #:phases
 492        (modify-phases %standard-phases
 493          (add-after 'unpack 'no-custom-css
 494            (lambda* (#:key inputs #:allow-other-keys)
 495               (substitute* "sparqlkernel/install.py"
 496                 (("install_custom_css\\( destd, PKGNAME \\)") ""))
 497               #t))
 498          (add-after 'install 'install-kernelspec
 499            (lambda* (#:key inputs outputs #:allow-other-keys)
 500              (let ((out (assoc-ref outputs "out")))
 501                (setenv "HOME" "/tmp")
 502                (add-installed-pythonpath inputs outputs)
 503                (invoke
 504                  (string-append out "/bin/jupyter-sparqlkernel")
 505                  "install"
 506                  (string-append "--InstallKernelSpec.prefix=" out))
 507                #t))))))
 508     (native-inputs
 509      (list python-traitlets python-jupyter-client python-notebook
 510            python-ipykernel python-html5lib-0.9))
 511     (propagated-inputs
 512      (list python-sparqlwrapper python-pygments))
 513     (home-page "https://github.com/paulovn/sparql-kernel")
 514     (synopsis "Jupyter kernel for SPARQL")
 515     (description "This module installs a Jupyter kernel for SPARQL.  It allows
 516 sending queries to an SPARQL endpoint and fetching & presenting the results in
 517 a notebook.")
 518     (license license:bsd-3)))
 519
 520 (define-public python-voila
 521   (package
 522     (name "python-voila")
 523     (version "0.2.10")
 524     (source
 525      (origin
 526        (method url-fetch)
 527        (uri (pypi-uri "voila" version))
 528        (sha256
 529         (base32
 530          "0krfc95yjlhjdmrsladhy6lpf4xs1zw49nmkyl4pkykndglvwa1m"))))
 531     (build-system python-build-system)
 532     (propagated-inputs
 533      (list python-jupyter-client python-jupyter-server python-nbclient
 534            python-nbconvert))
 535     (native-inputs
 536      (list python-ipywidgets
 537            python-jupyter-packaging
 538            python-matplotlib
 539            python-mock
 540            python-pytest
 541            python-pytest-tornasync
 542            python-setuptools
 543            python-tornado-6))
 544     (home-page "https://github.com/voila-dashboards/voila")
 545     (synopsis "Render live Jupyter notebooks with interactive widgets")
 546     (description
 547      "Voilà turns Jupyter notebooks into standalone web applications.  Unlike
 548 the usual HTML-converted notebooks, each user connecting to the Voilà tornado
 549 application gets a dedicated Jupyter kernel which can execute the callbacks to
 550 changes in Jupyter interactive widgets.")
 551     (license license:bsd-3)))