diff options
Diffstat (limited to 'gnu/packages/jupyter.scm')
| -rw-r--r-- | gnu/packages/jupyter.scm | 266 |
1 files changed, 265 insertions, 1 deletions
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm index 52869dbeeb..0de7ad998a 100644 --- a/gnu/packages/jupyter.scm +++ b/gnu/packages/jupyter.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2019 Ludovic Courtès <[email protected]> ;;; Copyright © 2021 Ricardo Wurmus <[email protected]> +;;; Copyright © 2021 Hugo Lecomte <[email protected]> ;;; ;;; This file is part of GNU Guix. ;;; @@ -24,18 +25,26 @@ #: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 xml)) + #:use-module (gnu packages sphinx) + #:use-module (gnu packages serialization) + #:use-module (gnu packages docker)) (define-public python-jupyter-protocol (package @@ -242,6 +251,73 @@ 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") @@ -310,3 +386,191 @@ are interactive HTML widgets for Jupyter notebooks and the IPython kernel.") "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))) |