diff options
Diffstat (limited to 'gnu/packages/jupyter.scm')
| -rw-r--r-- | gnu/packages/jupyter.scm | 399 |
1 files changed, 319 insertions, 80 deletions
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm index dd5d2a5a55..441e19bf47 100644 --- a/gnu/packages/jupyter.scm +++ b/gnu/packages/jupyter.scm @@ -1,8 +1,9 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2019 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2019, 2022 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2021 Hugo Lecomte <hugo.lecomte@inria.fr> ;;; Copyright © 2022 Marius Bakke <marius@gnu.org> +;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -21,6 +22,7 @@ (define-module (gnu packages jupyter) #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix gexp) #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) @@ -29,6 +31,7 @@ #:use-module (gnu packages bash) #:use-module (gnu packages check) #:use-module (gnu packages cpp) + #:use-module (gnu packages docker) #:use-module (gnu packages linux) #:use-module (gnu packages monitoring) #:use-module (gnu packages networking) @@ -37,6 +40,7 @@ #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) #:use-module (gnu packages python-crypto) + #:use-module (gnu packages python-science) #:use-module (gnu packages python-xyz) #:use-module (gnu packages python-web) #:use-module (gnu packages rdf) @@ -45,21 +49,24 @@ #:use-module (gnu packages tls) #:use-module (gnu packages sphinx) #:use-module (gnu packages serialization) - #:use-module (gnu packages docker)) + #:use-module (gnu packages version-control)) (define-public python-jupyter-protocol (package (name "python-jupyter-protocol") - (version "0.1.1") + (version "0.2.0") (source (origin (method url-fetch) (uri (pypi-uri "jupyter_protocol" version)) (sha256 (base32 - "1bk3as5yw9y5nmq6l15nr46aby34phmvsx9kxgqnm5pd5q2b5h57")))) + "075vbaak6hlk9606lw61ldv72p6694k938jd1kvkm6spd0pczpmn")))) (build-system python-build-system) (propagated-inputs - (list python-dateutil python-jupyter-core python-pyzmq + (list python-dateutil + python-ipython-genutils + python-jupyter-core + python-pyzmq python-traitlets)) (native-inputs (list python-ipykernel python-ipython python-mock python-pytest)) @@ -75,23 +82,40 @@ protocol} to be used by both clients and kernels.") (define-public python-jupyter-kernel-mgmt (package (name "python-jupyter-kernel-mgmt") - (version "0.4.0") + (version "0.5.1") (source (origin (method url-fetch) (uri (pypi-uri "jupyter_kernel_mgmt" version)) (sha256 (base32 - "0i7a78dn89ca8h0a42giyxwcmk6y4wrdr7q8h2ax9vybb84c795q")))) + "0977ixfi1pzjgy84hl0zycg4wpllmid98fhzcpy0lxd322w4sl7x")))) (build-system python-build-system) + (arguments + (list + ;; There are 8 test failures, most of them in 'test_client_loop.py' + ;; (see: https://github.com/takluyver/jupyter_kernel_mgmt/issues/48). + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp") + (invoke "pytest" "-vv" "jupyter_kernel_mgmt"))))))) (propagated-inputs (list python-dateutil python-entrypoints python-jupyter-core python-jupyter-protocol python-pyzmq + python-tornado python-traitlets)) (native-inputs - (list python-ipykernel python-ipython python-mock python-pytest)) + (list python-async-generator + python-ipykernel + python-ipython + python-pytest + python-pytest-asyncio)) (home-page "https://jupyter.org") (synopsis "Discover, launch, and communicate with Jupyter kernels") (description @@ -146,15 +170,15 @@ Messaging Protocol}.") (define-public xeus (package (name "xeus") - (version "0.23.2") + (version "2.4.1") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/QuantStack/xeus") + (url "https://github.com/jupyter-xeus/xeus") (commit version))) (sha256 (base32 - "1m1b6z1538r7mv2ggn7bdbd9570ja7cadplq64zl8rgl2c8vdi2a")) + "1k1h416qkw3yra6ayfa61nv0v4ify2wvp5x27slgbcw6c88w7fb1")) (file-name (git-file-name name version)))) (build-system cmake-build-system) (arguments @@ -166,7 +190,7 @@ Messaging Protocol}.") ;; The following inputs are used by the test suite. googletest python-pytest - python-3 + python-wrapper python-jupyter-kernel-test python-jupyter-client)) (inputs @@ -175,7 +199,7 @@ Messaging Protocol}.") cppzmq zeromq openssl - `(,util-linux "lib"))) ;libuuid + `(,util-linux "lib"))) ;libuuid (home-page "https://quantstack.net/xeus") (synopsis "C++ implementation of the Jupyter Kernel protocol") (description @@ -211,18 +235,82 @@ alternative Python kernel for Jupyter.") the JupyterLab CSS variables.") (license license:bsd-3))) +(define-public python-jupyterlab-server + (package + (name "python-jupyterlab-server") + (version "2.12.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "jupyterlab_server" version)) + (sha256 + (base32 "1gxbfa5s0v4z0v8kagkm2bz8hlli5pwhr89y68w5kxcrqfsg9q00")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" "-c" "/dev/null" "tests" + ;; XXX: These tests appear to fail due to the lack of + ;; locales. + "-k" "not locale and not language"))))))) + (propagated-inputs + (list python-babel + python-entrypoints + python-importlib-metadata ;TODO: remove after Python >= 3.10 + python-jinja2 + python-json5 + python-jsonschema + python-jupyter-server + python-packaging + python-requests)) + (native-inputs + (list python-ipykernel + python-jupyter-server + python-openapi-core + python-openapi-spec-validator + python-pytest + python-pytest-console-scripts + python-pytest-tornasync + python-ruamel.yaml + python-strict-rfc3339)) + (home-page "https://jupyter.org") + (synopsis "Server components for JupyterLab applications") + (description "JupyterLab Server sits between JupyterLab and Jupyter +Server, and provides a set of REST API handlers and utilities that are used by +JupyterLab. It is a separate project in order to accommodate creating +JupyterLab-like applications from a more limited scope.") + (license license:bsd-3))) + (define-public python-jupyter-packaging (package (name "python-jupyter-packaging") - (version "0.9.1") + (version "0.12.0") (source (origin (method url-fetch) (uri (pypi-uri "jupyter_packaging" version)) (sha256 (base32 - "0r015c0m713d19asmpimsw6bk2sqv2lpd2nccgjzjdj5h1crg0bg")))) + "1b7ssc627vgrdl21c09w9sxk5fc1ps3g7f70laxag4yw1bb5ax5j")))) (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; Disable isolation so that the package environment can be + ;; setup without connectivity. + (setenv "SOURCE_DATE_EPOCH" "315532800") + (substitute* "tests/test_build_api.py" + (("\"-m\", \"build\"" all) + (string-append all ", \"--no-isolation\""))) + (invoke "python" "-m" "pytest" "-vv"))))))) (propagated-inputs (list python-deprecation python-packaging python-setuptools python-tomlkit python-wheel)) @@ -239,14 +327,14 @@ JavaScript build steps.") (define-public python-jupyter-server (package (name "python-jupyter-server") - (version "1.10.2") + (version "1.16.0") (source (origin (method url-fetch) (uri (pypi-uri "jupyter_server" version)) (sha256 (base32 - "1gvjbsw5nl94hz02rnkr4g4kkvh9fz7i45vz17hzwyvdpj7bd8yk")))) + "0fj6l34m6vk3yic87isz9bzgg4qsbr285x1faamf512bsrxghmn7")))) (build-system python-build-system) (arguments `(#:phases @@ -273,7 +361,6 @@ JavaScript build steps.") (propagated-inputs (list python-anyio python-argon2-cffi - python-ipython-genutils python-jinja2 python-jupyter-client python-jupyter-core @@ -281,7 +368,6 @@ JavaScript build steps.") python-nbformat python-prometheus-client python-pyzmq - python-requests-unixsocket python-send2trash python-terminado python-tornado-6 @@ -323,49 +409,116 @@ endpoints—to Jupyter web applications.") are interactive HTML widgets for Jupyter notebooks and the IPython kernel.") (license license:bsd-3))) +(define-public python-jupyter-server-mathjax + (package + (name "python-jupyter-server-mathjax") + (version "0.2.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "jupyter_server_mathjax" version)) + (sha256 + (base32 "1cz7grhj9jih9mgw4xk7a4bqy1fwlb1jsawh6ykxnvpydn76rnb4")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (with-directory-excursion "/tmp" + (invoke "pytest" "-vv" + "--pyargs" "jupyter_server_mathjax")))))))) + (propagated-inputs (list python-jupyter-server)) + (native-inputs + (list python-jupyter-server + python-jupyter-packaging + python-pytest + python-pytest-tornasync)) + (home-page "https://jupyter.org") + (synopsis "Jupyter Server extension for serving Mathjax") + (description "This package provides a Jupyter Server extension for serving +Mathjax, the JavaScript display engine for mathematics.") + (license license:bsd-3))) + (define-public python-nbclient (package (name "python-nbclient") - (version "0.5.3") + (version "0.6.0") (source (origin (method url-fetch) (uri (pypi-uri "nbclient" version)) (sha256 (base32 - "172q4r6mq0lg394di0pc6ipvniy14jg38wkdsj48r366609jf5yv")))) + "0cbhs8l8ma5nzm1i4484gsrb7189m1lmniashp929pxsqq1s929z")))) (build-system python-build-system) - ;; Tests require a kernel via python-ipykernel, and also tools from - ;; nbconvert. + ;; Tests require tools from nbconvert, which would introduces a cycle. (arguments '(#:tests? #false)) (propagated-inputs - (list python-async-generator python-jupyter-client python-nbformat - python-nest-asyncio python-traitlets)) - (native-inputs - (list python-black - python-bumpversion - python-check-manifest - python-codecov - python-coverage - python-flake8 - ;; ("python-ipykernel" ,python-ipykernel) - ;; ("python-ipython" ,python-ipython) - ;; ("python-ipywidgets" ,python-ipywidgets) - python-mypy - python-pip - python-pytest - python-pytest-cov - python-setuptools - python-testpath - python-tox - python-twine - python-wheel - python-xmltodict)) + (list python-jupyter-client + python-nbformat + python-nest-asyncio + python-traitlets)) (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.}") + "This package provides a client library for executing notebooks. +It was formerly known as nbconvert's @code{ExecutePreprocessor.}") + (license license:bsd-3))) + +(define-public python-nbdime + (package + (name "python-nbdime") + (version "3.1.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "nbdime" version)) + (sha256 + (base32 "12v41lricbg713lzlfcx0cilfm9spndaanhp39q4ydvix4h76xk7")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'remove-ipython-genutils + ;; TODO: Remove when a release newer than 3.1.1 is made. + (lambda _ + (substitute* "nbdime/config.py" + (("from ipython_genutils import py3compat") + "") + (("py3compat\\.getcwd") + "os.getcwd"))))))) + (propagated-inputs + (list python-colorama + python-gitpython + python-jinja2 + python-jupyter-server + python-jupyter-server-mathjax + python-nbformat + python-pygments + python-requests + python-tornado-6)) + (native-inputs + (list python-jupyter-server + python-mock + python-notebook + python-pytest + python-pytest-tornado + python-tabulate)) + (home-page "https://nbdime.readthedocs.io") + (synopsis "Diff tools for Jupyter Notebooks") + (description "@code{nbdime} provides tools for diffing and merging of +Jupyter Notebooks. It includes the following commands: +@table @command +@item nbdiff compare notebooks in a terminal-friendly way +@item nbmerge three-way merge of notebooks with automatic conflict resolution +@item nbdiff-web rich rendered diff of notebooks +@item nbmerge-web web-based three-way merge tool for notebooks +nbshow present a single notebook in a terminal-friendly way +@end table") (license license:bsd-3))) (define-public repo2docker @@ -467,9 +620,10 @@ Docker registry.") (invoke "python" "-m" "bash_kernel.install" "--prefix" out) #t)))))) (inputs - (list bash)) - (propagated-inputs - (list python-pexpect python-ipykernel python-jupyter-client)) + (list bash + 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.") @@ -487,59 +641,144 @@ Docker registry.") "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) + (list + #:tests? #f ;no test suite + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'no-custom-css + (lambda _ (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)) + (("install_custom_css\\( destd, PKGNAME \\)") "")))) + (add-after 'add-install-to-pythonpath 'install-kernelspec + (lambda _ + (setenv "HOME" "/tmp") + (invoke + (string-append #$output "/bin/jupyter-sparqlkernel") + "install" + (string-append "--InstallKernelSpec.prefix=" #$output))))))) (propagated-inputs - (list python-sparqlwrapper python-pygments)) + (list python-ipykernel + python-notebook + python-pygments + python-rdflib + python-sparqlwrapper + python-traitlets)) (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 +sending queries to an SPARQL endpoint, fetching and presenting the results in a notebook.") (license license:bsd-3))) +(define-public python-ipympl + (package + (name "python-ipympl") + (version "0.9.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ipympl" version)) + (sha256 + (base32 "11rppjdqzgs4pfiq8gww5xkpbk21fp86vvv839v56b9rqq06j2b4")))) + (build-system python-build-system) + (propagated-inputs + (list python-ipython + python-ipython-genutils + python-ipywidgets + python-matplotlib + python-numpy + python-pillow + python-traitlets)) + (native-inputs + (list python-jupyter-packaging)) + (home-page "https://matplotlib.org/ipympl/") + (synopsis "Matplotlib Jupyter Extension") + (description "Leveraging the Jupyter interactive widgets framework, ipympl +enables the interactive features of matplotlib in the Jupyter notebook and in +JupyterLab.") + (license license:bsd-3))) + +(define-public python-ipydatawidgets + (package + (name "python-ipydatawidgets") + (version "4.2.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ipydatawidgets" version)) + (sha256 + (base32 "1g65nzlsb1cipmvh9v27b22kkmzwvg8zbf32hmg1c25mb65vbr6h")))) + (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-v"))))))) + (propagated-inputs + (list python-ipywidgets python-numpy python-six python-traittypes)) + (native-inputs + (list python-jupyter-packaging + python-nbval + python-pytest + python-pytest-cov)) + (home-page "https://github.com/vidartf/ipydatawidgets") + (synopsis "Widgets to help facilitate reuse of large datasets across widgets") + (description + "This package provides a set of widgets to help facilitate reuse of large +datasets across widgets.") + (license license:bsd-3))) + (define-public python-voila (package (name "python-voila") - (version "0.2.10") + (version "0.3.5") (source (origin - (method url-fetch) - (uri (pypi-uri "voila" version)) + (method git-fetch) ;no tests in pypi archive + (uri (git-reference + (url "https://github.com/voila-dashboards/voila") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0krfc95yjlhjdmrsladhy6lpf4xs1zw49nmkyl4pkykndglvwa1m")))) + "10qn34ddmcwcl9zxa0gwxarxr64k8hx4yysdwrf0iqvmzmkwmbbj")))) (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "setup.cfg" + (("nbclient>=0.4.0,<0.6") + "nbclient")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (setenv "HOME" "/tmp") + (invoke "pytest" "-vv" + ;; Many tests depend on Node JavaScript dependencies + ;; and a running HTTP server; ignore them. + "--ignore" "tests/app" + "--ignore" "tests/server"))))))) (propagated-inputs - (list python-jupyter-client python-jupyter-server python-nbclient - python-nbconvert)) + (list python-jupyter-client + python-jupyter-server + python-jupyterlab-server + python-nbclient + python-nbconvert + python-traitlets + python-websockets)) (native-inputs (list python-ipywidgets - python-jupyter-packaging python-matplotlib python-mock + python-numpy + python-pandas 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") |