diff options
Diffstat (limited to 'gnu/packages/jupyter.scm')
| -rw-r--r-- | gnu/packages/jupyter.scm | 467 |
1 files changed, 354 insertions, 113 deletions
diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm index 8c8c7b5347..9a3ef8b121 100644 --- a/gnu/packages/jupyter.scm +++ b/gnu/packages/jupyter.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2019, 2022 Ludovic Courtès <ludo@gnu.org> -;;; Copyright © 2021, 2022, 2023 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2021-2024 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> @@ -53,6 +53,81 @@ #:use-module (gnu packages serialization) #:use-module (gnu packages version-control)) +(define-public python-nbclassic + (package + (name "python-nbclassic") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "nbclassic" version)) + (sha256 + (base32 "1qrhzazq10dz64y9mawr3ns595fsdhrj1wvbb42xhmcl66r1xq8a")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-argon2-cffi + python-ipykernel + python-ipython-genutils + python-jinja2 + python-jupyter-client + python-jupyter-core + python-jupyter-server + python-nbconvert + python-nbformat + python-nest-asyncio + python-notebook-shim + python-prometheus-client + python-pyzmq + python-send2trash + python-terminado + python-tornado-6 + python-traitlets)) + (native-inputs (list python-coverage + python-nbval + python-jupyter-packaging + python-pytest + python-pytest-cov + python-pytest-jupyter + python-pytest-tornasync + python-requests + python-requests-unixsocket + python-testpath)) + (home-page "https://github.com/jupyter/nbclassic") + (synopsis "Jupyter Notebook as a Jupyter Server extension") + (description "NbClassic provides a backwards compatible Jupyter Notebook +interface that you can install side-by-side with the latest versions: That +way, you can fearlessly upgrade without worrying about your classic extensions +and customizations breaking. Because NbClassic provides the classic interface +on top of the new Jupyter Server backend, it can coexist with other frontends +like JupyterLab and Notebook 7 in the same installation. NbClassic preserves +the custom classic notebook experience under a new set of URL endpoints, under +the namespace @code{/nbclassic/}.") + (license license:bsd-3))) + +(define-public python-notebook-shim + (package + (name "python-notebook-shim") + (version "0.2.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "notebook_shim" version)) + (sha256 + (base32 "1jrqqrm5xjwsx13plyyh7wybb1g71yrzaqa3l9y3162xnshwzcml")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-jupyter-server)) + (native-inputs + (list python-hatchling + python-pytest + python-pytest-console-scripts + python-pytest-jupyter + python-pytest-tornasync)) + (home-page "https://pypi.org/project/notebook-shim/") + (synopsis "Shim layer for notebook traits and config") + (description + "This project provides a way for JupyterLab and other frontends to switch +to Jupyter Server for their Python Web application backend.") + (license license:bsd-3))) + (define-public python-jupyter-protocol (package (name "python-jupyter-protocol") @@ -110,7 +185,7 @@ protocol} to be used by both clients and kernels.") python-jupyter-core python-jupyter-protocol python-pyzmq - python-tornado + python-tornado-6 python-traitlets)) (native-inputs (list python-async-generator @@ -169,6 +244,52 @@ tests kernels for successful code execution and conformance with the Messaging Protocol}.") (license license:bsd-3))) +(define-public python-pytest-jupyter + (package + (name "python-pytest-jupyter") + (version "0.10.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pytest_jupyter" version)) + (sha256 + (base32 "114y9py29j6p2iymhc3vj55x65gg1ncbhwal5mads0g2z7p59pq0")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; This requires python-jupyter-server, which itself requires this + ;; package. + '(list "--ignore=tests/test_jupyter_server.py") + #:phases + '(modify-phases %standard-phases + ;; The jupyter_server tests requires python-jupyter-server, which + ;; itself requires this package. + (add-after 'unpack 'disable-tests + (lambda _ + (substitute* "tests/conftest.py" + (("\"pytest_jupyter.jupyter_server\",") "")))) + ;; Some tests require a writable HOME + (add-before 'check 'set-HOME + (lambda _ (setenv "HOME" "/tmp"))) + (add-after 'unpack 'ignore-deprecation-warnings + (lambda _ + (substitute* "pyproject.toml" + ((" \"module:datetime.*" m) + (string-append m "\n\"ignore:zmq.eventloop.ioloop is deprecated:DeprecationWarning\",")))))))) + (propagated-inputs (list python-jupyter-core python-nbformat)) + (native-inputs (list python-hatchling + python-ipykernel + python-pytest + python-pytest-timeout + python-tornado-6)) + (home-page "https://jupyter.org") + (synopsis "Pytest plugin for testing Jupyter libraries and extensions.") + (description + "This package provides a pytest plugin for testing Jupyter libraries and +extensions.") + (license license:bsd-4))) + (define-public xeus (package (name "xeus") @@ -240,28 +361,35 @@ the JupyterLab CSS variables.") (define-public python-jupyterlab-server (package (name "python-jupyterlab-server") - (version "2.12.0") + (version "2.27.1") (source (origin (method url-fetch) (uri (pypi-uri "jupyterlab_server" version)) (sha256 - (base32 "1gxbfa5s0v4z0v8kagkm2bz8hlli5pwhr89y68w5kxcrqfsg9q00")))) - (build-system python-build-system) + (base32 "07b3m34akrf79xpaim9cymhsac0ry5ry7if998lcfxmn173mlyq9")))) + (build-system pyproject-build-system) (arguments (list + #:test-flags + ;; XXX: These tests appear to fail due to the lack of + ;; locales. + '(list "-k" "not locale and not language") #: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"))))))) + '(modify-phases %standard-phases + (add-after 'unpack 'ignore-deprecation-warnings + (lambda _ + (substitute* "pyproject.toml" + ((" \"module:datetime.*" m) + (string-append + m + "\n\"ignore:zmq.eventloop.ioloop is deprecated:DeprecationWarning\"," + "\n\"ignore:There is no current event loop:DeprecationWarning\"," + "\n\"ignore:Spec is deprecated. Use SchemaPath from jsonschema-path package.:DeprecationWarning\"," ))))) + (add-before 'check 'set-HOME + (lambda _ (setenv "HOME" "/tmp")))))) (propagated-inputs (list python-babel - python-entrypoints python-importlib-metadata ;TODO: remove after Python >= 3.10 python-jinja2 python-json5 @@ -270,15 +398,20 @@ the JupyterLab CSS variables.") python-packaging python-requests)) (native-inputs - (list python-ipykernel - python-jupyter-server + (list python-hatchling + python-ipykernel python-openapi-core python-openapi-spec-validator python-pytest python-pytest-console-scripts - python-pytest-tornasync + python-pytest-cov + python-pytest-jupyter + python-pytest-timeout + python-requests-mock python-ruamel.yaml - python-strict-rfc3339)) + python-strict-rfc3339 + python-werkzeug + python-wheel)) (home-page "https://jupyter.org") (synopsis "Server components for JupyterLab applications") (description "JupyterLab Server sits between JupyterLab and Jupyter @@ -287,6 +420,43 @@ 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-events + (package + (name "python-jupyter-events") + (version "0.10.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "jupyter_events" version)) + (sha256 + (base32 "08jyhj16drl3hg594gr677bc5q991lpd4khlhb3jx26csclq42v7")))) + (build-system pyproject-build-system) + (arguments + ;; This passes the whole command line to shutil.which, instead of just + ;; the executable. + (list #:test-flags '(list "--ignore=tests/test_cli.py"))) + (propagated-inputs (list python-jsonschema + python-json-logger + python-pyyaml + python-referencing + python-rich + python-rfc3339-validator + python-rfc3986-validator + python-traitlets)) + (native-inputs (list python-click + python-hatchling + python-pytest + python-pytest-asyncio + python-pytest-console-scripts)) + (home-page "https://pypi.org/project/jupyter-events/") + (synopsis "Jupyter Event System library") + (description "Jupyter Events enables Jupyter Python +Applications (e.g. Jupyter Server, JupyterLab Server, JupyterHub, etc.) to +emit events—structured data describing things happening inside the +application. Other software (e.g. client applications like JupyterLab) can +listen and respond to these events.") + (license license:bsd-3))) + (define-public python-jupyter-packaging (package (name "python-jupyter-packaging") @@ -326,48 +496,83 @@ Jupyter Python packages that require a pre-build step that may include JavaScript build steps.") (license license:bsd-3))) +(define-public python-hatch-jupyter-builder + (package + (name "python-hatch-jupyter-builder") + (version "0.9.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "hatch_jupyter_builder" version)) + (sha256 + (base32 "1baqk80c5ddhksh73l48mb59vvaaa2ldrs65k6vldii4s6c829vr")))) + (build-system pyproject-build-system) + (arguments + ;; Don't attempt to build anything, because we don't have network access + ;; anyway. + (list #:test-flags '(list "-k" "not test_hatch_build"))) + (propagated-inputs (list python-hatchling)) + (native-inputs (list python-pytest + python-pytest-cov + python-pytest-mock + python-tomli + python-twine)) + (home-page "https://github.com/jupyterlab/hatch-jupyter-builder") + (synopsis "Hatch plugin to help build Jupyter packages") + (description + "This package provides a hatch plugin to help build Jupyter packages.") + (license license:bsd-3))) + (define-public python-jupyter-server (package (name "python-jupyter-server") - (version "1.16.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (pypi-uri "jupyter_server" version)) (sha256 (base32 - "0fj6l34m6vk3yic87isz9bzgg4qsbr285x1faamf512bsrxghmn7")))) - (build-system python-build-system) + "0xz69anflhib514lgpdrs0ppmbwp13zbg4vwzls3820jlp7594b5")))) + (build-system pyproject-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")))))))) + (list + #:test-flags + ;; Integration tests require a server. + '(list "-m" "not integration_test" + ;; This test fails just like the shutil test in + ;; python-jupyter-events fails. Odd, that. + "-k" "not test_server_extension_list") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'ignore-deprecation-warnings + (lambda _ + (substitute* "pyproject.toml" + ((" \"ignore:datetime.*" m) + (string-append m "\n\"ignore:zmq.eventloop.ioloop is deprecated:DeprecationWarning\"," + "\n\"ignore:There is no current event loop:DeprecationWarning\"," + "\n\"ignore:unclosed event loop:ResourceWarning\"," + ;; From tornado + "\n\"ignore:unclosed <socket.socket:ResourceWarning\","))))) + (add-before 'check 'pre-check + (lambda _ + (let ((home (string-append (getcwd) "/guix-home"))) + (setenv "HOME" home)) + ;; Add jupyter-server executable to PATH. + (setenv "PATH" + (string-append #$output "/bin:" (getenv "PATH")))))))) (propagated-inputs (list python-anyio python-argon2-cffi python-jinja2 python-jupyter-client python-jupyter-core + python-jupyter-events + python-jupyter-server-terminals python-nbconvert python-nbformat + python-overrides + python-packaging python-prometheus-client python-pyzmq python-send2trash @@ -376,13 +581,14 @@ JavaScript build steps.") python-traitlets python-websocket-client)) (native-inputs - (list python-coverage + (list python-flaky + python-hatchling + python-hatch-jupyter-builder python-ipykernel python-pytest python-pytest-console-scripts - python-pytest-cov - python-pytest-mock - python-pytest-tornasync + python-pytest-jupyter + python-pytest-timeout python-requests)) (home-page "https://jupyter.org") (synopsis "Core services, APIs, and REST endpoints for Jupyter web applications") @@ -391,20 +597,43 @@ JavaScript build steps.") endpoints—to Jupyter web applications.") (license license:expat))) +(define-public python-jupyter-server-terminals + (package + (name "python-jupyter-server-terminals") + (version "0.5.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "jupyter_server_terminals" version)) + (sha256 + (base32 "0sajiadhwncrr0inzzkrs7l1xc6jmw9b5zfw1v79l3i2cx8jkq2s")))) + (build-system pyproject-build-system) + ;; The tests require python-jupyter-server, but python-jupyter-server + ;; needs this package. + (arguments (list #:tests? #false)) + (propagated-inputs (list python-terminado)) + (native-inputs + (list python-hatchling)) + (home-page "https://pypi.org/project/jupyter-server-terminals/") + (synopsis "Jupyter Server extension providing terminals") + (description + "This package provides a Jupyter Server extension providing terminals.") + (license license:bsd-3))) + (define-public python-jupyterlab-widgets (package (name "python-jupyterlab-widgets") - (version "1.1.4") + (version "3.0.10") (source (origin (method url-fetch) (uri (pypi-uri "jupyterlab_widgets" version)) (sha256 (base32 - "0kdib439i9pbv90cscq5c7w4nvv8214k9ik4dnbd152yf897cvpa")))) + "1h04kln8hp56svdjjk2hbsb0z1mby71cv4gss3wy89v7jw2arwh4")))) (build-system pyproject-build-system) (native-inputs - (list python-jupyter-packaging python-setuptools)) + (list python-jupyter-packaging)) (home-page "https://github.com/jupyter-widgets/ipywidgets") (synopsis "Interactive widgets for Jupyter Notebooks") (description "ipywidgets, also known as jupyter-widgets or simply widgets, @@ -462,30 +691,23 @@ for authoring custom addons.") (define-public python-jupyter-server-mathjax (package (name "python-jupyter-server-mathjax") - (version "0.2.5") + (version "0.2.6") (source (origin (method url-fetch) (uri (pypi-uri "jupyter_server_mathjax" version)) (sha256 - (base32 "1cz7grhj9jih9mgw4xk7a4bqy1fwlb1jsawh6ykxnvpydn76rnb4")))) - (build-system python-build-system) + (base32 "0hrrl969r7ir6q683hlr7a4lid9x2s35hax2hviiyv38q1nnn7mv")))) + (build-system pyproject-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")))))))) + #:test-flags + '(list "--pyargs" "jupyter_server_mathjax"))) (propagated-inputs (list python-jupyter-server)) (native-inputs - (list python-jupyter-server - python-jupyter-packaging - python-pytest - python-pytest-tornasync)) + (list python-jupyter-packaging + python-pytest python-pytest-jupyter + python-setuptools python-wheel)) (home-page "https://jupyter.org") (synopsis "Jupyter Server extension for serving Mathjax") (description "This package provides a Jupyter Server extension for serving @@ -521,20 +743,28 @@ and a default CommManager that can be used.") (define-public python-nbclient (package (name "python-nbclient") - (version "0.6.6") + (version "0.10.0") (source (origin (method url-fetch) (uri (pypi-uri "nbclient" version)) (sha256 (base32 - "09whkb8ll1nfdn4h3k0shncgkfak4lglmiwn8wdni6nrc5wnmxqd")))) + "02dvb9ffpd237apyj4fw97a9371kv99lzny49624j7jkp9yingsb")))) (build-system pyproject-build-system) ;; Tests require tools from nbconvert, which would introduces a cycle. (arguments '(#:tests? #false)) (propagated-inputs (list python-jupyter-client python-jupyter-core python-nbformat python-traitlets)) + (native-inputs + (list python-hatchling + python-flaky + python-pytest + python-pytest-asyncio + python-pytest-cov + python-testpath + python-xmltodict)) (home-page "https://jupyter.org") (synopsis "Client library for executing notebooks") (description @@ -605,27 +835,27 @@ nbshow present a single notebook in a terminal-friendly way (sha256 (base32 "1n57nvxsc94gz9w8ymi83bjkfhfwkpmx4y14m6gjrmlqd49m1aw6")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - '(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'delete-bad-tests - (lambda _ - ;; These tests use git and hg, and they are sensitive to the - ;; exact printed output. - (for-each delete-file (list "tests/test-git.t" - "tests/test-hg.t" - "tests/test-status.t" - "tests/test-uninstall.t")))) - (add-before 'check 'set-CRAMSHELL - (lambda _ - (setenv "CRAMSHELL" (which "bash"))))))) + (list + ;; These tests use git and hg, and they are sensitive to the + ;; exact printed output. + #:test-flags '(map (lambda (test) + (string-append "--ignore=tests/test-" test ".t")) + '("git" "hg" "status" "uninstall")) + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'set-CRAMSHELL + (lambda _ + (setenv "CRAMSHELL" (which "bash"))))))) (propagated-inputs (list python-nbformat)) (native-inputs (list python-pytest python-pytest-cram python-pytest-flake8 - python-pytest-runner)) + python-pytest-runner + python-setuptools + python-wheel)) (home-page "https://github.com/kynan/nbstripout") (synopsis "Strips outputs from Jupyter and IPython notebooks") (description @@ -636,7 +866,7 @@ version to the original file.") (define-public repo2docker (package (name "repo2docker") - (version "2021.08.0") + (version "2024.03.0") (source (origin (method git-fetch) (uri (git-reference @@ -645,38 +875,38 @@ version to the original file.") (file-name (git-file-name name version)) (sha256 (base32 - "111irpghzys0s5ixs8paskz7465cls1sm9d5bg45a15jklcw84a9")))) + "1bcnl91j6p3315lk2mmn02jq6mjsn68m9rcw5rkln4c9fx1160rx")))) (outputs '("out" "doc")) - (build-system python-build-system) + (build-system pyproject-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|\ + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'patch-shebangs 'fix-install-miniforge + (lambda _ + (substitute* (find-files + #$output "^(install-miniforge|install-nix|\ nix-shell-wrapper|repo2docker-entrypoint)") - (("^#!(.*)/bin/bash") - "#!/bin/bash")) - (substitute* (find-files out "^freeze\\.py$") - (("^#!(.*)/bin/python3") - "#!/bin/python3\n"))))) - (add-after 'install 'make-doc - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "doc")) - (doc (string-append out "/share/doc/" - ,(package-name this-package)))) - (setenv "PYTHONPATH" - (string-append (getcwd) ":" - (getenv "GUIX_PYTHONPATH"))) - ;; Don't treat warnings as errors. - (substitute* "docs/Makefile" - (("(SPHINXOPTS[[:blank:]]+= )-W" _ group) - group)) - (with-directory-excursion "docs" - (invoke "make" "html") - (copy-recursively "build/html" - (string-append doc "/html"))))))))) + (("^#!(.*)/bin/bash") + "#!/bin/bash")) + (substitute* (find-files #$output "^freeze\\.py$") + (("^#!(.*)/bin/python3") + "#!/bin/python3\n")))) + (add-after 'install 'make-doc + (lambda _ + (let ((doc (string-append #$output:out "/share/doc/" + #$(package-name this-package)))) + (setenv "PYTHONPATH" + (string-append (getcwd) ":" + (getenv "GUIX_PYTHONPATH"))) + ;; Don't treat warnings as errors. + (substitute* "docs/Makefile" + (("(SPHINXOPTS[[:blank:]]+= )-W" _ group) + group)) + (with-directory-excursion "docs" + (invoke "make" "html") + (copy-recursively "build/html" + (string-append doc "/html"))))))))) (inputs (list python-traitlets python-toml @@ -690,8 +920,18 @@ nix-shell-wrapper|repo2docker-entrypoint)") python-docker python-chardet)) (native-inputs - (list python-sphinx python-entrypoints python-recommonmark - python-sphinxcontrib-autoprogram python-pydata-sphinx-theme)) + (list python-entrypoints + python-myst-parser + python-pydata-sphinx-theme + python-recommonmark + python-setuptools + python-sphinx + python-sphinx-autobuild + python-sphinx-copybutton + python-sphinxcontrib-autoprogram + python-sphinxext-opengraph + python-sphinxext-rediraffe + python-wheel)) (home-page "https://repo2docker.readthedocs.io/en/latest/index.html#") (synopsis "Generate docker images from repositories") (description @@ -762,6 +1002,7 @@ Docker registry.") (add-after 'unpack 'no-custom-css (lambda _ (substitute* "sparqlkernel/install.py" + (("notebook.DEFAULT_STATIC_FILES_PATH") "\"/does-not-matter\"") (("install_custom_css\\( destd, PKGNAME \\)") "")))) (add-after 'add-install-to-pythonpath 'install-kernelspec (lambda _ |