veit / jupyter-tutorial

Training materials for setting up and using a research infrastructure based on Jupyter notebooks: https://cusy.io/en/seminars
https://jupyter-tutorial.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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Scheduled weekly dependency update for week 16 #249

Closed pyup-bot closed 6 months ago

pyup-bot commented 6 months ago

Update docutils from 0.20.1 to 0.21.1.

Changelog ### 0.21.1 ``` =========================== The sdist in 0.21 was incomplete - pypi allows no file replacing - adding a postrelease suffix "post1": docutils-0.21.post1.tar.gz works on pypi, but fails with pip because the metadata differs. But if the metadata is 0.21.post1 pypi makes it a new release. 0.21.1 is the same code except for the version number. ``` ### 0.21 ``` ========================= * General: - Drop support for Python 3.7 and 3.8. - Provide ``rst2*`` "console_scripts" `entry points`_ (without the ``.py`` extension) instead of installing the ``rst2*.py`` `front end tools`_ in the binary PATH. []_ Exceptions: ``rstpep2html.py`` and ``rst2odt_prepstyles.py``: - Use ``docutils --reader=pep --writer=pep_html`` for a PEP preview. []_ - Use ``python -m docutils.writers.odf_odt.prepstyles`` to `strip the page size`__ from an ODT writer stylesheet. __ docs/user/odt.htmlpage-size .. [] Some Linux distributions already use the short names. .. [] The final rendering is done by a Sphinx-based build system (cf. :PEP:`676`). * reStructuredText: - Use the same CSV format for the ``:header:`` option and the main data of the "csv-table_" directive. - New option "loading" for the `"image" directive`_. Sets the new attribute loading__ of the <image> doctree element. __ docs/ref/doctree.htmlloading * Configuration changes: - New configuration setting root_prefix_. Configurable root directory for included files. - New configuration setting sources_ for the "buildhtml.py" application. - Simpler and more secure `input encoding`_ default behaviour: Do not use the locale encoding as fallback if Python is started in `UTF-8 mode`_. Stop using "latin1" as second fallback. Remove BOM (U+FEFF ZWNBSP at start of data) only if the `input_encoding`_ configuration setting is None, '', 'utf-8-sig', 'utf-16', or 'utf-32'. Do not remove other ZWNBSPs. * Output changes: HTML5: Stop setting the "footnote-reference" class value for footnote references. Use the CSS selector ``[role="doc-noteref"]`` (works since Docutils 0.18, see minimal.css for examples). Fix MathML rendering problems in Chrome/Chromium based browsers. Embed SVG images as ``<svg>`` instead of data-URI. manpage: Use .EE/.EX macros for literal blocks. Render URI references (do not use .UR/.UE). Use box option for tables. * Removed objects: `docutils.nodes.reprunicode`, `docutils.nodes.ensure_str()` Python 2 compatibility hacks `docutils.utils.Reporter.set_conditions()` obsolete `docutils.core.Publisher.setup_option_parser()` internal, obsolete * New files: ``docutils/writers/html5_polyglot/italic-field-names.css`` Alternative style for Docutils field-lists. * Removed files: ``install.py``, ``setup.py`` Metadata is now stored in ``pyproject.toml``, supported by pip_ since version 19.0 (2019-01-22). See README__ for installation alternatives. __ README.htmlinstallation * Bugfixes and improvements (see HISTORY_). .. _input encoding: docs/api/publisher.htmlencodings .. _csv-table: docs/ref/rst/directives.htmlcsv-table .. _"image" directive: docs/ref/rst/directives.htmlimage .. _root_prefix: docs/user/config.htmlroot-prefix .. _sources: docs/user/config.htmlsources ```
Links - PyPI: https://pypi.org/project/docutils - Changelog: https://data.safetycli.com/changelogs/docutils/

Update pyzmq from 26.0.0 to 26.0.2.

The bot wasn't able to find a changelog for this release. Got an idea?

Links - PyPI: https://pypi.org/project/pyzmq

Update regex from 2023.12.25 to 2024.4.16.

Changelog ### 2024.4.16 ``` Git issue 525: segfault when fuzzy matching empty list ```
Links - PyPI: https://pypi.org/project/regex - Changelog: https://data.safetycli.com/changelogs/regex/ - Repo: https://github.com/mrabarnett/mrab-regex

Update Sphinx from 7.2.6 to 7.3.7.

Changelog ### 7.3.7 ``` ===================================== Bugs fixed ---------- * 12299: Defer loading themes defined via entry points until their explicit use by the user or a child theme. Patch by Adam Turner. * 12305: Return the default value for ``theme.get_config()`` with an unsupported theme configuration section. Patch by Adam Turner. ``` ### 7.3.6 ``` ===================================== Bugs fixed ---------- * 12295: Re-export all AST types in the C and C++ domains. Patch by Adam Turner. * 12295: Re-export various objects from ``sphinx.domains.python._annotations`` in ``sphinx.domains.python``. Patch by Jacob Chesslo and Adam Turner. ``` ### 7.3.5 ``` ===================================== Bugs fixed ---------- * 12295: Re-export various objects from ``sphinx.domains.python._object`` in ``sphinx.domains.python``. Patch by Jacob Chesslo and Adam Turner. ``` ### 7.3.4 ``` ===================================== Bugs fixed ---------- * Handle cases when ``Any`` is not an instance of ``type``. Patch by Adam Turner. ``` ### 7.3.3 ``` ===================================== Bugs fixed ---------- * 12290: Fix a false-positive warning when setting a configuration value with ``Any`` as the valid type to a type other than the value's default. Patch by Adam Turner. ``` ### 7.3.2 ``` ===================================== Bugs fixed ---------- * Preload all themes defined via entry points. Patch by Adam Turner. * Fix a bad interaction between the ``'Furo'`` theme and the new-style for configuration values. Patch by Adam Turner. ``` ### 7.3.1 ``` ===================================== Dependencies ------------ * Require ``tomli`` on Python 3.10 and earlier. Patch by Adam Turner. ``` ### 7.3.0 ``` ===================================== Dependencies ------------ * 11858: Increase the minimum supported version of Alabaster to 0.7.14. Patch by Adam Turner. * 11411: Support `Docutils 0.21`_. Patch by Adam Turner. .. _Docutils 0.21: https://docutils.sourceforge.io/RELEASE-NOTES.html#release-0-21-2024-04-09 * 12012: Use ``types-docutils`` instead of ``docutils-stubs``. Deprecated ---------- * 11693: Support for old-style :file:`Makefile` and :file:`make.bat` output in :program:`sphinx-quickstart`, and the associated options :option:`!-M`, :option:`!-m`, :option:`!--no-use-make-mode`, and :option:`!--use-make-mode`. * 11285: Direct access to :attr:`!sphinx.testing.util.SphinxTestApp._status` or :attr:`!sphinx.testing.util.SphinxTestApp._warning` is deprecated. Use the public properties :attr:`!sphinx.testing.util.SphinxTestApp.status` and :attr:`!sphinx.testing.util.SphinxTestApp.warning` instead. Patch by Bénédikt Tran. * tests: :func:`!sphinx.testing.util.strip_escseq` is deprecated in favour of :func:`!sphinx.util.console.strip_colors`. Patch by Bénédikt Tran. Features added -------------- * 12265: Support theme configuration via ``theme.toml``. * 11701: HTML Search: Adopt the new `\<search\>`_ element. Patch by Bénédikt Tran. .. _`\<search\>`: https://developer.mozilla.org/en-US/docs/Web/HTML/Element/search * 11776: Add long option names to ``sphinx-build``. Patch by Hugo van Kemenade, Adam Turner, Bénédikt Tran, and Ezio Melotti. * Organise the ``sphinx-build`` options into groups. Patch by Adam Turner. * 11855: Defer computation of configuration values. Patch by Adam Turner. * Add ``:no-search:`` as an alias of the ``:nosearch:`` metadata field. Patch by Adam Turner. * 11803: autodoc: Use an overriden ``__repr__()`` function in an enum, if defined. Patch by Shengyu Zhang. * 11825: Allow custom targets in the manpage role. Patch by Nicolas Peugnet. * 11892: Improved performance when resolving cross references in the C++ domain. Patch by Rouslan Korneychuk. * 11905: Add a :rst:dir:`versionremoved` directive. Patch by Hugo van Kemenade, Adam Turner, and C.A.M. Gerlach. * 11981: Improve rendering of signatures using ``slice`` syntax, e.g., ``def foo(arg: np.float64[:,:]) -> None: ...``. * The manpage builder now adds `OSC 8`_ anchors to hyperlinks, using the `groff`_ device control command. .. _OSC 8: https://gist.github.com/egmontkob/eb114294efbcd5adb1944c9f3cb5feda .. _groff: https://lists.gnu.org/archive/html/groff/2021-10/msg00000.html * 11015: Change the text of the :rst:dir:`versionadded` directive from ``New in [...]`` to ``Added in [...]``. Patch by Bénédikt Tran. * 12131: Added :confval:`show_warning_types` configuration option. Patch by Chris Sewell. * 12193: Improve ``external`` warnings for unknown roles. In particular, suggest related role names if an object type is mistakenly used. Patch by Chris Sewell. * Add public type alias :class:`sphinx.util.typing.ExtensionMetadata`. This can be used by extension developers to annotate the return type of their ``setup`` function. Patch by Chris Sewell. Bugs fixed ---------- * 11668: Raise a useful error when ``theme.conf`` is missing. Patch by Vinay Sajip. * 11622: Ensure that the order of keys in ``searchindex.js`` is deterministic. Patch by Pietro Albini. * 11617: ANSI control sequences are stripped from the output when writing to a warnings file with :option:`-w <sphinx-build -w>`. Patch by Bénédikt Tran. * 11666: Skip all hidden directories in ``CatalogRepository.pofiles``. Patch by Aryaz Eghbali. * 9686: html builder: Fix MathJax lazy loading when equations appear in titles. Patch by Bénédikt Tran. * 11483: singlehtml builder: Fix MathJax lazy loading when the index does not contain any math equations. Patch by Bénédikt Tran. * 11697: HTML Search: add 'noindex' meta robots tag. Patch by James Addison. * 11678: Fix a possible ``ZeroDivisionError`` in ``sphinx.ext.coverage``. Patch by Stephen Finucane. * 11756: LaTeX: build error with recent TeXLive due to missing ``substitutefont`` package (triggered if using ``fontenc`` with ``T2A`` option and document language is not a Cyrillic one). Patch by Jean-François B. * 11675: Fix rendering of progression bars in environments that do not support ANSI control sequences. Patch by Bénédikt Tran. * 11861: Whitelist more types with an incorrect ``__module__`` attribute. Patch by Adam Turner. * 11715: Apply ``tls_verify`` and ``tls_cacerts`` config to ``ImageDownloader``. Patch by Nick Touran. * Allow hyphens in group names for :rst:dir:`productionlist` cross-references. Patch by Adam Turner. * 11433: Added the :confval:`linkcheck_allow_unauthorized` configuration option. Set this option to ``False`` to report HTTP 401 (unauthorized) server responses as broken. Patch by James Addison. * 11868: linkcheck: added a distinct ``timeout`` reporting status code. This can be enabled by setting :confval:`linkcheck_report_timeouts_as_broken` to ``False``. Patch by James Addison. * 11869: Refresh the documentation for the ``linkcheck_timeout`` setting. Patch by James Addison. * 11874: Configure a default 30-second value for ``linkcheck_timeout``. Patch by James Addison. * 11886: Print the Jinja2 template path chain in ``TemplateNotFound`` exceptions. Patch by Colin Marquardt. * 11598: Do not use query components in URLs for assets in EPUB rendering. Patch by David Runge. * 11904: Support unary subtraction when parsing annotations. Patch by James Addison. * 11925: Blacklist the ``sphinxprettysearchresults`` extension; the functionality it provides was merged into Sphinx v2.0.0. Patch by James Addison. * 11917: Fix rendering of annotated inherited members for Python 3.9. Patch by Janet Carson. * 11935: C Domain: Fix namespace-pop context. Patch by Frank Dana. * 11923: Avoid zombie processes when parallel builds fail. Patch by Felix von Drigalski. * 11353: Support enumeration classes inheriting from mixin or data types. Patch by Bénédikt Tran. * 11962: Fix target resolution when using ``:paramtype:`` fields. Patch by Bénédikt Tran. * 11944: Use anchor in search preview. Patch by Will Lachance. * 12008: Fix case-sensitive lookup of ``std:label`` names in intersphinx inventory. Patch by Michael Goerz. * 11958: HTML Search: Fix partial matches overwriting full matches. Patch by William Lachance. * 11959: Fix multiple term matching when word appears in both title and document. Patch by Will Lachance. * 11474: Fix doctrees caching causing files not be rebuilt in some cases, e.g., when :confval:`numfig` is ``True``. Patch by Bénédikt Tran. * 11278: autodoc: Fix rendering of :class:`functools.singledispatchmethod` combined with :func:`classmethod <classmethod>`. Patch by Bénédikt Tran. * 11894: Do not add checksums to css files if building using the htmlhelp builder. Patch by reduerK akiM. * 12052: Remove ``<script>`` and ``<style>`` tags from the content of search result summary snippets. Patch by James Addison. * 11578: HTML Search: Order non-main index entries after other results. Patch by Brad King. * 12147: autosummary: Fix a bug whereby the wrong file extension may be used, when multiple suffixes are specified in :confval:`source_suffix`. Patch by Sutou Kouhei. * 10786: improve the error message when a file to be copied (e.g., an asset) is removed during Sphinx execution. Patch by Bénédikt Tran. * 12040: HTML Search: Ensure that document titles that are partially-matched by the user search query are included in search results. Patch by James Addison. * 11970: singlehtml builder: make target URIs to be same-document references in the sense of :rfc:`RFC 3986, §4.4 <3986section-4.4>`, e.g., ``index.htmlfoo`` becomes ``foo``. Patch by Eric Norige. * 12271: Partially revert Docutils' r9562__ to fix EPUB files. Patch by Adam Turner. __ https://sourceforge.net/p/docutils/code/9562/ * 12253: Escape reserved path characters in the remote images post-transform download cache. Patch by James Addison and Adam Turner. Testing ------- * Reorganise tests into directories. Patch by Adam Turner. * Clean up global state in ``SphinxTestApp``. Patch by Adam Turner. * 11285: :func:`!pytest.mark.sphinx` and :class:`!sphinx.testing.util.SphinxTestApp` accept *warningiserror*, *keep_going* and *verbosity* as keyword arguments. Patch by Bénédikt Tran. * 11285: :class:`!sphinx.testing.util.SphinxTestApp` *status* and *warning* arguments are checked to be :class:`io.StringIO` objects (the public API incorrectly assumed this without checking it). Patch by Bénédikt Tran. * Report the result of ``test_run_epubcheck`` as ``skipped`` instead of ``success`` when either Java or ``epubcheck`` are not available. * Use dynamic allocation of unused port numbers for the test HTTP(S) servers. As a side-effect, this removes the need for test server lockfiles, meaning that any remaining ``tests/test-server.lock`` files can safely be deleted. ```
Links - PyPI: https://pypi.org/project/sphinx - Changelog: https://data.safetycli.com/changelogs/sphinx/

Update traitlets from 5.14.2 to 5.14.3.

Changelog ### 5.14.3 ``` ([Full Changelog](https://github.com/ipython/traitlets/compare/v5.14.2...5cf34f6c42b6e39aa1e53394443efca3d7329e3b)) Bugs fixed - Fix assigning string value to Set [903](https://github.com/ipython/traitlets/pull/903) ([azjps](https://github.com/azjps)) Maintenance and upkeep improvements - Bump the actions group with 1 update [899](https://github.com/ipython/traitlets/pull/899) ([dependabot](https://github.com/dependabot)) Contributors to this release ([GitHub contributors page for this release](https://github.com/ipython/traitlets/graphs/contributors?from=2024-03-12&to=2024-04-19&type=c)) [azjps](https://github.com/search?q=repo%3Aipython%2Ftraitlets+involves%3Aazjps+updated%3A2024-03-12..2024-04-19&type=Issues) | [dependabot](https://github.com/search?q=repo%3Aipython%2Ftraitlets+involves%3Adependabot+updated%3A2024-03-12..2024-04-19&type=Issues) <!-- <END NEW CHANGELOG ENTRY> --> ```
Links - PyPI: https://pypi.org/project/traitlets - Changelog: https://data.safetycli.com/changelogs/traitlets/