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Update sphinx requirement from <6,>=4.4.0 to >=4.4.0,<7 #2430

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merged 1 commit into from
Jan 3, 2023

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@dependabot dependabot bot commented on behalf of github Jan 2, 2023

Updates the requirements on sphinx to permit the latest version.

Release notes

Sourced from sphinx's releases.

v6.0.0

Changelog: https://www.sphinx-doc.org/en/master/changes.html

Changelog

Sourced from sphinx's changelog.

Release 6.0.0 (released Dec 29, 2022)

Dependencies

  • #10468: Drop Python 3.6 support
  • #10470: Drop Python 3.7, Docutils 0.14, Docutils 0.15, Docutils 0.16, and Docutils 0.17 support. Patch by Adam Turner

Incompatible changes

  • #7405: Removed the jQuery and underscore.js JavaScript frameworks.

    These frameworks are no longer be automatically injected into themes from Sphinx 6.0. If you develop a theme or extension that uses the jQuery, $, or $u global objects, you need to update your JavaScript to modern standards, or use the mitigation below.

    The first option is to use the sphinxcontrib.jquery_ extension, which has been developed by the Sphinx team and contributors. To use this, add sphinxcontrib.jquery to the extensions list in conf.py, or call app.setup_extension("sphinxcontrib.jquery") if you develop a Sphinx theme or extension.

    The second option is to manually ensure that the frameworks are present. To re-add jQuery and underscore.js, you will need to copy jquery.js and underscore.js from the Sphinx repository_ to your static directory, and add the following to your layout.html:

    .. code-block:: html+jinja

    {%- block scripts %} {{ super() }} {%- endblock %}

    .. _sphinxcontrib.jquery: https://github.com/sphinx-contrib/jquery/

    Patch by Adam Turner.

  • #10471, #10565: Removed deprecated APIs scheduled for removal in Sphinx 6.0. See :ref:dev-deprecated-apis for details. Patch by Adam Turner.

  • #10901: C Domain: Remove support for parsing pre-v3 style type directives and roles. Also remove associated configuration variables c_allow_pre_v3 and c_warn_on_allowed_pre_v3. Patch by Adam Turner.

Features added

... (truncated)

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Updates the requirements on [sphinx](https://github.com/sphinx-doc/sphinx) to permit the latest version.
- [Release notes](https://github.com/sphinx-doc/sphinx/releases)
- [Changelog](https://github.com/sphinx-doc/sphinx/blob/master/CHANGES)
- [Commits](sphinx-doc/sphinx@v4.4.0...v6.0.0)

---
updated-dependencies:
- dependency-name: sphinx
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Jan 2, 2023
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codecov bot commented Jan 2, 2023

Codecov Report

Merging #2430 (9eaa1ca) into latest (2f2c692) will increase coverage by 8.13%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           latest    #2430      +/-   ##
==========================================
+ Coverage   84.08%   92.22%   +8.13%     
==========================================
  Files         130      101      -29     
  Lines       15044    11496    -3548     
  Branches     2403     2403              
==========================================
- Hits        12650    10602    -2048     
+ Misses       2098      598    -1500     
  Partials      296      296              
Flag Coverage Δ
python 92.22% <ø> (ø)
rust ?

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
src/core/src/index/sbt/mod.rs
src/core/src/ffi/mod.rs
src/core/src/lib.rs
src/core/src/sketch/minhash.rs
src/core/src/index/search.rs
src/core/src/sketch/hyperloglog/estimators.rs
src/core/src/ffi/cmd/compute.rs
src/core/tests/minhash.rs
src/core/src/index/bigsi.rs
src/core/src/ffi/utils.rs
... and 19 more

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@ctb
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ctb commented Jan 3, 2023

This PR was occasioned by sphinx releasing v6.0.0.

When I test this in a separate environment with sphinx==6, the documentation looks good. However, myst-parser (latest: v0.18.1) does not yet (formally) support sphinx >= 6 so presumably that will limit actual installs of sphinx 6.

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ctb commented Jan 3, 2023

(which goes to say: I will merge, but we will still be on sphinx 5.x until myst-parser updates its requirements)

@ctb ctb merged commit 059d988 into latest Jan 3, 2023
@ctb ctb deleted the dependabot/pip/sphinx-gte-4.4.0-and-lt-7 branch January 3, 2023 15:05
@ctb ctb mentioned this pull request Mar 3, 2023
ctb added a commit that referenced this pull request Mar 3, 2023
# sourmash release 4.7.0

Major new features:

* provide an initial plugin architecture for sourmash that supports new
signature saving & loading mechanisms (#2428)
* add plugin support for new command-line subcommands (#2438)
* debias all containment values (#2243)

Minor new features:

* Use RankLineageInfo to simplify reading lineages (#2467)
* store taxids in lineageDB (#2466)
* Use new tax classes for taxonomic summarization (#2443)
* add tax summarization dataclasses for safety and flexibility (#2439)
* add `--scaled` to sourmash compare (#2414)
* replace `lca_utils.LineagePair` with `tax_utils.LineagePair` (#2441)
* Add new classes for lineage manipulation (#2437)

Cleanup and documentation updates:

* ReadTheDocs updates (#2445)
* update `sourmash compare` command-line docs (#2400)

Developer updates:

* fix python tests by bumping tox and pip cache versions (#2424)
* Update sphinx requirement from <6,>=4.4.0 to >=4.4.0,<7 (#2430)
* Build: replace milksnake with maturin (#2393)
* importlib_metadata is a dependency on old Python versions (#2484)
* Release docs: use two separate sed commands (#2483)
* minor fixes to release behavior (#2479)
* Use screed and maturin from nixpkgs in `flake.nix` (#2481)
* update release procedure after v4.6.0 and v4.6.1 (#2386)
* Update makefile and docs (#2432)

Dependabot updates:

* Bump once_cell from 1.17.0 to 1.17.1 (#2488)
* Bump ouroboros from 0.15.5 to 0.15.6 (#2487)
* Bump memmap2 from 0.5.8 to 0.5.9 (#2486)
* Bump supercharge/redis-github-action from 1.4.0 to 1.5.0 (#2485)
* Bump proptest from 1.0.0 to 1.1.0 (#2460)
* Bump web-sys from 0.3.60 to 0.3.61 (#2461)
* Bump serde_json from 1.0.91 to 1.0.93 (#2471)
* Bump wasm-bindgen-test from 0.3.33 to 0.3.34 (#2463)
* Bump cachix/install-nix-action from 18 to 19 (#2459)
* Bump wasm-bindgen from 0.2.83 to 0.2.84 (#2464)
* Bump typed-builder from 0.11.0 to 0.12.0 (#2451)
* Bump bumpalo from 3.9.1 to 3.12.0 (#2450)
* Bump pypa/cibuildwheel from 2.11.4 to 2.12.0 (#2447)
* Bump bzip2 from 0.4.3 to 0.4.4 (#2444)
* Bump once_cell from 1.14.0 to 1.17.0 (#2429)
* Bump serde from 1.0.151 to 1.0.152 (#2423)
* Bump pypa/cibuildwheel from 2.11.3 to 2.11.4 (#2422)
* Bump serde_json from 1.0.89 to 1.0.91 (#2418)
* Bump serde from 1.0.150 to 1.0.151 (#2419)
* Bump thiserror from 1.0.37 to 1.0.38 (#2417)
* Bump finch from 0.4.3 to 0.5.0 (#2416)
* Bump rayon from 1.6.0 to 1.6.1 (#2404)
* Bump serde from 1.0.149 to 1.0.150 (#2403)
* Bump pypa/cibuildwheel from 2.11.2 to 2.11.3 (#2402)
* Bump serde from 1.0.148 to 1.0.149 (#2397)
* Bump capnp from 0.14.5 to 0.14.11 (#2396)
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