RISPaDD / biospecdb

Biosample Spectral Repository
BSD 3-Clause "New" or "Revised" License
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Bump the all-minor-and-patch-dependency-updates group with 5 updates #365

Closed dependabot[bot] closed 4 months ago

dependabot[bot] commented 4 months ago

Bumps the all-minor-and-patch-dependency-updates group with 5 updates:

Package From To
boto3 1.34.143 1.34.152
django-nested-admin 4.0.2 4.1.0
plotly 5.22.0 5.23.0
pytest 8.2.2 8.3.2
ruff 0.5.1 0.5.5

Updates boto3 from 1.34.143 to 1.34.152

Commits
  • ba3d7ce Merge branch 'release-1.34.152'
  • be5b965 Bumping version to 1.34.152
  • 8723785 Add changelog entries from botocore
  • 64fb912 Merge branch 'release-1.34.151'
  • 533a186 Merge branch 'release-1.34.151' into develop
  • 37f7211 Bumping version to 1.34.151
  • 00f626a Add changelog entries from botocore
  • 0f53991 Merge branch 'release-1.34.150'
  • d2588d7 Merge branch 'release-1.34.150' into develop
  • a1cbd94 Bumping version to 1.34.150
  • Additional commits viewable in compare view


Updates django-nested-admin from 4.0.2 to 4.1.0

Release notes

Sourced from django-nested-admin's releases.

v4.1.0

What's Changed

New Contributors

Full Changelog: https://github.com/theatlantic/django-nested-admin/compare/v4.0.2...v4.1.0

Commits


Updates plotly from 5.22.0 to 5.23.0

Release notes

Sourced from plotly's releases.

v5.23.0

Updated

  • Updated Plotly.js from version 2.32.0 to version 2.34.0. See the plotly.js CHANGELOG for more information. These changes are reflected in the auto-generated plotly.graph_objects module. Notable changes include:
    • Add subtitle attribute to layout.title to enable adding subtitles to plots [#7012]
    • Introduce "u" and "s" pseudo html tags to add partial underline and strike-through styles to SVG text elements [#7043]
    • Add geometric mean functionality and 'geometric mean ascending' + 'geometric mean descending' to category_order on cartesian axes [#6223], with thanks to @​acxz and @​prabhathc for the contribution!
    • Add axis property ticklabelindex for drawing the label for each minor tick n positions away from a major tick, with thanks to @​my-tien for the contribution! [#7036]
    • Add property ticklabelstandoff and ticklabelshift to cartesian axes to adjust positioning of tick labels, with thanks to @​my-tien for the contribution! [#7006]
    • Add x0shift, x1shift, y0shift, y1shift to shapes to add control over positioning of shape vertices on (multi-)category axes, with thanks to @​my-tien for the contribution! [#7005]
Changelog

Sourced from plotly's changelog.

[5.23.0] - 2024-07-23

Updated

  • Updated Plotly.js from version 2.32.0 to version 2.34.0. See the plotly.js CHANGELOG for more information. These changes are reflected in the auto-generated plotly.graph_objects module. Notable changes include:
    • Add subtitle attribute to layout.title to enable adding subtitles to plots [#7012]
    • Introduce "u" and "s" pseudo html tags to add partial underline and strike-through styles to SVG text elements [#7043]
    • Add geometric mean functionality and 'geometric mean ascending' + 'geometric mean descending' to category_order on cartesian axes [#6223], with thanks to @​acxz and @​prabhathc for the contribution!
    • Add axis property ticklabelindex for drawing the label for each minor tick n positions away from a major tick, with thanks to @​my-tien for the contribution! [#7036]
    • Add property ticklabelstandoff and ticklabelshift to cartesian axes to adjust positioning of tick labels, with thanks to @​my-tien for the contribution! [#7006]
    • Add x0shift, x1shift, y0shift, y1shift to shapes to add control over positioning of shape vertices on (multi-)category axes, with thanks to @​my-tien for the contribution! [#7005]
  • Specify Python version 3.8-3.11 for development virtual environments and pin pytest at version 8.1.1 to match.
  • Update IntegerValidator to handle extras option to allow supporting additional keyword values. For example, 'bold' and 'normal' as well as integers as used in font weights #4612.
Commits
  • 83c7c85 version changes for v5.23.0
  • bf78a8a Merge pull request #4683 from plotly/add-latest-docs-updates
  • a32a981 Merge branch 'master' into add-latest-docs-updates
  • 9b5ec6a Merge pull request #4627 from plotly/update-plotly-js-version
  • bcbc571 Merge branch 'master' into update-plotly-js-version
  • e5fdd7c add text annotation example
  • 3de6e25 Merge pull request #4679 from plotly/fix-maps-docstring
  • 44bf20c specify which maps require token
  • 059433f add plot subtitle example
  • b9e178d update plotly.js to 2.34.0
  • Additional commits viewable in compare view


Updates pytest from 8.2.2 to 8.3.2

Release notes

Sourced from pytest's releases.

8.3.2

pytest 8.3.2 (2024-07-24)

Bug fixes

  • #12652: Resolve regression [conda]{.title-ref} environments where no longer being automatically detected.

    -- by RonnyPfannschmidt{.interpreted-text role="user"}

8.3.1

pytest 8.3.1 (2024-07-20)

The 8.3.0 release failed to include the change notes and docs for the release. This patch release remedies this. There are no other changes.

8.3.0

pytest 8.3.0 (2024-07-20)

New features

  • #12231: Added [--xfail-tb]{.title-ref} flag, which turns on traceback output for XFAIL results.

    • If the [--xfail-tb]{.title-ref} flag is not given, tracebacks for XFAIL results are NOT shown.
    • The style of traceback for XFAIL is set with [--tb]{.title-ref}, and can be [auto|long|short|line|native|no]{.title-ref}.
    • Note: Even if you have [--xfail-tb]{.title-ref} set, you won't see them if [--tb=no]{.title-ref}.

    Some history:

    With pytest 8.0, [-rx]{.title-ref} or [-ra]{.title-ref} would not only turn on summary reports for xfail, but also report the tracebacks for xfail results. This caused issues with some projects that utilize xfail, but don't want to see all of the xfail tracebacks.

    This change detaches xfail tracebacks from [-rx]{.title-ref}, and now we turn on xfail tracebacks with [--xfail-tb]{.title-ref}. With this, the default [-rx]{.title-ref}/ [-ra]{.title-ref} behavior is identical to pre-8.0 with respect to xfail tracebacks. While this is a behavior change, it brings default behavior back to pre-8.0.0 behavior, which ultimately was considered the better course of action.

  • #12281: Added support for keyword matching in marker expressions.

    Now tests can be selected by marker keyword arguments. Supported values are int{.interpreted-text role="class"}, (unescaped) str{.interpreted-text role="class"}, bool{.interpreted-text role="class"} & None{.interpreted-text role="data"}.

    See marker examples <marker_keyword_expression_example>{.interpreted-text role="ref"} for more information.

    -- by lovetheguitar{.interpreted-text role="user"}

  • #12567: Added --no-fold-skipped command line option.

    If this option is set, then skipped tests in short summary are no longer grouped by reason but all tests are printed individually with their nodeid in the same way as other statuses.

    -- by pbrezina{.interpreted-text role="user"}

... (truncated)

Commits
  • bbcec9c Prepare release version 8.3.2
  • 78fe8b6 Merge pull request #12657 from pytest-dev/patchback/backports/8.3.x/6c806b499...
  • 238bad2 Merge pull request #12656 from RonnyPfannschmidt/fix-12652-detect-conda-env
  • ae6034a Merge pull request #12641 from pytest-dev/patchback/backports/8.3.x/c03989cee...
  • 31337ab Merge pull request #12640 from pytest-dev/update-user
  • ca3070b Merge pull request #12637 from pytest-dev/release-8.3.1
  • de98446 Prepare release version 8.3.1
  • bd0a042 Merge pull request #12636 from pytest-dev/update-release-notes
  • 664325b doc/changelog: update 8.3.0 notes
  • 19d225d Merge pull request #12635 from pytest-dev/release-8.3.0
  • Additional commits viewable in compare view


Updates ruff from 0.5.1 to 0.5.5

Release notes

Sourced from ruff's releases.

0.5.5

Release Notes

Preview features

  • [fastapi] Implement fastapi-redundant-response-model (FAST001) and fastapi-non-annotated-dependency(FAST002) (#11579)
  • [pydoclint] Implement docstring-missing-exception (DOC501) and docstring-extraneous-exception (DOC502) (#11471)

Rule changes

  • [numpy] Fix NumPy 2.0 rule for np.alltrue and np.sometrue (#12473)
  • [numpy] Ignore NPY201 inside except blocks for compatibility with older numpy versions (#12490)
  • [pep8-naming] Avoid applying ignore-names to self and cls function names (N804, N805) (#12497)

Formatter

  • Fix incorrect placement of leading function comment with type params (#12447)

Server

  • Do not bail code action resolution when a quick fix is requested (#12462)

Bug fixes

  • Fix Ord implementation of cmp_fix (#12471)
  • Raise syntax error for unparenthesized generator expression in multi-argument call (#12445)
  • [pydoclint] Fix panic in DOC501 reported in #12428 (#12435)
  • [flake8-bugbear] Allow singleton tuples with starred expressions in B013 (#12484)

Documentation

  • Add Eglot setup guide for Emacs editor (#12426)
  • Add note about the breaking change in nvim-lspconfig (#12507)
  • Add note to include notebook files for native server (#12449)
  • Add setup docs for Zed editor (#12501)

Contributors

... (truncated)

Changelog

Sourced from ruff's changelog.

0.5.5

Preview features

  • [fastapi] Implement fastapi-redundant-response-model (FAST001) and fastapi-non-annotated-dependency(FAST002) (#11579)
  • [pydoclint] Implement docstring-missing-exception (DOC501) and docstring-extraneous-exception (DOC502) (#11471)

Rule changes

  • [numpy] Fix NumPy 2.0 rule for np.alltrue and np.sometrue (#12473)
  • [numpy] Ignore NPY201 inside except blocks for compatibility with older numpy versions (#12490)
  • [pep8-naming] Avoid applying ignore-names to self and cls function names (N804, N805) (#12497)

Formatter

  • Fix incorrect placement of leading function comment with type params (#12447)

Server

  • Do not bail code action resolution when a quick fix is requested (#12462)

Bug fixes

  • Fix Ord implementation of cmp_fix (#12471)
  • Raise syntax error for unparenthesized generator expression in multi-argument call (#12445)
  • [pydoclint] Fix panic in DOC501 reported in #12428 (#12435)
  • [flake8-bugbear] Allow singleton tuples with starred expressions in B013 (#12484)

Documentation

  • Add Eglot setup guide for Emacs editor (#12426)
  • Add note about the breaking change in nvim-lspconfig (#12507)
  • Add note to include notebook files for native server (#12449)
  • Add setup docs for Zed editor (#12501)

0.5.4

Rule changes

  • [ruff] Rename RUF007 to zip-instead-of-pairwise (#12399)

Bug fixes

  • [flake8-builtins] Avoid shadowing diagnostics for @override methods (#12415)
  • [flake8-comprehensions] Insert parentheses for multi-argument generators (#12422)
  • [pydocstyle] Handle escaped docstrings within docstring (D301) (#12192)

Documentation

  • Fix GitHub link to Neovim setup (#12410)

... (truncated)

Commits
  • fc16d8d Bump version to 0.5.5 (#12510)
  • 175e5d7 Add missing traceback line in f-string-in-exception docstring. (#12508)
  • c03f257 Add note about the breaking change in nvim-lspconfig (#12507)
  • 6bbb4a2 Add setup docs for Zed editor (#12501)
  • 2ce3e3a Fix the search path tests on MacOS (#12503)
  • 2a64ccc Avoid applying ignore-names to self and cls function names (#12497)
  • 928ffd6 Ignore NPY201 inside except blocks for compatibility with older numpy ver...
  • e52be09 [red-knot] Improve validation for search paths (#12376)
  • 8890735 [flake8-bugbear] Allow singleton tuples with starred expressions in B013 (#12...
  • eac965e [red-knot] Watch search paths (#12407)
  • Additional commits viewable in compare view


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codecov[bot] commented 4 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 90.79%. Comparing base (f96aebc) to head (3096df7). Report is 6 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #365 +/- ## ======================================= Coverage 90.79% 90.79% ======================================= Files 28 28 Lines 2237 2237 ======================================= Hits 2031 2031 Misses 206 206 ``` | [Flag](https://app.codecov.io/gh/RISPaDD/biospecdb/pull/365/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=RISPaDD) | Coverage Δ | | |---|---|---| | [unittests](https://app.codecov.io/gh/RISPaDD/biospecdb/pull/365/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=RISPaDD) | `90.79% <ø> (ø)` | | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=RISPaDD#carryforward-flags-in-the-pull-request-comment) to find out more.

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