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RISPaDD / biospecdb

Biosample Spectral Repository
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Bump the all-minor-and-patch-dependency-updates group with 8 updates #336

Closed dependabot[bot] closed 7 months ago

dependabot[bot] commented 7 months ago

Bumps the all-minor-and-patch-dependency-updates group with 8 updates:

Package From To
setuptools 69.2.0 69.5.1
tox 4.12.1 4.15.0
boto3 1.34.62 1.34.95
django-sql-explorer[charts] 4.0.2 4.2
pandas 2.2.1 2.2.2
plotly 5.19.0 5.22.0
pytest 8.1.1 8.2.0
ruff 0.3.5 0.4.2

Updates setuptools from 69.2.0 to 69.5.1

Changelog

Sourced from setuptools's changelog.

v69.5.1

No significant changes.

v69.5.0

Features

  • Refresh unpinned vendored dependencies. (#4253)
  • Updated vendored packaging to version 24.0. (#4301)

v69.4.2

Bugfixes

v69.4.1

No significant changes.

v69.4.0

Features

  • pypa/distutils#213#4298)

v69.3.1

Bugfixes

  • Remove attempt to canonicalize the version. It's already canonical enough. (#4302)

v69.3.0

... (truncated)

Commits


Updates tox from 4.12.1 to 4.15.0

Release notes

Sourced from tox's releases.

4.15.0

What's Changed

New Contributors

Full Changelog: https://github.com/tox-dev/tox/compare/4.14.2...4.15.0

4.14.2

What's Changed

New Contributors

Full Changelog: https://github.com/tox-dev/tox/compare/4.14.1...4.14.2

4.14.1

What's Changed

Full Changelog: https://github.com/tox-dev/tox/compare/4.14.0...4.14.1

4.14.0

What's Changed

... (truncated)

Changelog

Sourced from tox's changelog.

v4.15.0 (2024-04-26)

Features - 4.15.0

- Add support for multiple appending override options (-x, --override) on command line - by :user:`amitschang`. (:issue:`3261`)
- Add support for inverting exit code success criteria using bang (!) (:issue:`3271`)

Bugfixes - 4.15.0

  • Fix issue that the leading character c was dropped from packages in constraints files - by :user:jugmac00. (:issue:3247)
  • Allow appending to deps with --override testenv.deps+=foo - by :user:stefanor. (:issue:3256)
  • Fix non-existing branch rewrite in the documentation to main. (:issue:3257)
  • Update test typing for build 1.2.0, which has an explicit Distribution type - by :user:stefanor. (:issue:3260)
  • Fix broken input parsing for --discover flag. - by :user:mimre25 (:issue:3272)

Improved Documentation - 4.15.0

- Rephrase ``--discover`` flag's description to avoid confusion between paths and executables. - by :user:`mimre25` (:issue:`3274`)

v4.14.2 (2024-03-22)


Bugfixes - 4.14.2


- Add provision arguments to ToxParser to fix crash when provisioning new tox environment without list-dependencies by :user:`seyidaniels` (:issue:`3190`)

Improved Documentation - 4.14.2
</code></pre>
<ul>
<li>Removed unused line from the 'fresh_subprocess' documentation. (:issue:<code>3241</code>)</li>
</ul>
<h2>v4.14.1 (2024-03-06)</h2>
<p>Bugfixes - 4.14.1</p>
<pre><code>- Fix crash with fresh subprocess, if the build backend is setuptools automatically enable fresh subprocesses for
  build backend calls - by :user:`gaborbernat`. (:issue:`3235`)

v4.14.0 (2024-03-05)
--------------------

Features - 4.14.0
</code></pre>
<ul>
<li>Support enabling fresh subprocess for packaging build backends via :ref:<code>fresh_subprocess</code> - by :user:<code>gaborbernat</code>. (:issue:<code>3227</code>)</li>
<li>Allow plugins attaching additional information to <code>--version</code> via <code>tox_append_version_info</code> method in the plugin
module - by :user:<code>gaborbernat</code>. (:issue:<code>3234</code>)</li>
</ul>
<h2>v4.13.0 (2024-02-16)</h2>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>

<ul>
<li><a href="https://github.com/tox-dev/tox/commit/261b4ca55686059489b1314c440f0e2fca21aca5"><code>261b4ca</code></a> release 4.15.0</li>
<li><a href="https://github.com/tox-dev/tox/commit/c54dfbd9ad4aad9f0ef5503b7dff2558cdf64208"><code>c54dfbd</code></a> fix(parser): Fix --discover parsed incorrectly from env (<a href="https://redirect.github.com/tox-dev/tox/issues/3274">#3274</a>)</li>
<li><a href="https://github.com/tox-dev/tox/commit/809e10f9871e75cf7b07063f47393f9c10861174"><code>809e10f</code></a> Add bang to invert exit code (<a href="https://redirect.github.com/tox-dev/tox/issues/3271">#3271</a>)</li>
<li><a href="https://github.com/tox-dev/tox/commit/822c9d07699aa090fb8d37cb94247ea0d085125b"><code>822c9d0</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://redirect.github.com/tox-dev/tox/issues/3267">#3267</a>)</li>
<li><a href="https://github.com/tox-dev/tox/commit/0e5a3dbb9a1c7eb1df56421cc4bca5e187626ccd"><code>0e5a3db</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://redirect.github.com/tox-dev/tox/issues/3265">#3265</a>)</li>
<li><a href="https://github.com/tox-dev/tox/commit/f5850c0d3a893cbb6d9de192fe8e6e857573499b"><code>f5850c0</code></a> Support multiple override appends (<a href="https://redirect.github.com/tox-dev/tox/issues/3261">#3261</a>)</li>
<li><a href="https://github.com/tox-dev/tox/commit/c2be62972e7f7b3e79260e5c96e4fe5bf76f5929"><code>c2be629</code></a> Allow appending to deps with the command line (<a href="https://redirect.github.com/tox-dev/tox/issues/3259">#3259</a>)</li>
<li><a href="https://github.com/tox-dev/tox/commit/d28a9ee0ea28b2356b24a0d0e0ed70c0141d41cc"><code>d28a9ee</code></a> Update installation.rst (<a href="https://redirect.github.com/tox-dev/tox/issues/3257">#3257</a>)</li>
<li><a href="https://github.com/tox-dev/tox/commit/a19a9467cfae5a0fc2c1b6faf1845d412898c693"><code>a19a946</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://redirect.github.com/tox-dev/tox/issues/3258">#3258</a>)</li>
<li><a href="https://github.com/tox-dev/tox/commit/a22fe8ffce73acdfc2aefd70228ede0337aac19b"><code>a22fe8f</code></a> Fix type-checking (<a href="https://redirect.github.com/tox-dev/tox/issues/3260">#3260</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/tox-dev/tox/compare/4.12.1...4.15.0">compare view</a></li>
</ul>
</details>

<br />



Updates `boto3` from 1.34.62 to 1.34.95


Changelog

Sourced from boto3's changelog.




1.34.95


    

  • api-change:chime-sdk-voice: [botocore] Due to changes made by the Amazon Alexa service, GetSipMediaApplicationAlexaSkillConfiguration and PutSipMediaApplicationAlexaSkillConfiguration APIs are no longer available for use. For more information, refer to the Alexa Smart Properties page.
    • 

  • api-change:codeartifact: [botocore] Add support for the Ruby package format.
    • 

  • api-change:fms: [botocore] AWS Firewall Manager now supports the network firewall service stream exception policy feature for accounts within your organization.
    • 

  • api-change:omics: [botocore] Add support for workflow sharing and dynamic run storage
    • 

  • api-change:opensearch: [botocore] This release enables customers to create Route53 A and AAAA alias record types to point custom endpoint domain to OpenSearch domain's dualstack search endpoint.
    • 

  • api-change:pinpoint-sms-voice-v2: [botocore] Amazon Pinpoint has added two new features Multimedia services (MMS) and protect configurations. Use the three new MMS APIs to send media messages to a mobile phone which includes image, audio, text, or video files. Use the ten new protect configurations APIs to block messages to specific countries.
    • 

  • api-change:qbusiness: [botocore] This is a general availability (GA) release of Amazon Q Business. Q Business enables employees in an enterprise to get comprehensive answers to complex questions and take actions through a unified, intuitive web-based chat experience - using an enterprise's existing content, data, and systems.
    • 

  • api-change:quicksight: [botocore] New Q embedding supporting Generative Q&A
    • 

  • api-change:route53resolver: [botocore] Release of FirewallDomainRedirectionAction parameter on the Route 53 DNS Firewall Rule.  This allows customers to configure a DNS Firewall rule to inspect all the domains in the DNS redirection chain (default) , such as CNAME, ALIAS, DNAME, etc., or just the first domain and trust the rest.
    • 

  • api-change:sagemaker: [botocore] Amazon SageMaker Training now supports the use of attribute-based access control (ABAC) roles for training job execution roles. Amazon SageMaker Inference now supports G6 instance types.
    • 

  • api-change:signer: [botocore] Documentation updates for AWS Signer. Adds cross-account signing constraint and definitions for cross-account actions.
    • 



1.34.94


    

  • api-change:amplify: [botocore] Updating max results limit for listing any resources (Job, Artifacts, Branch, BackendResources, DomainAssociation) to 50 with the exception of list apps that where max results can be up to 100.
    • 

  • api-change:connectcases: [botocore] This feature releases DeleteField, DeletedLayout, and DeleteTemplate API's
    • 

  • api-change:inspector2: [botocore] Update Inspector2 to include new Agentless API parameters.
    • 

  • api-change:timestream-query: [botocore] This change allows users to update and describe account settings associated with their accounts.
    • 

  • api-change:transcribe: [botocore] This update provides error messaging for generative call summarization in Transcribe Call Analytics
    • 

  • api-change:trustedadvisor: [botocore] This release adds the BatchUpdateRecommendationResourceExclusion API to support batch updates of Recommendation Resource exclusion statuses and introduces a new exclusion status filter to the ListRecommendationResources and ListOrganizationRecommendationResources APIs.
    • 



1.34.93


    

  • api-change:codepipeline: [botocore] Add ability to manually and automatically roll back a pipeline stage to a previously successful execution.
    • 

  • api-change:cognito-idp: [botocore] Add LimitExceededException to SignUp errors
    • 

  • api-change:connectcampaigns: [botocore] This release adds support for specifying if Answering Machine should wait for prompt sound.
    • 

  • api-change:marketplace-entitlement: [botocore] Releasing minor endpoint updates.
    • 

  • api-change:oam: [botocore] This release introduces support for Source Accounts to define which Metrics and Logs to share with the Monitoring Account
    • 

  • api-change:rds: [botocore] SupportsLimitlessDatabase field added to describe-db-engine-versions to indicate whether the DB engine version supports Aurora Limitless Database.
    • 

  • api-change:support: [botocore] Releasing minor endpoint updates.
    • 



1.34.92


    

  • api-change:appsync: [botocore] UpdateGraphQLAPI documentation update and datasource introspection secret arn update
    • 

  • api-change:fms: [botocore] AWS Firewall Manager adds support for network ACL policies to manage Amazon Virtual Private Cloud (VPC) network access control lists (ACLs) for accounts in your organization.
    • 

  • api-change:ivs: [botocore] Bug Fix: IVS does not support arns with the svs prefix
    • 

  • api-change:ivs-realtime: [botocore] Bug Fix: IVS Real Time does not support ARNs using the svs prefix.
    • 

  • api-change:rds: [botocore] Updates Amazon RDS documentation for setting local time zones for RDS for Db2 DB instances.
    • 

  • api-change:stepfunctions: [botocore] Add new ValidateStateMachineDefinition operation, which performs syntax checking on the definition of a Amazon States Language (ASL) state machine.
    • 






... (truncated)





Commits

    

  • dc49ed5 Merge branch 'release-1.34.95'
    • 

  • ded69f6 Bumping version to 1.34.95
    • 

  • 9f4321d Add changelog entries from botocore
    • 

  • f474951 Merge branch 'release-1.34.94'
    • 

  • 32dabda Merge branch 'release-1.34.94' into develop
    • 

  • 5a5954d Bumping version to 1.34.94
    • 

  • 8b3a8f6 Add changelog entries from botocore
    • 

  • 98b2562 Merge branch 'release-1.34.93'
    • 

  • 9d2623a Merge branch 'release-1.34.93' into develop
    • 

  • b7f2abe Bumping version to 1.34.93
    • 

  • Additional commits viewable in compare view
    • 







Updates `django-sql-explorer[charts]` from 4.0.2 to 4.2


Release notes

Sourced from django-sql-explorer[charts]'s releases.




4.2.0


4.2.0_ (2024-04-26)


    

  • [#609](https://github.com/chrisclark/django-sql-explorer/issues/609)_: Tracking should be opt-in and not use the SECRET_KEY
    • 

  • [#610](https://github.com/chrisclark/django-sql-explorer/issues/610)_: Import error (sql_metadata) with 4.1 version
    • 

  • [#612](https://github.com/chrisclark/django-sql-explorer/issues/612)_: Accessing the database during app initialization
    • 

  • Regex-injection vulnerability
    • 

  • Improved assistant UI
    • 



4.2.0.beta1


4.2.0b1_ (2024-04-25)


    

  • [#609](https://github.com/chrisclark/django-sql-explorer/issues/609)_: Tracking should be opt-in and not use the SECRET_KEY
    • 

  • [#610](https://github.com/chrisclark/django-sql-explorer/issues/610)_: Import error (sql_metadata) with 4.1 version
    • 

  • [#612](https://github.com/chrisclark/django-sql-explorer/issues/612)_: Accessing the database during app initialization
    • 

  • Regex-injection vulnerability
    • 

  • Better anonymization for telemetry
    • 



4.1.0


4.1.0 (2024-04-23)


    

  • SQL Assistant: Built in query help via OpenAI (or LLM of choice), with relevant schema
automatically injected into the prompt. Enable by setting EXPLORER_AI_API_KEY.
    • 

  • Anonymous usage telemetry. Disable by setting EXPLORER_ENABLE_ANONYMOUS_STATS to False.
    • 

  • Refactor pip requirements to make 'extras' more robust and easier to manage.
    • 

  • [#592](https://github.com/chrisclark/django-sql-explorer/issues/592)_: Support user models with no email fields
    • 

  • [#594](https://github.com/chrisclark/django-sql-explorer/issues/594)_: Eliminate  tags to prevent potential Content Security Policy issues.
    • 



4.1.0.beta6


    

  • SQL Assistant: Built in query help via OpenAI (or LLM of choice), with relevant schema
automatically injected into the prompt. Enable by setting EXPLORER_AI_API_KEY.
    • 

  • Anonymous usage telemetry. Disable by setting EXPLORER_ENABLE_ANONYMOUS_STATS to False.
    • 

  • Refactor pip requirements to make 'extras' more robust and easier to manage.
    • 

  • [#592](https://github.com/chrisclark/django-sql-explorer/issues/592)_: Support user models with no email fields
    • 

  • [#594](https://github.com/chrisclark/django-sql-explorer/issues/594)_: Eliminate  tags to prevent potential Content Security Policy issues.
    • 



4.1.0.beta5


4.1.0b5_ (2024-04-18)


    

  • Fixes an issue in b2 with different DB backends throwing different exception types if migrations are not applied.
    • 

  • Refactor of requirements & fixed relative import issue in urls.py
    • 

  • SQL Assistant: Built in query help via OpenAI (or LLM of choice), with relevant schema
automatically injected into the prompt. Enable via setting EXPLORER_AI_API_KEY.
    • 

  • Anonymous usage telemetry. Can be disabled by setting EXPLORER_ENABLE_ANONYMOUS_STATS to False
    • 

  • #594_: Eliminate  tags to prevent potential Content Security Policy issues
    • 



4.1.0.beta4


4.1.0b4_ (2024-04-17)


    

  • Fixes an issue in b2 with different DB backends throwing different exception types if migrations are not applied.
    • 

  • SQL Assistant: Built in query help via OpenAI (or LLM of choice), with relevant schema
automatically injected into the prompt. Enable via setting EXPLORER_AI_API_KEY.
    • 






... (truncated)





Changelog

Sourced from django-sql-explorer[charts]'s changelog.




==========
Change Log


This document records all notable changes to django-sql-explorer <https://github.com/chrisclark/django-sql-explorer>.
This project adheres to Semantic Versioning <https://semver.org/>.


4.2.0_ (2024-04-26)


    

  • [#609](https://github.com/chrisclark/django-sql-explorer/issues/609)_: Tracking should be opt-in and not use the SECRET_KEY
    • 

  • [#610](https://github.com/chrisclark/django-sql-explorer/issues/610)_: Import error (sql_metadata) with 4.1 version
    • 

  • [#612](https://github.com/chrisclark/django-sql-explorer/issues/612)_: Accessing the database during app initialization
    • 

  • Regex-injection vulnerability
    • 

  • Improved assistant UI
    • 



4.1.0_ (2024-04-23)


    

  • SQL Assistant: Built in query help via OpenAI (or LLM of choice), with relevant schema
automatically injected into the prompt. Enable by setting EXPLORER_AI_API_KEY.
    • 

  • Anonymous usage telemetry. Disable by setting EXPLORER_ENABLE_ANONYMOUS_STATS to False.
    • 

  • Refactor pip requirements to make 'extras' more robust and easier to manage.
    • 

  • [#592](https://github.com/chrisclark/django-sql-explorer/issues/592)_: Support user models with no email fields
    • 

  • [#594](https://github.com/chrisclark/django-sql-explorer/issues/594)_: Eliminate  tags to prevent potential Content Security Policy issues.
    • 








Commits






Updates `pandas` from 2.2.1 to 2.2.2


Release notes

Sourced from pandas's releases.




Pandas 2.2.2


We are pleased to announce the release of pandas 2.2.2.
This release includes some new features, bug fixes, and performance improvements. We recommend that all users upgrade to this version.


See the full whatsnew for a list of all the changes.
Pandas 2.2.2 supports Python 3.9 and higher.


The release will be available on the defaults and conda-forge channels:


conda install pandas



Or via PyPI:


python3 -m pip install --upgrade pandas



Please report any issues with the release on the pandas issue tracker.


Thanks to all the contributors who made this release possible.







Commits






Updates `plotly` from 5.19.0 to 5.22.0


Release notes

Sourced from plotly's releases.




v5.22.0


Updated


    

  • Updated Plotly.js from version 2.31.1 to version 2.32.0. See the plotly.js CHANGELOG for more information. These changes are reflected in the auto-generated plotly.graph_objects module. Notable changes include:

      

    • Add "bold" weight, "italic" style and "small-caps" variant options to fonts #6956
      • 

    • Fix applying autotickangles on axes with showdividers as well as cases where tickson is set to "boundaries" #6967, with thanks to @​my-tien for the contribution!
      • 

    • Fix positioning of multi-line axis titles with standoff #6970, with thanks to @​my-tien for the contribution!
      • 

    

    • 



v5.21.0


Updated


    

  • Updated Plotly.js from version 2.30.0 to version 2.31.1. See the plotly.js CHANGELOG for more information. These changes are reflected in the auto-generated plotly.graph_objects module. Notable changes include:

      

    • Add zorder attribute to various cartesian traces for controlling stacking order of SVG traces drawn into a subplot [#6918, #6953],
This feature was anonymously sponsored: thank you to our sponsor!
      • 

    • Add "between" option to shape layer for placing them above grid lines and below traces [#6927],
with thanks to @​my-tien for the contribution!
      • 

    • Add "raw" sizemode to cone trace [#6938]
      • 

    • Add layout.hoversubplots to enable hover effects across multiple cartesian suplots sharing one axis [#6947, #6950]
      • 

    

    • 



Fixed


    

  • Fixed orjson loading issue [#4562]
    • 



v5.20.0


Updated


    

  • Updated Plotly.js from version 2.29.1 to version 2.30.0. See the plotly.js CHANGELOG for more information. These changes are reflected in the auto-generated plotly.graph_objects module. Notable changes include:

      

    • Add fill gradients for scatter traces [#6905], with thanks to @​lumip for the contribution!
      • 

    • Add indentation to legend [#6874], with thanks to @​my-tien for the contribution!
      • 

    

    • 








Changelog

Sourced from plotly's changelog.




[5.22.0] - 2024-05-01


Updated


    

  • Updated Plotly.js from version 2.31.1 to version 2.32.0. See the plotly.js CHANGELOG for more information. These changes are reflected in the auto-generated plotly.graph_objects module. Notable changes include:

      

    • Add "bold" weight, "italic" style and "small-caps" variant options to fonts #6956
      • 

    • Fix applying autotickangles on axes with showdividers as well as cases where tickson is set to "boundaries" #6967, with thanks to @​my-tien for the contribution!
      • 

    • Fix positioning of multi-line axis titles with standoff #6970, with thanks to @​my-tien for the contribution!
      • 

    

    • 



[5.21.0] - 2024-04-17


Updated


    

  • Updated Plotly.js from version 2.30.0 to version 2.31.1. See the plotly.js CHANGELOG for more information. These changes are reflected in the auto-generated plotly.graph_objects module. Notable changes include:

      

    • Add zorder attribute to various cartesian traces for controlling stacking order of SVG traces drawn into a subplot [#6918, #6953],
This feature was anonymously sponsored: thank you to our sponsor!
      • 

    • Add "between" option to shape layer for placing them above grid lines and below traces [#6927],
with thanks to @​my-tien for the contribution!
      • 

    • Add "raw" sizemode to cone trace [#6938]
      • 

    • Add layout.hoversubplots to enable hover effects across multiple cartesian suplots sharing one axis [#6947, #6950]
      • 

    

    • 



Fixed


    

  • Fixed orjson loading issue [#4562]
    • 



[5.20.0] - 2024-03-13


Updated


    

  • Updated Plotly.js from version 2.29.1 to version 2.30.0. See the plotly.js CHANGELOG for more information. These changes are reflected in the auto-generated plotly.graph_objects module. Notable changes include:

      

    • Add fill gradients for scatter traces [#6905], with thanks to @​lumip for the contribution!
      • 

    • Add indentation to legend [#6874], with thanks to @​my-tien for the contribution!
      • 

    

    • 








Commits

    

  • 34e8bdb version changes for v5.22.0
    • 

  • 9a158eb Merge pull request #4589 from plotly/recent-docs-updates
    • 

  • 6ed004b Merge branch 'master' into recent-docs-updates
    • 

  • 56ec663 Merge pull request #4587 from plotly/update-plotlyjs-version
    • 

  • 025eea7 add font example
    • 

  • f60b7f0 add textfont style, variant and weight
    • 

  • 2fa17d9 Merge pull request #4557 from rl-utility-man/patch-5
    • 

  • cd5fc87 update test to add new font attributes
    • 

  • 217ed66 Update doc/python/hover-text-and-formatting.md
    • 

  • 94c172e update plotly.js to 2.32
    • 

  • Additional commits viewable in compare view
    • 







Updates `pytest` from 8.1.1 to 8.2.0


Release notes

Sourced from pytest's releases.




8.2.0


pytest 8.2.0 (2024-04-27)


Deprecations


    

  • 

    #12069: A deprecation warning is now raised when implementations of one of the following hooks request a deprecated py.path.local parameter instead of the pathlib.Path parameter which replaced it:
    

      

    • pytest_ignore_collect{.interpreted-text role="hook"} - the path parameter - use collection_path instead.
      • 

    • pytest_collect_file{.interpreted-text role="hook"} - the path parameter - use file_path instead.
      • 

    • pytest_pycollect_makemodule{.interpreted-text role="hook"} - the path parameter - use module_path instead.
      • 

    • pytest_report_header{.interpreted-text role="hook"} - the startdir parameter - use start_path instead.
      • 

    • pytest_report_collectionfinish{.interpreted-text role="hook"} - the startdir parameter - use start_path instead.
      • 

    

    The replacement parameters are available since pytest 7.0.0.
The old parameters will be removed in pytest 9.0.0.
    

    See legacy-path-hooks-deprecated{.interpreted-text role="ref"} for more details.
    

    • 



Features


    

  • 

    #11871: Added support for reading command line arguments from a file using the prefix character @, like e.g.: pytest @tests.txt. The file must have one argument per line.
    

    See Read arguments from file <args-from-file>{.interpreted-text role="ref"} for details.
    

    • 



Improvements


    

  • 

    #11523: pytest.importorskip{.interpreted-text role="func"} will now issue a warning if the module could be found, but raised ImportError{.interpreted-text role="class"} instead of ModuleNotFoundError{.interpreted-text role="class"}.
    

    The warning can be suppressed by passing exc_type=ImportError to pytest.importorskip{.interpreted-text role="func"}.
    

    See import-or-skip-import-error{.interpreted-text role="ref"} for details.
    

    • 

  • 

    #11728: For unittest-based tests, exceptions during class cleanup (as raised by functions registered with TestCase.addClassCleanup <unittest.TestCase.addClassCleanup>{.interpreted-text role="meth"}) are now reported instead of silently failing.
    

    • 

  • 

    #11777: Text is no longer truncated in the short test summary info section when -vv is given.
    

    • 

  • 

    #12112: Improved namespace packages detection when consider_namespace_packages{.interpreted-text role="confval"} is enabled, covering more situations (like editable installs).
    

    • 

  • 

    #9502: Added PYTEST_VERSION{.interpreted-text role="envvar"} environment variable which is defined at the start of the pytest session and undefined afterwards. It contains the value of pytest.__version__, and among other things can be used to easily check if code is running from within a pytest run.
    

    • 



Bug Fixes


    

  • 

    #12065: Fixed a regression in pytest 8.0.0 where test classes containing setup_method and tests using @staticmethod or @classmethod would crash with AttributeError: 'NoneType' object has no attribute 'setup_method'.
    

    Now the request.instance <pytest.FixtureRequest.instance>{.interpreted-text role="attr"} attribute of tests using @staticmethod and @classmethod is no longer None, but a fresh instance of the class, like in non-static methods.
    

    • 






... (truncated)





Commits

    

  • 6bd3f31 Tweak changelog for 8.2.0
    • 

  • 9b6219b Prepare release version 8.2.0
    • 

  • 835765c Merge pull request #12130 from bluetech/fixtures-inline
    • 

  • 7e7503c unittest: report class cleanup exceptions (#12250)
    • 

  • 882c4da fixtures: inline fail_fixturefunc
    • 

  • 2e8fb9f fixtures: extract a _check_fixturedef method
    • 

  • acf2971 fixtures: inline _getnextfixturedef into _get_active_fixturedef
    • 

  • 3c77aec fixtures: move "request" check early
    • 

  • d217d68 fixtures: inline _compute_fixture_value
    • 

  • 530be28 fixtures: use early return in _get_active_fixturedef
    • 

  • Additional commits viewable in compare view
    • 







Updates `ruff` from 0.3.5 to 0.4.2


Release notes

Sourced from ruff's releases.




v0.4.2


Changes


Rule changes


    

  • [flake8-pyi] Allow for overloaded __exit__ and __aexit__ definitions (PYI036) (#11057)
    • 

  • [pyupgrade] Catch usages of "%s" % var and provide an unsafe fix (UP031) (#11019)
    • 

  • [refurb] Implement new rule that suggests min/max over sorted() (FURB192) (#10868)
    • 



Server


    

  • Fix an issue with missing diagnostics for Neovim and Helix (#11092)
    • 

  • Implement hover documentation for noqa codes (#11096)
    • 

  • Introduce common Ruff configuration options with new server settings (#11062)
    • 



Bug fixes


    

  • Use macos-12 for building release wheels to enable macOS 11 compatibility (#11146)
    • 

  • [flake8-blind-expect] Allow raise from in BLE001 (#11131)
    • 

  • [flake8-pyi] Allow simple assignments to None in enum class scopes (PYI026) (#11128)
    • 

  • [flake8-simplify] Avoid raising SIM911 for non-zip attribute calls (#11126)
    • 

  • [refurb] Avoid operator.itemgetter suggestion for single-item tuple (#11095)
    • 

  • [ruff] Respect per-file-ignores for RUF100 with no other diagnostics (#11058)
    • 

  • [ruff] Fix async comprehension false positive (RUF029) (#11070)
    • 



Documentation


    

  • [flake8-bugbear] Document explicitly disabling strict zip (B905) (#11040)
    • 

  • [flake8-type-checking] Mention lint.typing-modules in TCH001, TCH002, and TCH003 (#11144)
    • 

  • [isort] Improve documentation around custom isort sections (#11050)
    • 

  • [pylint] Fix documentation oversight for invalid-X-returns (#11094)
    • 



Performance


    

  • Use matchit to resolve per-file settings (#11111)
    • 



Contributors






... (truncated)





Changelog

Sourced from ruff's changelog.




0.4.2


Rule changes


    

  • [flake8-pyi] Allow for overloaded __exit__ and __aexit__ definitions (PYI036) (#11057)
    • 

  • [pyupgrade] Catch usages of "%s" % var and provide an unsafe fix (UP031) (#11019)
    • 

  • [refurb] Implement new rule that suggests min/max over sorted() (FURB192) (#10868)
    • 



Server


    

  • Fix an issue with missing diagnostics for Neovim and Helix (#11092)
    • 

  • Implement hover documentation for noqa codes (#11096)
    • 

  • Introduce common Ruff configuration options with new server settings (#11062)
    • 



Bug fixes


    

  • Use macos-12 for building release wheels to enable macOS 11 compatibility (#11146)
    • 

  • [flake8-blind-expect] Allow raise from in BLE001 (#11131)
    • 

  • [flake8-pyi] Allow simple assignments to None in enum class scopes (PYI026) (#11128)
    • 

  • [flake8-simplify] Avoid raising SIM911 for non-zip attribute calls (#11126)
    • 

  • [refurb] Avoid operator.itemgetter suggestion for single-item tuple (#11095)
    • 

  • [ruff] Respect per-file-ignores for RUF100 with no other diagnostics (#11058)
    • 

  • [ruff] Fix async comprehension false positive (RUF029) (#11070)
    • 



Documentation


    

  • [flake8-bugbear] Document explicitly disabling strict zip (B905) (#11040)
    • 

  • [flake8-type-checking] Mention lint.typing-modules in TCH001, TCH002, and TCH003 (#11144)
    • 

  • [isort] Improve documentation around custom isort sections (#11050)
    • 

  • [pylint] Fix documentation oversight for invalid-X-returns (#11094)
    • 



Performance


    

  • Use matchit to resolve per-file settings (#11111)
    • 



0.4.1


Preview features


    

  • [pylint] Implement invalid-hash-returned (PLE0309) (#10961)
    • 

  • [pylint] Implement invalid-index-returned (PLE0305) (#10962)
    • 



Bug fixes


    

  • [pylint] Allow NoReturn-like functions for __str__, __len__, etc. (PLE0307) (#11017)
    • 

  • Parser: Use empty range when there's "gap" in token source (#11032)
    • 

  • [ruff] Ignore stub functions in unused-async (RUF029) (#11026)
    • 

  • Parser: Expect indented case block instead of match stmt (#11033)
    • 



0.4.0





... (truncated)





Commits

    

  • 77c93fd Bump version to 0.4.2 (#11151)
    • 

  • 1c9f5e3 Display the AST even with syntax errors (#11147)
    • 

  • 263a0d2 Use macos-12 to build release wheels (#11146)
    • 

  • 4738e19 Remove unused lexical error types (#11145)
    • 

  • f428bd5 Docs: mention lint.typing-modules in TCH001, TCH002, TCH003 (#11144)
    • 

  • 4690890 ruff server: In 'publish diagnostics' mode, document diagnostics are cleare...
    • 

  • 19baabb README: add Apache Superset to project list (#11136)
    • 

  • cee38f3 [flake8-blind-expect] Allow raise from in BLE001 (#11131)
    • 

  • e3fde28 [flake8-pyi] Allow overloaded __exit__ and __aexit__ definitions (`PYI0...
    • 

  • 1c8849f Use Matchit to Resolve Per-File Settings (#11111)
    • 

  • Additional commits viewable in compare view
    • 







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codecov[bot] commented 7 months ago

Codecov Report

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

Project coverage is 90.73%. Comparing base (b2575d6) to head (3bf599d).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #336 +/- ## ======================================= Coverage 90.73% 90.73% ======================================= Files 28 28 Lines 2235 2235 ======================================= Hits 2028 2028 Misses 207 207 ``` | [Flag](https://app.codecov.io/gh/RISPaDD/biospecdb/pull/336/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/336/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=RISPaDD) | `90.73% <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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