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Bump the all-dependencies group with 11 updates #38

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merged 1 commit into from
Dec 23, 2024
Merged

Bump the all-dependencies group with 11 updates #38

merged 1 commit into from
Dec 23, 2024

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@dependabot dependabot bot commented on behalf of github Dec 23, 2024

Bumps the all-dependencies group with 11 updates:

Package From To
click 8.1.7 8.1.8
pydantic 2.10.3 2.10.4
attrs 24.2.0 24.3.0
bioregistry 0.11.28 0.11.29
curies 0.9.2 0.10.1
eval-type-backport 0.2.0 0.2.2
google-api-python-client 2.155.0 2.156.0
jinja2 3.1.4 3.1.5
protobuf 5.29.1 5.29.2
pydantic-core 2.27.1 2.27.2
urllib3 2.2.3 2.3.0

Updates click from 8.1.7 to 8.1.8

Release notes

Sourced from click's releases.

8.1.8

This is the Click 8.1.8 fix release, which fixes bugs but does not otherwise change behavior and should not result in breaking changes compared to the latest feature release.

PyPI: https://pypi.org/project/click/8.1.8/ Changes: https://click.palletsprojects.com/en/stable/changes/#version-8-1-8 Milestone https://github.com/pallets/click/milestones/23?closed=1

  • Fix an issue with type hints for click.open_file(). #2717
  • Fix issue where error message for invalid click.Path displays on multiple lines. #2697
  • Fixed issue that prevented a default value of "" from being displayed in the help for an option. #2500
  • The test runner handles stripping color consistently on Windows. #2705
  • Show correct value for flag default when using default_map. #2632
  • Fix click.echo(color=...) passing color to coloroma so it can be forced on Windows. #2606.
  • More robust bash version check, fixing problem on Windows with git-bash. #2638
  • Cache the help option generated by the help_option_names setting to respect its eagerness. #2811
  • Replace uses of os.system with subprocess.Popen. #1476
  • Exceptions generated during a command will use the context's color setting when being displayed. #2193
  • Error message when defining option with invalid name is more descriptive. #2452
  • Refactor code generating default --help option to deduplicate code. #2563
  • Test CLIRunner resets patched _compat.should_strip_ansi. #2732
Changelog

Sourced from click's changelog.

Version 8.1.8

Unreleased

  • Fix an issue with type hints for click.open_file(). :issue:2717
  • Fix issue where error message for invalid click.Path displays on multiple lines. :issue:2697
  • Fixed issue that prevented a default value of "" from being displayed in the help for an option. :issue:2500
  • The test runner handles stripping color consistently on Windows. :issue:2705
  • Show correct value for flag default when using default_map. :issue:2632
  • Fix click.echo(color=...) passing color to coloroma so it can be forced on Windows. :issue:2606.
Commits

Updates pydantic from 2.10.3 to 2.10.4

Release notes

Sourced from pydantic's releases.

v2.10.4 2024-12-18

What's Changed

Packaging

Fixes

New Contributors

Full Changelog: pydantic/pydantic@v2.10.3...v2.10.4

Changelog

Sourced from pydantic's changelog.

v2.10.4 (2024-12-18)

GitHub release

What's Changed

Packaging

Fixes

New Contributors

Commits

Updates attrs from 24.2.0 to 24.3.0

Commits

Updates bioregistry from 0.11.28 to 0.11.29

Commits

Updates curies from 0.9.2 to 0.10.1

Release notes

Sourced from curies's releases.

v0.10.1

What's Changed

Full Changelog: biopragmatics/curies@v0.10.0...v0.10.1

v0.10.0

What's Changed

Full Changelog: biopragmatics/curies@v0.9.2...v0.10.0

Commits

Updates eval-type-backport from 0.2.0 to 0.2.2

Commits

Updates google-api-python-client from 2.155.0 to 2.156.0

Release notes

Sourced from google-api-python-client's releases.

v2.156.0

2.156.0 (2024-12-17)

Features

Commits

Updates jinja2 from 3.1.4 to 3.1.5

Release notes

Sourced from jinja2's releases.

3.1.5

This is the Jinja 3.1.5 security fix release, which fixes security issues and bugs but does not otherwise change behavior and should not result in breaking changes compared to the latest feature release.

PyPI: https://pypi.org/project/Jinja2/3.1.5/ Changes: https://jinja.palletsprojects.com/changes/#version-3-1-5 Milestone: https://github.com/pallets/jinja/milestone/16?closed=1

  • The sandboxed environment handles indirect calls to str.format, such as by passing a stored reference to a filter that calls its argument. GHSA-q2x7-8rv6-6q7h
  • Escape template name before formatting it into error messages, to avoid issues with names that contain f-string syntax. #1792, GHSA-gmj6-6f8f-6699
  • Sandbox does not allow clear and pop on known mutable sequence types. #2032
  • Calling sync render for an async template uses asyncio.run. #1952
  • Avoid unclosed auto_aiter warnings. #1960
  • Return an aclose-able AsyncGenerator from Template.generate_async. #1960
  • Avoid leaving root_render_func() unclosed in Template.generate_async. #1960
  • Avoid leaving async generators unclosed in blocks, includes and extends. #1960
  • The runtime uses the correct concat function for the current environment when calling block references. #1701
  • Make |unique async-aware, allowing it to be used after another async-aware filter. #1781
  • |int filter handles OverflowError from scientific notation. #1921
  • Make compiling deterministic for tuple unpacking in a {% set ... %} call. #2021
  • Fix dunder protocol (copy/pickle/etc) interaction with Undefined objects. #2025
  • Fix copy/pickle support for the internal missing object. #2027
  • Environment.overlay(enable_async) is applied correctly. #2061
  • The error message from FileSystemLoader includes the paths that were searched. #1661
  • PackageLoader shows a clearer error message when the package does not contain the templates directory. #1705
  • Improve annotations for methods returning copies. #1880
  • urlize does not add mailto: to values like @a@b. #1870
  • Tests decorated with @pass_context can be used with the |select filter. #1624
  • Using set for multiple assignment (a, b = 1, 2) does not fail when the target is a namespace attribute. #1413
  • Using set in all branches of {% if %}{% elif %}{% else %} blocks does not cause the variable to be considered initially undefined. #1253
Changelog

Sourced from jinja2's changelog.

Version 3.1.5

Released 2024-12-21

  • The sandboxed environment handles indirect calls to str.format, such as by passing a stored reference to a filter that calls its argument. :ghsa:q2x7-8rv6-6q7h
  • Escape template name before formatting it into error messages, to avoid issues with names that contain f-string syntax. :issue:1792, :ghsa:gmj6-6f8f-6699
  • Sandbox does not allow clear and pop on known mutable sequence types. :issue:2032
  • Calling sync render for an async template uses asyncio.run. :pr:1952
  • Avoid unclosed auto_aiter warnings. :pr:1960
  • Return an aclose-able AsyncGenerator from Template.generate_async. :pr:1960
  • Avoid leaving root_render_func() unclosed in Template.generate_async. :pr:1960
  • Avoid leaving async generators unclosed in blocks, includes and extends. :pr:1960
  • The runtime uses the correct concat function for the current environment when calling block references. :issue:1701
  • Make |unique async-aware, allowing it to be used after another async-aware filter. :issue:1781
  • |int filter handles OverflowError from scientific notation. :issue:1921
  • Make compiling deterministic for tuple unpacking in a {% set ... %} call. :issue:2021
  • Fix dunder protocol (copy/pickle/etc) interaction with Undefined objects. :issue:2025
  • Fix copy/pickle support for the internal missing object. :issue:2027
  • Environment.overlay(enable_async) is applied correctly. :pr:2061
  • The error message from FileSystemLoader includes the paths that were searched. :issue:1661
  • PackageLoader shows a clearer error message when the package does not contain the templates directory. :issue:1705
  • Improve annotations for methods returning copies. :pr:1880
  • urlize does not add mailto: to values like @a@b. :pr:1870
  • Tests decorated with @pass_context`` can be used with the ``|select`` filter. :issue:1624`
  • Using set for multiple assignment (a, b = 1, 2) does not fail when the target is a namespace attribute. :issue:1413
  • Using set in all branches of {% if %}{% elif %}{% else %} blocks does not cause the variable to be considered initially undefined. :issue:1253
Commits
  • 877f6e5 release version 3.1.5
  • 8d58859 remove test pypi
  • eda8fe8 update dev dependencies
  • c8fdce1 Fix bug involving calling set on a template parameter within all branches of ...
  • 66587ce Fix bug where set would sometimes fail within if
  • fbc3a69 Add support for namespaces in tuple parsing (#1664)
  • b8f4831 more comments about nsref assignment
  • ee83219 Add support for namespaces in tuple assignment
  • 1d55cdd Triple quotes in docs (#2064)
  • 8a8eafc edit block assignment section
  • Additional commits viewable in compare view

Updates protobuf from 5.29.1 to 5.29.2

Commits
  • 2330983 Updating version.json and repo version numbers to: 29.2
  • 1772657 Automated rollback of commit 23aada230b2478c7a07fe7612489eb8e79b9c379. (#19692)
  • 8b9d76c Export environment variables so bazelisk picks them up (#19690)
  • a1c9b6a Pin staleness check to Bazel 7 (#19689)
  • 3649f87 Remove unused / invalid C++ lazy repeated field code from OSS. (#19682)
  • 3a7bb4a Remove CMake downgrade workaround from Windows CI tests (#19630)
  • d7d3da6 Merge pull request #19506 from protocolbuffers/29.x-202412032207
  • a3e9db8 Updating version.json and repo version numbers to: 29.2-dev
  • See full diff in compare view

Updates pydantic-core from 2.27.1 to 2.27.2

Release notes

Sourced from pydantic-core's releases.

v2.27.2 2024-12-18

What's Changed

Full Changelog: pydantic/pydantic-core@v2.27.1...v2.27.2

Commits

Updates urllib3 from 2.2.3 to 2.3.0

Release notes

Sourced from urllib3's releases.

2.3.0

🚀 urllib3 is fundraising for HTTP/2 support

urllib3 is raising ~$40,000 USD to release HTTP/2 support and ensure long-term sustainable maintenance of the project after a sharp decline in financial support for 2023. If your company or organization uses Python and would benefit from HTTP/2 support in Requests, pip, cloud SDKs, and thousands of other projects please consider contributing financially to ensure HTTP/2 support is developed sustainably and maintained for the long-haul.

Thank you for your support.

Features

  • Added HTTPResponse.shutdown() to stop any ongoing or future reads for a specific response. It calls shutdown(SHUT_RD) on the underlying socket. This feature was sponsored by LaunchDarkly. (urllib3/urllib3#2868)
  • Added support for JavaScript Promise Integration on Emscripten. This enables more efficient WebAssembly requests and streaming, and makes it possible to use in Node.js if you launch it as node --experimental-wasm-stack-switching. (urllib3/urllib3#3400)
  • Added the proxy_is_tunneling property to HTTPConnection and HTTPSConnection. (urllib3/urllib3#3285)
  • Added pickling support to NewConnectionError and NameResolutionError. (urllib3/urllib3#3480)

Bugfixes

  • Fixed an issue in debug logs where the HTTP version was rendering as "HTTP/11" instead of "HTTP/1.1". (urllib3/urllib3#3489)

Deprecations and Removals

Full Changelog: urllib3/urllib3@2.2.3...2.3.0

Changelog

Sourced from urllib3's changelog.

2.3.0 (2024-12-22)

Features

  • Added HTTPResponse.shutdown() to stop any ongoing or future reads for a specific response. It calls shutdown(SHUT_RD) on the underlying socket. This feature was sponsored by LaunchDarkly <https://opencollective.com/urllib3/contributions/815307>. ([#2868](https://github.com/urllib3/urllib3/issues/2868) <https://github.com/urllib3/urllib3/issues/2868>)
  • Added support for JavaScript Promise Integration on Emscripten. This enables more efficient WebAssembly requests and streaming, and makes it possible to use in Node.js if you launch it as node --experimental-wasm-stack-switching. ([#3400](https://github.com/urllib3/urllib3/issues/3400) <https://github.com/urllib3/urllib3/issues/3400>__)
  • Added the proxy_is_tunneling property to HTTPConnection and HTTPSConnection. ([#3285](https://github.com/urllib3/urllib3/issues/3285) <https://github.com/urllib3/urllib3/issues/3285>__)
  • Added pickling support to NewConnectionError and NameResolutionError. ([#3480](https://github.com/urllib3/urllib3/issues/3480) <https://github.com/urllib3/urllib3/issues/3480>__)

Bugfixes

  • Fixed an issue in debug logs where the HTTP version was rendering as "HTTP/11" instead of "HTTP/1.1". ([#3489](https://github.com/urllib3/urllib3/issues/3489) <https://github.com/urllib3/urllib3/issues/3489>__)

Deprecations and Removals

  • Removed support for Python 3.8. ([#3492](https://github.com/urllib3/urllib3/issues/3492) <https://github.com/urllib3/urllib3/issues/3492>__)
Commits

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@dependabot
Bump the all-dependencies group with 11 updates
fae543a 
Bumps the all-dependencies group with 11 updates:

| Package | From | To |
| --- | --- | --- |
| [click](https://github.com/pallets/click) | `8.1.7` | `8.1.8` |
| [pydantic](https://github.com/pydantic/pydantic) | `2.10.3` | `2.10.4` |
| [attrs](https://github.com/sponsors/hynek) | `24.2.0` | `24.3.0` |
| [bioregistry](https://github.com/biopragmatics/bioregistry) | `0.11.28` | `0.11.29` |
| [curies](https://github.com/biopragmatics/curies) | `0.9.2` | `0.10.1` |
| [eval-type-backport](https://github.com/alexmojaki/eval_type_backport) | `0.2.0` | `0.2.2` |
| [google-api-python-client](https://github.com/googleapis/google-api-python-client) | `2.155.0` | `2.156.0` |
| [jinja2](https://github.com/pallets/jinja) | `3.1.4` | `3.1.5` |
| [protobuf](https://github.com/protocolbuffers/protobuf) | `5.29.1` | `5.29.2` |
| [pydantic-core](https://github.com/pydantic/pydantic-core) | `2.27.1` | `2.27.2` |
| [urllib3](https://github.com/urllib3/urllib3) | `2.2.3` | `2.3.0` |


Updates `click` from 8.1.7 to 8.1.8
- [Release notes](https://github.com/pallets/click/releases)
- [Changelog](https://github.com/pallets/click/blob/main/CHANGES.rst)
- [Commits](pallets/click@8.1.7...8.1.8)

Updates `pydantic` from 2.10.3 to 2.10.4
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md)
- [Commits](pydantic/pydantic@v2.10.3...v2.10.4)

Updates `attrs` from 24.2.0 to 24.3.0
- [Commits](https://github.com/sponsors/hynek/commits)

Updates `bioregistry` from 0.11.28 to 0.11.29
- [Release notes](https://github.com/biopragmatics/bioregistry/releases)
- [Commits](biopragmatics/bioregistry@v0.11.28...v0.11.29)

Updates `curies` from 0.9.2 to 0.10.1
- [Release notes](https://github.com/biopragmatics/curies/releases)
- [Commits](biopragmatics/curies@v0.9.2...v0.10.1)

Updates `eval-type-backport` from 0.2.0 to 0.2.2
- [Commits](alexmojaki/eval_type_backport@v0.2.0...v0.2.2)

Updates `google-api-python-client` from 2.155.0 to 2.156.0
- [Release notes](https://github.com/googleapis/google-api-python-client/releases)
- [Commits](googleapis/google-api-python-client@v2.155.0...v2.156.0)

Updates `jinja2` from 3.1.4 to 3.1.5
- [Release notes](https://github.com/pallets/jinja/releases)
- [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst)
- [Commits](pallets/jinja@3.1.4...3.1.5)

Updates `protobuf` from 5.29.1 to 5.29.2
- [Release notes](https://github.com/protocolbuffers/protobuf/releases)
- [Changelog](https://github.com/protocolbuffers/protobuf/blob/main/protobuf_release.bzl)
- [Commits](protocolbuffers/protobuf@v5.29.1...v5.29.2)

Updates `pydantic-core` from 2.27.1 to 2.27.2
- [Release notes](https://github.com/pydantic/pydantic-core/releases)
- [Commits](pydantic/pydantic-core@v2.27.1...v2.27.2)

Updates `urllib3` from 2.2.3 to 2.3.0
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](urllib3/urllib3@2.2.3...2.3.0)

---
updated-dependencies:
- dependency-name: click
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-dependencies
- dependency-name: pydantic
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: all-dependencies
- dependency-name: attrs
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: all-dependencies
- dependency-name: bioregistry
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: all-dependencies
- dependency-name: curies
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: all-dependencies
- dependency-name: eval-type-backport
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: all-dependencies
- dependency-name: google-api-python-client
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: all-dependencies
- dependency-name: jinja2
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: all-dependencies
- dependency-name: protobuf
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: all-dependencies
- dependency-name: pydantic-core
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: all-dependencies
- dependency-name: urllib3
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: all-dependencies
...

Signed-off-by: dependabot[bot] <[email protected]>
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🚀 Deployed preview to https://geneontology.github.io/gocam-py/pr-preview/pr-38/
on branch gh-pages at 2024-12-23 02:33 UTC

@pkalita-lbl pkalita-lbl merged commit 4814f80 into main Dec 23, 2024
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@pkalita-lbl pkalita-lbl deleted the dependabot/pip/all-dependencies-889e94972c branch December 23, 2024 16:32
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