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Bump the all-dependencies group with 5 updates #57

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merged 1 commit into from
Feb 18, 2025

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@dependabot dependabot bot commented on behalf of github Feb 17, 2025

Bumps the all-dependencies group with 5 updates:

Package From To
bioregistry 0.11.35 0.12.0
google-api-python-client 2.160.0 2.161.0
googleapis-common-protos 1.66.0 1.67.0
jsbeautifier 1.15.2 1.15.3
lxml 5.3.0 5.3.1

Updates bioregistry from 0.11.35 to 0.12.0

Release notes

Sourced from bioregistry's releases.

v0.12.0

Commits

  • 1c69c14: Bump version: 0.11.35 → 0.11.36-dev (Charles Tapley Hoyt)
  • dc651ee: Add explicit contact and attribution policy (Charles Tapley Hoyt)
  • 39ba3f9: Add prefix: eubopen (#1378) (Nalika Palayoor) #1378
  • fa48931: Add prefix: deims (#1382) (github-actions[bot]) #1382
  • 57ab5ad: Generate JSON schema with Pydantic 2 (#1210) (Charles Tapley Hoyt) #1210
  • b5b8274: Apply black 2025 formatting (#1390) (Charles Tapley Hoyt) #1390
  • fedaae7: Require Pydantic 2 (#1391) (Charles Tapley Hoyt) #1391
  • f0a1f0f: Start applying ruff (#1371) (Charles Tapley Hoyt) #1371
  • e315071: Update predictions file with papers between 2025-01-02 and 2025-02-01 (github-actions[bot])
  • 177d904: Override URI format for SIO (#1395) (Benjamin M. Gyori) #1395
  • 9be5cd2: 🫀Health Report (GitHub Action)
  • ace8b61: Update ECCODE pattern to allow optional dashes (#1396) (Benjamin M. Gyori) #1396
  • e83e2f4: Adjust the dates for paper_ranking pipeline to be from the first to the last of the previous month (#1402) (Mufaddal Naguthanawala) #1402
  • 89221aa: Add prefix: mibig (#1408) (github-actions[bot]) #1408
  • a1283c3: New prefix: mirgenedb (#1393) (Nalika Palayoor) #1393
  • 3b9f87d: Update curated_papers.tsv with irrelevant curations (#1380) (Nalika Palayoor) #1380
  • cf18218: 🫀Health Report (GitHub Action)
  • 60c44c3: Fixing GO entries (#1411) (Chris Mungall) #1411
  • c0f9641: New schema field - contact page (#1392) (Charles Tapley Hoyt) #1392
  • 7fae7ba: Rename clingene to clingen.allele (#1412) (Mufaddal Naguthanawala) #1412
  • 7005a15: Update URI formats for tair.locus and tair.protein (#1386) (Benjamin M. Gyori) #1386
  • 7b35140: New publication: rgd (#1399) (Nalika Palayoor) #1399
  • ba174d0: New prefix: psskb (#1398) (Nalika Palayoor) #1398
  • 6fdc2c6: Rename eccode to ec (#1413) (Mufaddal Naguthanawala) #1413
  • 8436c96: New prefix: holofood (#1400) (Nalika Palayoor) #1400
  • c32768c: Update curated_papers.tsv with irrelevant curations (#1401) (Nalika Palayoor) #1401
  • 9fa6bdf: New schema field - secondary contact list (#1388) (Charles Tapley Hoyt) #1388
  • d97de9a: New schema field - group email (#1389) (Charles Tapley Hoyt) #1389
  • 8f33ba9: New schema element: secondary reviewers (#1415) (Charles Tapley Hoyt) #1415
  • 79f405f: Add prefix: mite (#1406) (github-actions[bot]) #1406
  • 38f25fe: Show provenance for annotations in web app (#1095) (Charles Tapley Hoyt) #1095
  • 04515e8: Bump version: 0.12.0-dev → 0.12.0 (Charles Tapley Hoyt)
Commits

Updates google-api-python-client from 2.160.0 to 2.161.0

Release notes

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

v2.161.0

2.161.0 (2025-02-11)

Features

... (truncated)

Commits

Updates googleapis-common-protos from 1.66.0 to 1.67.0

Release notes

Sourced from googleapis-common-protos's releases.

googleapis-common-protos: v1.67.0

1.67.0 (2025-02-12)

Features

  • A new field unversioned_package_disabled is added to message .google.api.PythonSettings (eb554e8)
  • add support for field generate_omitted_as_internal in selective gapic generation (#13482) (993ff4d)

Documentation

  • A comment for field content in message .google.api.Page is changed (eb554e8)
  • A comment for message RoutingRule is changed (eb554e8)
Commits
  • a31de41 chore: release main (#13491)
  • 50d43b1 docs: [google-apps-chat] Update Google chat app command documentation (#13519)
  • b1c3ce8 feat: [Many APIs] Add REST Interceptors which support reading metadata (#13495)
  • 2c92938 chore: delete erroneous $2 directory (#13518)
  • 38d410a build(php): [google-cloud-dialogflow] remove generation for google/cloud/dial...
  • 3f8ab82 feat: [google-cloud-memorystore] add Instance.Mode.CLUSTER_DISABLED value, an...
  • 3e64234 chore: [google-cloud-deploy] Add missing field-behavior annotations (#13513)
  • 559dea7 feat: [google-cloud-batch] promote cancel job API to GA (#13511)
  • a0910dd feat: [Many APIs] Add REST Interceptors which support reading metadata (#13499)
  • 5cdcc9d feat: [Many APIs] Add REST Interceptors which support reading metadata (#13502)
  • Additional commits viewable in compare view

Updates jsbeautifier from 1.15.2 to 1.15.3

Commits

Updates lxml from 5.3.0 to 5.3.1

Changelog

Sourced from lxml's changelog.

5.3.1 (2025-02-09)

Bugs fixed

  • GH#440: Some tests were adapted for libxml2 2.14.0. Patch by Nick Wellnhofer.

  • LP#2097175: DTD(external_id="…") erroneously required a byte string as ID value.

  • GH#450: iterparse() internally triggered the `DeprecationWarning`` added in lxml 5.3.0 when parsing HTML.

Other changes

  • GH#442: Binary wheels for macOS no longer use the linker flag -flat_namespace.
Commits
  • 1dd5001 Update changelog.
  • 7b177e4 CI: Fix dependency issues.
  • 088c9e5 CI: Use older Ubuntu image to fix builds.
  • 58af8b3 CI: Try to get legacy jobs working again.
  • 37cdbb5 Prepare release of lxml 5.3.1.
  • 64ac58f Build/CI: Update cache action from deprecated version.
  • 6b654c9 Buld: Downgrade Ubuntu build image to fix dependency issues.
  • 71fda3f Update changelog.
  • 306041e iterparse: ignore "strip_cdata" when parsing HTML (GH-450)
  • e73c466 Fix DTD(external_id="...") option.
  • Additional commits viewable in compare view

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Bumps the all-dependencies group with 5 updates:

| Package | From | To |
| --- | --- | --- |
| [bioregistry](https://github.com/biopragmatics/bioregistry) | `0.11.35` | `0.12.0` |
| [google-api-python-client](https://github.com/googleapis/google-api-python-client) | `2.160.0` | `2.161.0` |
| [googleapis-common-protos](https://github.com/googleapis/google-cloud-python) | `1.66.0` | `1.67.0` |
| [jsbeautifier](https://github.com/ghost6991/Jsbeautifier) | `1.15.2` | `1.15.3` |
| [lxml](https://github.com/lxml/lxml) | `5.3.0` | `5.3.1` |


Updates `bioregistry` from 0.11.35 to 0.12.0
- [Release notes](https://github.com/biopragmatics/bioregistry/releases)
- [Commits](biopragmatics/bioregistry@v0.11.35...v0.12.0)

Updates `google-api-python-client` from 2.160.0 to 2.161.0
- [Release notes](https://github.com/googleapis/google-api-python-client/releases)
- [Commits](googleapis/google-api-python-client@v2.160.0...v2.161.0)

Updates `googleapis-common-protos` from 1.66.0 to 1.67.0
- [Release notes](https://github.com/googleapis/google-cloud-python/releases)
- [Changelog](https://github.com/googleapis/google-cloud-python/blob/main/packages/google-cloud-documentai/CHANGELOG.md)
- [Commits](googleapis/google-cloud-python@googleapis-common-protos-v1.66.0...googleapis-common-protos-v1.67.0)

Updates `jsbeautifier` from 1.15.2 to 1.15.3
- [Commits](https://github.com/ghost6991/Jsbeautifier/commits)

Updates `lxml` from 5.3.0 to 5.3.1
- [Release notes](https://github.com/lxml/lxml/releases)
- [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt)
- [Commits](lxml/lxml@lxml-5.3.0...lxml-5.3.1)

---
updated-dependencies:
- dependency-name: bioregistry
  dependency-type: indirect
  update-type: version-update:semver-minor
  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: googleapis-common-protos
  dependency-type: indirect
  update-type: version-update:semver-minor
  dependency-group: all-dependencies
- dependency-name: jsbeautifier
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: all-dependencies
- dependency-name: lxml
  dependency-type: indirect
  update-type: version-update:semver-patch
  dependency-group: all-dependencies
...

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@pkalita-lbl pkalita-lbl merged commit a84d95c into main Feb 18, 2025
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@pkalita-lbl pkalita-lbl deleted the dependabot/pip/all-dependencies-06ca908581 branch February 18, 2025 17:19
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