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chore(deps): bump the minor-and-patch group across 1 directory with 8 updates - #178

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chore(deps): bump the minor-and-patch group across 1 directory with 8 updates#178
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Bumps the minor-and-patch group with 8 updates in the / directory:

Package From To
cpg-utils 5.6.0 5.6.1
grpcio 1.78.0 1.80.0
grpcio-status 1.78.0 1.80.0
build 1.4.2 1.5.0
coverage 7.13.5 7.14.0
ruff 0.15.7 0.15.12
mike 2.1.4 2.2.0
pyright 1.1.408 1.1.409

Updates cpg-utils from 5.6.0 to 5.6.1

Commits

Updates grpcio from 1.78.0 to 1.80.0

Release notes

Sourced from grpcio's releases.

Release v1.80.0

This is release 1.80.0 (glimmering) of gRPC Core.

For gRPC documentation, see grpc.io. For previous releases, see Releases.

This release contains refinements, improvements, and bug fixes, with highlights listed below.

Core

  • [ssl] Implement TLS private key signer in Python. (#41701)
  • [TLS Credentials]: Private Key Offload Implementation. (#41606)
  • Fix max sockaddr struct size on OpenBSD. (#40454)
  • [core] Enable EventEngine for Python by default, and EventEngine fork support in Python and Ruby. (#41432)
  • [TLS Credentials]: Create InMemoryCertificateProvider to update certificates independently. (#41484)
  • [Ruby] Build/test ruby 4.0 and build native gems with Ruby 4.0 support. (#41324)
  • [EventEngine] Remove an incorrect std::move in DNSServiceResolver constructor. (#41502)
  • [RR and WRR] enable change to connect from a random index. (#41472)
  • [xds] Implement gRFC A101. (#41051)

C++

  • [C++] Add SNI override option to C++ channel credentials options API. (#41460)

C#

  • [C# tools] Option to append Async to server side method names #39010. (#39797)

Objective-C

  • [Fix][Compiler] Plugins fall back to the edition 2023 for older protobuf. (#41357)

PHP

  • [PHP] Disable php infinite recursion check for callback from Core to PHP. (#41835)
  • [PHP] Fix runtime error with PHp8.5 alpha because zend_exception_get_defaul…. (#40337)

Python

  • [Python] Fix GRPC_TRACE not working when absl log initialized in cython. (#41814)
  • Revert "[Python] Align GRPC_ENABLE_FORK_SUPPORT env defaults in core and python (#41455)". (#41769)
  • [Python] Fix AsyncIO Server maximum_concurrent_rpcs enforcement preventing negative active_rpcs count. (#41532)
  • [Python] Docs: correct grpc.Compression references. (#41705)
  • [Python] [Typeguard] Part 4 - Add Typeguard to AIO stack in tests . (#40226)

... (truncated)

Commits
  • f5e2d6e [Release] Bump version to 1.80.0 (on v1.80.x branch) (#41857)
  • 938cfec [subchannel connection scaling] fix when we reset backoff (#41935)
  • 91778be [Backport][v1.80.x][Python] New _create method for aio.Metadata (#41888)
  • f10b9f2 [bzlmod] upgrade rules_swift to avoid BCR CI breakage on Windows with bazel 7...
  • be4c1c5 [subchannel] fix crash in connection scaling code (#41853)
  • a71df73 [Release] Bump version to 1.80.0-pre1 (on v1.80.x branch) (#41844)
  • 3ca09e4 [Python] Fix GRPC_TRACE and add test to check the GRPC_TRACE logs print (#41814)
  • 260c6fd [PHP] Disable php infinite recursion check for callback from Core to PHP (#41...
  • 50957c5 [Flakiness] Delete flaky iomgr fd_conservation_posix_test and create an Event...
  • e1e1d0a [Bzlmod] Turn off bzlmod for PSM python tests. (#41810)
  • Additional commits viewable in compare view

Updates grpcio-status from 1.78.0 to 1.80.0

Updates build from 1.4.2 to 1.5.0

Release notes

Sourced from build's releases.

1.5.0

What's Changed

Full Changelog: pypa/build@1.4.4...1.5.0

1.4.4

What's Changed

Full Changelog: pypa/build@1.4.3...1.4.4

1.4.3

What's Changed

... (truncated)

Changelog

Sourced from build's changelog.

#################### 1.5.0 (2026-04-30) ####################

Features

  • Drop Python 3.9 support - by :user:henryiii (:issue:1036)

Bugfixes

  • Make --ignore-installed opt-in from the API via fresh=True - by :user:henryiii (:issue:1056)

Miscellaneous

  • :issue:1033

#################### 1.4.4 (2026-04-22) ####################

Bugfixes

  • Fix release pipeline generating CHANGELOG.rst entries with inconsistent heading levels, which broke sphinx -W and pinned Read the Docs stable at 1.4.0 - by :user:gaborbernat. (:issue:1031)
  • Revert :pr:1039 from build 1.4.3, no longer check direct_url (for now) - by :user:henryiii (:issue:1039)
  • Add --ignore-installed to pip install command to prevent issues with packages already present in the isolated build environment - by :user:henryiii (:issue:1037) (:issue:1040)
  • Partial revert of :pr:973, keeping log messages in one entry, multiple lines. (:issue:1044)

Miscellaneous

  • :issue:1048, :issue:1049

#################### 1.4.3 (2026-04-10) ####################

Features

... (truncated)

Commits

Updates coverage from 7.13.5 to 7.14.0

Changelog

Sourced from coverage's changelog.

Version 7.14.0 — 2026-05-10

  • Feature: now when running one of the reporting commands, if there are parallel data files that need combining, they will be implicitly combined before creating the report. There is no option to avoid the combination; let us know if you have a use case that requires it. Thanks, Tim Hatch <pull 2162_>. Closes issue 1781.

  • Fix: the output from combine was too verbose, listing each file considered. Now it shows a single line with the counts of files combined, files skipped, and files with errors. The -q flag suppresses this line. The old detailed lines are available with the new --debug=combine option.

  • Fix: running a Python file through a symlink now sets the sys.path correctly, matching regular Python behavior. Fixes issue 2157_.

  • Fix: Collector.flush_data could fail with "RuntimeError: Set changed size during iteration" when a tracer in another thread added a line to the per-file set that add_lines (or add_arcs) was iterating. The values passed to CoverageData are now snapshotted via dict.copy() and set.copy(), which are atomic under the GIL. Thanks, Alex Vandiver <pull 2165_>_.

  • Fix: the soft keyword lazy is now bolded in HTML reports.

  • We are no longer testing eventlet support. Eventlet started issuing stern deprecation warnings that break our tests. Our support code is still there.

.. _issue 1781: coveragepy/coveragepy#1781 .. _issue 2157: coveragepy/coveragepy#2157 .. _pull 2162: coveragepy/coveragepy#2162 .. _pull 2165: coveragepy/coveragepy#2165

.. _changes_7-13-5:

Commits
  • 646351b docs: sample HTML for 7.14.0
  • 39cd015 docs: prep for 7.14.0
  • 649e8aa docs: thanks Alex Vandiver for #2165
  • 8cd392e fix: snapshot data in Collector.flush_data to avoid threading race (#2165)
  • c48e0ed fix: less output for combining
  • c2a3a28 docs: explain the change from #2162
  • 1cd47aa fix: implicit combine-during-report now removes the combined data files
  • 2d99fd7 feat: automatically combine coverage in report, thanks Tim Hatch (#2162)
  • 9fbdcdf fix: lazy soft keywords are bolded
  • 5de7d02 build: oops, misplaced quote
  • Additional commits viewable in compare view

Updates ruff from 0.15.7 to 0.15.12

Release notes

Sourced from ruff's releases.

0.15.12

Release Notes

Released on 2026-04-24.

Preview features

  • Implement #ruff:file-ignore file-level suppressions (#23599)
  • Implement #ruff:ignore logical-line suppressions (#23404)
  • Revert preview changes to displayed diagnostic severity in LSP (#24789)
  • [airflow] Implement task-branch-as-short-circuit (AIR004) (#23579)
  • [flake8-bugbear] Fix break/continue handling in loop-iterator-mutation (B909) (#24440)
  • [pylint] Fix PLC2701 for type parameter scopes (#24576)

Rule changes

  • [pandas-vet] Suggest .array as well in PD011 (#24805)

CLI

  • Respect default Unix permissions for cache files (#24794)

Documentation

  • [pylint] Fix PLR0124 description not to claim self-comparison always returns the same value (#24749)
  • [pyupgrade] Expand docs on reusable TypeVars and scoping (UP046) (#24153)
  • Improve rules table accessibility (#24711)

Contributors

Install ruff 0.15.12

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://releases.astral.sh/github/ruff/releases/download/0.15.12/ruff-installer.sh | sh

... (truncated)

Changelog

Sourced from ruff's changelog.

0.15.12

Released on 2026-04-24.

Preview features

  • Implement #ruff:file-ignore file-level suppressions (#23599)
  • Implement #ruff:ignore logical-line suppressions (#23404)
  • Revert preview changes to displayed diagnostic severity in LSP (#24789)
  • [airflow] Implement task-branch-as-short-circuit (AIR004) (#23579)
  • [flake8-bugbear] Fix break/continue handling in loop-iterator-mutation (B909) (#24440)
  • [pylint] Fix PLC2701 for type parameter scopes (#24576)

Rule changes

  • [pandas-vet] Suggest .array as well in PD011 (#24805)

CLI

  • Respect default Unix permissions for cache files (#24794)

Documentation

  • [pylint] Fix PLR0124 description not to claim self-comparison always returns the same value (#24749)
  • [pyupgrade] Expand docs on reusable TypeVars and scoping (UP046) (#24153)
  • Improve rules table accessibility (#24711)

Contributors

0.15.11

Released on 2026-04-16.

Preview features

  • [ruff] Ignore RUF029 when function is decorated with asynccontextmanager (#24642)
  • [airflow] Implement airflow-xcom-pull-in-template-string (AIR201) (#23583)
  • [flake8-bandit] Fix S103 false positives and negatives in mask analysis (#24424)

... (truncated)

Commits
  • 66f93cf Bump 0.15.12 (#24815)
  • 476a4d0 [ty] Complete support for more detailed diagnostics on possibly unbound error...
  • ed669ea Implement #ruff:file-ignore file-level suppressions (#23599)
  • e73d952 [ty] Include inferred type in invalid-key concise diagnostic for union/inte...
  • 80feb29 [ty] report only dead annotation-only locals as unused (#24811)
  • 0fbf2bc Drop deprecated license classifier (#24808)
  • 43b174c [ty] Infer lambda parameter types with Callable type context (#24317)
  • 4f449ae [ty] Add error context for intersection types (#24772)
  • 5b4e753 [ty] Add support for goto in literal enum member inlay hint (#24792)
  • e7cc762 [ty] Add error context for TypedDict assignments (#24790)
  • Additional commits viewable in compare view

Updates mike from 2.1.4 to 2.2.0

Release notes

Sourced from mike's releases.

v2.2.0

New features

Bug fixes

  • Use DST timestamps for new commits when DST is in effect
  • Support ISO8601 and RFC 2822 values for GIT_COMMITTER_DATE
Changelog

Sourced from mike's changelog.

v2.2.0 (2026-04-13)

New features

Bug fixes

  • Use DST timestamps for new commits when DST is in effect
  • Support ISO8601 and RFC 2822 values for GIT_COMMITTER_DATE
Commits

Updates pyright from 1.1.408 to 1.1.409

Commits

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@dependabot
chore(deps): bump the minor-and-patch group across 1 directory with 8…
43f802d 
… updates

Bumps the minor-and-patch group with 8 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [cpg-utils](https://github.com/populationgenomics/cpg-utils) | `5.6.0` | `5.6.1` |
| [grpcio](https://github.com/grpc/grpc) | `1.78.0` | `1.80.0` |
| [grpcio-status](https://grpc.io) | `1.78.0` | `1.80.0` |
| [build](https://github.com/pypa/build) | `1.4.2` | `1.5.0` |
| [coverage](https://github.com/coveragepy/coveragepy) | `7.13.5` | `7.14.0` |
| [ruff](https://github.com/astral-sh/ruff) | `0.15.7` | `0.15.12` |
| [mike](https://github.com/jimporter/mike) | `2.1.4` | `2.2.0` |
| [pyright](https://github.com/RobertCraigie/pyright-python) | `1.1.408` | `1.1.409` |



Updates `cpg-utils` from 5.6.0 to 5.6.1
- [Commits](https://github.com/populationgenomics/cpg-utils/commits)

Updates `grpcio` from 1.78.0 to 1.80.0
- [Release notes](https://github.com/grpc/grpc/releases)
- [Commits](grpc/grpc@v1.78.0...v1.80.0)

Updates `grpcio-status` from 1.78.0 to 1.80.0

Updates `build` from 1.4.2 to 1.5.0
- [Release notes](https://github.com/pypa/build/releases)
- [Changelog](https://github.com/pypa/build/blob/main/CHANGELOG.rst)
- [Commits](pypa/build@1.4.2...1.5.0)

Updates `coverage` from 7.13.5 to 7.14.0
- [Release notes](https://github.com/coveragepy/coveragepy/releases)
- [Changelog](https://github.com/coveragepy/coveragepy/blob/main/CHANGES.rst)
- [Commits](coveragepy/coveragepy@7.13.5...7.14.0)

Updates `ruff` from 0.15.7 to 0.15.12
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.15.7...0.15.12)

Updates `mike` from 2.1.4 to 2.2.0
- [Release notes](https://github.com/jimporter/mike/releases)
- [Changelog](https://github.com/jimporter/mike/blob/master/CHANGES.md)
- [Commits](jimporter/mike@v2.1.4...v2.2.0)

Updates `pyright` from 1.1.408 to 1.1.409
- [Release notes](https://github.com/RobertCraigie/pyright-python/releases)
- [Commits](RobertCraigie/pyright-python@v1.1.408...v1.1.409)

---
updated-dependencies:
- dependency-name: cpg-utils
  dependency-version: 5.6.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: minor-and-patch
- dependency-name: grpcio
  dependency-version: 1.80.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minor-and-patch
- dependency-name: grpcio-status
  dependency-version: 1.80.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minor-and-patch
- dependency-name: build
  dependency-version: 1.5.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: minor-and-patch
- dependency-name: coverage
  dependency-version: 7.14.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: minor-and-patch
- dependency-name: ruff
  dependency-version: 0.15.12
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: minor-and-patch
- dependency-name: mike
  dependency-version: 2.2.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: minor-and-patch
- dependency-name: pyright
  dependency-version: 1.1.409
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: minor-and-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code labels May 13, 2026
@dependabot
dependabot Bot requested a review from a team as a code owner May 13, 2026 21:40
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code labels May 13, 2026
@github-actions

github-actions Bot commented May 13, 2026

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Vulnerability Audit

Found 3 vulnerabilities across 2 packages.
2 actionable now, 1 blocked.

Actionable now — bump via uv.lock

Package Current → Fix CVEs Path
urllib3 2.6.3 → 2.7.0 CVE-2026-44432, CVE-2026-44431 metamist → urllib3
One-shot fix command 
uv lock \
  --upgrade-package urllib3

Blocked upstream — needs a fix in a parent package

Package Current → Fix CVEs Blocked by
bokeh 3.4.3 → 3.8.2 CVE-2026-21883 hail==0.2.137 pins <3.5,>=3

@github-actions

github-actions Bot commented May 13, 2026

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🐳 Docker Image Built

A new Docker image has been built for this PR:

Image: australia-southeast1-docker.pkg.dev/cpg-common/images-dev/cpg_flow:43f802d880172f0fcc8c25f32559ff0a421103e1

Pull command:

docker pull australia-southeast1-docker.pkg.dev/cpg-common/images-dev/cpg_flow:43f802d880172f0fcc8c25f32559ff0a421103e1

🔗 View in Google Cloud Console

This comment was automatically generated by the Docker workflow.

@dependabot @github

dependabot Bot commented on behalf of github May 20, 2026

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Looks like these dependencies are updatable in another way, so this is no longer needed.

@dependabot dependabot Bot closed this May 20, 2026
@dependabot
dependabot Bot deleted the dependabot/uv/minor-and-patch-5eefab36c2 branch May 20, 2026 23:58
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