[services] pytest update

[cjllanwarne]

Change Description

Regular pip and npm updates.

Also updates pytest to 9.0.3.

Doing so had the nice side effect of being able to remove a couple of clunky workarounds but required us to switch our uv compile from 3.10 to 3.11 (to avoid bringing in a couple of backport packages which are incompatible with new dependencies). Justification is that the only environments that need dev/pinned-requirements are 3.11 so this is fine, and that the custom builds on 3.10 don't need any dev packages.

Will supersede #15516 unless there are test issues with the new library version.

Security Assessment

• This change potentially impacts the Hail Batch instance as deployed by Broad Institute in GCP

Impact Rating

• This change has a low security impact

Impact Description

Standard regular updates

Appsec Review

• Required: The impact has been assessed and approved by appsec

[Copilot]

Pull request overview

Routine pip and npm dependency updates plus an upgrade of pytest to 9.0.3 (with related pytest-asyncio, pytest-html, pytest-xdist bumps). The Python version used to compile pinned-requirements.txt files moves from 3.10 to 3.11 to avoid pulling in backport packages (async-timeout, exceptiongroup, tomli, importlib-metadata, zipp) that are incompatible with newer dependencies. The bump in pytest-asyncio (>=0.23) allows removing the manual event_loop session fixtures and adopting asyncio_default_fixture_loop_scope = session in the pytest configs instead.

Changes:

• Bump --python-version used by uv from 3.10 to 3.11 in the two compile scripts and regenerate all pinned-requirements.txt files (drops backport packages, bumps idna, numpy, scipy, tornado, boto3/botocore, etc.).
• Upgrade pytest to 9.0.3 and remove the custom event_loop session fixture from batch/test/conftest.py, hail/python/test/hail/conftest.py, and hail/python/test/hailtop/conftest.py; add asyncio_default_fixture_loop_scope = session to all pytest.ini files.
• Refresh npm lockfile for services/ui (babel runtime/code-frame, es-toolkit, hasown, ws).

Reviewed changes

Copilot reviewed 18 out of 19 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
generate-pip-lockfile.sh	Switch uv compile target to Python 3.11.
check_pip_requirements.sh	Switch uv compile check target to Python 3.11.
auth/test/pytest.ini, batch/test/pytest.ini, ci/test/pytest.ini, monitoring/test/pytest.ini, hail/python/pytest.ini	Set asyncio_default_fixture_loop_scope = session for new pytest-asyncio.
batch/test/conftest.py, hail/python/test/hail/conftest.py, hail/python/test/hailtop/conftest.py	Remove now-redundant custom session-scoped event_loop fixture.
hail/python/dev/requirements.txt	Bump pytest stack (pytest 9, pytest-html 4, pytest-xdist 3, pytest-asyncio 1.4) and drop workaround pin.
hail/python/dev/pinned-requirements.txt	Regenerated lockfile reflecting Python 3.11 + new pytest stack (drops tomli, exceptiongroup, importlib-metadata, py, pytest-forked, zipp).
hail/python/pinned-requirements.txt, hail/python/hailtop/pinned-requirements.txt	Regenerated lockfiles; drop async-timeout, bump numpy/scipy/tornado/boto3/botocore/etc.
gear/pinned-requirements.txt, web_common/pinned-requirements.txt, batch/pinned-requirements.txt, ci/pinned-requirements.txt	Regenerated lockfiles for Python 3.11.
services/ui/package-lock.json	Bumps for @babel/code-frame, @babel/helper-validator-identifier, @babel/runtime, es-toolkit, hasown, ws.

Files not reviewed (1)

• services/ui/package-lock.json: Language not supported

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