Update template to v0.7.0

[scverse-bot]

cookiecutter-scverse released v0.7.0.

Changes

Changes

• Switch to dependency groups in pyproject.toml by @flying-sheep in Switch to dependency groups scverse/cookiecutter-scverse#449
• Use type instead of label for issue templates by @Zethson in Use type instead of label for issue templates scverse/cookiecutter-scverse#444
• use KaTeX Sphinx plugin for better math rendering @flying-sheep in chore: use KaTeX Sphinx plugin scverse/cookiecutter-scverse#446
• Make all-green check pass even if pre-release job fails by @grst in Make all-green check pass even if pre-release job fails scverse/cookiecutter-scverse#452

Fixes

• sphinx conf.py: use project instead of project_name by @ilia-kats in sphinx conf.py: use project instead of project_name scverse/cookiecutter-scverse#440
• Fix workflow badge and link in readme by @flying-sheep in Fix workflow badge and link in readme scverse/cookiecutter-scverse#441
• Enable OIDC in Codecov action by @grst in Enable OIDC in Codecov action scverse/cookiecutter-scverse#457

Additional remarks

• unsubscribe: If you don’t want to receive these PRs in the future,
  add skip: true to template-repos.yml using a PR or,
  if you never want to sync from the template again, delete the .cruft.json file in the root of your repository.
• If there are merge conflicts, you need to resolve them manually.
• The scverse template works best when the pre-commit.ci, readthedocs and codecov services are enabled.
  Make sure to activate those apps if you haven't already.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 49.68%. Comparing base (9ac4620) to head (5f46834).

Additional details and impacted files

@@             Coverage Diff             @@
##             main      #63       +/-   ##
===========================================
- Coverage   98.13%   49.68%   -48.45%     
===========================================
  Files          13       13               
  Lines         322      322               
===========================================
- Hits          316      160      -156     
- Misses          6      162      +156     

see 7 files with indirect coverage changes

[srivarra]

@greptile

[greptile-apps]

Greptile Overview

Greptile Summary

This PR updates the project template from cookiecutter-scverse v0.6.0 to v0.7.0, bringing significant infrastructure modernization:

Key Changes:

• Migrated to PEP 735 dependency groups in pyproject.toml, consolidating hatch.toml and ruff.toml into a single configuration file
• Minimum Python version bumped from 3.10 to 3.11, narwhals upgraded from 1.37.1 to 2.14 (major version change)
• CI/CD workflows overhauled to use hatch test matrix, now testing only Python 3.11 and 3.14 (stable + pre-release)
• Source code improvements: replaced inspect-based expression parsing with narwhals private API (with known nested expression limitation), and fixed truthiness checks to explicit is not None in filter/select functions
• ReadTheDocs configuration updated to Ubuntu 24.04 and Python 3.13
• Pre-commit hooks and various tools updated to latest versions

Issues Found:

• Test matrix only covers Python 3.11 and 3.14, but classifiers list 3.12 and 3.13 as supported
• New expression parsing uses narwhals private API which may break in future versions

Confidence Score: 3/5

• Requires attention due to test coverage gap and dependency on private API
• Template updates are generally well-tested, but critical issue: test matrix doesn't cover Python 3.12/3.13 despite being declared as supported. Additionally, the switch to narwhals private API (_expression_parsing) introduces brittleness with acknowledged limitations on nested expressions. The Python 3.10 drop and narwhals major version bump are breaking changes that need verification.
• Pay close attention to .github/workflows/test.yaml (missing Python version coverage) and src/annsel/core/utils.py (private API dependency with nested expression bugs)

Important Files Changed

Filename	Overview
pyproject.toml	Migrated to dependency groups (PEP 735), bumped Python minimum to 3.11, updated narwhals to 2.14+, consolidated ruff config from external file
src/annsel/core/utils.py	Replaced inspect-based expression parsing with narwhals private API _expression_parsing. Known limitation: doesn't handle nested expressions correctly
src/annsel/tl/_filter.py	Changed truthiness checks to explicit is not None checks for better handling of empty/falsy values
src/annsel/tl/_select.py	Changed truthiness checks to explicit is not None checks for better handling of empty/falsy values
.github/workflows/test.yaml	Complete rewrite to use hatch test matrix from pyproject.toml, tests only 3.11 and 3.14 (stable), 3.14 (pre-release), added all-green check job
.github/workflows/build.yaml	Simplified to check package build validity using twine, removed artifact upload and workflow dependencies

_{Last reviewed commit: ceacb2e}

[greptile-apps]

_{19 files reviewed, 4 comments}

_{Edit Code Review Agent Settings | Greptile}

[greptile-apps]

Greptile Overview

Greptile Summary

This PR updates the project template from cookiecutter-scverse v0.6.x to v0.7.0, bringing several infrastructure improvements and modernizations.

Key Changes:

• Migrated configuration from separate hatch.toml and ruff.toml files into pyproject.toml using dependency groups (PEP 735)
• Updated Python support: dropped 3.10, now testing 3.11 and 3.14 (with pre-release dependencies)
• Refactored CI workflows to dynamically discover test environments from hatch configuration
• Updated GitHub Actions (checkout v4→v5, setup-uv v6→v7, pypa/gh-action-pypi-publish to release/v1)
• Improved ReadTheDocs configuration to use hatch for docs building
• Enhanced issue templates with better session-info2 usage instructions
• Expanded contributing documentation with detailed hatch environment setup guide

Critical Issue Found:

• The pyproject.toml defines [tool.hatch.envs.hatch-test] but is missing the required scripts section. The CI workflow (.github/workflows/test.yaml) attempts to run run-cov, cov-combine, and cov-report scripts that don't exist, which will cause all test jobs to fail.

Confidence Score: 1/5

• This PR will break CI - tests cannot run without the missing hatch scripts
• The missing hatch-test scripts (run-cov, cov-combine, cov-report) in pyproject.toml will cause immediate CI failures when the test workflow attempts to execute them. This is a blocking issue that prevents merging.
• Pay close attention to pyproject.toml - must add the missing [tool.hatch.envs.hatch-test.scripts] section before merging

Important Files Changed

Filename	Overview
pyproject.toml	Critical issue: Migrated to dependency groups and hatch test matrix (3.11, 3.14), but missing required hatch-test scripts (run-cov, cov-combine, cov-report) that CI workflow expects
.github/workflows/test.yaml	Refactored to use dynamic hatch environment discovery, but references undefined hatch scripts that will cause CI failures
.github/workflows/build.yaml	Simplified to single-job package build check with twine validation, removed matrix strategy
.pre-commit-config.yaml	Updated ruff hook from 'ruff' to 'ruff-check' and excluded .cruft.json from biome-format
.readthedocs.yaml	Restructured to use hatch for docs build, updated to Ubuntu 24.04 and Python 3.13

_{Last reviewed commit: 5e7f4e9}

[greptile-apps]

_{16 files reviewed, 1 comment}

_{Edit Code Review Agent Settings | Greptile}

[greptile-apps]

Missing required hatch scripts. The CI workflow (.github/workflows/test.yaml:78-84) references run-cov, cov-combine, and cov-report scripts, but these aren't defined here.

Add after line 93:

Suggested change

	[tool.hatch.envs.hatch-test]
	dependency-groups = [ "dev", "test" ]
	dependency-groups = [ "dev", "test" ]
	[tool.hatch.envs.hatch-test.scripts]
	run = "pytest {args}"
	run-cov = "pytest --cov --cov-report=term-missing {args}"
	cov-combine = "coverage combine"
	cov-report = "coverage report"