build: PEP 735 dep group for dev tooling (closes #328 dev portion)

[robotrocketscience]

Summary

Closes the dev portion of #328: moves pytest, pytest-timeout, pyright from [project.optional-dependencies.dev] into [dependency-groups.dev] (PEP 735), drops their DEP002 deptry ignores, and updates CI workflows (ci.yml, mutation.yml, publish.yml) to install via --group dev instead of --extra dev.

Why

deptry was flagging dev tooling as DEP002 (declared-but-not-imported) because optional extras count as "project dependencies" from deptry's perspective. PEP 735 dependency groups don't, so the ignores can go.

Bench portion deferred

#328 also asked to move nltk/tiktoken/datasets/huggingface_hub to a [dependency-groups.bench] group. Skipped: pip install -e ".[benchmarks]" is a documented contract (benchmarks/README.md), and PEP 735 dep groups are not publishable extras. Their DEP002 ignores stay; comment in [tool.deptry.per_rule_ignores] now explains why. Filed as a comment on #328 — the issue stays open or gets rescoped.

Verification

• uv lock regenerated.
• uv sync --frozen --group dev --extra archive installs cleanly.
• uvx deptry src (CI invocation) → "Success! No dependency issues found."
• Full pytest suite: 1982 passed, 18 skipped.

Closes #328 (dev portion).

Summary by Sourcery

Move development tooling dependencies to a PEP 735 dependency group and update CI to install from that group instead of an optional extra.

Enhancements:

• Reorganize dev tooling dependencies (pytest, pytest-timeout, pyright) from project optional extras into a PEP 735 [dependency-groups.dev] group.
• Clarify deptry DEP002 ignore configuration to document why benchmark extras remain and are not imported from the main src package.

CI:

• Update CI workflows to install development dependencies via uv sync --group dev instead of --extra dev.

[sourcery-ai]

Reviewer's guide (collapsed on small PRs)

Reviewer's Guide

Migrates dev test/tooling dependencies from an optional dependency extra to a PEP 735 dependency group and updates deptry configuration and CI workflows to use the new dev group-based install strategy.

File-Level Changes

Change	Details	Files
Move dev tooling deps from optional extras to PEP 735 dependency group and adjust deptry ignores accordingly.	Remove pytest, pytest-timeout, and pyright from [project.optional-dependencies.dev]. Add pytest, pytest-timeout, and pyright to [dependency-groups.dev]. Narrow DEP002 deptry ignores to only benchmarks-related packages and expand the comment to explain why the benchmarks extra remains and why those ignores are still needed.	pyproject.toml
Update CI workflows to install dev dependencies via dependency groups instead of extras.	Change uv sync invocations in CI, mutation testing, and publish workflows from --extra dev to --group dev while preserving the archive extra. Ensure all workflows that run pytest still install the dev tooling via the new dependency group.	.github/workflows/ci.yml .github/workflows/mutation.yml .github/workflows/publish.yml
Regenerate uv.lock to reflect the dependency group reorganization.	Update lockfile metadata to align with moving dev tooling dependencies into [dependency-groups.dev].	uv.lock

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#328	Reorganize development tooling dependencies (pytest, pytest-timeout, pyright) from [project.optional-dependencies] into a PEP 735 [dependency-groups.dev] group, update CI to install via this group, and remove their DEP002 deptry ignores.	✅
#328	Reorganize benchmark-only dependencies (nltk, tiktoken, datasets, huggingface_hub) into a dedicated benchmark grouping as described (e.g. [project.optional-dependencies.bench]) and remove their DEP002 deptry ignores so deptry no longer ignores them.	❌	The PR explicitly defers the benchmark-related changes: it leaves nltk, tiktoken, datasets, and huggingface_hub in the DEP002 ignore list and does not move them into a new benchmark dependency grouping, documenting that this part of the issue is skipped.

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ℹ️ Review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

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Run ID: d37f55a7-33ed-4662-964e-de41e01c07c9

📥 Commits

Reviewing files that changed from the base of the PR and between 1531a8e and cbbbcf5.

⛔ Files ignored due to path filters (1)

• uv.lock is excluded by !**/*.lock, !**/*.lock

📒 Files selected for processing (4)

• .github/workflows/ci.yml
• .github/workflows/mutation.yml
• .github/workflows/publish.yml
• pyproject.toml

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[robotrocketscience]

[claim:review:Gylf:2026-05-01T15:51:20Z]

[robotrocketscience]

[release:review:Gylf:2026-05-01T15:53:34Z]