chore: migrate to uv, update dependencies, fix test markers and CI

[nllong]

Summary

Migrates the project's tooling from Poetry to uv, updates all dependencies to current stable releases, wires ruff/uv into pre-commit, and fixes CI so tests actually run.

This was prompted by CI currently failing on every dependency-bump PR (dependabot/pip/*) — see recent failed runs on main.

What changed

Dependency management: Poetry → uv

• Converted pyproject.toml from [tool.poetry] to PEP 621 [project] + [dependency-groups], with tool.uv.package = false (this is an app, not a library).
• Removed the unneeded pathlib PyPI backport dependency — it's dead weight on Python ≥3.12 (stdlib already provides pathlib).
• Replaced poetry.lock with uv.lock.

Dependency updates

Bumped all deps to current majors, e.g. pandas → 3.0.5, requests → 2.34, geopandas → 1.1.4, pyarrow → 25.0.0, pytest → 9.1.1, mypy → 2.3.0, pre-commit → 4.6.1.

Fixed a real breakage caused by the pandas 3.0 bump: GroupBy.apply() no longer implicitly retains the grouping columns in the sub-frame, which broke 01_data_sampling_example.ipynb with KeyError: 'in.county_name' (confirmed in the failed dependabot CI runs). Switched to the version-safe GroupBy.sample() instead of groupby(...).apply(lambda x: x.sample(...)).

Tests weren't actually connected to CI

7 of the 10 tests in tests/test_comstock_processor.py had no @pytest.mark.unit/@pytest.mark.integration marker. Since CI (and pytest.ini) uses --strict-markers with -m "unit" / -m "integration", those 7 tests were silently never executed by CI. Added the correct marker to every test so the whole suite runs.

mypy config was silently broken

[tool.mypy] pointed at a nonexistent your_module.py and used python_version = "3.8" for a >=3.12 project — mypy was effectively never checking real code. Fixed the config, which surfaced a genuine bug: process_building_time_series() was annotated -> None but actually returns a tuple of lists. Fixed the annotation/type hints; added a per-module override to keep tests loosely typed (standard practice). mypy now passes cleanly.

pre-commit

• Bumped ruff-pre-commit (v0.11.10 → v0.15.22) and nbstripout (0.8.1 → 0.9.1) to latest.
• Added astral-sh/uv-pre-commit's uv-lock hook so uv.lock always stays in sync with pyproject.toml.

CI

• Replaced the Poetry install/run steps with astral-sh/setup-uv + uv sync/uv run. Poetry itself was failing to install on the Python 3.9 job (Installing Poetry ... An error occurred), which is moot anyway since the project requires Python ≥3.12. Swapped the 3.9 job for 3.13 (now testing 3.12/ubuntu, 3.13/ubuntu, 3.12/windows).

README

Updated install/testing/pre-commit instructions to use uv instead of poetry.

Validation

All run locally against the new environment (uv sync --group dev):

• uv run pytest tests/ -m unit ✅
• uv run pytest tests/ -m integration (real network downloads from the ComStock S3 bucket) ✅ — all 8 pass
• uv run mypy ✅ no issues
• uv run pre-commit run --all-files ✅ all hooks pass (including the new uv-lock hook)
• Full notebook execution (jupyter nbconvert --execute) ✅ completes, confirming the pandas 3.0 fix