Fix mypy errors and align make lint with CI

[mogres]

Summary

Makes the CI lint gate pass green by clearing the pre-existing mypy type-checking debt (132 errors across 27 files), and aligns make lint with the CI config so local and CI behavior match.

Changes

mypy: 132 → 0 errors

• Exclude .*/notebooks/.* from [tool.mypy] exclude (66 errors), mirroring the ruff notebook per-file-ignore.
• Fix the remaining 66 library/workflow errors properly: add function/variable annotations, correct real type mismatches (ndarray/list, float/int, Figure | None narrowing, tuple return types), and use a few narrowly-scoped # type: ignore with reasons (e.g. np.mgrid float slices).

make lint now matches CI

• Drop the extra Makefile mypy flags (--disallow-untyped-calls --disallow-untyped-defs --disallow-incomplete-defs) so it runs plain mypy cellpack_analysis, identical to lint.yml.

Clear pre-existing ruff/black debt (independent of mypy; surfaced once lint was run end-to-end)

• Add "**/notebooks/*.py" = ["D", "E501"] ruff per-file-ignore.
• Hand-fix remaining ruff errors (E501 line wraps; a B007 false positive and a C901 via scoped # noqa).
• Apply black to 5 files.

Verification

All four CI lint steps pass clean:

ruff check cellpack_analysis   → All checks passed!
black --check cellpack_analysis → unchanged
isort --check cellpack_analysis → ok
mypy cellpack_analysis          → Success: no issues found

🤖 Generated with Claude Code

[Copilot]

Pull request overview

This PR clears existing mypy type-checking failures across the codebase and makes local make lint behavior match the CI lint workflow, so developers get consistent results locally and in CI.

Changes:

• Update mypy configuration and local lint invocation so CI and make lint run the same mypy command and scope.
• Add/adjust type annotations and narrow a few value types (notably NumPy scalar → float) to resolve mypy errors.
• Apply small refactors to satisfy lint/type tooling (e.g., Callable typing, figure/axes narrowing, minor array variable renames).

Reviewed changes

Copilot reviewed 20 out of 20 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
pyproject.toml	Excludes notebooks/ from mypy discovery and adds ruff notebook per-file ignores to keep linting consistent.
Makefile	Aligns make lint mypy invocation with CI by removing extra strict CLI flags.
cellpack_analysis/preprocessing/get_structure_coordinates.py	Ensures numeric outputs are JSON-serializable floats and adds explicit dict typing + return annotation.
cellpack_analysis/preprocessing/get_meshes_from_images.py	Adds explicit main() -> int return typing for script entrypoint.
cellpack_analysis/packing/run_packing_workflow.py	Adds return type to _run_packing_workflow() consistent with downstream usage (total_failed).
cellpack_analysis/packing/pack_recipes.py	Broadens internal dictionary typing to satisfy mypy where mixed value types are stored.
cellpack_analysis/lib/visualization.py	Tightens return types and figure retrieval/narrowing; resolves type issues around colormaps and plotting arrays.
cellpack_analysis/lib/stats.py	Clarifies tobs/tobs_joint numeric typing across envelope implementations.
cellpack_analysis/lib/simularium_utils.py	Adds Any typing for untyped external clients/dataframes to satisfy mypy.
cellpack_analysis/lib/s3_utils.py	Adds Any typing for boto3 S3 client plumbing and get_s3_client() return.
cellpack_analysis/lib/rule_interpolation.py	Adds precise Callable[...] annotations for MSE getter callbacks.
cellpack_analysis/lib/occupancy.py	Minor variable renames to keep types consistent through NumPy percentile/max operations.
cellpack_analysis/lib/mesh_tools.py	Adds narrowly-scoped type: ignore[misc] for np.mgrid float-slice stubs and simplifies return.
cellpack_analysis/lib/label_tables.py	Updates projection label mapping to a tuple form consistent with unpacking usage.
cellpack_analysis/lib/img_io.py	Declares generate_composite_thumbnail() as -> None to match behavior.
cellpack_analysis/lib/distance.py	Tightens return and intermediate collection types and normalizes dtypes in aggregation.
cellpack_analysis/data_release/run_data_release_workflow.py	Adds Any typing for helper return values and S3 client parameter typing.
cellpack_analysis/data_release/export_simularium_paths_as_csv.py	Adds Any typing and list annotations for script-level structures and processing lists.
cellpack_analysis/data_release/data_release_config.py	Adds explicit -> None return typing for internal setup methods.
cellpack_analysis/analysis/workflows/run_analysis_workflow.py	Adds explicit -> None return typing for internal methods and main().

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[mogres]

Verified linting updates do not break packing workflows