full typing per MyPy, fixed bugs revealed by MyPy, use pythonic names

pyproject.toml

@@ -11,7 +11,7 @@ packages = [
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.9,<4.0"
+python = ">=3.10,<4.0"
 numexpr = "^2.10.0"
 zarr = "^2.17.2"
 h5py = "^3.11.0"
@@ -20,6 +20,8 @@ numpy = "^1.26.4"
 orjson = "^3.10.3"
 vtk = "^9.3.1"
 pyvcell-fvsolver = "^0.0.4"
+typer = "^0.12.3"
+h5py-stubs = "^0.1.1"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.2.0"

pyvcell/simdata/main.py

@@ -14,7 +14,8 @@ def n5_to_zarr(
         sim_data_dir: Path = typer.Argument(..., help="path to vcell dataset directory"),
         sim_id: int = typer.Argument(..., help="simulation id (e.g. 946368938)"),
         job_id: int = typer.Argument(..., help="job id (e.g. 0"),
-        zarr_path: Path = typer.Argument(..., help="path to zarr dataset to write to")):
+        zarr_path: Path = typer.Argument(..., help="path to zarr dataset to write to")
+) -> None:
     pde_dataset = PdeDataSet(base_dir=sim_data_dir, log_filename=f"SimID_{sim_id}_{job_id}_.log")
     pde_dataset.read()
     data_functions = DataFunctions(function_file=sim_data_dir / f"SimID_{sim_id}_{job_id}_.functions")
@@ -25,9 +26,9 @@ def n5_to_zarr(
     write_zarr(pde_dataset=pde_dataset, data_functions=data_functions, mesh=mesh, zarr_dir=zarr_path)
 
 
-def main():
+def main() -> None:
     app()
 
 
 if __name__ == "__main__":
-    main()
+    main()