fix more type errors in __main

Author: DocOtak

src/cchdo/hydro/__main__.py

@@ -55,12 +55,14 @@ def _comment_loader(str_or_path: str) -> str:
     type=str,
     help="either a comment string or file path prefixed with @ (e.g. @README.txt)",
 )
-def convert_exchange(exchange_path, out_path, check_flag, precision_source, comments):
+def convert_exchange(
+    exchange_path, out_path, check_flag: bool, precision_source, comments
+):
     setup_logging("DEBUG")
     log.info("Loading read_exchange")
-    from .exchange import read_exchange
+    from .exchange import CheckOptions, read_exchange
 
-    checks = {"flags": check_flag}
+    checks: CheckOptions = {"flags": check_flag}
 
     ex = read_exchange(exchange_path, checks=checks, precision_source=precision_source)
     log.info("Saving to netCDF")
@@ -91,9 +93,9 @@ def convert_exchange(exchange_path, out_path, check_flag, precision_source, comm
 def convert_csv(csv_path, out_path, ftype, check_flag, precision_source, comments):
     setup_logging("DEBUG")
     log.info("Loading read_exchange")
-    from .exchange import read_csv
+    from .exchange import CheckOptions, read_csv
 
-    checks = {"flags": check_flag}
+    checks: CheckOptions = {"flags": check_flag}
 
     ex = read_csv(
         csv_path, ftype=ftype, checks=checks, precision_source=precision_source
@@ -134,9 +136,11 @@ def edit_comments(expocode, dtype):
     extant_ids = cruise_file_ids & files.keys()
     edit_files = list(
         filter(
-            lambda x: x["role"] == "dataset"
-            and x["data_format"] == "cf_netcdf"
-            and x["data_type"] == dtype,
+            lambda x: (
+                x["role"] == "dataset"
+                and x["data_format"] == "cf_netcdf"
+                and x["data_type"] == dtype
+            ),
             (files[id] for id in extant_ids),
         )
     )

src/cchdo/hydro/__main_helpers.py

@@ -5,7 +5,7 @@
 import xarray as xr
 
 from cchdo.hydro import accessors  # noqa: F401
-from cchdo.hydro.exchange import read_exchange
+from cchdo.hydro.exchange import CheckOptions, read_exchange
 from cchdo.hydro.exchange.exceptions import (
     ExchangeDataFlagPairError,
     ExchangeParameterUndefError,
@@ -24,7 +24,7 @@ def make_netcdf_file_json(path):
 
 def p_file(file_m):
     t_dir, file, file_metadata, roundtrip = file_m
-    checks = {"flags": False}
+    checks: CheckOptions = {"flags": False}
     unknown_params = []
 
     warnings.simplefilter("ignore")

src/cchdo/hydro/checks.py

@@ -131,7 +131,7 @@ def check_flags(dataset: xr.Dataset, raises=True):
             # TODO deal with strs
 
             if np.issubdtype(data.values.dtype, np.number):
-                fill_value_mismatch: xr.DataArray = ~(np.isfinite(data) ^ has_fill)  # type: ignore[assignment]
+                fill_value_mismatch: xr.DataArray = ~(np.isfinite(data) ^ has_fill)
                 if np.any(fill_value_mismatch):
                     fill_value_mismatch.attrs["comments"] = (
                         f"This is a boolean array in the same shape as '{data.name}' which is truthy where invalid values exist"