build: scope mypy workaround to bokeh imports

- remove file-level mypy disable pragmas added for bokeh 3.7\n- configure mypy override for bokeh modules in pyproject\n- keep type-checking active for project code while skipping bokeh stubs

Author: Sharon-codes

malariagen_data/anoph/cnv_data.py

@@ -1,4 +1,3 @@
-# mypy: disable-error-code="call-arg,arg-type,attr-defined,list-item"
 from typing import Dict, List, Optional, Tuple, Union
 
 import dask.array as da

malariagen_data/anoph/fst.py

@@ -1,4 +1,3 @@
-# mypy: disable-error-code="call-arg,arg-type,attr-defined,list-item"
 from typing import Tuple, Optional
 
 import numpy as np

malariagen_data/anoph/g123.py

@@ -1,4 +1,3 @@
-# mypy: disable-error-code="call-arg,arg-type,attr-defined,list-item"
 from collections import Counter
 from typing import Optional, Tuple, Dict, Mapping
 

malariagen_data/anoph/genome_features.py

@@ -1,4 +1,3 @@
-# mypy: disable-error-code="call-arg,arg-type,attr-defined,list-item"
 from typing import Dict, Optional, Tuple, Mapping
 
 import bokeh.models

malariagen_data/anoph/h12.py

@@ -1,4 +1,3 @@
-# mypy: disable-error-code="call-arg,arg-type,attr-defined,list-item"
 from typing import Optional, Tuple, Dict, Mapping
 
 import allel  # type: ignore

malariagen_data/anoph/h1x.py

@@ -1,4 +1,3 @@
-# mypy: disable-error-code="call-arg,arg-type,attr-defined,list-item"
 from typing import Optional, Tuple
 
 import allel  # type: ignore

malariagen_data/anoph/snp_data.py

@@ -1,4 +1,3 @@
-# mypy: disable-error-code="call-arg,arg-type,attr-defined,list-item"
 import warnings
 from functools import lru_cache
 from typing import Any, Dict, List, Optional, Tuple, Union

malariagen_data/anopheles.py

@@ -1,4 +1,3 @@
-# mypy: disable-error-code="call-arg,arg-type,attr-defined,list-item"
 from abc import abstractmethod
 from typing import Any, Dict, Mapping, Optional, Tuple, Sequence
 

pyproject.toml

@@ -107,3 +107,10 @@ line-length = 88
 
 [tool.ruff.lint]
 extend-select = []
+
+[tool.mypy]
+ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = ["bokeh", "bokeh.*"]
+follow_imports = "skip"