Merge pull request #83 from ImperialCollegeLondon/feature/mypy_options

Strict requirement for type hinting

docs/source/development/training/test_mfm.py

@@ -4,12 +4,12 @@
 from mfm import TimesTable, my_float_multiplier, my_picky_float_multiplier
 
 
-def test_fm():
+def test_fm() -> None:
 
     assert 10 == my_float_multiplier(2, 5)
 
 
-def test_pfm():
+def test_pfm() -> None:
 
     with pytest.raises(ValueError) as err_hndlr:
 
@@ -18,7 +18,7 @@ def test_pfm():
     assert str(err_hndlr.value) == "Both x and y must be of type float"
 
 
-def test_pfm_fail():
+def test_pfm_fail() -> None:
 
     with pytest.raises(ValueError) as err_hndlr:
 
@@ -36,7 +36,7 @@ def test_pfm_fail():
         (-1.5, -3.0, 4.5),
     ],
 )
-def test_pfm_param_noid(x, y, expected):
+def test_pfm_param_noid(x: float, y: float, expected: float) -> None:
 
     assert expected == my_picky_float_multiplier(x, y)
 
@@ -51,7 +51,7 @@ def test_pfm_param_noid(x, y, expected):
     ],
     ids=["++", "-+", "+-", "--"],
 )
-def test_pfm_param_ids(x, y, expected):
+def test_pfm_param_ids(x: float, y: float, expected: float) -> None:
 
     assert expected == my_picky_float_multiplier(x, y)
 
@@ -66,13 +66,13 @@ def test_pfm_param_ids(x, y, expected):
     argvalues=[(3.0,), (-3.0,)],
     ids=["+", "-"],
 )
-def test_pfm_twoparam(x, y):
+def test_pfm_twoparam(x: float, y: float) -> None:
 
     assert 4.5 == abs(my_picky_float_multiplier(x, y))
 
 
 @pytest.fixture
-def twoparam_expected():
+def twoparam_expected() -> dict[str, float]:
 
     expected = {"+-+": 4.5, "---": 4.5, "--+": -4.5, "+--": -4.5}
     return expected
@@ -88,27 +88,32 @@ def twoparam_expected():
     argvalues=[(3.0,), (-3.0,)],
     ids=["+", "-"],
 )
-def test_pfm_twoparam_fixture(request, twoparam_expected, x, y):
+def test_pfm_twoparam_fixture(
+    request: pytest.FixtureRequest,
+    twoparam_expected: dict[str, float],
+    x: float,
+    y: float,
+) -> None:
 
     expected = twoparam_expected[request.node.callspec.id]
 
     assert expected == my_picky_float_multiplier(x, y)
 
 
 @pytest.fixture()
-def times_table_instance():
+def times_table_instance() -> TimesTable:
     return TimesTable(num=7)
 
 
-def test_times_table_errors(times_table_instance):
+def test_times_table_errors(times_table_instance: TimesTable) -> None:
 
     with pytest.raises(TypeError) as err_hndlr:
-        times_table_instance.table(1.6, 23.9)
+        times_table_instance.table(1.6, 23.9)  # type: ignore
 
     assert str(err_hndlr.value) == "'float' object cannot be interpreted as an integer"
 
 
-def test_times_table_values(times_table_instance):
+def test_times_table_values(times_table_instance: TimesTable) -> None:
 
     value = times_table_instance.table(2, 7)
     assert value == [14, 21, 28, 35, 42, 49]

pyproject.toml

@@ -21,6 +21,7 @@ tomli-w = "^1.0.0"
 scipy = "^1.9.0"
 jsonschema = "^4.14.0"
 Shapely = "^1.8.4"
+types-jsonschema = "^4.16.1"
 
 [tool.poetry.dev-dependencies]
 pytest = "^7.1.2"

setup.cfg

@@ -21,12 +21,20 @@ extend-ignore =
 docstring-convention = google
 
 [mypy]
-ignore_missing_imports = True
+ignore_missing_imports = False
 strict_optional = False
+disallow_untyped_calls = True
+disallow_untyped_defs = True
+disallow_incomplete_defs = True
 
 [mypy-setup]
 ignore_errors = True
 
+[mypy-tests.*]
+disallow_untyped_calls = False
+disallow_untyped_defs = False
+disallow_incomplete_defs = False
+
 [isort]
 profile = black
 multi_line_output = 3

tests/conftest.py

@@ -1,11 +1,13 @@
 """Collection of fixtures to assist the testing scripts."""
 
+import pytest
+
 # An import of LOGGER is required for INFO logging events to be visible to tests
 # This can be removed as soon as a script that imports logger is imported
 import virtual_rainforest.core.logger  # noqa
 
 
-def log_check(caplog, expected_log):
+def log_check(caplog: pytest.LogCaptureFixture, expected_log: tuple[tuple]) -> None:
     """Helper function to check that the captured log is as expected.
 
     Arguments:

tests/test_config.py

@@ -32,7 +32,7 @@
         ),
     ],
 )
-def test_check_dict_leaves(d_a, d_b, overlap):
+def test_check_dict_leaves(d_a: dict, d_b: dict, overlap: list) -> None:
     """Checks overlapping dictionary search function."""
     assert overlap == config.check_dict_leaves(d_a, d_b, [])
 
@@ -203,7 +203,7 @@ def test_find_schema(caplog, config_dict, expected_exception, expected_log_entri
     log_check(caplog, expected_log_entries)
 
 
-def test_construct_combined_schema(caplog):
+def test_construct_combined_schema(caplog: pytest.LogCaptureFixture) -> None:
     """Checks errors for bad or missing json schema."""
 
     # Check that construct_combined_schema fails as expected
@@ -241,6 +241,8 @@ def test_construct_combined_schema(caplog):
 def test_final_validation_log(caplog, expected_log_entries):
     """Checks that validation passes as expected and produces the correct output."""
 
+    print(type(expected_log_entries))
+
     config.validate_config(["tests/fixtures"], out_file_name="complete_config")
 
     # Remove generated output file
@@ -321,7 +323,7 @@ def test_register_schema_errors(
     with pytest.raises(expected_exception):
 
         @register_schema(schema_name)
-        def to_be_decorated():
+        def to_be_decorated() -> dict:
             return schema
 
         to_be_decorated()

virtual_rainforest/core/__init__.py

@@ -5,7 +5,7 @@
 
 
 @register_schema("core")
-def schema():
+def schema() -> dict:
     """Defines the schema that the core module configuration should conform to."""
 
     schema_file = Path(__file__).parent.resolve() / "core_schema.json"

virtual_rainforest/core/config.py

@@ -11,7 +11,7 @@
 from pathlib import Path
 from typing import Callable, Union
 
-import dpath.util
+import dpath.util  # type: ignore
 import jsonschema
 import tomli_w
 
@@ -37,7 +37,7 @@ def register_schema(module_name: str) -> Callable:
         KeyError: If a module schema is missing one of the required keys
     """
 
-    def wrap(func: Callable):
+    def wrap(func: Callable) -> Callable:
         if module_name in SCHEMA_REGISTRY:
             log_and_raise(
                 f"The module schema {module_name} is used multiple times, this "
@@ -75,7 +75,9 @@ def wrap(func: Callable):
 COMPLETE_CONFIG: dict = {}
 
 
-def check_dict_leaves(d1: dict, d2: dict, conflicts: list = [], path: list = []):
+def check_dict_leaves(
+    d1: dict, d2: dict, conflicts: list = [], path: list = []
+) -> list:
     """Recursively checks if leaves are repeated between two nested dictionaries.
 
     Args:

virtual_rainforest/core/grid.py

@@ -12,11 +12,11 @@
 
 import json
 import logging
-from typing import Callable
+from typing import Any, Callable
 
 import numpy as np
-from shapely.affinity import scale, translate
-from shapely.geometry import Polygon
+from shapely.affinity import scale, translate  # type: ignore
+from shapely.geometry import Polygon  # type: ignore
 
 LOGGER = logging.getLogger("virtual_rainforest.core")
 
@@ -250,7 +250,7 @@ def __repr__(self) -> str:
             f"cell_ny={self.cell_ny})"
         )
 
-    def dumps(self, dp: int = 2, **kwargs) -> str:
+    def dumps(self, dp: int = 2, **kwargs: Any) -> str:
         """Export a grid as a GeoJSON string.
 
         The virtual_rainforest.core.Grid object assumes an unspecified projected
@@ -267,7 +267,7 @@ def dumps(self, dp: int = 2, **kwargs) -> str:
         content = self._get_geojson(dp=dp)
         return json.dumps(obj=content, **kwargs)
 
-    def dump(self, outfile: str, dp: int = 2, **kwargs) -> None:
+    def dump(self, outfile: str, dp: int = 2, **kwargs: Any) -> None:
         """Export a grid as a GeoJSON file.
 
         The virtual_rainforest.core.Grid object assumes an unspecified projected
@@ -287,7 +287,7 @@ def dump(self, outfile: str, dp: int = 2, **kwargs) -> None:
         with open(outfile, "w") as outf:
             json.dump(obj=content, fp=outf, **kwargs)
 
-    def _get_geojson(self, dp):
+    def _get_geojson(self, dp: int) -> dict:
         """Convert the grid to a GeoJSON structured dictionary.
 
         Args:

virtual_rainforest/plants/__init__.py

@@ -5,7 +5,7 @@
 
 
 @register_schema("plants")
-def schema():
+def schema() -> dict:
     """Defines the schema that the plant module configuration should conform to."""
 
     schema_file = Path(__file__).parent.resolve() / "plants_schema.json"