🔧⌨️ Made mypy optout instead of opt in and fixed some typing issues

glotaran · Nov 7, 2022 · aeb4de0 · aeb4de0
1 parent ece973f
commit aeb4de0
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Showing 8 changed files with 24 additions and 40 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -114,7 +114,6 @@ repos:
     rev: v0.982
     hooks:
       - id: mypy
-        files: "^glotaran/(plugin_system|utils|deprecation|testing|optimization|parameter|project|simulation|model|builtin/io/pandas)"
         exclude: "docs"
         additional_dependencies: [types-all, types-attrs]
 

diff --git a/benchmark/benchmarks/unit/analysis/bench_optimize.py b/benchmark/benchmarks/unit/analysis/bench_optimize.py
@@ -12,7 +12,12 @@
     from glotaran.simulation import simulate
 
     try:
-        from glotaran.optimization.test.models import MultichannelMulticomponentDecay
+        # isort: off
+        from glotaran.optimization.test.models import (  # type: ignore[attr-defined]
+            MultichannelMulticomponentDecay,
+        )
+
+        # isort: on
     except ImportError:
         # 0.7.0
         from glotaran.optimization.test.suites import MultichannelMulticomponentDecay

diff --git a/glotaran/builtin/io/yml/utils.py b/glotaran/builtin/io/yml/utils.py
@@ -30,6 +30,7 @@ def write_dict(
         stream = StringIO()
         yaml.dump(data, stream)
         return stream.getvalue()
+    return None
 
 
 def load_dict(source: str | Path, is_file: bool) -> dict[str, Any]:

diff --git a/glotaran/builtin/megacomplexes/coherent_artifact/test/test_coherent_artifact.py b/glotaran/builtin/megacomplexes/coherent_artifact/test/test_coherent_artifact.py
@@ -1,3 +1,5 @@
+from typing import Any
+
 import numpy as np
 import pytest
 import xarray as xr
@@ -18,7 +20,7 @@
     ("none", "dispersed", "shifted"),
 )
 def test_coherent_artifact(spectral_dependence: str):
-    model_dict = {
+    model_dict: dict[str, dict[str, Any]] = {
         "initial_concentration": {
             "j1": {"compartments": ["s1"], "parameters": ["irf_center"]},
         },
@@ -80,7 +82,7 @@ def test_coherent_artifact(spectral_dependence: str):
         **model_dict
     )
 
-    parameters = Parameters.from_list(parameter_list)
+    parameters = Parameters.from_list(parameter_list)  # type: ignore[arg-type]
 
     time = np.arange(0, 50, 1.5)
     spectral = np.asarray([200, 300, 400])

diff --git a/glotaran/builtin/megacomplexes/decay/test/test_decay_megacomplex.py b/glotaran/builtin/megacomplexes/decay/test/test_decay_megacomplex.py
@@ -163,7 +163,7 @@ class ThreeComponentParallel:
                 ["1", 501e-3],
                 ["2", 202e-4],
                 ["3", 105e-5],
-                {"non-negative": True},
+                {"non-negative": True},  # type: ignore[list-item]
             ],
             "irf": [["center", 1.3], ["width", 7.8]],
         }
@@ -223,7 +223,7 @@ class ThreeComponentSequential:
                 ["1", 501e-3],
                 ["2", 202e-4],
                 ["3", 105e-5],
-                {"non-negative": True},
+                {"non-negative": True},  # type: ignore[list-item]
             ],
             "irf": [["center", 1.3], ["width", 7.8]],
         }

diff --git a/glotaran/model/model.py b/glotaran/model/model.py
@@ -3,6 +3,7 @@
 
 from collections.abc import Callable
 from collections.abc import Generator
+from collections.abc import Iterable
 from collections.abc import Mapping
 from typing import Any
 from typing import ClassVar
@@ -256,7 +257,7 @@ def create_class(cls, attributes: dict[str, Attribute]) -> type[Model]:
 
     @classmethod
     def create_class_from_megacomplexes(
-        cls, megacomplexes: list[type[Megacomplex]]
+        cls, megacomplexes: Iterable[type[Megacomplex]]
     ) -> type[Model]:
         """Create model class for megacomplexes.
 

diff --git a/glotaran/testing/simulated_data/sequential_spectral_decay.py b/glotaran/testing/simulated_data/sequential_spectral_decay.py
@@ -10,13 +10,13 @@
 
 SIMULATION_MODEL_YML = generate_model_yml(
     generator_name="spectral_decay_sequential",
-    generator_arguments={"nr_compartments": 3, "irf": True},  # type:ignore[arg-type]
+    generator_arguments={"nr_compartments": 3, "irf": True},
 )
 SIMULATION_MODEL = load_model(SIMULATION_MODEL_YML, format_name="yml_str")
 
 MODEL_YML = generate_model_yml(
     generator_name="decay_sequential",
-    generator_arguments={"nr_compartments": 3, "irf": True},  # type:ignore[arg-type]
+    generator_arguments={"nr_compartments": 3, "irf": True},
 )
 MODEL = load_model(MODEL_YML, format_name="yml_str")
 

diff --git a/setup.cfg b/setup.cfg
@@ -96,38 +96,14 @@ show_error_codes = True
 warn_unused_configs = True
 warn_unused_ignores = True
 
-[mypy-glotaran.*]
+[mypy-glotaran.builtin.megacomplexes.*]
 ignore_errors = True
 
-[mypy-glotaran.plugin_system.*]
-ignore_errors = False
-
-[mypy-glotaran.utils.*]
-ignore_errors = False
-
-[mypy-glotaran.deprecation.*]
-ignore_errors = False
-
-[mypy-glotaran.optimization.*]
-ignore_errors = False
-
-[mypy-glotaran.optimization.test.*]
-ignore_errors = False
-
-[mypy-glotaran.project.generators.test.*]
-ignore_errors = False
-
-[mypy-glotaran.parameter.*]
-ignore_errors = False
-
-[mypy-glotaran.project.*]
-ignore_errors = False
-
-[mypy-glotaran.simulation.*]
-ignore_errors = False
+[mypy-glotaran.builtin.io.ascii.*]
+ignore_errors = True
 
-[mypy-glotaran.model.*]
-ignore_errors = False
+[mypy-glotaran.cli.*]
+ignore_errors = True
 
-[mypy-glotaran.builtin.io.pandas.*]
-ignore_errors = False
+[mypy-benchmark.*]
+ignore_errors = True