Fixing typing.

primitives/setup.cfg

@@ -5,21 +5,14 @@ max-line-length = 200
 description-file = README.md
 
 [mypy]
+pretty = True
+show_error_context = True
+show_column_numbers = True
+ignore_missing_imports = True
 warn_redundant_casts = True
-# TODO: Enable back once false positives are fixed.
-#       See: https://github.com/python/mypy/issues/4412
-#warn_unused_ignores = True
+warn_unused_ignores = True
 warn_unused_configs = True
 disallow_untyped_defs = True
-
-# TODO: Remove once this is fixed: https://github.com/python/mypy/issues/4300
-[mypy-d3m.container.list]
-ignore_errors = True
-
-# TODO: Remove once this is fixed: https://github.com/python/mypy/issues/4300
-[mypy-d3m.metadata.hyperparams]
-ignore_errors = True
-
-# TODO: Remove once this is fixed: https://github.com/python/mypy/pull/4384#issuecomment-354033177
-[mypy-d3m.primitive_interfaces.distance]
-ignore_errors = True
+disallow_incomplete_defs = True
+# TODO: Enable eventually.
+# disallow_untyped_decorators = True

primitives/test_primitives/abs_sum.py

 import os.path
 import typing
 
-import numpy as np  # type: ignore
+import numpy as np
 
 from d3m import container, utils, exceptions
 from d3m.metadata import hyperparams, base as metadata_base

primitives/test_primitives/container_hyperparam.py

 import os.path
 import typing
 
-import numpy as np  # type: ignore
+import numpy as np
 
 from d3m import container, utils
 from d3m.metadata import hyperparams, base as metadata_base

primitives/test_primitives/fail.py

@@ -80,6 +80,8 @@ class FailPrimitive(transformer.TransformerPrimitiveBase[Inputs, Outputs, Hyperp
         'primitive_family': metadata_base.PrimitiveFamily.OPERATOR,
     })
 
+    _fitted: bool
+
     def __init__(self, *, hyperparams: Hyperparams) -> None:
         super().__init__(hyperparams=hyperparams)
         self._conditional_fail('__init__')

primitives/test_primitives/file_reader.py

 import os
 import typing
 
-import numpy  # type: ignore
-import frozendict  # type: ignore
+import numpy
+import frozendict
 
 from d3m import container, utils as d3m_utils
 from d3m.base import primitives

primitives/test_primitives/monomial.py

@@ -75,14 +75,19 @@ class MonomialPrimitive(supervised_learning.SupervisedLearnerPrimitiveBase[Input
         'primitive_family': metadata_base.PrimitiveFamily.REGRESSION,
     })
 
+    _a: float
+    _training_inputs: typing.Optional[Inputs]
+    _training_outputs: typing.Optional[Outputs]
+    _fitted: bool
+
     # Random seed is not needed, but we need it in tests to test which random seed was passed to a primitive.
     def __init__(self, *, hyperparams: Hyperparams, random_seed: int = 0) -> None:
         super().__init__(hyperparams=hyperparams, random_seed=random_seed)
 
-        self._a: float = 0
-        self._training_inputs: Inputs = None
-        self._training_outputs: Outputs = None
-        self._fitted: bool = False
+        self._a = 0
+        self._training_inputs = None
+        self._training_outputs = None
+        self._fitted = False
 
     def produce(self, *, inputs: Inputs, timeout: float = None, iterations: int = None) -> base.CallResult[Outputs]:
         if self._a is None:
@@ -109,7 +114,7 @@ class MonomialPrimitive(supervised_learning.SupervisedLearnerPrimitiveBase[Input
         if self._fitted:
             return base.CallResult(None)
 
-        if not self._training_inputs or not self._training_inputs:
+        if self._training_inputs is None or self._training_outputs is None:
             raise ValueError("Missing training data.")
 
         quotients = [output / input for output, input in zip(self._training_outputs, self._training_inputs) if input != 0]

primitives/test_primitives/multi_data_hyperparam.py

 import os.path
 import typing
 
-import numpy as np  # type: ignore
+import numpy as np
 
 from d3m import container, utils
 from d3m.metadata import hyperparams, base as metadata_base

primitives/test_primitives/postgresql.py

@@ -9,8 +9,8 @@ import subprocess
 import time
 import typing
 
-import prctl  # type: ignore
-import psycopg2  # type: ignore
+import prctl
+import psycopg2
 
 from d3m import container, utils
 from d3m.metadata import base as metadata_base, hyperparams
@@ -92,13 +92,21 @@ class PostgreSQLPrimitive(transformer.TransformerPrimitiveBase[Inputs, Outputs,
         'primitive_family': metadata_base.PrimitiveFamily.OPERATOR,
     })
 
+    _connection: typing.Optional[psycopg2.connection]
+    _process: typing.Optional[subprocess.Popen]
+    _postgresql_base: typing.Optional[str]
+    _config_dir: str
+    _data_dir: str
+    _run_dir: str
+    _config_file: str
+
     def __init__(self, *, hyperparams: Hyperparams, temporary_directory: str = None) -> None:
         super().__init__(hyperparams=hyperparams, temporary_directory=temporary_directory)
 
         # Initialize it early so that "__del__" has access to these attributes.
-        self._connection: psycopg2.connection = None
-        self._process: subprocess.Popen = None
-        self._postgresql_base: str = None
+        self._connection = None
+        self._process = None
+        self._postgresql_base = None
 
         self._postgresql_base = tempfile.mkdtemp()
         os.chmod(self._postgresql_base, 0o755)
@@ -203,9 +211,14 @@ class PostgreSQLPrimitive(transformer.TransformerPrimitiveBase[Inputs, Outputs,
                 connection_error = error
                 time.sleep(0.1)
         else:
-            raise connection_error
+            if connection_error is None:
+                raise TimeoutError("Timeout waiting for the connection.")
+            else:
+                raise connection_error
 
     def produce(self, *, inputs: Inputs, timeout: float = None, iterations: int = None) -> base.CallResult[Outputs]:
+        assert self._connection is not None
+
         with self._connection.cursor() as cursor:
             cursor.execute("SELECT 42;")
             return base.CallResult(container.List([cursor.fetchone()[0]], generate_metadata=True))

primitives/test_primitives/primitive_hyperparam.py

 import os.path
 import typing
 
-import pandas as pd  # type: ignore
+import pandas as pd
 
 from d3m import container, utils
 from d3m.metadata import hyperparams, base as metadata_base

primitives/test_primitives/primitive_sum.py

@@ -2,7 +2,7 @@ import os.path
 import time
 import typing
 
-import numpy  # type: ignore
+import numpy
 
 from d3m import container, exceptions, utils
 from d3m.metadata import base as metadata_base, hyperparams

primitives/test_primitives/random.py

 import os.path
 import typing
 
-import numpy  # type: ignore
+import numpy
 
 from d3m import container, utils
 from d3m.metadata import base as metadata_base, hyperparams
@@ -151,4 +151,4 @@ class RandomPrimitive(generator.GeneratorPrimitiveBase[Outputs, None, Hyperparam
             A dict of values for each produce method wrapped inside ``MultiCallResult``.
         """
 
-        return self._fit_multi_produce(produce_methods=produce_methods, timeout=timeout, iterations=iterations, inputs=inputs)  # type: ignore
+        return self._fit_multi_produce(produce_methods=produce_methods, timeout=timeout, iterations=iterations, inputs=inputs)

primitives/test_primitives/random_classifier.py

@@ -63,14 +63,19 @@ class RandomClassifierPrimitive(SupervisedLearnerPrimitiveBase[Inputs, Outputs,
         ],
     })
 
+    _random: random.Random
+    _training_outputs: typing.Optional[Outputs]
+    _fitted: bool
+    _classes: typing.Optional[typing.List]
+
     def __init__(self, *, hyperparams: Hyperparams, random_seed: int = 0) -> None:
         super().__init__(hyperparams=hyperparams, random_seed=random_seed)
 
-        self._random: random.Random = random.Random()
+        self._random = random.Random()
         self._random.seed(random_seed)
-        self._training_outputs: Outputs = None
+        self._training_outputs = None
         self._fitted = False
-        self._classes: typing.List = []
+        self._classes = []
 
     def set_training_data(self, *, inputs: Inputs, outputs: Outputs) -> None:
         self._training_outputs = outputs

primitives/test_primitives/sum.py

@@ -3,7 +3,7 @@ import pickle
 import typing
 from http import client
 
-import numpy  # type: ignore
+import numpy
 
 from d3m import container, utils
 from d3m.metadata import base as metadata_base, hyperparams