flake8 and mypy

libbids/instruments/eeg_instrument.py

@@ -131,9 +131,9 @@ def device_read(self) -> Union[np.ndarray, List]:
     def device_stop(self) -> None:
         """Stop the device"""
         if isinstance(self.stop_fn, Callable):  # type: ignore
-            return case(Callable, self.stop_fn)()
+            return cast(Callable, self.stop_fn)()
 
-        fn, args, kwards = cast(Tuple, self.stop_fn)
+        fn, args, kwargs = cast(Tuple, self.stop_fn)
         return self.device.__getattribute__(fn)(*args, **kwargs)
 
     def flush(self) -> None:
@@ -185,10 +185,10 @@ def read(self, remainder: bool = False) -> Union[List, np.ndarray]:
             )
             has_data: np.bool_ = np.any([i.shape[0] > 0 for i in self.buffers])
             if (not remainder) and period_met:
-                n_periods: List = [
+                n_periodss: List[int] = [
                     i.shape[0] // j for i, j in zip(self.buffers, periods)
                 ]
-                period_boundaries: List = [i * j for i, j in zip(n_periods, periods)]
+                period_boundaries: List = [i * j for i, j in zip(n_periodss, periods)]
                 writebufs: List = [
                     i[:j] for i, j in zip(self.buffers, period_boundaries)
                 ]

libbids/instruments/ieeg_instrument.py

@@ -1,7 +1,3 @@
-import numpy as np  # type: ignore
-
-from datetime import datetime
-from pyedflib import EdfWriter  # type: ignore
 from typing import (
     Any,
     Callable,
@@ -10,7 +6,6 @@
     Tuple,
     TYPE_CHECKING,
     Union,
-    cast,
 )
 
 from .eeg_instrument import EEGInstrument

libbids/task.py

@@ -73,7 +73,9 @@ def add_run(self) -> Run:
         Run
             A run object that can be used to start the session
         """
-        return Run(self)
+        run: Run = Run(self)
+        self.on_new_run(run)
+        return run
 
     @abstractmethod
     def on_event_start(self, event: Event):
@@ -96,6 +98,17 @@ def on_event_end(self, event: Event):
         """
         raise Exception("Not Implemented")
 
+    @abstractmethod
+    def on_new_run(self, run: Run) -> None:
+        """Called when a new run is created
+
+        Parameters
+        ----------
+        run : Run
+            The instance of the Run that will process the task
+        """
+        raise Exception("Not Implemented")
+
     @abstractmethod
     def process(self, *args, **kwargs) -> np.ndarray:
         """This method is to be implemented by inheriting classes to define how

setup.py

@@ -1,7 +1,4 @@
-from skbuild import setup
-from setuptools import find_packages
+from skbuild import setup  # type: ignore
+from setuptools import find_packages  # type: ignore
 
-setup(
-    name="libbids",
-    packages=find_packages(exclude=["tests"])
-)
+setup(name="libbids", packages=find_packages(exclude=["tests"]))

tests/test_entity.py

@@ -1,9 +1,9 @@
 from typing import Optional
 
-from libbids.clibbids import Entity
+from libbids.clibbids import Entity  # type: ignore
 
 
-def test_constructor_with_name_and_optional_key_and_int_value():
+def test_constructor_with_name_and_optional_key_and_int_value() -> None:
     name = "Entity"
     key: Optional[str] = "KEY"
     value: int = 42
@@ -14,7 +14,7 @@ def test_constructor_with_name_and_optional_key_and_int_value():
     assert entity.id == "KEY-42"
 
 
-def test_constructor_with_name_and_optional_key_and_string_value():
+def test_constructor_with_name_and_optional_key_and_string_value() -> None:
     name = "Entity"
     key: Optional[str] = "KEY"
     value: str = "VALUE"
@@ -25,7 +25,7 @@ def test_constructor_with_name_and_optional_key_and_string_value():
     assert entity.id == "KEY-VALUE"
 
 
-def test_constructor_with_name_and_optional_key_and_invalid_string_value():
+def test_constructor_with_name_and_optional_key_and_invalid_string_value() -> None:
     name: str = "Entity"
     key: Optional[str] = "KEY"
     value: str = "INVALID"

tests/test_session.py

@@ -4,7 +4,8 @@
 
 from pathlib import Path
 from libbids import Dataset
-from libbids.clibbids import Session
+from libbids.clibbids import Session, Subject  # type: ignore
+from typing import cast
 
 
 # Test fixture for Session class
@@ -41,45 +42,45 @@ def setup(self):
         shutil.rmtree(self.test_dir)
 
     # Test the path() method of Session
-    def test_path_test(self):
+    def test_path_test(self) -> None:
         # Create a Session object with index 1
         session: Session = Session(self.subject, 1)
 
         # Expected path: subject path + session id
-        expected_path: Path = self.subject.path / "ses-01"
+        expected_path: Path = cast(Subject, self.subject).path / "ses-01"
 
         # Check if the calculated path matches the expected path
         assert session.path == expected_path
 
     # Test the prefix() method of Session
-    def test_prefix(self):
+    def test_prefix(self) -> None:
         # Create a Session object with index 2
         session: Session = Session(self.subject, 2)
 
         # Expected prefix: subject id + "_" + session id
-        expected_prefix: str = self.subject.id + "_" + session.id
+        expected_prefix: str = cast(Subject, self.subject).id + "_" + session.id
 
         # Check if the calculated prefix matches the expected prefix
         assert session.prefix == expected_prefix
 
     # test the label
-    def test_label(self):
+    def test_label(self) -> None:
         # Create a Session object with index 3
         session: Session = Session(self.subject, 3)
 
         # Check if the calculated prefix matches the expected prefix
         assert session.label == "03"
 
     # test padding
-    def test_padding(self):
+    def test_padding(self) -> None:
         # Create a Session object with index 4
         session: Session = Session(self.subject, 4)
 
         # Check if the calculated prefix matches the expected prefix
         assert session.padding == 2
 
     # test index
-    def test_index(self):
+    def test_index(self) -> None:
         # Creat a Session object with index 5
         session: Session = Session(self.subject, 5)
 

tests/test_subject.py

@@ -4,7 +4,7 @@
 
 from pathlib import Path
 from libbids import Dataset
-from libbids.clibbids import Session, Subject
+from libbids.clibbids import Session, Subject  # type: ignore
 
 
 # Test fixture for Subject class
@@ -40,7 +40,7 @@ def setup(self):
         shutil.rmtree(self.test_dir)
 
     # Test the path() method of Subject
-    def test_path_test(self):
+    def test_path_test(self) -> None:
         # Create a Subject object with index 1
         subject: Subject = Subject(
             self.dataset, dict(name="Jacob", participant_id="sub-01")
@@ -53,7 +53,7 @@ def test_path_test(self):
         assert subject.path == expected_path
 
     # Test the prefix() method of Subject
-    def test_prefix(self):
+    def test_prefix(self) -> None:
         # Create a Subject object with index 2
         subject: Subject = Subject(self.dataset, dict(participant_id="02"))
 
@@ -64,15 +64,15 @@ def test_prefix(self):
         assert subject.id == expected_prefix
 
     # test the label
-    def test_label(self):
+    def test_label(self) -> None:
         # Create a Subject object with index 3
         subject: Subject = Subject(self.dataset, dict(participant_id="sub-03"))
 
         # Check if the calculated prefix matches the expected prefix
         assert subject.get_participant_label() == "03"
 
     # Test adding a session
-    def test_add_session(self):
+    def test_add_session(self) -> None:
         # Create a Subject object with index 4
         subject: Subject = Subject(
             self.dataset, dict(participant_id="sub-04", name="J'Dinklage Morgoon")