change strict_stiminterval and ignore_first_ISI to bool type

efel/api.py

@@ -79,7 +79,7 @@ def set_dependency_file_location(location: str | Path) -> None:
     Raises:
         FileNotFoundError: If the path to the dependency file doesn't exist.
     """
-    _settings.set_setting('dependencyfile_path', str(location))
+    set_setting('dependencyfile_path', str(location))
 
 
 def get_dependency_file_location() -> str:
@@ -99,7 +99,7 @@ def set_threshold(new_threshold: float) -> None:
         new_threshold: The new spike detection threshold value (in the same units
                        as the traces, e.g. mV).
     """
-    _settings.set_setting('Threshold', new_threshold)
+    set_setting('Threshold', new_threshold)
 
 
 @deprecated("Use `set_setting('DerivativeThreshold', "
@@ -114,7 +114,7 @@ def set_derivative_threshold(new_derivative_threshold: float) -> None:
         new_derivative_threshold: The new derivative threshold value (in the same units
                                   as the traces, e.g. mV/ms).
     """
-    _settings.set_setting('DerivativeThreshold', new_derivative_threshold)
+    set_setting('DerivativeThreshold', new_derivative_threshold)
 
 
 def get_feature_names() -> list[str]:
@@ -216,6 +216,8 @@ def _initialise() -> None:
     # Set the settings in the cppcore
     settings_attrs = vars(_settings)
     for setting_name, setting_value in settings_attrs.items():
+        if isinstance(setting_value, bool):
+            setting_value = int(setting_value)
         if isinstance(setting_value, int):
             cppcore.setFeatureInt(setting_name, [setting_value])
         elif isinstance(setting_value, float):
@@ -230,19 +232,19 @@ def _initialise() -> None:
 @deprecated("Use `set_setting()` instead")
 def set_int_setting(setting_name: str, new_value: int) -> None:
     """Set a certain integer setting to a new value."""
-    _settings.set_int(setting_name, new_value)
+    set_setting(setting_name, new_value)
 
 
 @deprecated("Use `set_setting()` instead")
 def set_double_setting(setting_name: str, new_value: float) -> None:
     """Set a certain double setting to a new value."""
-    _settings.set_double(setting_name, new_value)
+    set_setting(setting_name, new_value)
 
 
 @deprecated("Use `set_setting()` instead")
 def set_str_setting(setting_name: str, new_value: str) -> None:
     """Set a certain string setting to a new value."""
-    _settings.set_str(setting_name, new_value)
+    set_setting(setting_name, new_value)
 
 
 @overload

efel/settings.py

@@ -53,7 +53,7 @@ class Settings:
         rise_end_perc (float): Rise end percentage (default: 1.0).
         initial_perc (float): Initial percentage (default: 0.1).
         min_spike_height (float): Minimum spike height (default: 20.0).
-        strict_stiminterval (int): Strict stimulus interval (default: 0).
+        strict_stiminterval (bool): Strict stimulus interval (default: False).
         initburst_freq_threshold (int): Initial burst frequency threshold
         (default: 50)
         initburst_sahp_start (int): Initial burst SAHP start (default: 5).
@@ -63,7 +63,7 @@ class Settings:
         current_base_mode (str): Current base mode (default: "mean").
         precision_threshold (float): Precision threshold (default: 1e-10).
         sahp_start (float): SAHP start (default: 5.0).
-        ignore_first_ISI (int): Ignore first ISI (default: 1).
+        ignore_first_ISI (bool): Ignore first ISI (default: True).
         impedance_max_freq (float): Impedance maximum frequency (default: 50.0).
     """
 
@@ -87,7 +87,7 @@ class Settings:
     rise_end_perc: float = 1.0
     initial_perc: float = 0.1
     min_spike_height: float = 20.0
-    strict_stiminterval: int = 0
+    strict_stiminterval: bool = False
     initburst_freq_threshold: int = 50
     initburst_sahp_start: int = 5
     initburst_sahp_end: int = 100
@@ -96,15 +96,17 @@ class Settings:
     current_base_mode: str = "mean"
     precision_threshold: float = 1e-10
     sahp_start: float = 5.0
-    ignore_first_ISI: int = 1
+    ignore_first_ISI: bool = True
     impedance_max_freq: float = 50.0
 
-    def set_setting(self, setting_name: str, new_value: Union[int, float, str]) -> None:
+    def set_setting(self,
+                    setting_name: str,
+                    new_value: Union[int, float, str, bool]) -> None:
         """Set a certain setting to a new value.
 
         Args:
             setting_name (str): Name of the setting to be modified.
-            new_value (Union[int, float, str]): New value for the setting.
+            new_value (Union[int, float, str, bool]): New value for the setting.
 
         Raises:
             ValueError: If the value is of the wrong type.
@@ -114,10 +116,9 @@ def set_setting(self, setting_name: str, new_value: Union[int, float, str]) -> N
         if hasattr(self, setting_name):
             expected_types = {f.name: f.type for f in fields(self)}
             expected_type = expected_types.get(setting_name)
-            if expected_type and expected_type != type(new_value):
-                expected_type_name = expected_type.__name__
+            if expected_type and not isinstance(new_value, expected_type):
                 raise ValueError(f"Invalid value for setting '{setting_name}'. "
-                                 f"Expected type: {expected_type_name}.")
+                                 f"Expected type: {expected_type.__name__}.")
         else:
             logger.warning("Setting '%s' not found in settings. "
                            "Adding it as a new setting.", setting_name)
@@ -130,18 +131,6 @@ def set_setting(self, setting_name: str, new_value: Union[int, float, str]) -> N
 
         setattr(self, setting_name, new_value)
 
-    @deprecated("Use set_setting instead")
-    def set_int(self, setting_name: str, new_value: int) -> None:
-        self.set_setting(setting_name, new_value)
-
-    @deprecated("Use set_setting instead")
-    def set_double(self, setting_name: str, new_value: float) -> None:
-        self.set_setting(setting_name, new_value)
-
-    @deprecated("Use set_setting instead")
-    def set_str(self, setting_name: str, new_value: str) -> None:
-        self.set_setting(setting_name, new_value)
-
     def reset_to_default(self):
         """Reset settings to their default values"""
         default_settings = Settings()

tests/test_basic.py

@@ -39,7 +39,6 @@
 from efel.io import load_ascii_input
 from efel.api import get_feature_values
 from efel.api import set_setting
-from efel.api import set_derivative_threshold
 from efel.api import get_distance
 
 
@@ -413,7 +412,7 @@ def test_setDerivativeThreshold():
             features)
     AP_begin_voltage_orig = feature_values[0]['AP_begin_voltage'][1]
 
-    set_derivative_threshold(5.0)
+    set_setting('DerivativeThreshold', 5.0)
     feature_values = \
         get_feature_values(
             [trace],
@@ -541,7 +540,7 @@ def test_min_AHP_indices_strict():
 
     import efel
 
-    for strict, n_of_ahp in [(0, 17), (1, 16)]:
+    for strict, n_of_ahp in [(False, 17), (True, 16)]:
         efel.reset()
         set_setting('strict_stiminterval', strict)
 
@@ -598,7 +597,7 @@ def test_strict_stiminterval():
 
     import efel
 
-    for strict, n_of_spikes in [(0, 5), (1, 3)]:
+    for strict, n_of_spikes in [(False, 5), (True, 3)]:
         efel.reset()
         set_setting("strict_stiminterval", strict)
 
@@ -681,7 +680,7 @@ def test_ISI_values_noIgnore():
 
     features = ['ISI_values']
 
-    set_setting("ignore_first_ISI", 0)
+    set_setting("ignore_first_ISI", False)
 
     feature_values = \
         get_feature_values(
@@ -690,7 +689,7 @@ def test_ISI_values_noIgnore():
     isi_values_no_ignore = feature_values[0]['ISI_values']
 
     efel.reset()
-    set_setting("ignore_first_ISI", 1)
+    set_setting("ignore_first_ISI", True)
 
     feature_values = \
         get_feature_values(
@@ -2038,7 +2037,7 @@ def test_unfinished_peak():
     """basic: Test if unfinished peak doesn't break spike_count"""
 
     import efel
-    set_setting('strict_stiminterval', 1)
+    set_setting('strict_stiminterval', True)
 
     dt = 0.1
     v = numpy.zeros(int(100 / dt)) - 70.0
@@ -2368,7 +2367,7 @@ def test_AP_width_between_threshold_strict():
 
     import efel
     efel.reset()
-    set_setting('strict_stiminterval', 1)
+    set_setting('strict_stiminterval', True)
 
     threshold = -48.0
     set_setting("Threshold", threshold)
@@ -3085,7 +3084,7 @@ def test_burst_indices():
     """basic: Test burst_begin_indices and burst_end_indices"""
     import efel
     efel.reset()
-    set_setting('ignore_first_ISI', 0)
+    set_setting('ignore_first_ISI', False)
 
     time, voltage = load_ascii_input(burst1_url)
     time, voltage = interpolate(time, voltage, 0.1)
@@ -3121,7 +3120,7 @@ def test_strict_burst_mean_freq():
     """basic: Test strict_burst_mean_freq"""
     import efel
     efel.reset()
-    set_setting('ignore_first_ISI', 0)
+    set_setting('ignore_first_ISI', False)
 
     time, voltage = load_ascii_input(burst1_url)
     time, voltage = interpolate(time, voltage, 0.1)
@@ -3168,7 +3167,7 @@ def test_strict_burst_number():
     """basic: Test strict_burst_number"""
     import efel
     efel.reset()
-    set_setting('ignore_first_ISI', 0)
+    set_setting('ignore_first_ISI', False)
 
     time, voltage = load_ascii_input(burst1_url)
     time, voltage = interpolate(time, voltage, 0.1)
@@ -3216,7 +3215,7 @@ def test_strict_interburst_voltage():
     """basic: Test strict_interburst_voltage"""
     import efel
     efel.reset()
-    set_setting('ignore_first_ISI', 0)
+    set_setting('ignore_first_ISI', False)
 
     time, voltage = load_ascii_input(burst1_url)
     time, voltage = interpolate(time, voltage, 0.1)
@@ -3278,7 +3277,7 @@ def test_AP_width_spike_before_stim_start():
 
     assert len(ap_width) == 15
 
-    set_setting('strict_stiminterval', 1)
+    set_setting('strict_stiminterval', True)
     feature_values = \
         get_feature_values(
             [trace],
@@ -3316,7 +3315,7 @@ def test_ADP_peak_amplitude():
     """basic: Test ADP_peak_amplitude"""
     import efel
     efel.reset()
-    set_setting('strict_stiminterval', 1)
+    set_setting('strict_stiminterval', True)
 
     stim_start = 250.0
     stim_end = 1600.0

tests/test_isi.py

@@ -142,7 +142,7 @@ def test_single_burst_ratio(self):
         assert self.feature_values["single_burst_ratio"] is None
 
         # set ignore_first_ISI=False
-        efel.set_setting("ignore_first_ISI", 0)
+        efel.set_setting("ignore_first_ISI", False)
         self.feature_values = get_feature_values(
             [self.trace],
             self.features, raise_warnings=False)[0]

tests/test_settings.py

@@ -31,13 +31,10 @@
 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 """
 
-from pathlib import Path
-import numpy
-
 import pytest
 
 from efel.settings import Settings
-from efel.api import set_setting
+from efel.api import set_setting, get_settings
 
 
 def test_set_setting():
@@ -51,24 +48,16 @@ def test_set_setting_invalid_type():
     """Test that the set_setting method raises a ValueError
     when given an invalid type."""
     settings = Settings()
-    try:
+    with pytest.raises(ValueError):
         settings.set_setting("Threshold", "-30.0")
-    except ValueError:
-        assert True
-    else:
-        assert False
 
 
 def test_set_setting_dependencyfile_path_not_found():
     """Test that the set_setting method raises a FileNotFoundError
     when given a nonexistent file."""
     settings = Settings()
-    try:
+    with pytest.raises(FileNotFoundError):
         settings.set_setting("dependencyfile_path", "nonexistent_file.txt")
-    except FileNotFoundError:
-        assert True
-    else:
-        assert False
 
 
 def test_reset_to_default():
@@ -78,3 +67,45 @@ def test_reset_to_default():
     settings.Threshold = -30.0
     settings.reset_to_default()
     assert settings.Threshold == -20.0
+
+
+def test_get_settings():
+    """Test that the get_settings method returns an instance of efel.Settings."""
+    settings = get_settings()
+    assert isinstance(settings, Settings)
+
+
+def test_str_method():
+    """Test that the __str__ method returns the correct string representation."""
+    settings = Settings()
+    expected_output = (
+        "Threshold: -20.0\n"
+        "DerivativeThreshold: 10.0\n"
+        "DownDerivativeThreshold: -12.0\n"
+        f"dependencyfile_path: {settings.dependencyfile_path}\n"
+        "spike_skipf: 0.1\n"
+        "max_spike_skip: 2\n"
+        "interp_step: 0.1\n"
+        "burst_factor: 1.5\n"
+        "strict_burst_factor: 2.0\n"
+        "voltage_base_start_perc: 0.9\n"
+        "voltage_base_end_perc: 1.0\n"
+        "current_base_start_perc: 0.9\n"
+        "current_base_end_perc: 1.0\n"
+        "rise_start_perc: 0.0\n"
+        "rise_end_perc: 1.0\n"
+        "initial_perc: 0.1\n"
+        "min_spike_height: 20.0\n"
+        "strict_stiminterval: False\n"
+        "initburst_freq_threshold: 50\n"
+        "initburst_sahp_start: 5\n"
+        "initburst_sahp_end: 100\n"
+        "DerivativeWindow: 3\n"
+        "voltage_base_mode: mean\n"
+        "current_base_mode: mean\n"
+        "precision_threshold: 1e-10\n"
+        "sahp_start: 5.0\n"
+        "ignore_first_ISI: True\n"
+        "impedance_max_freq: 50.0"
+    )
+    assert str(settings) == expected_output