Linting.

src/quackseq/__init__.py

@@ -0,0 +1 @@
+"""The base module for the quackseq pulse programming library."""

src/quackseq/event.py

@@ -1,3 +1,5 @@
+"""Event class for the pulse sequence. Every pulse sequence consists of events, that are executed subsequently and have different parameters."""
+
 import logging
 from collections import OrderedDict
 
@@ -21,7 +23,9 @@ class Event:
         pulse_sequence (PulseSequence): The pulse sequence the event belongs to
     """
 
-    def __init__(self, name: str, duration: float | str, pulse_sequence : "PulseSequence") -> None:
+    def __init__(
+        self, name: str, duration: float | str, pulse_sequence: "PulseSequence"
+    ) -> None:
         """Initializes the event."""
         self.parameters = OrderedDict()
         self.name = name
@@ -36,9 +40,7 @@ class Event:
         pulse_parameters = self.pulse_sequence.pulse_parameter_options
         for name, pulse_parameter_class in pulse_parameters.items():
             logger.debug("Adding pulse parameter %s to event %s", name, self.name)
-            self.parameters[name] = pulse_parameter_class(
+            self.parameters[name] = pulse_parameter_class(name)
-                name
-            )
             logger.debug(
                 "Created pulse parameter %s with object id %s",
                 name,

src/quackseq/options.py

@@ -1,8 +1,11 @@
+"""Options for the pulse parameters. Options can be of different types, for example boolean, numeric or function. Generally pulse parameters have different values for the different events in a pulse sequence."""
+
 import logging
 from quackseq.functions import Function
 
 logger = logging.getLogger(__name__)
 
+
 class Option:
     """Defines options for the pulse parameters which can then be set accordingly.
 
@@ -102,6 +105,7 @@ class NumericOption(Option):
             is_float (bool): If the value is a float.
             min_value: The minimum value of the option.
             max_value: The maximum value of the option.
+            slider (bool): If the option should be displayed as a slider. This is not used for the pulseq module, but visualizations can use this information.
         """
         super().__init__(name, value)
         self.is_float = is_float
@@ -116,7 +120,7 @@ class NumericOption(Option):
             self.value_changed.emit()
         elif value >= self.max_value:
             self.value = self.max_value
-            self.value_changed.emit() 
+            self.value_changed.emit()
         else:
             raise ValueError(
                 f"Value {value} is not in the range of {self.min_value} to {self.max_value}. This should have been caught earlier."

src/quackseq/pulsesequence.py

@@ -62,8 +62,10 @@ class PulseSequence:
             event (Event): The event to add
         """
         if event.name in self.get_event_names():
-            raise ValueError(f"Event with name {event.name} already exists in the pulse sequence")
+            raise ValueError(
-        
+                f"Event with name {event.name} already exists in the pulse sequence"
+            )
+
         self.events.append(event)
 
     def create_event(self, event_name: str, duration: str) -> "Event":
@@ -78,8 +80,10 @@ class PulseSequence:
         """
         event = Event(event_name, duration, self)
         if event.name in self.get_event_names():
-            raise ValueError(f"Event with name {event.name} already exists in the pulse sequence")
+            raise ValueError(
-        
+                f"Event with name {event.name} already exists in the pulse sequence"
+            )
+
         self.events.append(event)
         return event
 
@@ -224,7 +228,13 @@ class QuackSequence(PulseSequence):
         self.add_pulse_parameter_option(self.RX_READOUT, RXReadout)
 
     def add_blank_event(self, event_name: str, duration: float):
-        event = self.create_event(event_name, duration)
+        """Adds a blank event to the pulse sequence.
+
+        Args:
+            event_name (str): The name of the event
+            duration (float): The duration of the event with a unit suffix (n, u, m)
+        """
+        _ = self.create_event(event_name, duration)
 
     def add_pulse_event(
         self,
@@ -234,24 +244,44 @@ class QuackSequence(PulseSequence):
         phase: float,
         shape: Function = RectFunction(),
     ):
+        """Adds a pulse event to the pulse sequence.
+
+        Args:
+            event_name (str): The name of the event
+            duration (float): The duration of the event with a unit suffix (n, u, m)
+            amplitude (float): The amplitude of the transmit pulse in percent
+            phase (float): The phase of the transmit pulse
+            shape (Function): The shape of the transmit pulse
+        """
         event = self.create_event(event_name, duration)
         self.set_tx_amplitude(event, amplitude)
         self.set_tx_phase(event, phase)
         self.set_tx_shape(event, shape)
 
     def add_readout_event(self, event_name: str, duration: float):
+        """Adds a readout event to the pulse sequence.
+
+        Args:
+            event_name (str): The name of the event
+            duration (float): The duration of the event with a unit suffix (n, u, m)
+        """
         event = self.create_event(event_name, duration)
         self.set_rx(event, True)
 
     # TX Specific functions
 
     def set_tx_amplitude(self, event, amplitude: float) -> None:
-        """Sets the amplitude of the transmitter.
+        """Sets the relative amplitude of the transmit pulse in percent (larger 0 - max 100).
 
         Args:
             event (Event): The event to set the amplitude for
-            amplitude (float): The amplitude of the transmitter
+            amplitude (float): The amplitude of the transmit pulse in percent
         """
+        if amplitude <= 0 or amplitude > 100:
+            raise ValueError(
+                "Amplitude needs to be larger than 0 and smaller or equal to 100"
+            )
+
         event.parameters[self.TX_PULSE].get_option_by_name(
             TXPulse.RELATIVE_AMPLITUDE
         ).value = amplitude
@@ -268,11 +298,11 @@ class QuackSequence(PulseSequence):
         ).value = phase
 
     def set_tx_shape(self, event, shape: Function) -> None:
-        """Sets the shape of the transmitter.
+        """Sets the shape of the transmit pulse.
 
         Args:
             event (Event): The event to set the shape for
-            shape (Any): The shape of the transmitter
+            shape (Function): The shape of the transmit pulse
         """
         event.parameters[self.TX_PULSE].get_option_by_name(
             TXPulse.TX_PULSE_SHAPE

src/quackseq/spectrometer/spectrometer.py

@@ -1,7 +1,7 @@
-from typing import Any
+"""The base class for the spectrometer used in quackseq. This class is just a skeleton and should be inherited by all spectrometer implementations."""
 
 
-class Spectrometer():
+class Spectrometer:
     """Base class for spectrometers.
 
     This class should be inherited by all spectrometers.
@@ -15,11 +15,10 @@ class Spectrometer():
         """
         raise NotImplementedError
 
-    def set_frequency(self, value : float):
+    def set_frequency(self, value: float):
         """Sets the frequency of the spectrometer."""
         raise NotImplementedError
 
-    def set_averages(self, value : int):
+    def set_averages(self, value: int):
         """Sets the number of averages."""
         raise NotImplementedError
-    

src/quackseq/spectrometer/spectrometer_controller.py

@@ -7,7 +7,8 @@ from quackseq.pulsesequence import QuackSequence
 
 logger = logging.getLogger(__name__)
 
-class SpectrometerController():
+
+class SpectrometerController:
     """The base class for all spectrometer controllers."""
 
     def run_sequence(self, sequence):
@@ -17,14 +18,14 @@ class SpectrometerController():
         """
         raise NotImplementedError
 
-    def set_frequency(self, value : float):
+    def set_frequency(self, value: float):
         """Sets the frequency of the spectrometer."""
         raise NotImplementedError
 
-    def set_averages(self, value : int):
+    def set_averages(self, value: int):
         """Sets the number of averages."""
         raise NotImplementedError
-    
+
     def translate_rx_event(self, sequence: QuackSequence) -> tuple:
         """This method translates the RX event of the pulse sequence to the limr object.
 
@@ -62,7 +63,7 @@ class SpectrometerController():
 
         else:
             return None, None
-        
+
     def calculate_simulation_length(self, sequence: QuackSequence) -> float:
         """This method calculates the simulation length based on the settings and the pulse sequence.
 

src/quackseq/spectrometer/spectrometer_model.py

@@ -2,29 +2,54 @@
 
 import logging
 from collections import OrderedDict
-from typing import Any
 from quackseq.spectrometer.spectrometer_settings import Setting
 
 logger = logging.getLogger(__name__)
 
+
 class QuackSettings(OrderedDict):
+    """The Quack settings class makes the different settings of the spectrometer accessible as attributes. Additionally, it provides methods to get the settings by category."""
+
     def __getattr__(self, key):
+        """Gets the value of a setting by its key.
+
+        Args:
+            key (str) : The key of the setting
+
+        Returns:
+            The value of the setting
+        """
         return self[key].value
 
     def __setattr__(self, key, value):
+        """Sets the value of a setting by its key.
+
+        Args:
+            key (str) : The key of the setting
+            value : The value to set
+        """
         self[key].value = value
 
     @property
     def categories(self):
+        """The categories of the settings."""
         categories = []
 
         for setting in self.values():
-            if not setting.category in categories:
+            if setting.category not in categories:
                 categories.append(setting.category)
 
         return categories
-        
+
     def get_settings_by_category(self, category):
+        """Gets the settings by category.
+
+        Args:
+            category (str) : The category of the settings
+
+        Returns:
+            dict : The settings with the specified category
+        """
         settings = dict()
 
         for key, setting in self.items():
@@ -33,7 +58,8 @@ class QuackSettings(OrderedDict):
 
         return settings
 
-class SpectrometerModel():
+
+class SpectrometerModel:
     """The base class for all spectrometer models.
 
     It contains the settings and pulse parameters of the spectrometer.
@@ -48,8 +74,7 @@ class SpectrometerModel():
         """Initializes the spectrometer model."""
         self.settings = QuackSettings()
 
-
+    def add_setting(self, name: str, setting: Setting) -> None:
-    def add_setting(self,name: str, setting: Setting) -> None:
         """Adds a setting to the spectrometer.
 
         Args:
@@ -72,10 +97,10 @@ class SpectrometerModel():
         """
         if name in self.settings:
             return self.settings[name]
-        
+
         raise ValueError(f"No setting with name {name} found")
-    
+
-    def get_setting_by_display_name(self, display_name : str) -> Setting:
+    def get_setting_by_display_name(self, display_name: str) -> Setting:
         """Gets a setting by its display name.
 
         Args:
@@ -92,7 +117,7 @@ class SpectrometerModel():
                 return setting
 
         raise ValueError(f"No setting with display name {display_name} found")
-    
+
     @property
     def target_frequency(self):
         """The target frequency of the spectrometer in Hz. This is the frequency where the magnetic resonance experiment is performed."""

src/quackseq/spectrometer/spectrometer_settings.py

@@ -5,7 +5,7 @@ import logging
 logger = logging.getLogger(__name__)
 
 
-class Setting():
+class Setting:
     """A setting for the spectrometer is a value that is the same for all events in a pulse sequence.
 
     E.g. the Transmit gain or the number of points in a spectrum.
@@ -18,23 +18,27 @@ class Setting():
 
     Attributes:
         name (str) : The name of the setting
+        category (str) : The category of the setting
         description (str) : A description of the setting
         value : The value of the setting
         category (str) : The category of the setting
     """
 
-    def __init__(self, name: str, category : str, description: str = None, default=None) -> None:
+    def __init__(
+        self, name: str, category: str, description: str = None, default=None
+    ) -> None:
         """Create a new setting.
 
         Args:
             name (str): The name of the setting.
+            category (str): The category of the setting.
             description (str): A description of the setting.
             default: The default value of the setting.
         """
         self.name = name
         self.category = category
         self.description = description
-        self.default =  default
+        self.default = default
         if default is not None:
             self.value = default
             # Update the description with the default value
@@ -48,7 +52,13 @@ class NumericalSetting(Setting):
     """
 
     def __init__(
-        self, name: str, category: str, description: str, default, min_value=None, max_value=None
+        self,
+        name: str,
+        category: str,
+        description: str,
+        default,
+        min_value=None,
+        max_value=None,
     ) -> None:
         """Create a new numerical setting."""
         super().__init__(
@@ -104,7 +114,7 @@ class FloatSetting(NumericalSetting):
         description: str,
         min_value: float = None,
         max_value: float = None,
-        slider = False
+        slider=False,
     ) -> None:
         """Create a new float setting."""
         super().__init__(name, category, description, default, min_value, max_value)
@@ -117,7 +127,7 @@ class FloatSetting(NumericalSetting):
 
     @value.setter
     def value(self, value):
-        logger.debug(f"Setting {self.name} to {value}")      
+        logger.debug(f"Setting {self.name} to {value}")
         self._value = float(value)
 
 
@@ -141,13 +151,12 @@ class IntSetting(NumericalSetting):
         description: str,
         min_value=None,
         max_value=None,
-        slider = False
+        slider=False,
     ) -> None:
         """Create a new int setting."""
         super().__init__(name, category, description, default, min_value, max_value)
         self.slider = slider
 
-
     @property
     def value(self):
         """The value of the setting. In this case, an int."""
@@ -157,7 +166,7 @@ class IntSetting(NumericalSetting):
     def value(self, value):
         logger.debug(f"Setting {self.name} to {value}")
         value = int(float(value))
-        
+
         self._value = value
 
 
@@ -171,11 +180,12 @@ class BooleanSetting(Setting):
         description (str) : A description of the setting
     """
 
-    def __init__(self, name: str, category : str, default: bool, description: str) -> None:
+    def __init__(
+        self, name: str, category: str, default: bool, description: str
+    ) -> None:
         """Create a new boolean setting."""
         super().__init__(name, category, description, default)
 
-
     @property
     def value(self):
         """The value of the setting. In this case, a bool."""
@@ -189,7 +199,6 @@ class BooleanSetting(Setting):
             raise ValueError("Value must be a bool")
 
 
-
 class SelectionSetting(Setting):
     """A setting that is a selection from a list of options.
 
@@ -202,7 +211,7 @@ class SelectionSetting(Setting):
     """
 
     def __init__(
-        self, name: str, category : str, options: list, default: str, description: str
+        self, name: str, category: str, options: list, default: str, description: str
     ) -> None:
         """Create a new selection setting."""
         super().__init__(name, category, description, default)
@@ -212,7 +221,6 @@ class SelectionSetting(Setting):
 
         self.options = options
 
-
     @property
     def value(self):
         """The value of the setting. In this case, a string."""
@@ -241,7 +249,9 @@ class StringSetting(Setting):
         description (str) : A description of the setting
     """
 
-    def __init__(self, name: str, category :str, default: str, description: str) -> None:
+    def __init__(
+        self, name: str, category: str, default: str, description: str
+    ) -> None:
         """Create a new string setting."""
         super().__init__(name, category, description, default)