[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

docs/conf.py

@@ -106,6 +106,7 @@
 
 
 def setup(app):
+
     def skip(app, what, name, obj, skip, options):
         members = [
             '__init__',

episimmer/agent.py

@@ -9,6 +9,7 @@ class Agent():
         state: The state of the agent.
         info_dict: Information of each agent taken from the agents file.
     """
+
     def __init__(self, state: Union[str, None], info_dict: Dict[str, str]):
         self.state: Union[str, None] = state
         self.next_state: Union[str, None] = None

episimmer/location.py

@@ -8,6 +8,7 @@ class Location():
     Args:
         info_dict: Information of each location taken from the locations file .
     """
+
     def __init__(self, info_dict: Dict[str, str]):
         self.info: Dict[str, str] = info_dict
         self.index: str = info_dict['Location Index']

episimmer/model.py

@@ -20,6 +20,7 @@ class BaseModel():
     Args:
         name: Name of Disease Model
     """
+
     def __init__(self, name: str):
         self.name: str = name
 
@@ -380,6 +381,7 @@ def __init__(self):
         infected_states: The states that are infectious
         state_proportion: Starting proportions of each state
     """
+
     def __init__(self, individual_state_types: List[str],
                  infected_states: List[str],
                  state_proportion: Dict[str, Union[float, int]]):
@@ -750,6 +752,7 @@ def __init__(self):
                 self.set_event_contribution_fn(event_contribute_fn)
                 self.set_event_receive_fn(event_receive_fn)
     """
+
     def __init__(self):
         super().__init__('Scheduled Model')
         self.individual_state_types: List[str] = []

episimmer/policy/base.py

@@ -12,6 +12,7 @@ class Policy():
     Args:
         policy_type: Type of Agent Policy
     """
+
     def __init__(self, policy_type: str):
         self.policy_type: str = policy_type
 
@@ -67,6 +68,7 @@ class AgentPolicy(Policy):
     Args:
         policy_type: Type of Agent Policy
     """
+
     def __init__(self, policy_type: str):
         super().__init__(policy_type)
 
@@ -124,5 +126,6 @@ class EventPolicy(Policy):
     Args:
         policy_type: Type of Event Policy
     """
+
     def __init__(self, policy_type: str):
         super().__init__(policy_type)

episimmer/policy/contact_tracing_policy.py

@@ -12,6 +12,7 @@ class ContactList():
     """
     Class built to implement an ordered and unique list of contacts
     """
+
     def __init__(self):
         self.contacts: List[str] = []
 
@@ -94,6 +95,7 @@ def generate_policy():
         attribute : Parameter (attribute) type of agents
         value_list: List of attribute values of agents
     """
+
     def __init__(self,
                  num_of_days: int,
                  attribute: Union[str, None] = None,

episimmer/policy/lockdown_policy.py

@@ -18,6 +18,7 @@ class AgentLockdownPolicy(AgentPolicy):
         do_lockdown_fn: User-defined function to specify which time step(s) to enforce lockdown in
         p: Probability of agent to contribute and receive infection from any source of infection under lockdown
     """
+
     def __init__(self, do_lockdown_fn: Callable, p: float):
         super().__init__('Restrict')
         self.do_lockdown_fn: Callable = do_lockdown_fn
@@ -64,6 +65,7 @@ def lockdown_fn(time_step):
         do_lockdown_fn: User-defined function to specify which time step(s) to enforce lockdown in
         p: Probability of agent to contribute and receive infection from any source of infection under lockdown
     """
+
     def __init__(self, do_lockdown_fn: Callable, p: float = 0.0):
         super().__init__(do_lockdown_fn, p)
 
@@ -119,6 +121,7 @@ def lockdown_fn(time_step):
         do_lockdown_fn: User-defined function to specify which time step(s) to enforce lockdown in
         p: Probability of agent to contribute and receive infection from any source of infection under lockdown
     """
+
     def __init__(self,
                  attribute: str,
                  value_list: List[str],
@@ -209,6 +212,7 @@ def generate_policy():
         contact_tracing: Boolean specifying whether lockdown for contacts of positively tested agents is enabled or not
         p: Probability of agent to contribute and receive infection from any source of infection under lockdown
     """
+
     def __init__(self,
                  do_lockdown_fn: Callable,
                  lockdown_period: int,
@@ -290,6 +294,7 @@ class EventLockdownPolicy(EventPolicy):
         do_lockdown_fn: User-defined function to specify which time step(s) to enforce lockdown in
         p: Probability of an event occurring during lockdown
     """
+
     def __init__(self, do_lockdown_fn: Callable, p: float):
         super().__init__('Restrict')
         self.do_lockdown_fn: Callable = do_lockdown_fn
@@ -334,6 +339,7 @@ def generate_policy():
         do_lockdown_fn: User-defined function to specify which time step(s) to enforce lockdown in
         p: Probability of an event occurring during lockdown
     """
+
     def __init__(self,
                  attribute: str,
                  value_list: List[str],

episimmer/policy/testing_policy.py

@@ -26,6 +26,7 @@ class TestResult():
         time_step_done: Time step machine completed test
         valid_period: Number of time steps the test is considered to be valid
     """
+
     def __init__(self, result: str, agent: Agent, machine_name: str,
                  time_step: int, machine_start_step: int, time_step_done: int,
                  valid_period: int):
@@ -69,6 +70,7 @@ class TestTube():
     """
     Class for a Testtube.
     """
+
     def __init__(self):
         self.testtube_agent_dict: Dict[Agent, Dict[str, Union[str, int]]] = {}
         self.testtube_result: Union[str, None] = None
@@ -154,6 +156,7 @@ class Machine():
         capacity: Capacity of the machine for tests
         valid_period: Number of time steps the test is considered to be valid
     """
+
     def __init__(self, machine_name: str, cost: int,
                  false_positive_rate: float, false_negative_rate: float,
                  turnaround_time: int, capacity: int, valid_period: int):
@@ -423,6 +426,7 @@ def generate_policy():
     Args:
         agents_per_step_fn: User-defined function to specify the number of agents to test per time step
     """
+
     def __init__(self, agents_per_step_fn: Callable):
         super().__init__('Testing')
         self.register_agent_testtube_func: Union[Callable, None] = None

episimmer/policy/vaccination_policy.py

@@ -23,6 +23,7 @@ class VaccineResult():
         decay_days: Number of days of protection offered by the vaccine
         current_dose: The dose of the vaccine administered to the agent
     """
+
     def __init__(self, vaccine_name: str, agent: Agent, result: str,
                  time_step: int, efficacy: float, decay_days: int,
                  current_dose: int):
@@ -57,6 +58,7 @@ class VaccineType():
         interval: List specifying minimum days to pass before the administration of the next dose, for each dose of a
                   multi-dose vaccine
     """
+
     def __init__(self,
                  name: str,
                  cost: int,
@@ -154,6 +156,7 @@ def generate_policy():
     Args:
         agents_per_step_fn: User-defined function to specify the number of agents to vaccinate per time step
     """
+
     def __init__(self, agents_per_step_fn: Callable):
         super().__init__('Vaccination')
 
@@ -437,10 +440,10 @@ def full_multi_dose_vaccination(self, attribute: Union[str, None],
                       and lh.vaccine_name in self.available_vaccines
                       and self.available_vaccines[lh.vaccine_name]['type']
                       == 'Multi'):
-                    if (lh.current_dose <
-                            self.available_vaccines[lh.vaccine_name]['dose']
-                            and time_step - lh.time_stamp >=
-                            self.available_vaccines[lh.vaccine_name]
+                    if (lh.current_dose
+                            < self.available_vaccines[lh.vaccine_name]['dose']
+                            and time_step - lh.time_stamp
+                            >= self.available_vaccines[lh.vaccine_name]
                         ['interval'][lh.current_dose - 1]):
                         current_vaccine = None
                         for vaccine in self.vaccines:

episimmer/read_file.py

@@ -19,6 +19,7 @@ class ReadConfiguration():
     Args:
         filename: Name of the directory containing simulation files
     """
+
     def __init__(self, filename: str):
 
         self.filename: str = filename
@@ -246,6 +247,7 @@ class ReadVDConfiguration():
     Args:
         filename: Name of the directory containing simulation files
     """
+
     def __init__(self, filename: str):
         self.filename: str = filename
         self.example_path: str = osp.dirname(filename)
@@ -320,6 +322,7 @@ class ReadFilesList():
     Args:
         filename: Name of the files list file
     """
+
     def __init__(self, filename: str):
         self.filename: str = filename
         self.file_list: List[str] = []
@@ -345,6 +348,7 @@ class BaseReadFile():
     """
     Base class for reading agents, locations, interactions and events from a file.
     """
+
     def __init__(self):
         pass
 
@@ -374,6 +378,7 @@ class ReadAgents(BaseReadFile):
         config_obj: An object of class :class:`~episimmer.read_file.ReadConfiguration` containing the simulation
                     configurations.
     """
+
     def __init__(self, filename: str, config_obj: ReadConfiguration):
         super().__init__()
         self.filename: str = filename
@@ -457,6 +462,7 @@ class ReadInteractions(BaseReadFile):
                     configurations.
         agents_obj: An object of class :class:`ReadAgents` containing agent information
     """
+
     def __init__(self, filename: str, config_obj: ReadConfiguration,
                  agents_obj: ReadAgents):
         super().__init__()
@@ -556,6 +562,7 @@ class ReadProbabilisticInteractions(BaseReadFile):
                     configurations.
         agents_obj: An object of class :class:`ReadAgents` containing agent information
     """
+
     def __init__(self, filename: str, config_obj: ReadConfiguration,
                  agents_obj: ReadAgents):
         super().__init__()
@@ -664,6 +671,7 @@ class ReadLocations(BaseReadFile):
         config_obj: An object of class :class:`ReadConfiguration` containing the simulation
                     configurations.
     """
+
     def __init__(self, filename: str, config_obj: ReadConfiguration):
         super().__init__()
         self.filename: str = filename
@@ -727,6 +735,7 @@ class ReadEvents(BaseReadFile):
         locations_obj: An object of class :class:`ReadLocations` containing location information
         agents_obj: An object of class :class:`ReadAgents` containing agent information
     """
+
     def __init__(self,
                  filename: str,
                  config_obj: Union[ReadConfiguration, None] = None,
@@ -824,6 +833,7 @@ class ReadOneTimeEvents(ReadEvents):
     Args:
         filename: Name of the file containing one time event information.
     """
+
     def __init__(self, filename: str):
         super().__init__(filename)
         self.event_info_keys: str = ''

episimmer/simulate.py

@@ -26,6 +26,7 @@ class Simulate():
         agents_obj: An object of class :class:`~episimmer.read_file.ReadAgents`
         locations_obj: An object of class :class:`~episimmer.read_file.ReadLocations`
     """
+
     def __init__(self, config_obj: ReadConfiguration, model: BaseModel,
                  policy_list: List[Policy], agents_obj: ReadAgents,
                  locations_obj: ReadLocations):

episimmer/utils/statistics.py

@@ -237,7 +237,9 @@ def save_stats(
     Returns:
         Callable function
     """
+
     def decorator(func: Callable) -> Callable:
+
         @functools.wraps(func)
         def wrapper(ref: 'Simulate', *args, **kwargs) -> None:
             func(ref, *args, **kwargs)
@@ -270,7 +272,9 @@ def write_stats(pickle_file: str, text_file: str) -> Callable:
     Returns:
         Callable function
     """
+
     def decorator(func: Callable) -> Callable:
+
         @functools.wraps(func)
         def wrapper(*args, **kwargs):
             func(*args, **kwargs)

episimmer/utils/visualize.py

@@ -142,8 +142,8 @@ def get_interaction_graph_from_object(obj: 'Simulate') -> nx.Graph:
         if agent.can_contribute_infection > 0:
             for int_agent in agent.contact_list:
                 int_agent_indx = int_agent['Interacting Agent Index']
-                if (agents_obj.agents[int_agent_indx].can_receive_infection >
-                        0):
+                if (agents_obj.agents[int_agent_indx].can_receive_infection
+                        > 0):
                     g.add_edge(agent.index, int_agent_indx, color='black')
 
     # Events
@@ -155,8 +155,8 @@ def get_interaction_graph_from_object(obj: 'Simulate') -> nx.Graph:
                            pos=(-1500 - 500 * j, 500 * i))
                 for agent in event_info['Agents']:
                     if (agents_obj.agents[agent].can_receive_infection > 0 or
-                            agents_obj.agents[agent].can_contribute_infection >
-                            0):
+                            agents_obj.agents[agent].can_contribute_infection
+                            > 0):
                         g.add_edge(event_info['Location Index'] + '_event' +
                                    str(i),
                                    agent,
@@ -172,7 +172,9 @@ def save_env_graph() -> Callable:
     Returns:
         Callable function
     """
+
     def decorator(func: Callable) -> Callable:
+
         @functools.wraps(func)
         def wrapper(ref: 'Simulate', *args, **kwargs) -> None:
             func(ref, *args, **kwargs)
@@ -279,7 +281,9 @@ def store_animated_dynamic_graph() -> Callable:
     Returns:
         Callable function
     """
+
     def decorator(func: Callable) -> Callable:
+
         @functools.wraps(func)
         def wrapper(ref: 'Simulate', *args, **kwargs) -> None:
             if ref.config_obj.worlds - 1 == Time.get_current_world():

episimmer/vulnerability_detection/agent_vd.py

@@ -54,6 +54,7 @@ class SimpleVulnerableAgent(VulnerableAgent):
         world_obj: World object of simulation
         parameter_dict: Dictionary of parameters relevant to the algorithm
     """
+
     def __init__(self, world_obj: World,
                  parameter_dict: Dict[str, Union[List[str], int]]):
         super().__init__(world_obj)
@@ -133,6 +134,7 @@ class EarlyVulnerableAgent(VulnerableAgent):
         world_obj: World object of simulation
         parameter_dict: Dictionary of parameters relevant to the algorithm
     """
+
     def __init__(self, world_obj: World,
                  parameter_dict: Dict[str, Union[List[str], int]]):
         super().__init__(world_obj)
@@ -275,6 +277,7 @@ class SimpleAgentVulnerability(AgentVulnerability):
         world_obj: World object of simulation
         parameter_dict: Dictionary of parameters relevant to the algorithm
     """
+
     def __init__(self, world_obj: World,
                  parameter_dict: Dict[str, Union[List[str], int]]):
         super().__init__(world_obj)
@@ -426,6 +429,7 @@ class ChunkAgentVulnerability(AgentVulnerability):
         world_obj: World object of simulation
         parameter_dict: Dictionary of parameters relevant to the algorithm
     """
+
     def __init__(self, world_obj: World,
                  parameter_dict: Dict[str, Union[List[str], int, List[int]]]):
         super().__init__(world_obj)
@@ -693,6 +697,7 @@ class BanditAlgos(AgentVulnerability):
         world_obj: World object of simulation
         parameter_dict: Dictionary of parameters relevant to the algorithm
     """
+
     def __init__(self, world_obj: World,
                  parameter_dict: Dict[str, Union[List[str], int, str]]):
         super().__init__(world_obj)