diff --git a/.gitignore b/.gitignore index 6ebf11f8..598e06c2 100644 --- a/.gitignore +++ b/.gitignore @@ -39,3 +39,6 @@ simulations/validation simulations/poc/local/ simulations/regression_tests/poc simulations/regression_tests/poc_configs +dist/* +testing/tests/import_cadCAD.nbconvert.ipynb +testing/tests/cadCAD_memory_address.json diff --git a/CHANGELOG.md b/CHANGELOG.md index a86333e4..6b28e7f6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,15 @@ ### February 15, 2023 * **Fixes:** - Package has been cleaned-up for working with Python 3.10 +### 0.4.29.1 + +#### Changes +- Parallel executor uses the context manager handling the Process Pool lifetime + +### 0.4.29 + +- Merged repo with the `cadCAD_tweaked`, which includes performance improvements +- Python 3.10 compatible ### September 28, 2021 #### New Features: * **ver. ≥ `0.4.28`:** @@ -217,16 +226,16 @@ as a 2 dimensional `list` +----+------------+-----------+----+---------------------+-----+---------+----------+ ``` -* **Flattened Configuration List:** The `cadCAD.configs` (System Model Configuration) `list` has been **temporarily** +* **Flattened Configuration list:** The `cadCAD.configs` (System Model Configuration) `list` has been **temporarily** flattened to contain single run `cadCAD.configuration.Configuration` objects to both fault-tolerant simulation and elastic workloads. This functionality will be restored in a subsequent release by a class that returns `cadCAD.configs`'s original representation in ver. `0.3.1`. * The conversion utilities have been provided to restore its original representation of configurations with runs >= 1 * [System Configuration Conversions](documentation/System_Configuration.md) - * Configuration as List of Configuration Objects (as in ver. `0.3.1`) + * Configuration as list of Configuration Objects (as in ver. `0.3.1`) * New: System Configuration as a Pandas DataFrame - * New: System Configuration as List of Dictionaries + * New: System Configuration as list of Dictionaries ###### Examples: * Notes: diff --git a/cadCAD/configuration/__init__.py b/cadCAD/configuration/__init__.py index 3e5d07e4..9c9d0b12 100644 --- a/cadCAD/configuration/__init__.py +++ b/cadCAD/configuration/__init__.py @@ -90,19 +90,12 @@ def append_model( sim_config = t[0] sim_config['subset_id'] = subset_id sim_config['subset_window'] = self.subset_window - N = sim_config['N'] - if N > 1: - for n in range(N): - sim_config['simulation_id'] = self.simulation_id - sim_config['run_id'] = n - sim_config['N'] = 1 - new_sim_configs.append(deepcopy(sim_config)) - del sim_config - else: + N: int = sim_config['N'] + for n in range(0, N): sim_config['simulation_id'] = self.simulation_id - sim_config['run_id'] = 0 - new_sim_configs.append(deepcopy(sim_config)) - + sim_config['run_id'] = n + sim_config['N'] = 1 + new_sim_configs.append((sim_config.copy())) sim_cnt_local += 1 if model_id == None: @@ -128,7 +121,7 @@ def append_model( if run_id >= max_runs: sim_config['N'] = run_id - (max_runs - 1) - self.exp_window = deepcopy(self.exp_window) + self.exp_window = self.exp_window.copy() config = Configuration( exp_creation_ts=self.exp_creation_ts, @@ -192,19 +185,19 @@ def __init__(self, policy_id: Dict[str, int] = {'identity': 0}) -> None: def p_identity(self, var_dict, sub_step, sL, s, **kwargs): return self.beh_id_return_val - def policy_identity(self, k: str) -> Callable: + def policy_identity(self, k: str) -> callable: return self.p_identity def no_state_identity(self, var_dict, sub_step, sL, s, _input, **kwargs): return None - def state_identity(self, k: str) -> Callable: + def state_identity(self, k: str) -> callable: return lambda var_dict, sub_step, sL, s, _input, **kwargs: (k, s[k]) # state_identity = cloudpickle.dumps(state_identity) def apply_identity_funcs(self, - identity: Callable, + identity: callable, df: DataFrame, cols: List[str]) -> DataFrame: """ @@ -239,7 +232,7 @@ def create_matrix_field(self, partial_state_updates, key: str) -> DataFrame: return pd.DataFrame({'empty': []}) def generate_config(self, initial_state, partial_state_updates, exo_proc - ) -> List[Tuple[List[Callable], List[Callable]]]: + ) -> List[tuple[list[callable], List[callable]]]: def no_update_handler(bdf, sdf): if (bdf.empty == False) and (sdf.empty == True): diff --git a/cadCAD/configuration/utils/__init__.py b/cadCAD/configuration/utils/__init__.py index fce7bcb7..7ebac29a 100644 --- a/cadCAD/configuration/utils/__init__.py +++ b/cadCAD/configuration/utils/__init__.py @@ -1,7 +1,6 @@ import pandas as pd # type: ignore from datetime import datetime, timedelta from collections import Counter -from copy import deepcopy from functools import reduce from funcy import curry # type: ignore from cadCAD.types import * @@ -144,7 +143,7 @@ def trigger(end_substep, y, f): def env_trigger(end_substep): def trigger(end_substep, trigger_field, trigger_vals, funct_list): def env_update(state_dict, sweep_dict, target_value): - state_dict_copy = deepcopy(state_dict) + state_dict_copy = state_dict.copy() # Use supstep to simulate current sysMetrics if state_dict_copy['substep'] == end_substep: state_dict_copy['timestep'] = state_dict_copy['timestep'] + 1 @@ -189,6 +188,7 @@ def config_sim(config_dict: ConfigurationDict): return config_dict elif (1 in param_values_length_set): return [{**config_dict, "M": M} + for M in flatten_tabulated_dict(tabulate_dict(params))] else: raise Exception('When sweeping, `M` list lengths should either be 1 and/or equal. ') @@ -259,8 +259,8 @@ def sweep_partial_states(_type, in_config): for partial_state, state_dict in filtered_partial_states.items(): for state, state_funcs in state_dict.items(): for f in state_funcs: - config = deepcopy(in_config) - config.partial_state_update_blocks[partial_state][_type][state] = f + config = in_config.copy() + config.partial_state_updates[partial_state][_type][state] = f configs.append(config) del config else: @@ -275,8 +275,8 @@ def sweep_states(state_type, states, in_config): if len(filtered_states) > 0: for state, state_funcs in filtered_states.items(): for f in state_funcs: - config = deepcopy(in_config) - exploded_states = deepcopy(states) + config = in_config.copy() + exploded_states = states.copy() exploded_states[state] = f if state_type == 'exogenous': config.exogenous_states = exploded_states diff --git a/cadCAD/configuration/utils/depreciationHandler.py b/cadCAD/configuration/utils/depreciationHandler.py index 1c24fbff..43173a01 100644 --- a/cadCAD/configuration/utils/depreciationHandler.py +++ b/cadCAD/configuration/utils/depreciationHandler.py @@ -15,7 +15,7 @@ def sanitize_config(config): def sanitize_partial_state_updates(partial_state_updates): - new_partial_state_updates = deepcopy(partial_state_updates) + new_partial_state_updates = partial_state_updates.copy() def rename_keys(d): if 'behaviors' in d: d['policies'] = d.pop('behaviors') diff --git a/cadCAD/engine/__init__.py b/cadCAD/engine/__init__.py index 59e49d6b..24d977d4 100644 --- a/cadCAD/engine/__init__.py +++ b/cadCAD/engine/__init__.py @@ -1,5 +1,6 @@ from time import time from typing import Callable, Dict, List, Any, Tuple, Union +from tqdm.auto import tqdm from cadCAD.utils import flatten from cadCAD.utils.execution import print_exec_info @@ -9,10 +10,10 @@ from cadCAD.engine.execution import single_proc_exec, parallelize_simulations, local_simulations from cadCAD.types import * -VarDictType = Dict[str, List[Any]] -StatesListsType = List[Dict[str, Any]] -ConfigsType = List[Tuple[List[Callable], List[Callable]]] -EnvProcessesType = Dict[str, Callable] +VarDictType = Dict[str, List[object]] +StatesListsType = List[dict[str, object]] +ConfigsType = List[tuple[list[callable], List[callable]]] +EnvProcessesType = Dict[str, callable] class ExecutionMode: @@ -79,7 +80,7 @@ def __init__(self, self.configs = configs self.empty_return = empty_return - def execute(self) -> Tuple[Any, Any, Dict[str, Any]]: + def execute(self) -> Tuple[object, object, Dict[str, object]]: if self.empty_return is True: return [], [], [] @@ -99,7 +100,9 @@ def execute(self) -> Tuple[Any, Any, Dict[str, Any]]: print_exec_info(self.exec_context, configs_as_objs(self.configs)) t1 = time() - for x in self.configs: + for x in tqdm(self.configs, + total=len(self.configs), + desc="Initializing configurations"): sessions.append( { 'user_id': x.user_id, 'experiment_id': x.experiment_id, 'session_id': x.session_id, @@ -145,7 +148,9 @@ def get_final_results(simulations: List[StateHistory], sessions: List[SessionDict], remote_threshold: int): flat_timesteps, tensor_fields = [], [] - for sim_result, psu, ep in list(zip(simulations, psus, eps)): + for sim_result, psu, ep in tqdm(list(zip(simulations, psus, eps)), + total=len(simulations), + desc='Flattening results'): flat_timesteps.append(flatten(sim_result)) tensor_fields.append(create_tensor_field(psu, ep)) diff --git a/cadCAD/engine/execution.py b/cadCAD/engine/execution.py index febafffe..4a26218f 100644 --- a/cadCAD/engine/execution.py +++ b/cadCAD/engine/execution.py @@ -1,13 +1,13 @@ from typing import Callable, Dict, List, Any, Tuple -from pathos.multiprocessing import ProcessPool as PPool # type: ignore +from pathos.multiprocessing import ProcessPool # type: ignore from collections import Counter from cadCAD.types import * from cadCAD.utils import flatten -VarDictType = Dict[str, List[Any]] -StatesListsType = List[Dict[str, Any]] -ConfigsType = List[Tuple[List[Callable], List[Callable]]] -EnvProcessesType = Dict[str, Callable] +VarDictType = Dict[str, List[object]] +StatesListsType = List[dict[str, object]] +ConfigsType = List[tuple[list[callable], List[callable]]] +EnvProcessesType = Dict[str, callable] def single_proc_exec( @@ -96,13 +96,10 @@ def parallelize_simulations( def process_executor(params): if len_configs_structs > 1: - pp = PPool(processes=len_configs_structs) - results = pp.map( - lambda t: t[0](t[1], t[2], t[3], t[4], t[5], t[6], t[7], t[8], t[9], configured_n, additional_objs), params - ) - pp.close() - pp.join() - pp.clear() + with ProcessPool(processes=len_configs_structs) as pp: + results = pp.map( + lambda t: t[0](t[1], t[2], t[3], t[4], t[5], t[6], t[7], t[8], t[9], configured_n), params + ) else: t = params[0] results = t[0](t[1], t[2], t[3], t[4], t[5], t[6], t[7], t[8], t[9], configured_n) diff --git a/cadCAD/engine/simulation.py b/cadCAD/engine/simulation.py index d97d083e..76d7d909 100644 --- a/cadCAD/engine/simulation.py +++ b/cadCAD/engine/simulation.py @@ -8,15 +8,47 @@ from cadCAD.engine.utils import engine_exception from cadCAD.types import * -id_exception: Callable = curry(engine_exception)(KeyError)(KeyError)(None) - +id_exception: callable = curry(engine_exception)(KeyError)(KeyError)(None) + +Aggregator = Callable[[object, object], object] + + +def policy_scope_tuner(args: tuple, + additional_objs: object, + f: PolicyFunction) -> dict: + """ + Execute cadCAD policy function. + """ + (sweep_dict, sub_step, sL, s) = args + if additional_objs is None: + return f(sweep_dict, sub_step, sL, s) + else: + return f(sweep_dict, sub_step, sL, s, additional_objs) + + +def compose(init_reduction_funct: Aggregator, + funct_list: List[Aggregator], + val_list: dict) -> object: + """ + Reduce the nested policy input dict into a simple one. + """ + result, i = None, 0 + def composition(x): return [reduce( + init_reduction_funct, x.values())] + funct_list + for g in composition(val_list): + if i == 0: + result = g + i = 1 + else: + result = g(result) + return result class Executor: def __init__( self, policy_ops, - policy_update_exception: Callable = id_exception, - state_update_exception: Callable = id_exception + policy_update_exception: callable = id_exception, + state_update_exception: callable = id_exception ) -> None: self.policy_ops = policy_ops @@ -25,62 +57,66 @@ def __init__( def get_policy_input( self, - sweep_dict: Dict[str, List[Any]], + sweep_dict: Dict[str, List[object]], sub_step: int, - sL: List[Dict[str, Any]], - s: Dict[str, Any], - funcs: List[Callable], + sL: List[dict[str, object]], + s: Dict[str, object], + funcs: List[callable], additional_objs - ) -> Dict[str, Any]: + ) -> Dict[str, object]: + """ + Retrieves the Policy Input for usage on State Update Functions + + Arguments: + sweep_dict - System Parameters + sub_step - Execution order in regards to PSUBs + sL - History of the variables state + s - Current variables state + funcs - list of cadCAD Policies to be executed + """ ops = self.policy_ops - def get_col_results(sweep_dict, sub_step, sL, s, funcs): - def policy_scope_tuner(additional_objs, f): - if additional_objs is None: - return f(sweep_dict, sub_step, sL, s) - else: - return f(sweep_dict, sub_step, sL, s, additional_objs) - return list(map(lambda f: policy_scope_tuner(additional_objs, f), funcs)) - - def compose(init_reduction_funct, funct_list, val_list): - result, i = None, 0 - composition = lambda x: [reduce(init_reduction_funct, x)] + funct_list - for g in composition(val_list): - if i == 0: - result = g - i = 1 + args = (sweep_dict, sub_step, sL, s) + def execute_policy(f: PolicyFunction) -> dict: + return policy_scope_tuner(args, additional_objs, f) + + col_results: List[PolicyOutput] = map(execute_policy, funcs) + # Create a nested dict containing all results combination + # new_dict[policy_input][policy_ordinal] = policy_input_value + new_dict: dict = {} + for i, col_result in enumerate(col_results): + for label, value in col_result.items(): + if label not in new_dict.keys(): + new_dict[label] = {} else: - result = g(result) - return result - - col_results = get_col_results(sweep_dict, sub_step, sL, s, funcs) - try: - reducer_arg = list(map(lambda x: list(x.keys()), col_results)) - except: - raise ValueError("There is a Policy Function that has not properly returned a Dictionary") - reducer_function = lambda a, b: a + b - key_set = list(set(reduce(reducer_function, reducer_arg))) - new_dict = {k: [] for k in key_set} - for d in col_results: - for k in d.keys(): - new_dict[k].append(d[k]) + pass + new_dict[label][i] = value + # Aggregator functions ops_head, *ops_tail = ops - return { - k: compose( - init_reduction_funct=ops_head, - funct_list=ops_tail, - val_list=val_list - ) for k, val_list in new_dict.items() - } + + # Function for aggregating a combination of policy inputs + # for the same signal + def f(val_list): + return compose(init_reduction_funct=ops_head, + funct_list=ops_tail, + val_list=val_list) + + # Generate dict to be consumed by SUFs + policy_input = { + label: f(val_list) + for label, val_list + in new_dict.items()} + + return policy_input def apply_env_proc( self, sweep_dict, - env_processes: Dict[str, Callable], - state_dict: Dict[str, Any] - ) -> Dict[str, Any]: + env_processes: Dict[str, callable], + state_dict: Dict[str, object] + ) -> Dict[str, object]: def env_composition(target_field, state_dict, target_value): function_type = type(lambda x: x) @@ -95,9 +131,11 @@ def env_composition(target_field, state_dict, target_value): return target_value - filtered_state_dict = {k: v for k, v in state_dict.items() if k in env_processes.keys()} + filtered_state_dict = { + k: v for k, v in state_dict.items() if k in env_processes.keys()} env_proc_dict = { - target_field: env_composition(target_field, state_dict, target_value) + target_field: env_composition( + target_field, state_dict, target_value) for target_field, target_value in filtered_state_dict.items() } @@ -111,7 +149,7 @@ def partial_state_update( self, sweep_dict: Parameters, sub_step: Substep, - sL: list[State], + sL: List[State], sH: StateHistory, state_funcs: List[StateUpdateFunction], policy_funcs: List[PolicyFunction], @@ -119,7 +157,7 @@ def partial_state_update( time_step: int, run: int, additional_objs - ) -> List[Dict[str, Any]]: + ) -> List[dict[str, object]]: if type(additional_objs) == dict: if additional_objs.get('deepcopy_off', False) == True: @@ -172,29 +210,29 @@ def transfer_missing_fields(source, destination): # mech_pipeline - state_update_block def state_update_pipeline( self, - sweep_dict: Dict[str, List[Any]], + sweep_dict: Dict[str, List[object]], simulation_list, - configs: List[Tuple[List[Callable], List[Callable]]], - env_processes: Dict[str, Callable], + configs: List[tuple[list[callable], List[callable]]], + env_processes: Dict[str, callable], time_step: int, run: int, additional_objs - ) -> List[Dict[str, Any]]: + ) -> List[dict[str, object]]: sub_step = 0 - states_list_copy: List[Dict[str, Any]] = tuple(simulation_list[-1]) - genesis_states: Dict[str, Any] = states_list_copy[-1].copy() -# genesis_states: Dict[str, Any] = states_list_copy[-1] + states_list_copy: List[dict[str, object]] = tuple(simulation_list[-1]) + genesis_states: Dict[str, object] = states_list_copy[-1].copy() +# genesis_states: Dict[str, object] = states_list_copy[-1] if len(states_list_copy) == 1: genesis_states['substep'] = sub_step del states_list_copy - states_list: List[Dict[str, Any]] = [genesis_states] + states_list: List[dict[str, object]] = [genesis_states] sub_step += 1 for [s_conf, p_conf] in configs: - states_list: List[Dict[str, Any]] = self.partial_state_update( + states_list: List[dict[str, object]] = self.partial_state_update( sweep_dict, sub_step, states_list, simulation_list, s_conf, p_conf, env_processes, time_step, run, additional_objs ) @@ -207,19 +245,19 @@ def state_update_pipeline( # state_update_pipeline def run_pipeline( self, - sweep_dict: Dict[str, List[Any]], - states_list: List[Dict[str, Any]], - configs: List[Tuple[List[Callable], List[Callable]]], - env_processes: Dict[str, Callable], + sweep_dict: Dict[str, List[object]], + states_list: List[dict[str, object]], + configs: List[tuple[list[callable], List[callable]]], + env_processes: Dict[str, callable], time_seq: range, run: int, additional_objs - ) -> List[List[Dict[str, Any]]]: + ) -> List[list[dict[str, object]]]: time_seq: List[int] = [x + 1 for x in time_seq] - simulation_list: List[List[Dict[str, Any]]] = [states_list] + simulation_list: List[list[dict[str, object]]] = [states_list] for time_step in time_seq: - pipe_run: List[Dict[str, Any]] = self.state_update_pipeline( + pipe_run: List[dict[str, object]] = self.state_update_pipeline( sweep_dict, simulation_list, configs, env_processes, time_step, run, additional_objs ) _, *pipe_run = pipe_run @@ -245,19 +283,20 @@ def simulation( run += 1 subset_window.appendleft(subset_id) - def execute_run(sweep_dict, states_list, configs, env_processes, time_seq, _run) -> List[Dict[str, Any]]: + def execute_run(sweep_dict, states_list, configs, env_processes, time_seq, _run) -> List[dict[str, object]]: def generate_init_sys_metrics(genesis_states_list, sim_id, _subset_id, _run, _subset_window): for D in genesis_states_list: - d = deepcopy(D) + d = D.copy() d['simulation'], d['subset'], d['run'], d['substep'], d['timestep'] = \ sim_id, _subset_id, _run, 0, 0 yield d - states_list_copy: List[Dict[str, Any]] = list( - generate_init_sys_metrics(tuple(states_list), simulation_id, subset_id, run, subset_window) + states_list_copy: List[dict[str, object]] = list( + generate_init_sys_metrics( + tuple(states_list), simulation_id, subset_id, run, subset_window) ) - first_timestep_per_run: List[Dict[str, Any]] = self.run_pipeline( + first_timestep_per_run: List[dict[str, object]] = self.run_pipeline( sweep_dict, states_list_copy, configs, env_processes, time_seq, run, additional_objs ) del states_list_copy @@ -265,7 +304,8 @@ def generate_init_sys_metrics(genesis_states_list, sim_id, _subset_id, _run, _su return first_timestep_per_run pipe_run = flatten( - [execute_run(sweep_dict, states_list, configs, env_processes, time_seq, run)] + [execute_run(sweep_dict, states_list, configs, + env_processes, time_seq, run)] ) return pipe_run diff --git a/cadCAD/types.py b/cadCAD/types.py index d2658e48..d5b9302f 100644 --- a/cadCAD/types.py +++ b/cadCAD/types.py @@ -3,7 +3,7 @@ State = Dict[str, object] Parameters = Dict[str, object] -SweepableParameters = Dict[str, list[object]] +SweepableParameters = Dict[str, List[object]] Substep = int StateHistory = List[List[State]] PolicyOutput = Dict[str, object] @@ -26,7 +26,7 @@ class ConfigurationDict(TypedDict): TargetValue = object EnvProcess: Callable[[State, SweepableParameters, TargetValue], TargetValue] -EnvProcesses = dict[str, Callable] +EnvProcesses = Dict[str, Callable] TimeSeq = Iterator SimulationID = int Run = int diff --git a/cadCAD/utils/__init__.py b/cadCAD/utils/__init__.py index cb7977a0..7b944a35 100644 --- a/cadCAD/utils/__init__.py +++ b/cadCAD/utils/__init__.py @@ -1,5 +1,4 @@ from functools import reduce -from typing import Dict, List from collections import defaultdict from itertools import product import warnings @@ -16,15 +15,22 @@ class SilentDF(DataFrame): def __repr__(self): return str(hex(id(DataFrame))) - #"pandas.core.frame.DataFrame" -def append_dict(dict, new_dict): +def append_dict(dict: dict, new_dict: dict) -> dict: + """ + >>> append_dict({1: 2, 3: 4}, {3: 5}) + {1: 2, 3: 5} + """ dict.update(new_dict) return dict -def arrange_cols(df, reverse=False): +def arrange_cols(df: DataFrame, reverse=False) -> DataFrame: + """ + Reorders `df` columns so that the variable order is `session_metrics` + followed by `sys_metrics` and `results_cols` + """ session_metrics = ['session_id', 'user_id', 'simulation_id', 'run_id'] sys_metrics = ['run', 'timestep', 'substep'] result_cols = list(set(df.columns) - set(session_metrics) - set(sys_metrics)) @@ -41,35 +47,45 @@ def __call__(self): return self.i -def compose(*functions): +def compose(*functions: Tuple[callable]) -> object: return reduce(lambda f, g: lambda x: f(g(x)), functions, lambda x: x) -def pipe(x): +def pipe(x: object) -> object: return x -def print_pipe(x): +def print_pipe(x: object) -> object: print(x) return x -def flattenDict(l): - def tupalize(k, vs): - l = [] - if isinstance(vs, list): - for v in vs: - l.append((k, v)) - else: - l.append((k, vs)) - return l - +def tupalize(k: object, vs: Union[list, dict]): + """ + >>> tupalize(1, 1) + [(1, 1)] + >>> tupalize(1, [2, 3]) + [(1, 2), (1, 3)] + """ + l = [] + if isinstance(vs, list): + for v in vs: + l.append((k, v)) + else: + l.append((k, vs)) + return l + +def flattenDict(l: dict) -> list: + """ + >>> flattenDict({1: [1, 2, 3], 4: 5}) + [{1: 1, 4: 5}, {1: 2, 4: 5}, {1: 3, 4: 5}] + """ flat_list = [tupalize(k, vs) for k, vs in l.items()] flat_dict = [dict(items) for items in product(*flat_list)] return flat_dict -def flatten(l): +def flatten(l: Union[list, dict]): if isinstance(l, list): return functools.reduce(operator.iconcat, l, []) elif isinstance(l, dict): @@ -100,9 +116,9 @@ def tabulate_dict(d: Dict[str, List[int]]) -> Dict[str, List[int]]: return _d -def flatten_tabulated_dict(d: Dict[str, List[int]]) -> List[Dict[str, int]]: +def flatten_tabulated_dict(d: Dict[str, List[int]]) -> List[dict[str, int]]: max_len = get_max_dict_val_len(d) - dl: list[dict] = [{} for i in range(max_len)] + dl: List[dict] = [{} for i in range(max_len)] for k, vl in d.items(): for v, i in zip(vl, list(range(len(vl)))): diff --git a/dist/cadCAD-0.4.28-py3-none-any.whl b/dist/cadCAD-0.4.28-py3-none-any.whl deleted file mode 100644 index db314a31..00000000 Binary files a/dist/cadCAD-0.4.28-py3-none-any.whl and /dev/null differ diff --git a/dist/cadCAD-0.4.28.tar.gz b/dist/cadCAD-0.4.28.tar.gz deleted file mode 100644 index 84524405..00000000 Binary files a/dist/cadCAD-0.4.28.tar.gz and /dev/null differ diff --git a/documentation/Historically_State_Access.md b/documentation/Historically_State_Access.md index ec139775..3bb4033b 100644 --- a/documentation/Historically_State_Access.md +++ b/documentation/Historically_State_Access.md @@ -5,11 +5,11 @@ The current state (values of state variables) is accessed through the `s` list. variable values, they may be accessed through the state history list, `sH`. Accessing the state history should be implemented without creating unintended feedback loops on the current state. -The 3rd parameter of state and policy update functions (labeled as `sH` of type `List[List[dict]]`) provides access to +The 3rd parameter of state and policy update functions (labeled as `sH` of type `list[list[dict]]`) provides access to past Partial State Update Block (PSUB) given a negative offset number. `access_block` is used to access past PSUBs -(`List[dict]`) from `sH`. For example, an offset of `-2` denotes the second to last PSUB. +(`list[dict]`) from `sH`. For example, an offset of `-2` denotes the second to last PSUB. -#### Exclusion List +#### Exclusion list Create a list of states to exclude from the reported PSU. ```python exclusion_list = [ diff --git a/documentation/README.md b/documentation/README.md index 1c8ca8c4..439ef66c 100644 --- a/documentation/README.md +++ b/documentation/README.md @@ -31,7 +31,7 @@ exp.append_model( Parameters: `append_model` * **model_id** : str - OPTIONAL: System Model label * **initial_state** : _dict_ - [State Variables](#State-Variables) and their initial values -* **partial_state_update_blocks** : List[dict[dict]] - List of [Partial State Update Blocks](#Partial-State-Update-Blocks) +* **partial_state_update_blocks** : List[dict[dict]] - list of [Partial State Update Blocks](#Partial-State-Update-Blocks) * **policy_ops** : List[functions] - See [Policy Aggregation](Policy_Aggregation.md) * **sim_configs** - See [System Model Parameter Sweep](System_Model_Parameter_Sweep.md) * **user_id** : str - OPTIONAL: Configuration User ID @@ -203,7 +203,7 @@ impact the State Update Functions and Policy Functions in that PSUB - only those ![](https://i.imgur.com/9rlX9TG.png) -Partial State Update Blocks are passed to `append_model` as a List of Python `dicts` where the `dict_keys` are named +Partial State Update Blocks are passed to `append_model` as a list of Python `dicts` where the `dict_keys` are named `"policies"` and `"variables"` and the values are also Python `dicts` where the keys are the names of the policy and state update functions and the values are the functions. diff --git a/documentation/System_Configuration.md b/documentation/System_Configuration.md index b495ce4a..73dc36a4 100644 --- a/documentation/System_Configuration.md +++ b/documentation/System_Configuration.md @@ -10,9 +10,9 @@ subsequent release by a class that returns the original representation in ver. ` * The conversion utilities have been provided to restore its original representation of configurations with runs >= 1 * System Configuration Conversions: - * Configuration as List of Configuration Objects (as in ver. `0.3.1`) + * Configuration as list of Configuration Objects (as in ver. `0.3.1`) * New: System Configuration as a Pandas DataFrame - * New: System Configuration as List of Dictionaries + * New: System Configuration as list of Dictionaries ## Conversions ##### Note: The following applies as a result of simulation execution @@ -22,7 +22,7 @@ runs >= 1 from cadCAD.configuration.utils import configs_as_objs, configs_as_dataframe, configs_as_dicts ``` -#### System Configurations as List of Configuration Objects +#### System Configurations as list of Configuration Objects Example: * `configs` is temporarily returned in a flattened format and reformatted into its intended format. * `Configuration` objects at `0x10790e470` and `0x1143dd630` are reconstituted into objects at `0x10790e7b8` @@ -74,7 +74,7 @@ configs_df = configs_as_dataframe(configs) configs_df ``` -#### System Configurations as List of Dictionaries +#### System Configurations as list of Dictionaries ```python configs_dicts: list = configs_as_dicts(configs) pprint(configs_dicts[0]['sim_config']) diff --git a/documentation/examples/cadCAD_tools_example.ipynb b/documentation/examples/cadCAD_tools_example.ipynb index 5316dfc6..893c3fba 100644 --- a/documentation/examples/cadCAD_tools_example.ipynb +++ b/documentation/examples/cadCAD_tools_example.ipynb @@ -9,7 +9,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 1, "metadata": {}, "outputs": [ { @@ -38,7 +38,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -117,8 +117,8 @@ " 'prey_deaths': p_prey_deaths,\n", " },\n", " 'variables': {\n", - " 'predator_population': s_prey_population,\n", - " 'prey_population': s_predator_population\n", + " 'prey_population': s_prey_population,\n", + " 'predator_population': s_predator_population\n", " }\n", " },\n", " {\n", @@ -135,7 +135,17 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "import sys\n", + "sys.path.append(\"../..\")" + ] + }, + { + "cell_type": "code", + "execution_count": 4, "metadata": {}, "outputs": [ { @@ -154,10 +164,44 @@ "Execution Mode: local_proc\n", "Simulation Dimensions:\n", "Entire Simulation: (Models, Unique Timesteps, Params, Total Runs, Sub-States) = (1, 100, 5, 30, 2)\n", - " Simulation 0: (Timesteps, Params, Runs, Sub-States) = (100, 5, 30, 2)\n", + " Simulation 0: (Timesteps, Params, Runs, Sub-States) = (100, 5, 30, 2)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Initializing configurations: 100%|██████████| 30/30 [00:00<00:00, 669.03it/s]" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ "Execution Method: parallelize_simulations\n", - "Execution Mode: parallelized\n", - "Total execution time: 7.03s\n" + "Execution Mode: parallelized\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n", + "Flattening results: 100%|██████████| 30/30 [00:00<00:00, 324.56it/s]" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Total execution time: 0.86s\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n" ] } ], @@ -175,7 +219,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 5, "metadata": {}, "outputs": [ { @@ -201,1214 +245,1214 @@ "type": "scattergl", "x": [ 100, - 99.48169166436244, - 99.48169166436244, - 98.69341338983048, - 98.69341338983048, - 97.98718084927222, - 97.98718084927222, - 98.58395102883834, - 98.58395102883834, - 98.40369622245535, - 98.40369622245535, - 97.77553464781573, - 97.77553464781573, - 97.56411646679972, - 97.56411646679972, - 98.1122974546651, - 98.1122974546651, - 98.14244748338534, - 98.14244748338534, - 98.47898168561089, - 98.47898168561089, - 97.7270427545823, - 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{ "scrolled": true }, @@ -13343,10 +13387,44 @@ "Execution Mode: local_proc\n", "Simulation Dimensions:\n", "Entire Simulation: (Models, Unique Timesteps, Params, Total Runs, Sub-States) = (1, 20, 5, 30, 3)\n", - " Simulation 0: (Timesteps, Params, Runs, Sub-States) = (20, 5, 30, 3)\n", + " Simulation 0: (Timesteps, Params, Runs, Sub-States) = (20, 5, 30, 3)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "Initializing configurations: 100%|██████████| 30/30 [00:00<00:00, 662.65it/s]" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ "Execution Method: parallelize_simulations\n", - "Execution Mode: parallelized\n", - "Total execution time: 7.56s\n" + "Execution Mode: parallelized\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n", + "Flattening results: 100%|██████████| 30/30 [00:00<00:00, 666.25it/s]" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Total execution time: 0.48s\n" 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0.00006914138793945312, + 0.00006890296936035156, + 0.00006914138793945312 ], "y0": " ", "yaxis": "y" @@ -16011,34 +16089,43 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - " 0%| | 0/200 [00:00 3\u001b[0m visualize_substep_impact(df, relative\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n", - "File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/cadCAD_tools/profiling/visualizations.py:54\u001b[0m, in \u001b[0;36mvisualize_substep_impact\u001b[0;34m(df, relative, **kwargs)\u001b[0m\n\u001b[1;32m 52\u001b[0m g_df\u001b[38;5;241m.\u001b[39mloc[substep_row, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mpsub_time\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m dt\n\u001b[1;32m 53\u001b[0m g_df \u001b[38;5;241m=\u001b[39m g_df\u001b[38;5;241m.\u001b[39mset_index(indexes)\n\u001b[0;32m---> 54\u001b[0m new_df\u001b[38;5;241m.\u001b[39mloc[g_df\u001b[38;5;241m.\u001b[39mindex, \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mpsub_time\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m g_df\u001b[38;5;241m.\u001b[39mpsub_time\n\u001b[1;32m 56\u001b[0m fig_df \u001b[38;5;241m=\u001b[39m new_df\u001b[38;5;241m.\u001b[39mreset_index()\u001b[38;5;241m.\u001b[39mdropna(subset\u001b[38;5;241m=\u001b[39m[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mpsub_time\u001b[39m\u001b[38;5;124m'\u001b[39m])\n\u001b[1;32m 59\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124msubstep_label\u001b[39m\u001b[38;5;124m'\u001b[39m \u001b[38;5;129;01min\u001b[39;00m fig_df\u001b[38;5;241m.\u001b[39mcolumns:\n", - "File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/pandas/core/indexing.py:885\u001b[0m, in \u001b[0;36m_LocationIndexer.__setitem__\u001b[0;34m(self, key, value)\u001b[0m\n\u001b[1;32m 882\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_has_valid_setitem_indexer(key)\n\u001b[1;32m 884\u001b[0m iloc \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mname \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124miloc\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mobj\u001b[38;5;241m.\u001b[39miloc\n\u001b[0;32m--> 885\u001b[0m iloc\u001b[38;5;241m.\u001b[39m_setitem_with_indexer(indexer, value, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mname)\n", - "File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/pandas/core/indexing.py:1893\u001b[0m, in \u001b[0;36m_iLocIndexer._setitem_with_indexer\u001b[0;34m(self, indexer, value, name)\u001b[0m\n\u001b[1;32m 1890\u001b[0m \u001b[38;5;66;03m# align and set the values\u001b[39;00m\n\u001b[1;32m 1891\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m take_split_path:\n\u001b[1;32m 1892\u001b[0m \u001b[38;5;66;03m# We have to operate column-wise\u001b[39;00m\n\u001b[0;32m-> 1893\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_setitem_with_indexer_split_path(indexer, value, name)\n\u001b[1;32m 1894\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 1895\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_setitem_single_block(indexer, value, name)\n", - "File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/pandas/core/indexing.py:1914\u001b[0m, in \u001b[0;36m_iLocIndexer._setitem_with_indexer_split_path\u001b[0;34m(self, indexer, value, name)\u001b[0m\n\u001b[1;32m 1911\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m (\u001b[38;5;28misinstance\u001b[39m(value, ABCSeries) \u001b[38;5;129;01mand\u001b[39;00m name \u001b[38;5;241m!=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124miloc\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(value, \u001b[38;5;28mdict\u001b[39m):\n\u001b[1;32m 1912\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mpandas\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Series\n\u001b[0;32m-> 1914\u001b[0m value \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_align_series(indexer, Series(value))\n\u001b[1;32m 1916\u001b[0m \u001b[38;5;66;03m# Ensure we have something we can iterate over\u001b[39;00m\n\u001b[1;32m 1917\u001b[0m info_axis \u001b[38;5;241m=\u001b[39m indexer[\u001b[38;5;241m1\u001b[39m]\n", - "File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/pandas/core/indexing.py:2340\u001b[0m, in \u001b[0;36m_iLocIndexer._align_series\u001b[0;34m(self, indexer, ser, multiindex_indexer, using_cow)\u001b[0m\n\u001b[1;32m 2337\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ser\n\u001b[1;32m 2338\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ser\u001b[38;5;241m.\u001b[39m_values\u001b[38;5;241m.\u001b[39mcopy()\n\u001b[0;32m-> 2340\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m ser\u001b[38;5;241m.\u001b[39mreindex(new_ix)\u001b[38;5;241m.\u001b[39m_values\n\u001b[1;32m 2342\u001b[0m \u001b[38;5;66;03m# 2 dims\u001b[39;00m\n\u001b[1;32m 2343\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m single_aligner:\n\u001b[1;32m 2344\u001b[0m \u001b[38;5;66;03m# reindex along index\u001b[39;00m\n", + "File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/pandas/core/frame.py:12304\u001b[0m, in \u001b[0;36m_reindex_for_setitem\u001b[0;34m(value, index)\u001b[0m\n\u001b[1;32m 12303\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m> 12304\u001b[0m reindexed_value \u001b[38;5;241m=\u001b[39m value\u001b[38;5;241m.\u001b[39mreindex(index)\u001b[38;5;241m.\u001b[39m_values\n\u001b[1;32m 12305\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m err:\n\u001b[1;32m 12306\u001b[0m \u001b[38;5;66;03m# raised in MultiIndex.from_tuples, see test_insert_error_msmgs\u001b[39;00m\n", "File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/pandas/core/series.py:4977\u001b[0m, in \u001b[0;36mSeries.reindex\u001b[0;34m(self, index, axis, method, copy, level, fill_value, limit, tolerance)\u001b[0m\n\u001b[1;32m 4960\u001b[0m \u001b[38;5;129m@doc\u001b[39m(\n\u001b[1;32m 4961\u001b[0m NDFrame\u001b[38;5;241m.\u001b[39mreindex, \u001b[38;5;66;03m# type: ignore[has-type]\u001b[39;00m\n\u001b[1;32m 4962\u001b[0m klass\u001b[38;5;241m=\u001b[39m_shared_doc_kwargs[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mklass\u001b[39m\u001b[38;5;124m\"\u001b[39m],\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 4975\u001b[0m tolerance\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m,\n\u001b[1;32m 4976\u001b[0m ) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m Series:\n\u001b[0;32m-> 4977\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28msuper\u001b[39m()\u001b[38;5;241m.\u001b[39mreindex(\n\u001b[1;32m 4978\u001b[0m index\u001b[38;5;241m=\u001b[39mindex,\n\u001b[1;32m 4979\u001b[0m method\u001b[38;5;241m=\u001b[39mmethod,\n\u001b[1;32m 4980\u001b[0m copy\u001b[38;5;241m=\u001b[39mcopy,\n\u001b[1;32m 4981\u001b[0m level\u001b[38;5;241m=\u001b[39mlevel,\n\u001b[1;32m 4982\u001b[0m fill_value\u001b[38;5;241m=\u001b[39mfill_value,\n\u001b[1;32m 4983\u001b[0m limit\u001b[38;5;241m=\u001b[39mlimit,\n\u001b[1;32m 4984\u001b[0m tolerance\u001b[38;5;241m=\u001b[39mtolerance,\n\u001b[1;32m 4985\u001b[0m )\n", - "File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/pandas/core/generic.py:5521\u001b[0m, in \u001b[0;36mNDFrame.reindex\u001b[0;34m(self, labels, index, columns, axis, method, copy, level, fill_value, limit, tolerance)\u001b[0m\n\u001b[1;32m 5518\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_reindex_multi(axes, copy, fill_value)\n\u001b[1;32m 5520\u001b[0m \u001b[38;5;66;03m# perform the reindex on the axes\u001b[39;00m\n\u001b[0;32m-> 5521\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_reindex_axes(\n\u001b[1;32m 5522\u001b[0m axes, level, limit, tolerance, method, fill_value, copy\n\u001b[1;32m 5523\u001b[0m )\u001b[38;5;241m.\u001b[39m__finalize__(\u001b[38;5;28mself\u001b[39m, method\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mreindex\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", - "File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/pandas/core/generic.py:5544\u001b[0m, in \u001b[0;36mNDFrame._reindex_axes\u001b[0;34m(self, axes, level, limit, tolerance, method, fill_value, copy)\u001b[0m\n\u001b[1;32m 5541\u001b[0m \u001b[38;5;28;01mcontinue\u001b[39;00m\n\u001b[1;32m 5543\u001b[0m ax \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_axis(a)\n\u001b[0;32m-> 5544\u001b[0m new_index, indexer \u001b[38;5;241m=\u001b[39m ax\u001b[38;5;241m.\u001b[39mreindex(\n\u001b[1;32m 5545\u001b[0m labels, level\u001b[38;5;241m=\u001b[39mlevel, limit\u001b[38;5;241m=\u001b[39mlimit, tolerance\u001b[38;5;241m=\u001b[39mtolerance, method\u001b[38;5;241m=\u001b[39mmethod\n\u001b[1;32m 5546\u001b[0m )\n\u001b[1;32m 5548\u001b[0m axis \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_axis_number(a)\n\u001b[1;32m 5549\u001b[0m obj \u001b[38;5;241m=\u001b[39m obj\u001b[38;5;241m.\u001b[39m_reindex_with_indexers(\n\u001b[1;32m 5550\u001b[0m {axis: [new_index, indexer]},\n\u001b[1;32m 5551\u001b[0m fill_value\u001b[38;5;241m=\u001b[39mfill_value,\n\u001b[1;32m 5552\u001b[0m copy\u001b[38;5;241m=\u001b[39mcopy,\n\u001b[1;32m 5553\u001b[0m allow_dups\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m,\n\u001b[1;32m 5554\u001b[0m )\n", - "File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/pandas/core/indexes/base.py:4430\u001b[0m, in \u001b[0;36mIndex.reindex\u001b[0;34m(self, target, method, level, limit, tolerance)\u001b[0m\n\u001b[1;32m 4426\u001b[0m indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_indexer(\n\u001b[1;32m 4427\u001b[0m target, method\u001b[38;5;241m=\u001b[39mmethod, limit\u001b[38;5;241m=\u001b[39mlimit, tolerance\u001b[38;5;241m=\u001b[39mtolerance\n\u001b[1;32m 4428\u001b[0m )\n\u001b[1;32m 4429\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_is_multi:\n\u001b[0;32m-> 4430\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcannot handle a non-unique multi-index!\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 4431\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mis_unique:\n\u001b[1;32m 4432\u001b[0m \u001b[38;5;66;03m# GH#42568\u001b[39;00m\n\u001b[1;32m 4433\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcannot reindex on an axis with duplicate labels\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", - "\u001b[0;31mValueError\u001b[0m: cannot handle a non-unique multi-index!" + "File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/pandas/core/generic.py:5521\u001b[0m, in \u001b[0;36mNDFrame.reindex\u001b[0;34m(self, labels, index, columns, axis, method, copy, level, fill_value, limit, tolerance)\u001b[0m\n\u001b[1;32m 5520\u001b[0m \u001b[38;5;66;03m# perform the reindex on the axes\u001b[39;00m\n\u001b[0;32m-> 5521\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_reindex_axes(\n\u001b[1;32m 5522\u001b[0m axes, level, limit, tolerance, method, fill_value, copy\n\u001b[1;32m 5523\u001b[0m )\u001b[38;5;241m.\u001b[39m__finalize__(\u001b[38;5;28mself\u001b[39m, method\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mreindex\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", + "File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/pandas/core/generic.py:5544\u001b[0m, in \u001b[0;36mNDFrame._reindex_axes\u001b[0;34m(self, axes, level, limit, tolerance, method, fill_value, copy)\u001b[0m\n\u001b[1;32m 5543\u001b[0m ax \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_axis(a)\n\u001b[0;32m-> 5544\u001b[0m new_index, indexer \u001b[38;5;241m=\u001b[39m ax\u001b[38;5;241m.\u001b[39mreindex(\n\u001b[1;32m 5545\u001b[0m labels, level\u001b[38;5;241m=\u001b[39mlevel, limit\u001b[38;5;241m=\u001b[39mlimit, tolerance\u001b[38;5;241m=\u001b[39mtolerance, method\u001b[38;5;241m=\u001b[39mmethod\n\u001b[1;32m 5546\u001b[0m )\n\u001b[1;32m 5548\u001b[0m axis \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_axis_number(a)\n", + "File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/pandas/core/indexes/base.py:4437\u001b[0m, in \u001b[0;36mIndex.reindex\u001b[0;34m(self, target, method, level, limit, tolerance)\u001b[0m\n\u001b[1;32m 4435\u001b[0m indexer, _ \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mget_indexer_non_unique(target)\n\u001b[0;32m-> 4437\u001b[0m target \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_wrap_reindex_result(target, indexer, preserve_names)\n\u001b[1;32m 4438\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m target, indexer\n", + "File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/pandas/core/indexes/multi.py:2602\u001b[0m, in \u001b[0;36mMultiIndex._wrap_reindex_result\u001b[0;34m(self, target, indexer, preserve_names)\u001b[0m\n\u001b[1;32m 2601\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m-> 2602\u001b[0m target \u001b[38;5;241m=\u001b[39m MultiIndex\u001b[38;5;241m.\u001b[39mfrom_tuples(target)\n\u001b[1;32m 2603\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m:\n\u001b[1;32m 2604\u001b[0m \u001b[38;5;66;03m# not all tuples, see test_constructor_dict_multiindex_reindex_flat\u001b[39;00m\n", + "File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/pandas/core/indexes/multi.py:220\u001b[0m, in \u001b[0;36mnames_compat..new_meth\u001b[0;34m(self_or_cls, *args, **kwargs)\u001b[0m\n\u001b[1;32m 218\u001b[0m kwargs[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mnames\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m kwargs\u001b[38;5;241m.\u001b[39mpop(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mname\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 220\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m meth(self_or_cls, \u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n", + "File \u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/pandas/core/indexes/multi.py:615\u001b[0m, in \u001b[0;36mMultiIndex.from_tuples\u001b[0;34m(cls, tuples, sortorder, names)\u001b[0m\n\u001b[1;32m 613\u001b[0m tuples \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39masarray(tuples\u001b[38;5;241m.\u001b[39m_values)\n\u001b[0;32m--> 615\u001b[0m arrays \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(lib\u001b[38;5;241m.\u001b[39mtuples_to_object_array(tuples)\u001b[38;5;241m.\u001b[39mT)\n\u001b[1;32m 616\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(tuples, \u001b[38;5;28mlist\u001b[39m):\n", + "File \u001b[0;32mlib.pyx:2977\u001b[0m, in \u001b[0;36mpandas._libs.lib.tuples_to_object_array\u001b[0;34m()\u001b[0m\n", + "\u001b[0;31mValueError\u001b[0m: Buffer dtype mismatch, expected 'Python object' but got 'long'", + "\nThe above exception was the direct cause of the following exception:\n", + "\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)", + "\u001b[0;32m/var/folders/y4/dvc6qr5j30s3frwztjt5shg40000gn/T/ipykernel_61363/3498303338.py\u001b[0m in \u001b[0;36m?\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mcadCAD_tools\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mprofiling\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mvisualizations\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mvisualize_substep_impact\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mvisualize_substep_impact\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdf\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mrelative\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", + "\u001b[0;32m/opt/homebrew/Caskroom/miniconda/base/lib/python3.11/site-packages/cadCAD_tools/profiling/visualizations.py\u001b[0m in \u001b[0;36m?\u001b[0;34m(df, relative, **kwargs)\u001b[0m\n\u001b[1;32m 61\u001b[0m \u001b[0mx_col\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'substep'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 62\u001b[0m \u001b[0mfig_df\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mx_col\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfig_df\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mx_col\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m/\u001b[0m \u001b[0;36m2\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 63\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 64\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mrelative\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 65\u001b[0;31m \u001b[0mfig_df\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfig_df\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0massign\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrelative_psub_time\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mfig_df\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgroupby\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mindexes\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpsub_time\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;32mlambda\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m:\u001b[0m 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err\n\u001b[1;32m 12314\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mreindexed_value\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", + "\u001b[0;31mTypeError\u001b[0m: incompatible index of inserted column with frame index" ] } ], diff --git a/documentation/examples/param_sweep.py b/documentation/examples/param_sweep.py index 61e53a03..0d0299ac 100644 --- a/documentation/examples/param_sweep.py +++ b/documentation/examples/param_sweep.py @@ -1,5 +1,4 @@ import pprint -from typing import Dict, List import pandas as pd from tabulate import tabulate diff --git a/requirements.txt b/requirements.txt index e4aa76e1..763c639c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,4 +11,6 @@ pathos>=0.2.8 numpy>=1.22.0 pytz>=2021.1 setuptools>=69.0.2 -graphviz>=0.20.1 \ No newline at end of file +graphviz>=0.20.1 +tqdm>=4.65.0 +pytest>=7.4.3 \ No newline at end of file diff --git a/setup.py b/setup.py index dfd786c4..eef999fa 100644 --- a/setup.py +++ b/setup.py @@ -21,7 +21,7 @@ """ name = "cadCAD" -version = "0.4.28" +version = "0.4.29" setup(name=name, version=version, @@ -38,7 +38,8 @@ "dill", "pathos", "numpy", - "pytz" - ], - python_requires='>=3.6.13' + "pytz", + "six" + ], + python_requires='>=3.8.0' ) \ No newline at end of file diff --git a/testing/generic_test.py b/testing/generic_test.py index 015312ce..658fbc87 100644 --- a/testing/generic_test.py +++ b/testing/generic_test.py @@ -1,7 +1,6 @@ import unittest from functools import reduce -from tabulate import tabulate # type: ignore -from parameterized import parameterized +from tabulate import tabulate def generate_assertions_df(df, expected_results, target_cols, evaluations): test_names = [] diff --git a/testing/models/param_sweep.py b/testing/models/param_sweep.py index b2558bef..8c1549b3 100644 --- a/testing/models/param_sweep.py +++ b/testing/models/param_sweep.py @@ -1,9 +1,9 @@ import pprint -from typing import Dict, List from cadCAD import experiment from cadCAD.configuration import Experiment from cadCAD.configuration.utils import env_trigger, var_substep_trigger, config_sim, psub_list +from typing import Dict, List pp = pprint.PrettyPrinter(indent=4) diff --git a/testing/results_comparison.py b/testing/results_comparison.py index 22866571..2a8e5501 100644 --- a/testing/results_comparison.py +++ b/testing/results_comparison.py @@ -1,7 +1,7 @@ import unittest -import pandas as pd -from tabulate import tabulate -from pandas._testing import assert_frame_equal +import pandas as pd # type: ignore +from tabulate import tabulate # type: ignore +from pandas._testing import assert_frame_equal # type: ignore def compare_results(result_diff): diff --git a/testing/test_arg_count.py b/testing/test_arg_count.py index 556c8cfa..0078b9e3 100644 --- a/testing/test_arg_count.py +++ b/testing/test_arg_count.py @@ -13,10 +13,10 @@ def test_sufs(): psubs = [ { 'policies': { - 'p_A': lambda _1, _2, _3, _4, _5: {} + 'p_A': lambda _1, _2, _3, _4: {} }, 'variables': { - 'v_A': lambda _1, _2, _3, _4, _5, _6: ('a', 1) + 'v_A': lambda _1, _2, _3, _4, _5: ('a', 1) } } ] diff --git a/testing/tests/append_mod_test.py b/testing/tests/append_mod_test.py index 51a43627..a6e628c7 100644 --- a/testing/tests/append_mod_test.py +++ b/testing/tests/append_mod_test.py @@ -7,7 +7,6 @@ from testing.models.param_sweep import env_process as env_process_a from testing.models.param_sweep import partial_state_update_blocks as psubs_a - def append_model_id(model_ids, sim_config, genesis_states, env_process, psubs): exp_copy = deepcopy(exp) for mod_id in model_ids: