Merge branch 'master' into hard_to_debug_msg

.github/workflows/cadcad-ci.yml

@@ -0,0 +1,61 @@
+# This workflow will install Python dependencies and run tests with multiple versions of Python
+
+name: cadCAD CI
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    continue-on-error: true
+
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        os: [ubuntu-latest, macos-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+
+    - name: Display Python version
+      run: python -c "import sys; print(sys.version)"
+
+    - name: Install test and build dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install jupyter
+        pip install -r requirements.txt
+
+    - name: Build cadCAD
+      run: |
+        python setup.py bdist_wheel
+        python -m pip install dist/*.whl --force-reinstall
+
+    - name: Run tests
+      run: |
+        python testing/tests/multi_model_row_count.py
+        python testing/tests/param_sweep.py
+        python testing/tests/policy_aggregation.py
+        python testing/tests/timestep1psub0.py
+        python testing/tests/runs_not_zero.py
+        python testing/tests/run1psub0.py
+        python testing/tests/append_mod_test.py
+        python testing/tests/cadCAD_exp.py
+
+    - name: Run Jupyter test
+      run: |
+        python testing/tests/import_cadCAD_test.py

AUTHORS.txt

@@ -1,30 +1,41 @@
 Authors
 =======
 
-cadCAD was implemented by Joshua E. Jodesty and designed by Michael Zargham, Markus B. Koch, and
-Matthew V. Barlin from 2018 to 2020.
+cadCAD was originally implemented by Joshua E. Jodesty and designed by Michael Zargham, Markus B. Koch, and
+Matthew V. Barlin in 2018. Since then, upgrades and improvements were further committed by Danilo L. Bernardineli, Tyler D. Mace
+and Emanuel Lima.
+
 
 
-Project Maintainers:
-- Joshua E. Jodesty <[email protected]>
-- Markus B. Koch <[email protected]>
-- Michael Zargham <[email protected]>
+Current Project Maintainers:
+- Emanuel Lima <[email protected]> @emanuellima1
+- Michael Zargham <[email protected]> @mzargham
 
 
-Original Contributors:
-- Joshua E. Jodesty
-- Markus B. Koch
-- Matthew V. Barlin
-- Michael Zargham
-- Zixuan Zhang
-- Charles Rice
+Active and Past Contributors:
+- Joshua E. Jodesty @JEJodesty
+- Markus B. Koch @markusbkoch
+- Matthew V. Barlin @matttyb80
+- Michael Zargham @mzargham
+- Danilo L. Bernardineli @danlessa
+- Tyler D. Mace @tylerdmace
+- Emanuel Lima @emanuellima1
+- Zixuan Zhang @zixuanzh
+- Charles Rice @charles-rice
+- Benjamin Scholz @BenSchZA
 
 
 We’d also like to thank:
-- Andrew Clark
-- Nick Hirannet
-- Jonathan Gabler
-- Harry Goodnight
+- Andrew Clark @aclarkData
+- Nick Hirannet @nick-phl-7
+- Jonathan Gabler 
+- Harry Goodnight @
 - Charlie Hoppes
 - Nikhil Jamdade
 - Chris Frazier
+- Griff Green @GriffGreen
+- Isaac @eenti
+- Jonny Dubowsky @jonnydubowsky
+- Sem Brestels @sembrestels
+- @fjribi
+- Andrea Maria Piana @cammellos

cadCAD/engine/__init__.py

@@ -1,5 +1,5 @@
 from time import time
-from typing import Callable, Dict, List, Any, Tuple
+from typing import Callable, Dict, List, Any, Tuple, Union
 
 from cadCAD.utils import flatten
 from cadCAD.utils.execution import print_exec_info
@@ -39,6 +39,7 @@ def auto_mode_switcher(config_amt: int):
 class ExecutionContext:
     def __init__(self, context=ExecutionMode.local_mode, method=None, additional_objs=None) -> None:
         self.name = context
+        self.additional_objs = additional_objs
         if context == 'local_proc':
             self.method = local_simulations
         elif context == 'single_proc':
@@ -74,6 +75,7 @@ def __init__(self,
         self.SimExecutor = SimExecutor
         self.exec_method = exec_context.method
         self.exec_context = exec_context.name
+        self.additional_objs = exec_context.additional_objs
         self.configs = configs
         self.empty_return = empty_return
 
@@ -174,7 +176,7 @@ def get_final_results(simulations: List[StateHistory],
             print("Execution Method: " + self.exec_method.__name__)
             simulations_results = self.exec_method(
                 sim_executors, var_dict_list, states_lists, configs_structs, env_processes_list, Ts, SimIDs, RunIDs,
-                ExpIDs, SubsetIDs, SubsetWindows, original_N
+                ExpIDs, SubsetIDs, SubsetWindows, original_N, self.additional_objs
             )
 
             final_result = get_final_results(

cadCAD/engine/execution.py

@@ -22,7 +22,8 @@ def single_proc_exec(
     ExpIDs: List[int],
     SubsetIDs: List[SubsetID],
     SubsetWindows: List[SubsetWindow],
-    configured_n: List[N_Runs]
+    configured_n: List[N_Runs],
+    additional_objs=None
 ):
 
     # HACK for making it run with N_Runs=1
@@ -38,7 +39,7 @@ def single_proc_exec(
         map(lambda x: x.pop(), raw_params)
     )
     result = simulation_exec(
-        var_dict_list, states_list, config, env_processes, T, sim_id, N, subset_id, subset_window, configured_n
+        var_dict_list, states_list, config, env_processes, T, sim_id, N, subset_id, subset_window, configured_n, additional_objs
     )
     return flatten(result)
 
@@ -58,7 +59,8 @@ def parallelize_simulations(
     ExpIDs: List[int],
     SubsetIDs: List[SubsetID],
     SubsetWindows: List[SubsetWindow],
-    configured_n: List[N_Runs]
+    configured_n: List[N_Runs],
+    additional_objs=None
 ):
 
     print(f'Execution Mode: parallelized')
@@ -96,7 +98,7 @@ 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), params
+                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()
@@ -123,18 +125,19 @@ def local_simulations(
     ExpIDs: List[int],
     SubsetIDs: List[SubsetID],
     SubsetWindows: List[SubsetWindow],
-    configured_n: List[N_Runs]
+    configured_n: List[N_Runs],
+    additional_objs=None
     ):
     config_amt = len(configs_structs)
 
     if config_amt == 1: # and configured_n != 1
         return single_proc_exec(
             simulation_execs, var_dict_list, states_lists, configs_structs, env_processes_list,
-            Ts, SimIDs, Ns, ExpIDs, SubsetIDs, SubsetWindows, configured_n
+            Ts, SimIDs, Ns, ExpIDs, SubsetIDs, SubsetWindows, configured_n, additional_objs
         )
     elif config_amt > 1: # and configured_n != 1
         return parallelize_simulations(
             simulation_execs, var_dict_list, states_lists, configs_structs, env_processes_list,
-            Ts, SimIDs, Ns, ExpIDs, SubsetIDs, SubsetWindows, configured_n
+            Ts, SimIDs, Ns, ExpIDs, SubsetIDs, SubsetWindows, configured_n, additional_objs
         )
         # elif config_amt > 1 and configured_n == 1:

cadCAD/engine/simulation.py

@@ -1,10 +1,12 @@
 from typing import Any, Callable, Dict, List, Tuple
 from copy import deepcopy
+from types import MappingProxyType
 from functools import reduce
-from funcy import curry
+from funcy import curry # type: ignore
 
 from cadCAD.utils import flatten
 from cadCAD.engine.utils import engine_exception
+from cadCAD.types import *
 
 id_exception: Callable = curry(engine_exception)(KeyError)(KeyError)(None)
 
@@ -107,20 +109,30 @@ def env_composition(target_field, state_dict, target_value):
     # mech_step
     def partial_state_update(
         self,
-        sweep_dict: Dict[str, List[Any]],
-        sub_step: int,
-        sL,
-        sH,
-        state_funcs: List[Callable],
-        policy_funcs: List[Callable],
-        env_processes: Dict[str, Callable],
+        sweep_dict: Parameters,
+        sub_step: Substep,
+        sL: list[State],
+        sH: StateHistory,
+        state_funcs: List[StateUpdateFunction],
+        policy_funcs: List[PolicyFunction],
+        env_processes: EnvProcesses,
         time_step: int,
         run: int,
         additional_objs
     ) -> List[Dict[str, Any]]:
 
-        # last_in_obj: Dict[str, Any] = MappingProxyType(sL[-1])
-        last_in_obj: Dict[str, Any] = deepcopy(sL[-1])
+        if type(additional_objs) == dict:
+            if additional_objs.get('deepcopy_off', False) == True:
+                last_in_obj = MappingProxyType(sL[-1])
+                if len(additional_objs) == 1:
+                    additional_objs = None 
+                    # XXX: drop the additional objects if only used for deepcopy
+                    # toggling.
+            else:
+                last_in_obj = deepcopy(sL[-1])
+        else:
+            last_in_obj = deepcopy(sL[-1])
+
         _input: Dict[str, Any] = self.policy_update_exception(
             self.get_policy_input(sweep_dict, sub_step, sH, last_in_obj, policy_funcs, additional_objs)
         )
@@ -217,18 +229,18 @@ def run_pipeline(
 
     def simulation(
         self,
-        sweep_dict: Dict[str, List[Any]],
-        states_list: List[Dict[str, Any]],
+        sweep_dict: SweepableParameters,
+        states_list: StateHistory,
         configs,
-        env_processes: Dict[str, Callable],
-        time_seq: range,
-        simulation_id: int,
+        env_processes: EnvProcesses,
+        time_seq: TimeSeq,
+        simulation_id: SimulationID,
         run: int,
-        subset_id,
-        subset_window,
-        configured_N,
+        subset_id: SubsetID,
+        subset_window: SubsetWindow,
+        configured_N: int,
         # remote_ind
-        additional_objs=None
+        additional_objs: Union[None, Dict]=None
     ):
         run += 1
         subset_window.appendleft(subset_id)

cadCAD/types.py

@@ -24,16 +24,16 @@ class ConfigurationDict(TypedDict):
     N: int # Number of MC Runs
     M: Union[Parameters, SweepableParameters] # Parameters / List of Parameter to Sweep
 
-
-EnvProcesses = object
+TargetValue = object
+EnvProcess: Callable[[State, SweepableParameters, TargetValue], TargetValue]
+EnvProcesses = dict[str, Callable]
 TimeSeq = Iterator
 SimulationID = int
 Run = int
 SubsetID = int
 SubsetWindow = Iterator
 N_Runs = int
 
-
 ExecutorFunction = Callable[[Parameters, StateHistory, StateUpdateBlocks, EnvProcesses, TimeSeq, SimulationID, Run, SubsetID, SubsetWindow, N_Runs], object]
 ExecutionParameter = Tuple[ExecutorFunction, Parameters, StateHistory, StateUpdateBlocks, EnvProcesses, TimeSeq, SimulationID, Run, SubsetID, SubsetWindow, N_Runs]
 
@@ -45,4 +45,4 @@ class SessionDict(TypedDict):
     simulation_id: int
     run_id: int
     subset_id: int
-    subset_window: deque
+    subset_window: deque