From c84bfa6bc62c6e5e017b2e6f3bd02f0b7c25e8fc Mon Sep 17 00:00:00 2001 From: Danilo Lessa Bernardineli Date: Mon, 18 Dec 2023 17:41:31 -0300 Subject: [PATCH 1/3] change to v0.5.0 --- CHANGELOG.md | 28 +++++++++++++++++++--------- README.md | 6 +++--- cadCAD/__init__.py | 2 +- setup.py | 2 +- 4 files changed, 24 insertions(+), 14 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6b28e7f6..1f4469a9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,18 +1,28 @@ # Changelog: +### 0.5.0 - December 18 2023 -### February 15, 2023 -* **Fixes:** - - Package has been cleaned-up for working with Python 3.10 -### 0.4.29.1 +#### New User Features + +- Added toggle for enabling users to deactivate deepcopying. This is done by passing an additional object on the `ExecutionContext`, eg. `ExecutionContext(mode, additional_objs={'deepcopy_off': True})` + +#### New Submodules + +- A collection of type annotations for encapsuling `cadCAD` projects is now implemented through the `cadCAD.types` submodules +- Added `cadCAD.tools` as a submodule, which is originated from the `cadCAD_tools` Python package. This submodule contains several helper functions for making the simulation experience more straightforward as well as a collection of performance profiling tools. +- Added `cadCAD.diagram` as a submodule, which is originated from the `cadCAD_diagram` Python package. This submodule contains functions for programatically generating block diagrams from existing models. +- More informative error messages when policies and SUFs are wrongly implemented. (Issues #288 and #258) + +#### Backend Improvements + +- Merged repo with the `cadCAD_legacy_devel`, which includes performance improvements. In particular, simulations will start up faster due to code optimizations. +- `cadCAD` now uses `pytest` as the testing framework. This was made possible by isolating the existing tests and wrapping them into functions. -#### Changes -- Parallel executor uses the context manager handling the Process Pool lifetime +#### Fixes -### 0.4.29 +- cadCAD is now Python 3.10+ compatible (Issue #306 and #301) +- Proper support for `ExecutionMode.single_mode` (Issue #253 and #254) -- Merged repo with the `cadCAD_tweaked`, which includes performance improvements -- Python 3.10 compatible ### September 28, 2021 #### New Features: * **ver. ≥ `0.4.28`:** diff --git a/README.md b/README.md index e5151fa8..ea165f20 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ / ___/ __` / __ / / / /| | / / / / / /__/ /_/ / /_/ / /___/ ___ |/ /_/ / \___/\__,_/\__,_/\____/_/ |_/_____/ -by cadCAD ver. 0.4.28 +by cadCAD ver. 0.5.0 ====================================== Complex Adaptive Dynamics o i e @@ -20,7 +20,7 @@ through simulation, with support for Monte Carlo methods, A/B testing and parame # Getting Started -#### Change Log: [ver. 0.4.28](CHANGELOG.md) +#### Change Log: [ver. 0.5.0](CHANGELOG.md) [Previous Stable Release (No Longer Supported)](https://github.com/cadCAD-org/cadCAD/tree/b9cc6b2e4af15d6361d60d6ec059246ab8fbf6da) @@ -47,7 +47,7 @@ $ ## 1. Installation: Requires [>= Python 3.6.13](https://www.python.org/downloads/) -**Option A:** Install Using **[pip](https://pypi.org/project/cadCAD/0.4.28/)** +**Option A:** Install Using **[pip](https://pypi.org/project/cadCAD/)** ```bash pip3 install cadCAD ``` diff --git a/cadCAD/__init__.py b/cadCAD/__init__.py index fbfbaf52..8a276188 100644 --- a/cadCAD/__init__.py +++ b/cadCAD/__init__.py @@ -2,7 +2,7 @@ from cadCAD.configuration import Experiment name = "cadCAD" -version = "0.4.28" +version = "0.5.0" experiment = Experiment() configs = experiment.configs diff --git a/setup.py b/setup.py index eef999fa..785f3aee 100644 --- a/setup.py +++ b/setup.py @@ -21,7 +21,7 @@ """ name = "cadCAD" -version = "0.4.29" +version = "0.5.0" setup(name=name, version=version, From 9fc2ffcf9783305b5ff93414550f1d87917d0890 Mon Sep 17 00:00:00 2001 From: Danilo Lessa Bernardineli Date: Thu, 4 Apr 2024 09:21:59 -0300 Subject: [PATCH 2/3] update tests --- testing/test_param_count.py | 20 +++++---- testing/test_results_signature.py | 70 +++++++++++++++++++++++++++++++ testing/test_row_count.py | 9 ++-- 3 files changed, 88 insertions(+), 11 deletions(-) create mode 100644 testing/test_results_signature.py diff --git a/testing/test_param_count.py b/testing/test_param_count.py index 513c07d0..efb97e7a 100644 --- a/testing/test_param_count.py +++ b/testing/test_param_count.py @@ -3,6 +3,7 @@ from cadCAD.engine import Executor, ExecutionContext, ExecutionMode import pytest + P_no_lst = {'pA': 1, 'pB': 2, 'pC': 3} P_single_lst = {'pA': [1], 'pB': [1], 'pC': [3]} P_single_swp = {'pA': [4, 5, 6], 'pB': [1], 'pC': [3]} @@ -10,9 +11,13 @@ P_all_but_one_swp = {'pA': [7, 8, 9], 'pB': [1, 2, 3], 'pC': [1]} Ps = [P_no_lst, P_single_lst, P_single_swp, P_all_swp, P_all_but_one_swp] -CONFIG_SIGNATURES_TO_TEST = [(3, 3, 3, 3, 3), (1, 3, 3, 3, 3), - (3, 1, 3, 3, 3), (1, 1, 3, 3, 3), - (3, 3, 1, 3, 3), (1, 3, 1, 3, 3), (1, 1, 1, 3, 3)] +CONFIG_SIGNATURES_TO_TEST = [(3, 3, 3, 3, 3), + (1, 3, 3, 3, 3), + (3, 1, 3, 3, 3), + (1, 1, 3, 3, 3), + (3, 3, 1, 3, 3), + (1, 3, 1, 3, 3), + (1, 1, 1, 3, 3)] def run_experiment(exp: Experiment, mode: str): @@ -35,10 +40,12 @@ def p_test_param_count(params, _2, _3, _4): return {'sigA': None} return p_test_param_count + def create_experiments(N_simulations=3, N_sweeps=3, N_runs=3, N_timesteps=3, N_substeps=3, params={}) -> Experiment: INITIAL_STATE = {'varA': None} - PSUBs = [{'policies': {'sigA': param_count_test_policy_generator(params)}, 'variables': {'varA': param_count_test_suf_generator(params)}}] * N_substeps + PSUBs = [{'policies': {'sigA': param_count_test_policy_generator( + params)}, 'variables': {'varA': param_count_test_suf_generator(params)}}] * N_substeps SIM_CONFIG = config_sim( { @@ -58,8 +65,8 @@ def create_experiments(N_simulations=3, N_sweeps=3, N_runs=3, N_timesteps=3, N_s return exp -def expected_rows(N_simulations, N_sweeps, N_runs, N_timesteps, N_substeps,P) -> int: - return N_simulations * N_sweeps * N_runs * (N_timesteps * N_substeps + 1) +def expected_rows(N_simulations, N_sweeps, N_runs, N_timesteps, N_substeps, P) -> int: + return N_simulations * N_sweeps * N_runs * (N_timesteps * N_substeps + 1) @pytest.mark.parametrize("N_sim,N_sw,N_r,N_t,N_s", CONFIG_SIGNATURES_TO_TEST) @@ -69,7 +76,6 @@ def test_row_count_single(N_sim, N_sw, N_r, N_t, N_s, P): len(run_experiment(create_experiments(*args), 'single_proc')) - @pytest.mark.parametrize("N_sim,N_sw,N_r,N_t,N_s", CONFIG_SIGNATURES_TO_TEST) @pytest.mark.parametrize("P", Ps) def test_row_count_local(N_sim, N_sw, N_r, N_t, N_s, P): diff --git a/testing/test_results_signature.py b/testing/test_results_signature.py new file mode 100644 index 00000000..af50d955 --- /dev/null +++ b/testing/test_results_signature.py @@ -0,0 +1,70 @@ +from cadCAD.configuration import Experiment +from cadCAD.configuration.utils import config_sim +from cadCAD.engine import Executor, ExecutionContext, ExecutionMode +import pytest +import pandas as pd # type: ignore +from typing import Dict, List + +# (N_simulations, N_sweeps, N_runs, N_timesteps, N_substeps) + + +CONFIG_SIGNATURES_TO_TEST = [ + (1, 20, 5, 10, 5), (3, 3, 3, 3, 3), (1, 3, 3, 3, 3), + (3, 1, 3, 3, 3), (1, 1, 3, 3, 3), + (3, 3, 1, 3, 3), (1, 3, 1, 3, 3), (1, 1, 1, 3, 3)] + + +def run_experiment(exp: Experiment, mode: str) -> List[Dict]: + exec_context = ExecutionContext(mode) + executor = Executor(exec_context=exec_context, configs=exp.configs) + (records, tensor_field, _) = executor.execute() + return records + + +def create_experiments(N_simulations=3, N_sweeps=3, N_runs=3, N_timesteps=3, N_substeps=3) -> Experiment: + + INITIAL_STATE = {'varA': None} + PSUBs = [{'policies': {}, 'variables': {}}] * N_substeps + params = {'A': [None] * N_sweeps, + 'B': [None]} + + SIM_CONFIG = config_sim( + { + "N": N_runs, + "T": range(N_timesteps), + "M": params, # Optional + } + ) + + exp = Experiment() + for i_sim in range(N_simulations): + exp.append_model( + sim_configs=SIM_CONFIG, + initial_state=INITIAL_STATE, + partial_state_update_blocks=PSUBs + ) + return exp + + +def expected_rows(N_simulations, N_sweeps, N_runs, N_timesteps, N_substeps) -> int: + return N_simulations * N_sweeps * N_runs * (N_timesteps * N_substeps + 1) + + +@pytest.mark.parametrize("N_sim,N_sw,N_r,N_t,N_s", CONFIG_SIGNATURES_TO_TEST) +def test_identifiers_value_counts_single(N_sim, N_sw, N_r, N_t, N_s): + args = (N_sim, N_sw, N_r, N_t, N_s) + results = run_experiment(create_experiments(*args), 'single_proc') + df = pd.DataFrame(results).query("timestep > 0") + assert len(set(df.timestep.value_counts().values)) == 1 + assert len(set(df.subset.value_counts().values)) == 1 + assert len(set(df.run.value_counts().values)) == 1 + + +@pytest.mark.parametrize("N_sim,N_sw,N_r,N_t,N_s", CONFIG_SIGNATURES_TO_TEST[:-1]) +def test_identifiers_value_counts_multi(N_sim, N_sw, N_r, N_t, N_s): + args = (N_sim, N_sw, N_r, N_t, N_s) + results = run_experiment(create_experiments(*args), 'multi_proc') + df = pd.DataFrame(results).query("timestep > 0") + assert len(set(df.timestep.value_counts().values)) == 1 + assert len(set(df.subset.value_counts().values)) == 1 + assert len(set(df.run.value_counts().values)) == 1 diff --git a/testing/test_row_count.py b/testing/test_row_count.py index a1d78f14..834c844b 100644 --- a/testing/test_row_count.py +++ b/testing/test_row_count.py @@ -2,13 +2,14 @@ from cadCAD.configuration.utils import config_sim from cadCAD.engine import Executor, ExecutionContext, ExecutionMode import pytest - +import pandas as pd # type: ignore +from typing import Dict, List CONFIG_SIGNATURES_TO_TEST = [(3, 3, 3, 3, 3), (1, 3, 3, 3, 3), (3, 1, 3, 3, 3), (1, 1, 3, 3, 3), (3, 3, 1, 3, 3), (1, 3, 1, 3, 3), (1, 1, 1, 3, 3)] -def run_experiment(exp: Experiment, mode: str): +def run_experiment(exp: Experiment, mode: str) -> List[Dict]: exec_context = ExecutionContext(mode) executor = Executor(exec_context=exec_context, configs=exp.configs) (records, tensor_field, _) = executor.execute() @@ -44,11 +45,11 @@ def expected_rows(N_simulations, N_sweeps, N_runs, N_timesteps, N_substeps) -> i return N_simulations * N_sweeps * N_runs * (N_timesteps * N_substeps + 1) - @pytest.mark.parametrize("N_sim,N_sw,N_r,N_t,N_s", CONFIG_SIGNATURES_TO_TEST) def test_row_count_single(N_sim, N_sw, N_r, N_t, N_s): args = (N_sim, N_sw, N_r, N_t, N_s) - assert len(run_experiment(create_experiments(*args), 'single_proc')) == expected_rows(*args) + results = run_experiment(create_experiments(*args), 'single_proc') + assert len(results) == expected_rows(*args) @pytest.mark.parametrize("N_sim,N_sw,N_r,N_t,N_s", CONFIG_SIGNATURES_TO_TEST) From d5e762c431d73bd8ded90f7c22f306478e569183 Mon Sep 17 00:00:00 2001 From: Danilo Lessa Bernardineli Date: Thu, 11 Apr 2024 23:42:17 -0300 Subject: [PATCH 3/3] fix --- cadCAD/configuration/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cadCAD/configuration/__init__.py b/cadCAD/configuration/__init__.py index 9c9d0b12..9e2f0c79 100644 --- a/cadCAD/configuration/__init__.py +++ b/cadCAD/configuration/__init__.py @@ -126,7 +126,7 @@ def append_model( exp_creation_ts=self.exp_creation_ts, sim_config=sim_config, - initial_state=initial_state, + initial_state=deepcopy(initial_state), seeds=seeds, exogenous_states=exogenous_states, env_processes=env_processes,