import importlib import os import pickle as pkl import tempfile import traceback import unittest import warnings from pathlib import Path import numpy as np import pandas as pd import sympy # type: ignore from sklearn.utils.estimator_checks import check_estimator from pysr import PySRRegressor, install, jl from pysr.export_latex import sympy2latex from pysr.feature_selection import _handle_feature_selection, run_feature_selection from pysr.julia_helpers import init_julia from pysr.sr import ( _check_assertions, _process_constraints, _suggest_keywords, idx_model_selection, ) from pysr.utils import _csv_filename_to_pkl_filename from .params import ( DEFAULT_NCYCLES, DEFAULT_NITERATIONS, DEFAULT_PARAMS, DEFAULT_POPULATIONS, ) # Disables local saving: os.environ["SYMBOLIC_REGRESSION_IS_TESTING"] = os.environ.get( "SYMBOLIC_REGRESSION_IS_TESTING", "true" ) class TestPipeline(unittest.TestCase): def setUp(self): # Using inspect, # get default niterations from PySRRegressor, and double them: self.default_test_kwargs = dict( progress=False, model_selection="accuracy", niterations=DEFAULT_NITERATIONS * 2, populations=DEFAULT_POPULATIONS * 2, temp_equation_file=True, ) self.rstate = np.random.RandomState(0) self.X = self.rstate.randn(100, 5) def test_linear_relation(self): y = self.X[:, 0] model = PySRRegressor( **self.default_test_kwargs, early_stop_condition="stop_if(loss, complexity) = loss < 1e-4 && complexity == 1", ) model.fit(self.X, y) print(model.equations_) self.assertLessEqual(model.get_best()["loss"], 1e-4) def test_linear_relation_named(self): y = self.X[:, 0] model = PySRRegressor( **self.default_test_kwargs, early_stop_condition="stop_if(loss, complexity) = loss < 1e-4 && complexity == 1", ) model.fit(self.X, y, variable_names=["c1", "c2", "c3", "c4", "c5"]) self.assertIn("c1", model.equations_.iloc[-1]["equation"]) def test_linear_relation_weighted_bumper(self): y = self.X[:, 0] weights = np.ones_like(y) model = PySRRegressor( **self.default_test_kwargs, early_stop_condition="stop_if(loss, complexity) = loss < 1e-4 && complexity == 1", bumper=True, ) model.fit(self.X, y, weights=weights) print(model.equations_) self.assertLessEqual(model.get_best()["loss"], 1e-4) self.assertEqual( jl.seval("((::Val{x}) where x) -> x")(model.julia_options_.bumper), True ) def test_multiprocessing_turbo_custom_objective(self): rstate = np.random.RandomState(0) y = self.X[:, 0] y += rstate.randn(*y.shape) * 1e-4 model = PySRRegressor( **self.default_test_kwargs, # Turbo needs to work with unsafe operators: unary_operators=["sqrt"], procs=2, multithreading=False, turbo=True, early_stop_condition="stop_if(loss, complexity) = loss < 1e-10 && complexity == 1", loss_function=""" function my_objective(tree::Node{T}, dataset::Dataset{T}, options::Options) where T prediction, flag = eval_tree_array(tree, dataset.X, options) !flag && return T(Inf) abs3(x) = abs(x) ^ 3 return sum(abs3, prediction .- dataset.y) / length(prediction) end """, ) model.fit(self.X, y) print(model.equations_) best_loss = model.equations_.iloc[-1]["loss"] self.assertLessEqual(best_loss, 1e-10) self.assertGreaterEqual(best_loss, 0.0) # Test options stored: self.assertEqual( jl.seval("((::Val{x}) where x) -> x")(model.julia_options_.turbo), True ) def test_multiline_seval(self): # The user should be able to run multiple things in a single seval call: num = jl.seval( """ function my_new_objective(x) x^2 end 1.5 """ ) self.assertEqual(num, 1.5) def test_high_precision_search_custom_loss(self): y = 1.23456789 * self.X[:, 0] model = PySRRegressor( **self.default_test_kwargs, early_stop_condition="stop_if(loss, complexity) = loss < 1e-4 && complexity == 3", elementwise_loss="my_loss(prediction, target) = (prediction - target)^2", precision=64, parsimony=0.01, warm_start=True, ) model.fit(self.X, y) # We should have that the model state is now a Float64 hof: test_state = model.raw_julia_state_ self.assertTrue(jl.typeof(test_state[1]).parameters[1] == jl.Float64) # Test options stored: self.assertEqual( jl.seval("((::Val{x}) where x) -> x")(model.julia_options_.turbo), False ) def test_multioutput_custom_operator_quiet_custom_complexity(self): y = self.X[:, [0, 1]] ** 2 model = PySRRegressor( unary_operators=["square_op(x) = x^2"], extra_sympy_mappings={"square_op": lambda x: x**2}, complexity_of_operators={"square_op": 2, "plus": 1}, binary_operators=["plus"], verbosity=0, **self.default_test_kwargs, procs=0, # Test custom operators with turbo: turbo=True, # Test custom operators with constraints: nested_constraints={"square_op": {"square_op": 3}}, constraints={"square_op": 10}, early_stop_condition="stop_if(loss, complexity) = loss < 1e-4 && complexity == 3", ) model.fit(self.X, y) equations = model.equations_ print(equations) self.assertIn("square_op", model.equations_[0].iloc[-1]["equation"]) self.assertLessEqual(equations[0].iloc[-1]["loss"], 1e-4) self.assertLessEqual(equations[1].iloc[-1]["loss"], 1e-4) test_y1 = model.predict(self.X) test_y2 = model.predict(self.X, index=[-1, -1]) mse1 = np.average((test_y1 - y) ** 2) mse2 = np.average((test_y2 - y) ** 2) self.assertLessEqual(mse1, 1e-4) self.assertLessEqual(mse2, 1e-4) def test_custom_variable_complexity(self): for outer in (True, False): for case in (1, 2): y = self.X[:, [0, 1]] if case == 1: kwargs = dict(complexity_of_variables=[2, 3]) elif case == 2: kwargs = dict(complexity_of_variables=2) if outer: outer_kwargs = kwargs inner_kwargs = dict() else: outer_kwargs = dict() inner_kwargs = kwargs model = PySRRegressor( binary_operators=["+"], verbosity=0, **self.default_test_kwargs, early_stop_condition=( f"stop_if_{case}(l, c) = l < 1e-8 && c <= {3 if case == 1 else 2}" ), **outer_kwargs, ) model.fit(self.X[:, [0, 1]], y, **inner_kwargs) self.assertLessEqual(model.get_best()[0]["loss"], 1e-8) self.assertLessEqual(model.get_best()[1]["loss"], 1e-8) self.assertEqual(model.get_best()[0]["complexity"], 2) self.assertEqual( model.get_best()[1]["complexity"], 3 if case == 1 else 2 ) def test_error_message_custom_variable_complexity(self): X = np.ones((10, 2)) y = np.ones((10,)) model = PySRRegressor() with self.assertRaises(ValueError) as cm: model.fit(X, y, complexity_of_variables=[1, 2, 3]) self.assertIn( "number of elements in `complexity_of_variables`", str(cm.exception) ) def test_error_message_both_variable_complexity(self): X = np.ones((10, 2)) y = np.ones((10,)) model = PySRRegressor(complexity_of_variables=[1, 2]) with self.assertRaises(ValueError) as cm: model.fit(X, y, complexity_of_variables=[1, 2, 3]) self.assertIn( "You cannot set `complexity_of_variables` at both `fit` and `__init__`.", str(cm.exception), ) def test_multioutput_weighted_with_callable_temp_equation(self): X = self.X.copy() y = X[:, [0, 1]] ** 2 w = self.rstate.rand(*y.shape) w[w < 0.5] = 0.0 w[w >= 0.5] = 1.0 # Double equation when weights are 0: y = (2 - w) * y # Thus, pysr needs to use the weights to find the right equation! model = PySRRegressor( unary_operators=["sq(x) = x^2"], binary_operators=["plus"], extra_sympy_mappings={"sq": lambda x: x**2}, **self.default_test_kwargs, procs=0, delete_tempfiles=False, early_stop_condition="stop_if(loss, complexity) = loss < 1e-4 && complexity == 2", ) model.fit(X.copy(), y, weights=w) # These tests are flaky, so don't fail test: try: np.testing.assert_almost_equal( model.predict(X.copy())[:, 0], X[:, 0] ** 2, decimal=3 ) except AssertionError: print("Error in test_multioutput_weighted_with_callable_temp_equation") print("Model equations: ", model.sympy()[0]) print("True equation: x0^2") try: np.testing.assert_almost_equal( model.predict(X.copy())[:, 1], X[:, 1] ** 2, decimal=3 ) except AssertionError: print("Error in test_multioutput_weighted_with_callable_temp_equation") print("Model equations: ", model.sympy()[1]) print("True equation: x1^2") def test_complex_equations_anonymous_stop(self): X = self.rstate.randn(100, 3) + 1j * self.rstate.randn(100, 3) y = (2 + 1j) * np.cos(X[:, 0] * (0.5 - 0.3j)) model = PySRRegressor( binary_operators=["+", "-", "*"], unary_operators=["cos"], **self.default_test_kwargs, early_stop_condition="(loss, complexity) -> loss <= 1e-4 && complexity <= 6", ) model.niterations = DEFAULT_NITERATIONS * 10 model.fit(X, y) test_y = model.predict(X) self.assertTrue(np.issubdtype(test_y.dtype, np.complexfloating)) self.assertLessEqual(np.average(np.abs(test_y - y) ** 2), 1e-4) def test_empty_operators_single_input_warm_start(self): X = self.rstate.randn(100, 1) y = X[:, 0] + 3.0 regressor = PySRRegressor( unary_operators=[], binary_operators=["plus"], **self.default_test_kwargs, early_stop_condition="stop_if(loss, complexity) = loss < 1e-4 && complexity == 3", ) self.assertTrue("None" in regressor.__repr__()) regressor.fit(X, y) self.assertTrue("None" not in regressor.__repr__()) self.assertTrue(">>>>" in regressor.__repr__()) self.assertLessEqual(regressor.equations_.iloc[-1]["loss"], 1e-4) np.testing.assert_almost_equal(regressor.predict(X), y, decimal=1) # Test if repeated fit works: regressor.set_params( niterations=1, ncycles_per_iteration=2, warm_start=True, early_stop_condition=None, ) # We should have that the model state is now a Float32 hof: test_state = regressor.julia_state_ self.assertTrue( jl.first(jl.typeof(jl.last(test_state)).parameters) == jl.Float32 ) # This should exit almost immediately, and use the old equations regressor.fit(X, y) self.assertLessEqual(regressor.equations_.iloc[-1]["loss"], 1e-4) np.testing.assert_almost_equal(regressor.predict(X), y, decimal=1) # Tweak model selection: regressor.set_params(model_selection="best") self.assertEqual(regressor.get_params()["model_selection"], "best") self.assertTrue("None" not in regressor.__repr__()) self.assertTrue(">>>>" in regressor.__repr__()) def test_warm_start_set_at_init(self): # Smoke test for bug where warm_start=True is set at init y = self.X[:, 0] regressor = PySRRegressor(warm_start=True, max_evals=10) regressor.fit(self.X, y) def test_noisy_builtin_variable_names(self): y = self.X[:, [0, 1]] ** 2 + self.rstate.randn(self.X.shape[0], 1) * 0.05 model = PySRRegressor( # Test that passing a single operator works: unary_operators="sq(x) = x^2", binary_operators="plus", extra_sympy_mappings={"sq": lambda x: x**2}, **self.default_test_kwargs, procs=0, denoise=True, early_stop_condition="stop_if(loss, complexity) = loss < 0.05 && complexity == 2", ) # We expect in this case that the "best" # equation should be the right one: model.set_params(model_selection="best") # Also try without a temp equation file: model.set_params(temp_equation_file=False) # We also test builtin variable names model.fit(self.X, y, variable_names=["exec", "hash", "x3", "x4", "x5"]) self.assertLessEqual(model.get_best()[1]["loss"], 1e-2) self.assertLessEqual(model.get_best()[1]["loss"], 1e-2) self.assertIn("exec", model.latex()[0]) self.assertIn("hash", model.latex()[1]) def test_pandas_resample_with_nested_constraints(self): X = pd.DataFrame( { "T": self.rstate.randn(500), "x": self.rstate.randn(500), "unused_feature": self.rstate.randn(500), } ) def true_fn(x): return np.array(x["T"] + x["x"] ** 2 + 1.323837) y = true_fn(X) noise = self.rstate.randn(500) * 0.01 y = y + noise # We also test y as a pandas array: y = pd.Series(y) # Resampled array is a different order of features: Xresampled = pd.DataFrame( { "unused_feature": self.rstate.randn(100), "x": self.rstate.randn(100), "T": self.rstate.randn(100), } ) model = PySRRegressor( unary_operators=[], binary_operators=["+", "*", "/", "-"], **self.default_test_kwargs, denoise=True, nested_constraints={"/": {"+": 1, "-": 1}, "+": {"*": 4}}, early_stop_condition="stop_if(loss, complexity) = loss < 1e-3 && complexity == 7", ) model.fit(X, y, Xresampled=Xresampled) self.assertNotIn("unused_feature", model.latex()) self.assertIn("T", model.latex()) self.assertIn("x", model.latex()) self.assertLessEqual(model.get_best()["loss"], 1e-1) fn = model.get_best()["lambda_format"] X2 = pd.DataFrame( { "T": self.rstate.randn(100), "unused_feature": self.rstate.randn(100), "x": self.rstate.randn(100), } ) self.assertLess(np.average((fn(X2) - true_fn(X2)) ** 2), 1e-1) self.assertLess(np.average((model.predict(X2) - true_fn(X2)) ** 2), 1e-1) def test_high_dim_selection_early_stop(self): X = pd.DataFrame({f"k{i}": self.rstate.randn(10000) for i in range(10)}) Xresampled = pd.DataFrame({f"k{i}": self.rstate.randn(100) for i in range(10)}) y = X["k7"] ** 2 + np.cos(X["k9"]) * 3 model = PySRRegressor( unary_operators=["cos"], select_k_features=3, early_stop_condition=1e-4, # Stop once most accurate equation is <1e-4 MSE maxsize=12, **self.default_test_kwargs, ) model.set_params(model_selection="accuracy") model.fit(X, y, Xresampled=Xresampled) self.assertLess(np.average((model.predict(X) - y) ** 2), 1e-4) # Again, but with numpy arrays: model.fit(X.values, y.values, Xresampled=Xresampled.values) self.assertLess(np.average((model.predict(X.values) - y.values) ** 2), 1e-4) def test_load_model(self): """See if we can load a ran model from the equation file.""" csv_file_data = """Complexity,Loss,Equation 1,0.19951081,"1.9762075" 3,0.12717344,"(f0 + 1.4724599)" 4,0.104823045,"pow_abs(2.2683423, cos(f3))\"""" # Strip the indents: csv_file_data = "\n".join([line.strip() for line in csv_file_data.split("\n")]) for from_backup in [False, True]: rand_dir = Path(tempfile.mkdtemp()) equation_filename = str(rand_dir / "equation.csv") with open(equation_filename + (".bkup" if from_backup else ""), "w") as f: f.write(csv_file_data) model = PySRRegressor.from_file( equation_filename, n_features_in=5, feature_names_in=["f0", "f1", "f2", "f3", "f4"], binary_operators=["+", "*", "/", "-", "^"], unary_operators=["cos"], ) X = self.rstate.rand(100, 5) y_truth = 2.2683423 ** np.cos(X[:, 3]) y_test = model.predict(X, 2) np.testing.assert_allclose(y_truth, y_test) def test_load_model_simple(self): # Test that we can simply load a model from its equation file. y = self.X[:, [0, 1]] ** 2 model = PySRRegressor( # Test that passing a single operator works: unary_operators="sq(x) = x^2", binary_operators="plus", extra_sympy_mappings={"sq": lambda x: x**2}, **self.default_test_kwargs, procs=0, denoise=True, early_stop_condition="stop_if(loss, complexity) = loss < 0.05 && complexity == 2", ) rand_dir = Path(tempfile.mkdtemp()) equation_file = rand_dir / "equations.csv" model.set_params(temp_equation_file=False) model.set_params(equation_file=equation_file) model.fit(self.X, y) # lambda functions are removed from the pickling, so we need # to pass it during the loading: model2 = PySRRegressor.from_file( model.equation_file_, extra_sympy_mappings={"sq": lambda x: x**2} ) np.testing.assert_allclose(model.predict(self.X), model2.predict(self.X)) # Try again, but using only the pickle file: for file_to_delete in [str(equation_file), str(equation_file) + ".bkup"]: if os.path.exists(file_to_delete): os.remove(file_to_delete) # pickle_file = rand_dir / "equations.pkl" model3 = PySRRegressor.from_file( model.equation_file_, extra_sympy_mappings={"sq": lambda x: x**2} ) np.testing.assert_allclose(model.predict(self.X), model3.predict(self.X)) def test_jl_function_error(self): # TODO: Move this to better class with self.assertRaises(ValueError) as cm: PySRRegressor(unary_operators=["1"]).fit([[1]], [1]) self.assertIn( "When building `unary_operators`, `'1'` did not return a Julia function", str(cm.exception), ) def manually_create_model(equations, feature_names=None): if feature_names is None: feature_names = ["x0", "x1"] model = PySRRegressor( progress=False, niterations=1, extra_sympy_mappings={}, output_jax_format=False, model_selection="accuracy", equation_file="equation_file.csv", ) # Set up internal parameters as if it had been fitted: if isinstance(equations, list): # Multi-output. model.equation_file_ = "equation_file.csv" model.nout_ = len(equations) model.selection_mask_ = None model.feature_names_in_ = np.array(feature_names, dtype=object) for i in range(model.nout_): equations[i]["complexity loss equation".split(" ")].to_csv( f"equation_file.csv.out{i+1}.bkup" ) else: model.equation_file_ = "equation_file.csv" model.nout_ = 1 model.selection_mask_ = None model.feature_names_in_ = np.array(feature_names, dtype=object) equations["complexity loss equation".split(" ")].to_csv( "equation_file.csv.bkup" ) model.refresh() return model class TestBest(unittest.TestCase): def setUp(self): self.rstate = np.random.RandomState(0) self.X = self.rstate.randn(10, 2) self.y = np.cos(self.X[:, 0]) ** 2 equations = pd.DataFrame( { "equation": ["1.0", "cos(x0)", "square(cos(x0))"], "loss": [1.0, 0.1, 1e-5], "complexity": [1, 2, 3], } ) self.model = manually_create_model(equations) self.equations_ = self.model.equations_ def test_best(self): self.assertEqual(self.model.sympy(), sympy.cos(sympy.Symbol("x0")) ** 2) def test_index_selection(self): self.assertEqual(self.model.sympy(-1), sympy.cos(sympy.Symbol("x0")) ** 2) self.assertEqual(self.model.sympy(2), sympy.cos(sympy.Symbol("x0")) ** 2) self.assertEqual(self.model.sympy(1), sympy.cos(sympy.Symbol("x0"))) self.assertEqual(self.model.sympy(0), 1.0) def test_best_tex(self): self.assertEqual(self.model.latex(), "\\cos^{2}{\\left(x_{0} \\right)}") def test_best_lambda(self): X = self.X y = self.y for f in [self.model.predict, self.equations_.iloc[-1]["lambda_format"]]: np.testing.assert_almost_equal(f(X), y, decimal=3) def test_all_selection_strategies(self): equations = pd.DataFrame( dict( loss=[1.0, 0.1, 0.01, 0.001 * 1.4, 0.001], score=[0.5, 1.0, 0.5, 0.5, 0.3], ) ) idx_accuracy = idx_model_selection(equations, "accuracy") self.assertEqual(idx_accuracy, 4) idx_best = idx_model_selection(equations, "best") self.assertEqual(idx_best, 3) idx_score = idx_model_selection(equations, "score") self.assertEqual(idx_score, 1) class TestFeatureSelection(unittest.TestCase): def setUp(self): self.rstate = np.random.RandomState(0) def test_feature_selection(self): X = self.rstate.randn(20000, 5) y = X[:, 2] ** 2 + X[:, 3] ** 2 selected = run_feature_selection(X, y, select_k_features=2) np.testing.assert_array_equal(selected, [False, False, True, True, False]) def test_feature_selection_handler(self): X = self.rstate.randn(20000, 5) y = X[:, 2] ** 2 + X[:, 3] ** 2 var_names = [f"x{i}" for i in range(5)] selected_X, selection = _handle_feature_selection( X, select_k_features=2, variable_names=var_names, y=y, ) np.testing.assert_array_equal(selection, [False, False, True, True, False]) selected_var_names = [var_names[i] for i in range(5) if selection[i]] self.assertEqual(set(selected_var_names), set("x2 x3".split(" "))) np.testing.assert_array_equal( np.sort(selected_X, axis=1), np.sort(X[:, [2, 3]], axis=1) ) class TestMiscellaneous(unittest.TestCase): """Test miscellaneous functions.""" def test_csv_to_pkl_conversion(self): """Test that csv filename to pkl filename works as expected.""" tmpdir = Path(tempfile.mkdtemp()) equation_file = tmpdir / "equations.389479384.28378374.csv" expected_pkl_file = tmpdir / "equations.389479384.28378374.pkl" # First, test inputting the paths: test_pkl_file = _csv_filename_to_pkl_filename(equation_file) self.assertEqual(test_pkl_file, str(expected_pkl_file)) # Next, test inputting the strings. test_pkl_file = _csv_filename_to_pkl_filename(str(equation_file)) self.assertEqual(test_pkl_file, str(expected_pkl_file)) def test_pickle_with_temp_equation_file(self): """If we have a temporary equation file, unpickle the estimator.""" model = PySRRegressor( populations=int(1 + DEFAULT_POPULATIONS / 5), temp_equation_file=True, procs=0, multithreading=False, ) nout = 3 X = np.random.randn(100, 2) y = np.random.randn(100, nout) model.fit(X, y) contents = model.equation_file_contents_.copy() y_predictions = model.predict(X) equation_file_base = model.equation_file_ for i in range(1, nout + 1): assert not os.path.exists(str(equation_file_base) + f".out{i}.bkup") with tempfile.NamedTemporaryFile() as pickle_file: pkl.dump(model, pickle_file) pickle_file.seek(0) model2 = pkl.load(pickle_file) contents2 = model2.equation_file_contents_ cols_to_check = ["equation", "loss", "complexity"] for frame1, frame2 in zip(contents, contents2): pd.testing.assert_frame_equal(frame1[cols_to_check], frame2[cols_to_check]) y_predictions2 = model2.predict(X) np.testing.assert_array_almost_equal(y_predictions, y_predictions2) def test_scikit_learn_compatibility(self): """Test PySRRegressor compatibility with scikit-learn.""" model = PySRRegressor( niterations=int(1 + DEFAULT_NITERATIONS / 10), populations=int(1 + DEFAULT_POPULATIONS / 3), ncycles_per_iteration=int(2 + DEFAULT_NCYCLES / 10), verbosity=0, progress=False, random_state=0, deterministic=True, # Deterministic as tests require this. procs=0, multithreading=False, warm_start=False, temp_equation_file=True, ) # Return early. check_generator = check_estimator(model, generate_only=True) exception_messages = [] for _, check in check_generator: if check.func.__name__ == "check_complex_data": # We can use complex data, so avoid this check. continue try: with warnings.catch_warnings(): warnings.simplefilter("ignore") check(model) print("Passed", check.func.__name__) except Exception: error_message = str(traceback.format_exc()) exception_messages.append( f"{check.func.__name__}:\n" + error_message + "\n" ) print("Failed", check.func.__name__, "with:") # Add a leading tab to error message, which # might be multi-line: print("\n".join([(" " * 4) + row for row in error_message.split("\n")])) # If any checks failed don't let the test pass. self.assertEqual(len(exception_messages), 0) def test_param_groupings(self): """Test that param_groupings are complete""" param_groupings_file = Path(__file__).parent.parent / "param_groupings.yml" if not param_groupings_file.exists(): return # Read the file, discarding lines ending in ":", # and removing leading "\s*-\s*": params = [] with open(param_groupings_file, "r") as f: for line in f.readlines(): if line.strip().endswith(":"): continue if line.strip().startswith("-"): params.append(line.strip()[1:].strip()) regressor_params = [ p for p in DEFAULT_PARAMS.keys() if p not in ["self", "kwargs"] ] # Check the sets are equal: self.assertSetEqual(set(params), set(regressor_params)) class TestHelpMessages(unittest.TestCase): """Test user help messages.""" def test_deprecation(self): """Ensure that deprecation works as expected. This should give a warning, and sets the correct value. """ with self.assertWarns(FutureWarning): model = PySRRegressor(fractionReplaced=0.2) # This is a deprecated parameter, so we should get a warning. # The correct value should be set: self.assertEqual(model.fraction_replaced, 0.2) def test_deprecated_functions(self): with self.assertWarns(FutureWarning): install() _jl = None with self.assertWarns(FutureWarning): _jl = init_julia() self.assertEqual(_jl, jl) def test_power_law_warning(self): """Ensure that a warning is given for a power law operator.""" with self.assertWarns(UserWarning): _process_constraints(["^"], [], {}) def test_size_warning(self): """Ensure that a warning is given for a large input size.""" model = PySRRegressor() X = np.random.randn(10001, 2) y = np.random.randn(10001) with warnings.catch_warnings(): warnings.simplefilter("error") with self.assertRaises(Exception) as context: model.fit(X, y) self.assertIn("more than 10,000", str(context.exception)) def test_feature_warning(self): """Ensure that a warning is given for large number of features.""" model = PySRRegressor() X = np.random.randn(100, 10) y = np.random.randn(100) with warnings.catch_warnings(): warnings.simplefilter("error") with self.assertRaises(Exception) as context: model.fit(X, y) self.assertIn("with 10 features or more", str(context.exception)) def test_deterministic_warnings(self): """Ensure that warnings are given for determinism""" model = PySRRegressor(random_state=0) X = np.random.randn(100, 2) y = np.random.randn(100) with warnings.catch_warnings(): warnings.simplefilter("error") with self.assertRaises(Exception) as context: model.fit(X, y) self.assertIn("`deterministic`", str(context.exception)) def test_deterministic_errors(self): """Setting deterministic without random_state should error""" model = PySRRegressor(deterministic=True) X = np.random.randn(100, 2) y = np.random.randn(100) with self.assertRaises(ValueError): model.fit(X, y) def test_extra_sympy_mappings_undefined(self): """extra_sympy_mappings=None errors for custom operators""" model = PySRRegressor(unary_operators=["square2(x) = x^2"]) X = np.random.randn(100, 2) y = np.random.randn(100) with self.assertRaises(ValueError): model.fit(X, y) def test_sympy_function_fails_as_variable(self): model = PySRRegressor() X = np.random.randn(100, 2) y = np.random.randn(100) with self.assertRaises(ValueError) as cm: model.fit(X, y, variable_names=["x1", "N"]) self.assertIn("Variable name", str(cm.exception)) def test_bad_variable_names_fail(self): model = PySRRegressor() X = np.random.randn(100, 1) y = np.random.randn(100) with self.assertRaises(ValueError) as cm: model.fit(X, y, variable_names=["Tr(Tij)"]) self.assertIn("Invalid variable name", str(cm.exception)) with self.assertRaises(ValueError) as cm: model.fit(X, y, variable_names=["f{c}"]) self.assertIn("Invalid variable name", str(cm.exception)) def test_bad_kwargs(self): bad_kwargs = [ dict( kwargs=dict( elementwise_loss="g(x, y) = 0.0", loss_function="f(*args) = 0.0" ), error=ValueError, ), dict( kwargs=dict(maxsize=3), error=ValueError, ), dict( kwargs=dict(tournament_selection_n=10, population_size=3), error=ValueError, ), dict( kwargs=dict(optimizer_algorithm="COBYLA"), error=NotImplementedError, ), dict( kwargs=dict( constraints={ "+": (3, 5), } ), error=NotImplementedError, ), dict( kwargs=dict(binary_operators=["α(x, y) = x - y"]), error=ValueError, ), dict( kwargs=dict(model_selection="unknown"), error=NotImplementedError, ), ] for opt in bad_kwargs: model = PySRRegressor(**opt["kwargs"], niterations=1) with self.assertRaises(opt["error"]): model.fit([[1]], [1]) model.get_best() print("Failed", opt["kwargs"]) def test_suggest_keywords(self): # Easy self.assertEqual( _suggest_keywords(PySRRegressor, "loss_function"), ["loss_function"] ) # More complex, and with error with self.assertRaises(TypeError) as cm: PySRRegressor(ncyclesperiterationn=5) self.assertIn( "`ncyclesperiterationn` is not a valid keyword", str(cm.exception) ) self.assertIn("Did you mean", str(cm.exception)) self.assertIn("`ncycles_per_iteration`, ", str(cm.exception)) self.assertIn("`niterations`", str(cm.exception)) # Farther matches (this might need to be changed) with self.assertRaises(TypeError) as cm: PySRRegressor(operators=["+", "-"]) self.assertIn("`unary_operators`, `binary_operators`", str(cm.exception)) def test_issue_666(self): # Try the equivalent of `from pysr import *` pysr_module = importlib.import_module("pysr") names_to_import = pysr_module.__all__ for name in names_to_import: getattr(pysr_module, name) TRUE_PREAMBLE = "\n".join( [ r"\usepackage{breqn}", r"\usepackage{booktabs}", "", "...", "", ] ) class TestLaTeXTable(unittest.TestCase): def setUp(self): equations = pd.DataFrame( dict( equation=["x0", "cos(x0)", "x0 + x1 - cos(x1 * x0)"], loss=[1.052, 0.02315, 1.12347e-15], complexity=[1, 2, 8], ) ) self.model = manually_create_model(equations) self.maxDiff = None def create_true_latex(self, middle_part, include_score=False): if include_score: true_latex_table_str = r""" \begin{table}[h] \begin{center} \begin{tabular}{@{}cccc@{}} \toprule Equation & Complexity & Loss & Score \\ \midrule""" else: true_latex_table_str = r""" \begin{table}[h] \begin{center} \begin{tabular}{@{}ccc@{}} \toprule Equation & Complexity & Loss \\ \midrule""" true_latex_table_str += middle_part true_latex_table_str += r"""\bottomrule \end{tabular} \end{center} \end{table} """ # First, remove empty lines: true_latex_table_str = "\n".join( [line.strip() for line in true_latex_table_str.split("\n") if len(line) > 0] ) return true_latex_table_str.strip() def test_simple_table(self): latex_table_str = self.model.latex_table( columns=["equation", "complexity", "loss"] ) middle_part = r""" $y = x_{0}$ & $1$ & $1.05$ \\ $y = \cos{\left(x_{0} \right)}$ & $2$ & $0.0232$ \\ $y = x_{0} + x_{1} - \cos{\left(x_{0} x_{1} \right)}$ & $8$ & $1.12 \cdot 10^{-15}$ \\ """ true_latex_table_str = ( TRUE_PREAMBLE + "\n" + self.create_true_latex(middle_part) ) self.assertEqual(latex_table_str, true_latex_table_str) def test_other_precision(self): latex_table_str = self.model.latex_table( precision=5, columns=["equation", "complexity", "loss"] ) middle_part = r""" $y = x_{0}$ & $1$ & $1.0520$ \\ $y = \cos{\left(x_{0} \right)}$ & $2$ & $0.023150$ \\ $y = x_{0} + x_{1} - \cos{\left(x_{0} x_{1} \right)}$ & $8$ & $1.1235 \cdot 10^{-15}$ \\ """ true_latex_table_str = ( TRUE_PREAMBLE + "\n" + self.create_true_latex(middle_part) ) self.assertEqual(latex_table_str, true_latex_table_str) def test_include_score(self): latex_table_str = self.model.latex_table() middle_part = r""" $y = x_{0}$ & $1$ & $1.05$ & $0.0$ \\ $y = \cos{\left(x_{0} \right)}$ & $2$ & $0.0232$ & $3.82$ \\ $y = x_{0} + x_{1} - \cos{\left(x_{0} x_{1} \right)}$ & $8$ & $1.12 \cdot 10^{-15}$ & $5.11$ \\ """ true_latex_table_str = ( TRUE_PREAMBLE + "\n" + self.create_true_latex(middle_part, include_score=True) ) self.assertEqual(latex_table_str, true_latex_table_str) def test_last_equation(self): latex_table_str = self.model.latex_table( indices=[2], columns=["equation", "complexity", "loss"] ) middle_part = r""" $y = x_{0} + x_{1} - \cos{\left(x_{0} x_{1} \right)}$ & $8$ & $1.12 \cdot 10^{-15}$ \\ """ true_latex_table_str = ( TRUE_PREAMBLE + "\n" + self.create_true_latex(middle_part) ) self.assertEqual(latex_table_str, true_latex_table_str) def test_multi_output(self): equations1 = pd.DataFrame( dict( equation=["x0", "cos(x0)", "x0 + x1 - cos(x1 * x0)"], loss=[1.052, 0.02315, 1.12347e-15], complexity=[1, 2, 8], ) ) equations2 = pd.DataFrame( dict( equation=["x1", "cos(x1)", "x0 * x0 * x1"], loss=[1.32, 0.052, 2e-15], complexity=[1, 2, 5], ) ) equations = [equations1, equations2] model = manually_create_model(equations) middle_part_1 = r""" $y_{0} = x_{0}$ & $1$ & $1.05$ & $0.0$ \\ $y_{0} = \cos{\left(x_{0} \right)}$ & $2$ & $0.0232$ & $3.82$ \\ $y_{0} = x_{0} + x_{1} - \cos{\left(x_{0} x_{1} \right)}$ & $8$ & $1.12 \cdot 10^{-15}$ & $5.11$ \\ """ middle_part_2 = r""" $y_{1} = x_{1}$ & $1$ & $1.32$ & $0.0$ \\ $y_{1} = \cos{\left(x_{1} \right)}$ & $2$ & $0.0520$ & $3.23$ \\ $y_{1} = x_{0} x_{0} x_{1}$ & $5$ & $2.00 \cdot 10^{-15}$ & $10.3$ \\ """ true_latex_table_str = "\n\n".join( self.create_true_latex(part, include_score=True) for part in [middle_part_1, middle_part_2] ) true_latex_table_str = TRUE_PREAMBLE + "\n" + true_latex_table_str latex_table_str = model.latex_table() self.assertEqual(latex_table_str, true_latex_table_str) def test_latex_float_precision(self): """Test that we can print latex expressions with custom precision""" expr = sympy.Float(4583.4485748, dps=50) self.assertEqual(sympy2latex(expr, prec=6), r"4583.45") self.assertEqual(sympy2latex(expr, prec=5), r"4583.4") self.assertEqual(sympy2latex(expr, prec=4), r"4583.") self.assertEqual(sympy2latex(expr, prec=3), r"4.58 \cdot 10^{3}") self.assertEqual(sympy2latex(expr, prec=2), r"4.6 \cdot 10^{3}") # Multiple numbers: x = sympy.Symbol("x") expr = x * 3232.324857384 - 1.4857485e-10 self.assertEqual( sympy2latex(expr, prec=2), r"3.2 \cdot 10^{3} x - 1.5 \cdot 10^{-10}" ) self.assertEqual( sympy2latex(expr, prec=3), r"3.23 \cdot 10^{3} x - 1.49 \cdot 10^{-10}" ) self.assertEqual( sympy2latex(expr, prec=8), r"3232.3249 x - 1.4857485 \cdot 10^{-10}" ) def test_latex_break_long_equation(self): """Test that we can break a long equation inside the table""" long_equation = """ - cos(x1 * x0) + 3.2 * x0 - 1.2 * x1 + x1 * x1 * x1 + x0 * x0 * x0 + 5.2 * sin(0.3256 * sin(x2) - 2.6 * x0) + x0 * x0 * x0 * x0 * x0 + cos(cos(x1 * x0) + 3.2 * x0 - 1.2 * x1 + x1 * x1 * x1 + x0 * x0 * x0) """ long_equation = "".join(long_equation.split("\n")).strip() equations = pd.DataFrame( dict( equation=["x0", "cos(x0)", long_equation], loss=[1.052, 0.02315, 1.12347e-15], complexity=[1, 2, 30], ) ) model = manually_create_model(equations) latex_table_str = model.latex_table() middle_part = r""" $y = x_{0}$ & $1$ & $1.05$ & $0.0$ \\ $y = \cos{\left(x_{0} \right)}$ & $2$ & $0.0232$ & $3.82$ \\ \begin{minipage}{0.8\linewidth} \vspace{-1em} \begin{dmath*} y = x_{0} x_{0} x_{0} + x_{0} x_{0} x_{0} x_{0} x_{0} + 3.20 x_{0} - 1.20 x_{1} + x_{1} x_{1} x_{1} + 5.20 \sin{\left(- 2.60 x_{0} + 0.326 \sin{\left(x_{2} \right)} \right)} - \cos{\left(x_{0} x_{1} \right)} + \cos{\left(x_{0} x_{0} x_{0} + 3.20 x_{0} - 1.20 x_{1} + x_{1} x_{1} x_{1} + \cos{\left(x_{0} x_{1} \right)} \right)} \end{dmath*} \end{minipage} & $30$ & $1.12 \cdot 10^{-15}$ & $1.09$ \\ """ true_latex_table_str = ( TRUE_PREAMBLE + "\n" + self.create_true_latex(middle_part, include_score=True) ) self.assertEqual(latex_table_str, true_latex_table_str) class TestDimensionalConstraints(unittest.TestCase): def setUp(self): self.default_test_kwargs = dict( progress=False, model_selection="accuracy", niterations=DEFAULT_NITERATIONS * 2, populations=DEFAULT_POPULATIONS * 2, temp_equation_file=True, ) self.rstate = np.random.RandomState(0) self.X = self.rstate.randn(100, 5) def test_dimensional_constraints(self): y = np.cos(self.X[:, [0, 1]]) model = PySRRegressor( binary_operators=[ "my_add(x, y) = x + y", "my_sub(x, y) = x - y", "my_mul(x, y) = x * y", ], unary_operators=["my_cos(x) = cos(x)"], **self.default_test_kwargs, early_stop_condition=1e-8, select_k_features=3, extra_sympy_mappings={ "my_cos": sympy.cos, "my_add": lambda x, y: x + y, "my_sub": lambda x, y: x - y, "my_mul": lambda x, y: x * y, }, ) model.fit(self.X, y, X_units=["m", "m", "m", "m", "m"], y_units=["m", "m"]) # The best expression should have complexity larger than just 2: for i in range(2): self.assertGreater(model.get_best()[i]["complexity"], 2) self.assertLess(model.get_best()[i]["loss"], 1e-6) simple_eqs = model.equations_[i].query("complexity <= 2") self.assertTrue(len(simple_eqs) == 0 or simple_eqs.loss.min() > 1e-6) def test_unit_checks(self): """This just checks the number of units passed""" use_custom_variable_names = False variable_names = None complexity_of_variables = 1 weights = None args = ( use_custom_variable_names, variable_names, complexity_of_variables, weights, ) valid_units = [ (np.ones((10, 2)), np.ones(10), ["m/s", "s"], "m"), (np.ones((10, 1)), np.ones(10), ["m/s"], None), (np.ones((10, 1)), np.ones(10), None, "km/s"), (np.ones((10, 1)), np.ones(10), None, ["m/s"]), (np.ones((10, 1)), np.ones((10, 1)), None, ["m/s"]), (np.ones((10, 1)), np.ones((10, 2)), None, ["m/s", ""]), ] for X, y, X_units, y_units in valid_units: _check_assertions( X, *args, y, X_units, y_units, ) invalid_units = [ (np.ones((10, 2)), np.ones(10), ["m/s", "s", "s^2"], None), (np.ones((10, 2)), np.ones(10), ["m/s", "s", "s^2"], "km"), (np.ones((10, 2)), np.ones((10, 2)), ["m/s", "s"], ["m"]), (np.ones((10, 1)), np.ones((10, 1)), "m/s", ["m"]), ] for X, y, X_units, y_units in invalid_units: with self.assertRaises(ValueError): _check_assertions( X, *args, y, X_units, y_units, ) def test_unit_propagation(self): """Check that units are propagated correctly. This also tests that variables have the correct names. """ X = np.ones((100, 3)) y = np.ones((100, 1)) temp_dir = Path(tempfile.mkdtemp()) equation_file = str(temp_dir / "equation_file.csv") model = PySRRegressor( binary_operators=["+", "*"], early_stop_condition="(l, c) -> l < 1e-6 && c == 3", progress=False, model_selection="accuracy", niterations=DEFAULT_NITERATIONS * 2, populations=DEFAULT_POPULATIONS * 2, complexity_of_constants=10, weight_mutate_constant=0.0, should_optimize_constants=False, multithreading=False, deterministic=True, procs=0, random_state=0, equation_file=equation_file, warm_start=True, ) model.fit( X, y, X_units=["m", "s", "A"], y_units=["m*A"], ) best = model.get_best() self.assertIn("x0", best["equation"]) self.assertNotIn("x1", best["equation"]) self.assertIn("x2", best["equation"]) self.assertEqual(best["complexity"], 3) self.assertTrue( model.equations_.iloc[0].complexity > 1 or model.equations_.iloc[0].loss > 1e-6 ) # With pkl file: pkl_file = str(temp_dir / "equation_file.pkl") model2 = PySRRegressor.from_file(pkl_file) best2 = model2.get_best() self.assertIn("x0", best2["equation"]) # From csv file alone (we need to delete pkl file:) # First, we delete the pkl file: os.remove(pkl_file) model3 = PySRRegressor.from_file( equation_file, binary_operators=["+", "*"], n_features_in=X.shape[1] ) best3 = model3.get_best() self.assertIn("x0", best3["equation"]) # Try warm start, but with no units provided (should # be a different dataset, and thus different result): model.early_stop_condition = "(l, c) -> l < 1e-6 && c == 1" model.fit(X, y) self.assertEqual(model.equations_.iloc[0].complexity, 1) self.assertLess(model.equations_.iloc[0].loss, 1e-6) # TODO: Determine desired behavior if second .fit() call does not have units def runtests(just_tests=False): """Run all tests in test.py.""" test_cases = [ TestPipeline, TestBest, TestFeatureSelection, TestMiscellaneous, TestHelpMessages, TestLaTeXTable, TestDimensionalConstraints, ] if just_tests: return test_cases suite = unittest.TestSuite() loader = unittest.TestLoader() for test_case in test_cases: suite.addTests(loader.loadTestsFromTestCase(test_case)) runner = unittest.TextTestRunner() return runner.run(suite)