Rename loss => elementwise_loss and full_objective => loss_function

README.md

@@ -214,7 +214,7 @@ model = PySRRegressor(
     ],
     extra_sympy_mappings={"inv": lambda x: 1 / x},
     # ^ Define operator for SymPy as well
-    loss="loss(prediction, target) = (prediction - target)^2",
+    elementwise_loss="loss(prediction, target) = (prediction - target)^2",
     # ^ Custom loss function (julia syntax)
 )
 ```

docs/examples.md

@@ -144,7 +144,7 @@ but there are still some additional steps you can take to reduce the effect of n
 
 One thing you could do, which we won't detail here, is to create a custom log-likelihood
 given some assumed noise model. By passing weights to the fit function, and
-defining a custom loss function such as `loss="myloss(x, y, w) = w * (x - y)^2"`,
+defining a custom loss function such as `elementwise_loss="myloss(x, y, w) = w * (x - y)^2"`,
 you can define any sort of log-likelihood you wish. (However, note that it must be bounded at zero)
 
 However, the simplest thing to do is preprocessing, just like for feature selection. To do this,
@@ -380,7 +380,7 @@ end
 model = PySRRegressor(
     niterations=100,
     binary_operators=["*", "+", "-"],
-    full_objective=objective,
+    loss_function=objective,
 )
 ```
 
@@ -462,7 +462,7 @@ let's also create a custom loss function
 that looks at the error in log-space:
 
 ```python
-loss = """function loss_fnc(prediction, target)
+elementwise_loss = """function loss_fnc(prediction, target)
     scatter_loss = abs(log((abs(prediction)+1e-20) / (abs(target)+1e-20)))
     sign_loss = 10 * (sign(prediction) - sign(target))^2
     return scatter_loss + sign_loss
@@ -476,7 +476,7 @@ Now let's define our model:
 model = PySRRegressor(
     binary_operators=["+", "-", "*", "/"],
     unary_operators=["square"],
-    loss=loss,
+    elementwise_loss=elementwise_loss,
     complexity_of_constants=2,
     maxsize=25,
     niterations=100,

docs/options.md

@@ -243,7 +243,7 @@ train the parameters within JAX (and is differentiable).
 
 The default loss is mean-square error, and weighted mean-square error.
 One can pass an arbitrary Julia string to define a custom loss, using,
-e.g., `loss="myloss(x, y) = abs(x - y)^1.5"`. For more details,
+e.g., `elementwise_loss="myloss(x, y) = abs(x - y)^1.5"`. For more details,
 see the
 [Losses](https://milescranmer.github.io/SymbolicRegression.jl/dev/losses/)
 page for SymbolicRegression.jl.
@@ -253,26 +253,26 @@ Here are some additional examples:
 abs(x-y) loss
 
 ```python
-PySRRegressor(..., loss="f(x, y) = abs(x - y)^1.5")
+PySRRegressor(..., elementwise_loss="f(x, y) = abs(x - y)^1.5")
 ```
 
 Note that the function name doesn't matter:
 
 ```python
-PySRRegressor(..., loss="loss(x, y) = abs(x * y)")
+PySRRegressor(..., elementwise_loss="loss(x, y) = abs(x * y)")
 ```
 
 With weights:
 
 ```python
-model = PySRRegressor(..., loss="myloss(x, y, w) = w * abs(x - y)")
+model = PySRRegressor(..., elementwise_loss="myloss(x, y, w) = w * abs(x - y)")
 model.fit(..., weights=weights)
 ```
 
 Weights can be used in arbitrary ways:
 
 ```python
-model = PySRRegressor(..., weights=weights, loss="myloss(x, y, w) = abs(x - y)^2/w^2")
+model = PySRRegressor(..., weights=weights, elementwise_loss="myloss(x, y, w) = abs(x - y)^2/w^2")
 model.fit(..., weights=weights)
 ```
 
@@ -280,13 +280,13 @@ Built-in loss (faster) (see [losses](https://astroautomata.com/SymbolicRegressio
 This one computes the L3 norm:
 
 ```python
-PySRRegressor(..., loss="LPDistLoss{3}()")
+PySRRegressor(..., elementwise_loss="LPDistLoss{3}()")
 ```
 
 Can also uses these losses for weighted (weighted-average):
 
 ```python
-model = PySRRegressor(..., weights=weights, loss="LPDistLoss{3}()")
+model = PySRRegressor(..., weights=weights, elementwise_loss="LPDistLoss{3}()")
 model.fit(..., weights=weights)
 ```
 

example.py

@@ -18,7 +18,7 @@ model = PySRRegressor(
     ],
     extra_sympy_mappings={"inv": lambda x: 1 / x},
     # ^ Define operator for SymPy as well
-    loss="loss(x, y) = (x - y)^2",
+    elementwise_loss="loss(x, y) = (x - y)^2",
     # ^ Custom loss function (julia syntax)
 )
 

examples/pysr_demo.ipynb

@@ -576,7 +576,7 @@
    "outputs": [],
    "source": [
     "model = PySRRegressor(\n",
-    "    loss=\"myloss(x, y, w) = w * abs(x - y)\",  # Custom loss function with weights.\n",
+    "    elementwise_loss=\"myloss(x, y, w) = w * abs(x - y)\",  # Custom loss function with weights.\n",
     "    niterations=20,\n",
     "    populations=20,  # Use more populations\n",
     "    binary_operators=[\"+\", \"*\"],\n",

pysr/__init__.py

@@ -4,10 +4,9 @@
 from .julia_import import jl, SymbolicRegression  # isort:skip
 
 from . import sklearn_monkeypatch
-from .deprecated import best, best_callable, best_row, best_tex, pysr
+from .deprecated import best, best_callable, best_row, best_tex, install, pysr
 from .export_jax import sympy2jax
 from .export_torch import sympy2torch
-from .julia_helpers import install
 from .sr import PySRRegressor
 
 # This file is created by setuptools_scm during the build process:
@@ -28,5 +27,4 @@ __all__ = [
     "best_tex",
     "pysr",
     "__version__",
-    "install",
 ]

pysr/deprecated.py

@@ -2,6 +2,22 @@
 import warnings
 
 
+def install(*args, **kwargs):
+    del args, kwargs
+    warnings.warn(
+        "The `install` function has been removed. "
+        "PySR now uses the `juliacall` package to install its dependencies automatically at import time. "
+    )
+
+
+def init_julia(*args, **kwargs):
+    del args, kwargs
+    warnings.warn(
+        "The `init_julia` function has been removed. "
+        "Julia is now initialized automatically at import time."
+    )
+
+
 def pysr(X, y, weights=None, **kwargs):  # pragma: no cover
     from .sr import PySRRegressor
 
@@ -55,39 +71,28 @@ def best_callable(*args, **kwargs):  # pragma: no cover
     )
 
 
-def make_deprecated_kwargs_for_pysr_regressor():
-    """Create dict of deprecated kwargs."""
-
-    deprecation_string = """
-        fractionReplaced => fraction_replaced
-        fractionReplacedHof => fraction_replaced_hof
-        npop => population_size
-        hofMigration => hof_migration
-        shouldOptimizeConstants => should_optimize_constants
-        weightAddNode => weight_add_node
-        weightDeleteNode => weight_delete_node
-        weightDoNothing => weight_do_nothing
-        weightInsertNode => weight_insert_node
-        weightMutateConstant => weight_mutate_constant
-        weightMutateOperator => weight_mutate_operator
-        weightSwapOperands => weight_swap_operands
-        weightRandomize => weight_randomize
-        weightSimplify => weight_simplify
-        crossoverProbability => crossover_probability
-        perturbationFactor => perturbation_factor
-        batchSize => batch_size
-        warmupMaxsizeBy => warmup_maxsize_by
-        useFrequency => use_frequency
-        useFrequencyInTournament => use_frequency_in_tournament
-        ncyclesperiteration => ncycles_per_iteration
-    """
-    # Turn this into a dict:
-    deprecated_kwargs = {}
-    for line in deprecation_string.splitlines():
-        line = line.replace(" ", "")
-        if line == "":
-            continue
-        old, new = line.split("=>")
-        deprecated_kwargs[old] = new
-
-    return deprecated_kwargs
+DEPRECATED_KWARGS = {
+    "fractionReplaced": "fraction_replaced",
+    "fractionReplacedHof": "fraction_replaced_hof",
+    "npop": "population_size",
+    "hofMigration": "hof_migration",
+    "shouldOptimizeConstants": "should_optimize_constants",
+    "weightAddNode": "weight_add_node",
+    "weightDeleteNode": "weight_delete_node",
+    "weightDoNothing": "weight_do_nothing",
+    "weightInsertNode": "weight_insert_node",
+    "weightMutateConstant": "weight_mutate_constant",
+    "weightMutateOperator": "weight_mutate_operator",
+    "weightSwapOperands": "weight_swap_operands",
+    "weightRandomize": "weight_randomize",
+    "weightSimplify": "weight_simplify",
+    "crossoverProbability": "crossover_probability",
+    "perturbationFactor": "perturbation_factor",
+    "batchSize": "batch_size",
+    "warmupMaxsizeBy": "warmup_maxsize_by",
+    "useFrequency": "use_frequency",
+    "useFrequencyInTournament": "use_frequency_in_tournament",
+    "ncyclesperiteration": "ncycles_per_iteration",
+    "loss": "elementwise_loss",
+    "full_objective": "loss_function",
+}

pysr/julia_helpers.py

@@ -1,9 +1,9 @@
 """Functions for initializing the Julia environment and installing deps."""
-import warnings
 
 import numpy as np
 from juliacall import convert as jl_convert  # type: ignore
 
+from .deprecated import init_julia, install
 from .julia_import import jl
 
 jl.seval("using Serialization: Serialization")
@@ -15,14 +15,6 @@ PythonCall = jl.PythonCall
 jl.seval("using SymbolicRegression: plus, sub, mult, div, pow")
 
 
-def install(*args, **kwargs):
-    del args, kwargs
-    warnings.warn(
-        "The `install` function has been removed. "
-        "PySR now uses the `juliacall` package to install its dependencies automatically at import time. "
-    )
-
-
 def _escape_filename(filename):
     """Turn a path into a string with correctly escaped backslashes."""
     str_repr = str(filename)

pysr/param_groupings.yml

@@ -10,8 +10,8 @@
     - population_size
     - ncycles_per_iteration
   - The Objective:
-    - loss
-    - full_objective
+    - elementwise_loss
+    - loss_function
     - model_selection
     - dimensional_constraint_penalty
   - Working with Complexities:

pysr/sr.py

@@ -25,7 +25,7 @@ from sklearn.utils import check_array, check_consistent_length, check_random_sta
 from sklearn.utils.validation import _check_feature_names_in, check_is_fitted
 
 from .denoising import denoise, multi_denoise
-from .deprecated import make_deprecated_kwargs_for_pysr_regressor
+from .deprecated import DEPRECATED_KWARGS
 from .export_jax import sympy2jax
 from .export_latex import sympy2latex, sympy2latextable, sympy2multilatextable
 from .export_numpy import sympy2numpy
@@ -268,7 +268,7 @@ class PySRRegressor(MultiOutputMixin, RegressorMixin, BaseEstimator):
         arguments are treated the same way, and the max of each
         argument is constrained.
         Default is `None`.
-    loss : str
+    elementwise_loss : str
         String of Julia code specifying an elementwise loss function.
         Can either be a loss from LossFunctions.jl, or your own loss
         written as a function. Examples of custom written losses include:
@@ -284,11 +284,11 @@ class PySRRegressor(MultiOutputMixin, RegressorMixin, BaseEstimator):
         `ModifiedHuberLoss()`, `L2MarginLoss()`, `ExpLoss()`,
         `SigmoidLoss()`, `DWDMarginLoss(q)`.
         Default is `"L2DistLoss()"`.
-    full_objective : str
+    loss_function : str
         Alternatively, you can specify the full objective function as
         a snippet of Julia code, including any sort of custom evaluation
         (including symbolic manipulations beforehand), and any sort
-        of loss function or regularizations. The default `full_objective`
+        of loss function or regularizations. The default `loss_function`
         used in SymbolicRegression.jl is roughly equal to:
         ```julia
         function eval_loss(tree, dataset::Dataset{T,L}, options)::L where {T,L}
@@ -637,7 +637,7 @@ class PySRRegressor(MultiOutputMixin, RegressorMixin, BaseEstimator):
     ...         "inv(x) = 1/x",  # Custom operator (julia syntax)
     ...     ],
     ...     model_selection="best",
-    ...     loss="loss(x, y) = (x - y)^2",  # Custom loss function (julia syntax)
+    ...     elementwise_loss="loss(x, y) = (x - y)^2",  # Custom loss function (julia syntax)
     ... )
     >>> model.fit(X, y)
     >>> model
@@ -675,8 +675,8 @@ class PySRRegressor(MultiOutputMixin, RegressorMixin, BaseEstimator):
         timeout_in_seconds: Optional[float] = None,
         constraints: Optional[Dict[str, Union[int, Tuple[int, int]]]] = None,
         nested_constraints: Optional[Dict[str, Dict[str, int]]] = None,
-        loss: Optional[str] = None,
-        full_objective: Optional[str] = None,
+        elementwise_loss: Optional[str] = None,
+        loss_function: Optional[str] = None,
         complexity_of_operators: Optional[Dict[str, Union[int, float]]] = None,
         complexity_of_constants: Union[int, float] = 1,
         complexity_of_variables: Union[int, float] = 1,
@@ -769,8 +769,8 @@ class PySRRegressor(MultiOutputMixin, RegressorMixin, BaseEstimator):
         self.timeout_in_seconds = timeout_in_seconds
         self.early_stop_condition = early_stop_condition
         # - Loss parameters
-        self.loss = loss
-        self.full_objective = full_objective
+        self.elementwise_loss = elementwise_loss
+        self.loss_function = loss_function
         self.complexity_of_operators = complexity_of_operators
         self.complexity_of_constants = complexity_of_constants
         self.complexity_of_variables = complexity_of_variables
@@ -849,11 +849,10 @@ class PySRRegressor(MultiOutputMixin, RegressorMixin, BaseEstimator):
         # Once all valid parameters have been assigned handle the
         # deprecated kwargs
         if len(kwargs) > 0:  # pragma: no cover
-            deprecated_kwargs = make_deprecated_kwargs_for_pysr_regressor()
             for k, v in kwargs.items():
                 # Handle renamed kwargs
-                if k in deprecated_kwargs:
-                    updated_kwarg_name = deprecated_kwargs[k]
+                if k in DEPRECATED_KWARGS:
+                    updated_kwarg_name = DEPRECATED_KWARGS[k]
                     setattr(self, updated_kwarg_name, v)
                     warnings.warn(
                         f"{k} has been renamed to {updated_kwarg_name} in PySRRegressor. "
@@ -1251,8 +1250,10 @@ class PySRRegressor(MultiOutputMixin, RegressorMixin, BaseEstimator):
                 "to True and `procs` to 0 will result in non-deterministic searches. "
             )
 
-        if self.loss is not None and self.full_objective is not None:
-            raise ValueError("You cannot set both `loss` and `full_objective`.")
+        if self.elementwise_loss is not None and self.loss_function is not None:
+            raise ValueError(
+                "You cannot set both `elementwise_loss` and `loss_function`."
+            )
 
         # NotImplementedError - Values that could be supported at a later time
         if self.optimizer_algorithm not in VALID_OPTIMIZER_ALGORITHMS:
@@ -1587,9 +1588,13 @@ class PySRRegressor(MultiOutputMixin, RegressorMixin, BaseEstimator):
             complexity_of_operators_str += ")"
             complexity_of_operators = jl.seval(complexity_of_operators_str)
 
-        custom_loss = jl.seval(str(self.loss) if self.loss is not None else "nothing")
+        custom_loss = jl.seval(
+            str(self.elementwise_loss)
+            if self.elementwise_loss is not None
+            else "nothing"
+        )
         custom_full_objective = jl.seval(
-            str(self.full_objective) if self.full_objective is not None else "nothing"
+            str(self.loss_function) if self.loss_function is not None else "nothing"
         )
 
         early_stop_condition = jl.seval(

pysr/test/test.py

@@ -80,7 +80,7 @@ class TestPipeline(unittest.TestCase):
             multithreading=False,
             turbo=True,
             early_stop_condition="stop_if(loss, complexity) = loss < 1e-10 && complexity == 1",
-            full_objective="""
+            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)
@@ -100,7 +100,7 @@ class TestPipeline(unittest.TestCase):
         model = PySRRegressor(
             **self.default_test_kwargs,
             early_stop_condition="stop_if(loss, complexity) = loss < 1e-4 && complexity == 3",
-            loss="my_loss(prediction, target) = (prediction - target)^2",
+            elementwise_loss="my_loss(prediction, target) = (prediction - target)^2",
             precision=64,
             parsimony=0.01,
             warm_start=True,