Merge branch 'master' of github.com:erp12/pyshgp

README.md

@@ -46,13 +46,14 @@ Although PushGP is constantly changing through research and publication, `pyshgp
 ```sh
 pip install pyshgp
 ```
+- That's it! Read through the docs and examples to learn more.
 
-### Build Frome source
+### Build From source
 
 - Clone the repo
 - cd into the `pyshgp` repo directory
 - run `pip install . --upgrade`
-- Thats it! Check out the examples and documentation.
+- That's it! Read through the docs and examples to learn more.
 
 ### Running Tests
 

examples/integer_regression.py

@@ -46,6 +46,3 @@ def target_function(a, b):
     )
 
     est.fit(X=X, y=y)
-    print(est.solution.program.pretty_str())
-    print(est.predict(X))
-    print(est.score(X, y))

examples/leaky_relu.py

@@ -57,6 +57,3 @@ def target_function(x: float) -> (float, float):
     )
 
     est.fit(X=X, y=y)
-    print(est.solution.program.pretty_str())
-    print(est.predict(X))
-    print(est.score(X, y))

examples/odd.py

@@ -30,6 +30,3 @@
     )
 
     est.fit(X, y)
-    print(est.solution.program.pretty_str())
-    print(est.predict(X))
-    print(est.score(X, y))

examples/point_distance.py

@@ -114,6 +114,7 @@ def point_from_floats(f1, f2):
 
 if __name__ == "__main__":
     est.fit(X, y)
+    print("Best program found:")
     print(est.solution.program.pretty_str())
-    print(est.predict(X))
+    print("Errors:")
     print(est.score(X, y))

examples/software_synthesis/replace_space_with_newline.py

@@ -118,9 +118,8 @@ def random_char():
     start = time.time()
     est.fit(X=X_train, y=y_train)
     end = time.time()
-    print("train_error: ", est.solution.total_error)
-    print("test_error: ", np.sum(est.score(X_test, y_test)))
-    print("runtime: ", end - start)
-    print("final_generation: ", est.search.generation)
-    print("best_genome: ", est.solution.genome)
-    print("best_program_str:", est.solution.program.pretty_str())
+    print("========================================")
+    print("post-evolution stats")
+    print("========================================")
+    print("Runtime: ", end - start)
+    print("Test Error: ", np.sum(est.score(X_test, y_test)))

examples/string_demo.py

@@ -54,6 +54,7 @@ def target_function(s):
     )
 
     est.fit(X=X, y=y)
+    print("Best program found:")
     print(est.solution.program.pretty_str())
-    print(est.predict(X))
+    print("Errors:")
     print(est.score(X, y))

examples/string_demo_annealing.py

@@ -56,6 +56,7 @@ def target_function(s):
     )
 
     est.fit(X=X, y=y)
+    print("Best program found:")
     print(est.solution.program.pretty_str())
-    print(est.predict(X))
+    print("Errors:")
     print(est.score(X, y))

pyshgp/gp/estimators.py

@@ -11,7 +11,7 @@
 from pyshgp.push.interpreter import PushInterpreter, DEFAULT_INTERPRETER
 from pyshgp.push.config import PushConfig
 from pyshgp.push.program import ProgramSignature
-from pyshgp.tap import tap
+from pyshgp.tap import tap, set_verbosity
 from pyshgp.utils import list_rindex
 from pyshgp.validation import check_is_fitted, check_X_y
 
@@ -90,6 +90,7 @@ def __init__(self,
         self.parallelism = parallelism
         self.verbose = verbose
         self.ext = kwargs
+        set_verbosity(self.verbose)
 
         # Initialize attributes that will be set later.
         self.evaluator = None
@@ -126,8 +127,7 @@ def _build_search_algo(self):
             initial_genome_size=self.initial_genome_size,
             simplification_steps=self.simplification_steps,
             parallelism=self.parallelism,
-            push_config=self.push_config,
-            verbose=self.verbose
+            push_config=self.push_config
         )
         self.search = sr.get_search_algo(self._search_name, config=search_config, **self.ext)
 
@@ -154,6 +154,8 @@ def fit(self, X, y):
         self.evaluator = DatasetEvaluator(X, y, interpreter=self.interpreter)
         self._build_search_algo()
         self.solution = self.search.run()
+        if self.search.config.parallel_context is not None:
+            self.search.config.parallel_context.pool.close()
 
     def predict(self, X):
         """Execute the synthesized push program on a dataset.

pyshgp/gp/search.py

@@ -8,7 +8,7 @@
 from multiprocessing import Pool, Manager
 
 from pyshgp.push.program import ProgramSignature
-from pyshgp.tap import tap, set_verbosity
+from pyshgp.tap import tap
 from pyshgp.utils import DiscreteProbDistrib
 from pyshgp.gp.evaluation import Evaluator
 from pyshgp.gp.genome import GeneSpawner, GenomeSimplifier
@@ -90,7 +90,6 @@ def __init__(self,
                  initial_genome_size: Tuple[int, int] = (10, 50),
                  simplification_steps: int = 2000,
                  parallelism: Union[int, bool] = True,
-                 verbose: int = 0,
                  **kwargs):
         self.signature = signature
         self.evaluator = evaluator
@@ -100,9 +99,7 @@ def __init__(self,
         self.error_threshold = error_threshold
         self.initial_genome_size = initial_genome_size
         self.simplification_steps = simplification_steps
-        self.verbose = verbose
         self.ext = kwargs
-        set_verbosity(self.verbose)
 
         self.parallel_context = None
         if isinstance(parallelism, bool):

pyshgp/gp/selection.py

@@ -34,6 +34,7 @@ def select_one(self, population: Population) -> Individual:
         pass
 
     @tap
+    @abstractmethod
     def select(self, population: Population, n: int = 1) -> Sequence[Individual]:
         """Return `n` individuals from the population.
 

pyshgp/tap.py

@@ -18,7 +18,7 @@
 import numpy as np
 from abc import ABC
 from functools import wraps
-from typing import Dict, Sequence, Optional, MutableMapping
+from typing import Dict, Sequence, Optional, MutableMapping, Tuple
 
 
 class Tap(ABC):
@@ -28,31 +28,31 @@ class Tap(ABC):
     that state will change code behavior.
     """
 
-    def pre(self, id: str, args, kwargs):
+    def pre(self, id: str, args: Tuple, kwargs: Dict):
         """Perform a particular side-effect directly before the associated function/method is called.
 
         Parameters
         ----------
         id : str
             The ID of the tap, generated based off of the name qualified name of the function.
-        args : list
+        args : Tuple
             The positional of the function call. For methods, ``args[0]`` is the class instance.
-        kwargs : dict
+        kwargs : Dict
             The keyword args of the function call.
 
         """
         pass
 
-    def post(self, id: str, args, kwargs, returned):
+    def post(self, id: str, args: Tuple, kwargs: Dict, returned):
         """Perform a particular side-effect directly before the associated function/method is called.
 
         Parameters
         ----------
         id : str
             The ID of the tap, generated based off of the name qualified name of the function.
-        args : list
+        args : Tuple
             The positional of the function call. For methods, ``args[0]`` is the class instance.
-        kwargs : dict
+        kwargs : Dict
             The keyword args of the function call.
         returned : Any
             The returned value of the function call.
@@ -215,6 +215,9 @@ def __init__(self, *,
     def pre(self, id: str, args, kwargs, obj=None):
         """Print run config and/or all atoms to stdout."""
         search = args[0]
+        print("========================================")
+        print("Setup")
+        print("========================================")
         if self.pre_print_config:
             print("Search Configuration:")
             attrs = ["signature", "evaluator", "spawner", "population_size", "max_generations", "error_threshold",
@@ -228,21 +231,27 @@ def pre(self, id: str, args, kwargs, obj=None):
             print(search.config.spawner.literals)
             print("ERC Generators:")
             print(search.config.spawner.erc_generators)
+        print("========================================")
+        print("Start Run")
+        print("========================================")
 
     def post(self, id: str, args, kwargs, returned, obj=None):
         """Print a summary of the run result to stdout."""
         search = args[0]
+        print("========================================")
+        print("End Run")
+        print("========================================")
         if search.is_solved():
             print("Solution found.")
         else:
             print("No solution found.")
 
         if self.post_print_best:
-            print("Best individual found:")
-            print("Genome:", search.best_seen.genome)
-            print("Program:", search.best_seen.program)
-            print("Error vector:", search.best_seen.error_vector)
-            print("Total error:", search.best_seen.total_error)
+            print("Best Seen Individual")
+            print("\tGenome:\n\t", search.best_seen.genome)
+            print("\tProgram:\n\t", search.best_seen.program.pretty_str())
+            print("\tError vector:\n\t", search.best_seen.error_vector)
+            print("\tTotal error:\n\t", search.best_seen.total_error)
 
 
 class StdOutSearchStepTap(Tap):

setup.py

@@ -20,7 +20,7 @@ def read(fname):
     keywords=["push gp", "genetic programming", "pushgp", "gp", "push"],
     author="Eddie Pantridge",
     author_email="[email protected]",
-    license="LGPL",
+    license="MIT",
     url="https://github.com/erp12/pyshgp",
     packages=find_packages(
         exclude=('examples', 'examples.*', 'tests', 'tests.*', 'docs', 'docs_source')