Merge pull request #139 from perib/new_search_space_def

New search space def

setup.py

@@ -28,7 +28,7 @@ def calculate_version():
 
 ''',
     zip_safe=True,
-    install_requires=['numpy>=1.26.4',
+    install_requires=['numpy==1.26.4',
                       'scipy>=1.3.1',
                       'scikit-learn>=1.3.0',
                       'update_checker>=0.16',

tox.ini

@@ -27,4 +27,4 @@ commands = flake8 tpot2
 basepython = python3.10
 deps =
     -r{toxinidir}/requirements_dev.txt
-commands = mypy tpot2
+commands = mypy tpot2

tpot2/evolvers/steady_state_evolver.py

@@ -299,17 +299,18 @@ def optimize(self):
                                 eval_error = "INVALID"
                     else: #if future is not done
 
-                        #check if the future has been running for too long, cancel the future
-                        if time.time() - submitted_futures[completed_future]["time"] > self.max_eval_time_seconds*1.25:
-                            completed_future.cancel()
+                        if self.max_eval_time_seconds is not None:
+                            #check if the future has been running for too long, cancel the future
+                            if time.time() - submitted_futures[completed_future]["time"] > self.max_eval_time_seconds*1.25:
+                                completed_future.cancel()
 
-                            if self.verbose >= 4:
-                                print(f'WARNING AN INDIVIDUAL TIMED OUT (Fallback): \n {submitted_futures[completed_future]} \n')
+                                if self.verbose >= 4:
+                                    print(f'WARNING AN INDIVIDUAL TIMED OUT (Fallback): \n {submitted_futures[completed_future]} \n')
 
-                            scores = [np.nan for _ in range(len(self.objective_names))]
-                            eval_error = "TIMEOUT"
-                        else:
-                            continue #otherwise, continue to next future
+                                scores = [np.nan for _ in range(len(self.objective_names))]
+                                eval_error = "TIMEOUT"
+                            else:
+                                continue #otherwise, continue to next future
 
 
 

tpot2/search_spaces/base.py

@@ -15,23 +15,31 @@
 
 
 
+
 class SklearnIndividual(tpot2.BaseIndividual):
 
+    def __init_subclass__(cls):
+        cls.crossover = cls.validate_same_type(cls.crossover)
+
+
     def __init__(self,) -> None:
         super().__init__()
 
     def mutate(self, rng=None):
         return
 
-    @final
     def crossover(self, other, rng=None, **kwargs):
-        if not isinstance(other, type(self)):
-            return False
-        return self._crossover(other, rng=rng, **kwargs)
+        return 
 
-    @abstractmethod
-    def _crossover(self, other, rng=None):
-        return
+    @final
+    def validate_same_type(func):
+
+        def wrapper(self, other, rng=None, **kwargs):
+            if not isinstance(other, type(self)):
+                return False
+            return func(self, other, rng=None, **kwargs)
+
+        return wrapper
 
     def export_pipeline(self) -> BaseEstimator:
         return

tpot2/search_spaces/nodes/estimator_node.py

@@ -60,7 +60,7 @@ def mutate(self, rng=None):
         self.check_hyperparameters_for_None()
         return True
 
-    def _crossover(self, other, rng=None):
+    def crossover(self, other, rng=None):
         if isinstance(self.space, dict):
             return False
 

tpot2/search_spaces/nodes/fss_node.py

@@ -51,7 +51,7 @@ def mutate(self, rng=None):
         self.sel_subset = self.subset_dict[self.selected_subset_name]
 
 
-    def _crossover(self, other, rng=None):
+    def crossover(self, other, rng=None):
         self.selected_subset_name = other.selected_subset_name
         self.sel_subset = other.sel_subset
 

tpot2/search_spaces/nodes/genetic_feature_selection.py

@@ -31,16 +31,16 @@ def __init__(   self,
                     start_p=0.2,
                     mutation_rate = 0.5,
                     crossover_rate = 0.5,
-                    mutation_rate_rate = 0,
-                    crossover_rate_rate = 0,
                     rng=None,
                 ):
 
         self.start_p = start_p
         self.mutation_rate = mutation_rate
         self.crossover_rate = crossover_rate
-        self.mutation_rate_rate = mutation_rate_rate
-        self.crossover_rate_rate = crossover_rate_rate
+        self.mutation_rate_rate = 0
+        self.crossover_rate_rate = 0
+
+
 
         rng = np.random.default_rng(rng)
 
@@ -69,7 +69,7 @@ def mutate(self, rng=None):
 
         return rng.choice(self.mutation_list)(rng)
 
-    def _crossover(self, other, rng=None):
+    def crossover(self, other, rng=None):
         rng = np.random.default_rng(rng)
 
         if rng.uniform() < self.crossover_rate_rate:

tpot2/search_spaces/pipelines/choice.py

@@ -29,7 +29,7 @@ def _mutate_select_new_node(self, rng=None):
     def _mutate_node(self, rng=None):
         return self.node.mutate(rng)
 
-    def _crossover(self, other, rng=None):
+    def crossover(self, other, rng=None):
         return self.node.crossover(other.node, rng)
 
     def export_pipeline(self):

tpot2/search_spaces/pipelines/dynamic_linear.py

@@ -26,7 +26,7 @@ def __init__(self, search_space : SklearnIndividualGenerator, max_length: int ,
         self.pipeline = self._generate_pipeline(rng)
 
     def _generate_pipeline(self, rng=None):
-        rng = np.random.default_rng()
+        rng = np.random.default_rng(rng)
         pipeline = []
         length = rng.integers(self.min_length, self.max_length)
         length = min(length, 3)
@@ -37,7 +37,7 @@ def _generate_pipeline(self, rng=None):
 
 
     def mutate(self, rng=None):
-        rng = np.random.default_rng()
+        rng = np.random.default_rng(rng)
         options = []
         if len(self.pipeline) > self.min_length:
             options.append(self._mutate_remove_node)
@@ -48,28 +48,28 @@ def mutate(self, rng=None):
         return rng.choice(options)(rng)
 
     def _mutate_add_node(self, rng=None):
-        rng = np.random.default_rng()
+        rng = np.random.default_rng(rng)
         new_node = self.search_space.generate(rng)
         idx = rng.integers(len(self.pipeline))
         self.pipeline.insert(idx, new_node)
 
     def _mutate_remove_node(self, rng=None):
-        rng = np.random.default_rng()
+        rng = np.random.default_rng(rng)
         idx = rng.integers(len(self.pipeline))
         self.pipeline.pop(idx)
 
     def _mutate_step(self, rng=None):
         #choose a random step in the pipeline and mutate it
-        rng = np.random.default_rng()
+        rng = np.random.default_rng(rng)
         step = rng.choice(self.pipeline)
         return step.mutate(rng)
 
 
-    def _crossover(self, other, rng=None):
+    def crossover(self, other, rng=None):
         #swap a random step in the pipeline with the corresponding step in the other pipeline
 
-        rng = np.random.default_rng()
-        cx_funcs = [self._crossover_swap_random_steps, self._crossover_inner_step]
+        rng = np.random.default_rng(rng)
+        cx_funcs = [self._crossover_swap_multiple_nodes, self._crossover_node]
 
         rng.shuffle(cx_funcs)
         for cx_func in cx_funcs:
@@ -78,8 +78,8 @@ def _crossover(self, other, rng=None):
 
         return False
 
-    def _crossover_swap_random_steps(self, other, rng):
-        rng = np.random.default_rng()
+    def _crossover_swap_multiple_nodes(self, other, rng):
+        rng = np.random.default_rng(rng)
 
         max_steps = int(min(len(self.pipeline), len(other.pipeline))/2)
         max_steps = max(max_steps, 1)
@@ -99,21 +99,21 @@ def _crossover_swap_random_steps(self, other, rng):
 
         return True
 
-    def _crossover_swap_step(self, other, rng):
+    def _crossover_swap_node(self, other, rng):
         if len(self.pipeline) != len(other.pipeline):
             return False
 
         if len(self.pipeline) < 2:
             return False
 
-        rng = np.random.default_rng()
+        rng = np.random.default_rng(rng)
         idx = rng.integers(1,len(self.pipeline))
 
         self.pipeline[idx], other.pipeline[idx] = other.pipeline[idx], self.pipeline[idx]
         return True
 
-    def _crossover_inner_step(self, other, rng):
-        rng = np.random.default_rng()
+    def _crossover_node(self, other, rng):
+        rng = np.random.default_rng(rng)
 
         pipeline1_indexes= list(range(len(self.pipeline)))
         pipeline2_indexes= list(range(len(other.pipeline)))