Summertime release (0.8a1.dev16)

README.md

@@ -4,7 +4,7 @@
 [![License: Apache 2.0](https://img.shields.io/badge/license-apache--2.0-green.svg)](https://opensource.org/licenses/Apache-2.0) 
 [![Status: Actrive](https://img.shields.io/badge/status-active-brightgreen.svg)](https://github.com/cad-polito-it/byron)
 ![Language: Python](https://img.shields.io/badge/language-python-blue.svg)
-![Version: 0.1.dev2](https://img.shields.io/badge/version-0.8a1.dev15-orange.svg)
+![Version: 0.1.dev2](https://img.shields.io/badge/version-0.8a1.dev16-orange.svg)
 ![Codename: Don Juan](https://img.shields.io/badge/codename-Don_Juan-pink.svg)
 [![Documentation Status](https://readthedocs.org/projects/byron/badge/?version=pre-alpha)](https://byron.readthedocs.io/en/pre-alpha/?badge=pre-alpha)
 

byron/classes/individual.py

@@ -248,7 +248,7 @@ def fitness(self, value: FitnessABC) -> None:
             value << i.fitness or not value.is_distinguishable(i.fitness) for i in self.lineage.parents
         ):
             self._lineage.operator.stats.failures += 1
-        logger.debug(f"Individual: Fitness of {self} is {value}")
+        logger.debug(f"Individual: Fitness of {self}/{self.lineage} is {value}")
 
     @property
     def as_message(self) -> list[int]:

byron/classes/selement.py

@@ -177,7 +177,7 @@ def _is_valid_debug(self, node_ref: 'NodeReference') -> None:
         check_result = True
         for f in self.__class__.NODE_CHECKS:
             if not f(node_ref):
-                logger.info(f"{PARANOIA_SYSTEM_ERROR}: Failed check on {node_ref} ({f})")
+                logger.info(f"is_valid: Failed check on {node_ref}: {f}")
                 check_result = False
         return check_result
 

byron/functions.py

@@ -58,7 +58,7 @@ def mutate(parameter: ParameterABC, /, strength: float) -> None:
         or counter < 100
         or strength < 0.01
         or performance_warning(
-            f"Failed to mutate {parameter.__class__.__name__} with strength {strength} ({counter:,} failed attempts)",
+            f"Failed to mutate {parameter!r} with strength {strength} ({counter:,} failed attempts)",
             stacklevel_offset=2,
         )
     )

byron/global_symbols.py

@@ -64,7 +64,7 @@
 from collections import defaultdict
 import multiprocessing
 
-__version__ = "0.8a1.dev15"
+__version__ = "0.8a1.dev16"
 __date__ = "25-08-2023"
 __codename__ = "Don Juan"
 __author__ = "Giovanni Squillero and Alberto Tonda"

byron/operators/single_node_crossovers.py

@@ -27,6 +27,7 @@
 # v1 / August 2023 / Squillero (GX)
 
 from copy import deepcopy
+from collections import defaultdict
 
 from .ea_tools import *
 from byron.classes import *
@@ -35,50 +36,92 @@
 from byron.tools.graph import *
 from byron.user_messages import *
 
-# unfussy vs. chosy
 
+def _generic_node_crossover(
+    parent1: Individual, parent2: Individual, *, choosy: bool = False, only_targets: bool = False, link_type: str
+):
+    # assert parent1.run_paranoia_checks()
+    # assert parent2.run_paranoia_checks()
+
+    common_selements_raw = group_selements([parent1, parent2], only_targets=only_targets, choosy=choosy)
+    common_selements = defaultdict(lambda: defaultdict(list))
+    for path, elements in common_selements_raw.items():
+        if len(elements) < 2:
+            continue
+        for ind, nodes in elements.items():
+            plausible_nodes = [
+                n for n in nodes if link_type in set(t for u, v, t in ind.genome.in_edges(n, data='_type'))
+            ]
+            if not plausible_nodes:
+                continue
+            common_selements[path][ind] = plausible_nodes
+        if len(common_selements[path]) != 2:
+            del common_selements[path]
 
-def _generic_node_crossover(parent1: Individual, parent2: Individual, link_type: str):
-    assert parent1.run_paranoia_checks()
-    assert parent2.run_paranoia_checks()
-    common_selements = {k: v for k, v in group_selements([parent1, parent2], only_targets=True).items() if len(v) == 2}
     if not common_selements:
         raise ByronOperatorFailure
+
     target = rrandom.choice(list(common_selements.keys()))
     node1 = rrandom.choice(common_selements[target][parent1])
     node2 = rrandom.choice(common_selements[target][parent2])
     new_genome = nx.compose(deepcopy(parent1.genome), deepcopy(parent2.genome))
-    node1_fanin = new_genome.in_edges(node1, data='_type', keys=True)
-    node2_fanin = new_genome.in_edges(node2, data='_type', keys=True)
+    node1_fanin = new_genome.in_edges(node1, data=True, keys=True)
+    node2_fanin = new_genome.in_edges(node2, data=True, keys=True)
     try:
-        node1_parent_link = rrandom.choice([(u, v, k, t) for u, v, k, t in node1_fanin if t == link_type])
-        node2_parent_link = rrandom.choice([(u, v, k, t) for u, v, k, t in node2_fanin if t == node1_parent_link[3]])
+        node1_parent_link = rrandom.choice([(u, v, k, d) for u, v, k, d in node1_fanin if d['_type'] == link_type])
+        node2_parent_link = rrandom.choice(
+            [(u, v, k, d) for u, v, k, d in node2_fanin if d['_type'] == node1_parent_link[3]['_type']]
+        )
     except:
         raise ByronOperatorFailure
 
-    new_genome.remove_edge(node1_parent_link[0], node1_parent_link[1], node1_parent_link[2])
-    new_genome.remove_edge(node2_parent_link[0], node2_parent_link[1], node2_parent_link[2])
-    new_genome.add_edge(node1_parent_link[0], node2_parent_link[1], node1_parent_link[2], _type=node1_parent_link[3])
-    new_genome.add_edge(node2_parent_link[0], node1_parent_link[1], node2_parent_link[2], _type=node1_parent_link[3])
+    # NOTE[GX]: replace link in node1_parent -> node1 with node1_parent -> node2 preserving links order
+    parent1_complete_fanout = list(new_genome.edges(node1_parent_link[0], data=True, keys=True))
+    for edge in parent1_complete_fanout:
+        new_genome.remove_edge(edge[0], edge[1], key=edge[2])
+    for edge in parent1_complete_fanout:
+        if edge == node1_parent_link:
+            new_genome.add_edge(
+                node1_parent_link[0], node2_parent_link[1], node1_parent_link[2], **node1_parent_link[3]
+            )
+        else:
+            new_genome.add_edge(edge[0], edge[1], key=edge[2], **edge[3])
+    # NOTE[GX]: replace link in node2_parent -> node2 with node2_parent -> node1 preserving links order
+    parent2_complete_fanout = list(new_genome.edges(node1_parent_link[0], data=True, keys=True))
+    for edge in parent2_complete_fanout:
+        new_genome.remove_edge(edge[0], edge[1], key=edge[2])
+    for edge in parent2_complete_fanout:
+        if edge == node2_parent_link:
+            new_genome.add_edge(
+                node2_parent_link[0], node1_parent_link[1], node2_parent_link[2], **node2_parent_link[3]
+            )
+        else:
+            new_genome.add_edge(edge[0], edge[1], key=edge[2], **edge[3])
+
     discard_useless_components(new_genome)
 
     if not get_structure_tree(new_genome):
         raise ByronOperatorFailure
 
     Node.reset_labels(new_genome)
     new_individual = Individual(parent1.top_frame, new_genome)
-    assert new_individual.run_paranoia_checks()
+    # assert new_individual.run_paranoia_checks()
 
-    assert parent1.run_paranoia_checks()
-    assert parent2.run_paranoia_checks()
+    # assert parent1.run_paranoia_checks()
+    # assert parent2.run_paranoia_checks()
     return [new_individual]
 
 
-@genetic_operator(num_parents=2)
+# @genetic_operator(num_parents=2)
 def linked_node_crossover(parent1: Individual, parent2: Individual):
-    return _generic_node_crossover(parent1, parent2, LINK)
+    return _generic_node_crossover(parent1, parent2, only_targets=True, link_type=LINK)
+
+
+@genetic_operator(num_parents=2)
+def leaf_crossover_unfussy(parent1: Individual, parent2: Individual):
+    return _generic_node_crossover(parent1, parent2, choosy=False, only_targets=False, link_type=FRAMEWORK)
 
 
 @genetic_operator(num_parents=2)
-def leaf_crossover(parent1: Individual, parent2: Individual):
-    return _generic_node_crossover(parent1, parent2, FRAMEWORK)
+def leaf_crossover_choosy(parent1: Individual, parent2: Individual):
+    return _generic_node_crossover(parent1, parent2, choosy=True, only_targets=False, link_type=FRAMEWORK)

byron/tools/graph.py

@@ -44,6 +44,7 @@
 import networkx as nx
 
 from byron.global_symbols import *
+from byron.user_messages import *
 from byron.classes.node_reference import NodeReference
 from byron.classes.parameter import ParameterABC, ParameterStructuralABC
 from byron.classes.selement import *

examples/onemax/onemax-go/golang.py

@@ -24,7 +24,7 @@ def framework():
     int64 = byron.f.integer_parameter(0, 2**64)
     math_op = byron.f.choice_parameter(['+', '-', '*', '/', '&', '^', '|'])
     variable = byron.f.macro('var {_node} uint64', _label='')
-    variable.force_parent('prologue')
+    # variable.force_parent('prologue')
 
     # standard
     main_prologue = byron.f.macro('package main\nfunc evolved_function() uint64 {{')
@@ -50,7 +50,7 @@ def framework():
     subs_prologue = byron.f.macro('func {_node}(foo uint64) uint64 {{', _label='')
     subs_math = byron.f.macro('foo {op}= {num}', op=math_op, num=int64)
     subs_epilogue = byron.f.macro('return foo\n}}')
-    subs = byron.f.sequence([subs_prologue, byron.f.bunch([subs_math], size=2), subs_epilogue], name='function')
+    subs = byron.f.sequence([subs_prologue, byron.f.bunch([subs_math], size=(2, 10)), subs_epilogue], name='function')
 
     call = byron.f.macro(
         '{var1} = {sub}({var2})',
@@ -59,5 +59,8 @@ def framework():
         var2=byron.f.global_reference(variable),
     )
 
-    code = byron.f.bunch([imath, vmath, call], size=5, name='body')
-    return byron.f.sequence((main_prologue, code, main_epilogue), max_instances=1)
+    few_default_vars = byron.f.bunch([variable], size=2)
+    # NOTE[GX]: Force all newly created variables to appear after the few default ones
+    variable.force_parent(few_default_vars)
+    code = byron.f.bunch([imath, vmath, call], weights=(3, 3, 1), size=(2, 20), name='body')
+    return byron.f.sequence((main_prologue, few_default_vars, code, main_epilogue), max_instances=1)

examples/onemax/onemax-go/onemax-go.py

@@ -20,23 +20,23 @@
 
 @byron.fitness_function
 def dummy_fitness(text):
-    return len(text)
+    return 1 / len(text)
 
 
 def main():
     top_frame = golang.framework()
 
+    # evaluator = byron.evaluator.ScriptEvaluator('./evaluate-all.sh', filename_format="individual{i:06}.go")
+    evaluator = byron.evaluator.ParallelScriptEvaluator(
+        'go', 'onemax.go', other_required_files=('main.go',), flags=('run',), timeout=10, default_result='-1'
+    )
     # evaluator = byron.evaluator.PythonEvaluator(dummy_fitness)
-    evaluator = byron.evaluator.ScriptEvaluator('./evaluate-all.sh', filename_format="individual{i:06}.go")
-    # evaluator = byron.evaluator.ParallelScriptEvaluator(
-    #     'go', 'onemax.go', other_required_files=('main.go',), flags=('run',), timeout=10, default_result='-1'
-    # )
 
     byron.f.set_option('$dump_node_info', True)
     final_population = byron.ea.vanilla_ea(
         top_frame,
         evaluator,
-        max_generation=100,
+        max_generation=1_000,
         mu=50,
         lambda_=20,
         max_fitness=64.0,

pyproject.toml

@@ -10,7 +10,7 @@
 
 [tool.poetry]
 name = "byron"
-version = "0.8a1.dev15"
+version = "0.8a1.dev16"
 description = "Multi-purpose extensible self-adaptive optimizer and fuzzer"
 authors = [
     "Giovanni Squillero <giovanni.squillero@polito.it>",
@@ -96,7 +96,7 @@ max-line-length = 120
 source-roots = ['src']
 
 [bumpver]
-current_version = "0.8a1.dev15"
+current_version = "0.8a1.dev16"
 version_pattern = "MAJOR.MINOR[PYTAGNUM].devINC0"
 commit_message = "Bump version to {new_version}"
 commit = false