Merge pull request #78 from Morridin/master

Add support for Particle Swarm Optimisation to Propulate

.gitignore

@@ -3,7 +3,7 @@
 *.py[cod]
 *.so
 *.cfg
-!.isort.cfg
+!propulate/.isort.cfg
 !setup.cfg
 *.orig
 *.log
@@ -49,11 +49,6 @@ MANIFEST
 # Per-project virtualenvs
 .venv*/
 
-*.pkl
-
+*.pickle
 MNIST
-*cpt.p
-*cpt.p.bkp
-scripts/*.png
-
-voucher_propulate.txt
+*.bkp

README.md

@@ -63,3 +63,6 @@ OpenMPI.
 
 
 
+
+
+

propulate/__init__.py

@@ -11,16 +11,22 @@
     del get_distribution, DistributionNotFound
 
 from .islands import Islands
+from .population import Individual, Particle
 from .propulator import Propulator
 from .migrator import Migrator
 from .pollinator import Pollinator
 from .utils import get_default_propagator, set_logger_config
 
+from . import propagators
+
 __all__ = [
     "Islands",
+    "Individual",
+    "Particle",
     "Propulator",
     "Migrator",
     "Pollinator",
     "get_default_propagator",
     "set_logger_config",
+    "propagators",
 ]

propulate/islands.py

@@ -1,16 +1,16 @@
+import logging
+import platform
 import random
 from pathlib import Path
 from typing import Callable, Union, List, Type
-import logging
 
-from mpi4py import MPI
 import numpy as np
+from mpi4py import MPI
 
-from .propagators import Propagator, SelectMin, SelectMax
 from .migrator import Migrator
 from .pollinator import Pollinator
 from .population import Individual
-
+from .propagators import Propagator, SelectMin, SelectMax
 
 log = logging.getLogger(__name__)  # Get logger instance.
 
@@ -97,22 +97,25 @@ def __init__(
             print(
                 "#################################################\n"
                 "# PROPULATE: Parallel Propagator of Populations #\n"
-                "#################################################\n\n"
-                "        ⠀⠀⠀⠈⠉⠛⢷⣦⡀⠀⣀⣠⣤⠤⠄⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀\n"
-                "⠀        ⠀⠀⠀⠀⠀⣀⣻⣿⣿⣿⣋⣀⡀⠀⠀⢀⣠⣤⣄⡀⠀⠀⠀⠀⠀⠀⠀⠀⠀\n"
-                "⠀        ⠀⠀⣠⠾⠛⠛⢻⣿⣿⣿⠟⠛⠛⠓⠢⠀⠀⠉⢿⣿⣆⣀⣠⣤⣀⣀⠀⠀⠀\n"
-                "⠀        ⠀⠘⠁⠀⠀⣰⡿⠛⠿⠿⣧⡀⠀⠀⢀⣤⣤⣤⣼⣿⣿⣿⡿⠟⠋⠉⠉⠀⠀\n"
-                "⠀        ⠀⠀⠀⠀⠠⠋⠀⠀⠀⠀⠘⣷⡀⠀⠀⠀⠀⠹⣿⣿⣿⠟⠻⢶⣄⠀⠀⠀⠀\n"
-                "⠀⠀        ⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠸⣧⠀⠀⠀⠀⢠⡿⠁⠀⠀⠀⠀⠈⠀⠀⠀⠀\n"
-                "⠀⠀        ⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢿⡄⠀⠀⢠⡟⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀\n"
-                "⠀⠀        ⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢸⡇⠀⠀⣾⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀\n"
-                "⠀        ⣤⣤⣤⣤⣤⣤⡤⠄⠀⠀⣀⡀⢸⡇⢠⣤⣁⣀⠀⠀⠠⢤⣤⣤⣤⣤⣤⣤⠀\n"
-                "⠀⠀⠀⠀⠀        ⠀⣀⣤⣶⣾⣿⣿⣷⣤⣤⣾⣿⣿⣿⣿⣷⣶⣤⣀⠀⠀⠀⠀⠀⠀\n"
-                "        ⠀⠀⠀⣠⣴⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣦⣄⠀⠀⠀\n"
-                "⠀        ⠀⠼⠿⣿⣿⠿⠛⠉⠉⠉⠙⠛⠿⣿⣿⠿⠛⠛⠛⠛⠿⢿⣿⣿⠿⠿⠇⠀⠀\n"
-                "⠀        ⢶⣤⣀⣀⣠⣴⠶⠛⠋⠙⠻⣦⣄⣀⣀⣠⣤⣴⠶⠶⣦⣄⣀⣀⣠⣤⣤⡶⠀\n"
-                "        ⠀⠀⠈⠉⠉⠉⠀⠀⠀⠀⠀⠀⠀⠉⠉⠉⠉⠀⠀⠀⠀⠀⠉⠉⠉⠉⠀⠀⠀⠀\n"
+                "#################################################\n"
             )
+            if "Windows" not in platform.system():
+                print(
+                    "        ⠀⠀⠀⠈⠉⠛⢷⣦⡀⠀⣀⣠⣤⠤⠄⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀\n"
+                    "⠀        ⠀⠀⠀⠀⠀⣀⣻⣿⣿⣿⣋⣀⡀⠀⠀⢀⣠⣤⣄⡀⠀⠀⠀⠀⠀⠀⠀⠀⠀\n"
+                    "⠀        ⠀⠀⣠⠾⠛⠛⢻⣿⣿⣿⠟⠛⠛⠓⠢⠀⠀⠉⢿⣿⣆⣀⣠⣤⣀⣀⠀⠀⠀\n"
+                    "⠀        ⠀⠘⠁⠀⠀⣰⡿⠛⠿⠿⣧⡀⠀⠀⢀⣤⣤⣤⣼⣿⣿⣿⡿⠟⠋⠉⠉⠀⠀\n"
+                    "⠀        ⠀⠀⠀⠀⠠⠋⠀⠀⠀⠀⠘⣷⡀⠀⠀⠀⠀⠹⣿⣿⣿⠟⠻⢶⣄⠀⠀⠀⠀\n"
+                    "⠀⠀        ⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠸⣧⠀⠀⠀⠀⢠⡿⠁⠀⠀⠀⠀⠈⠀⠀⠀⠀\n"
+                    "⠀⠀        ⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢿⡄⠀⠀⢠⡟⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀\n"
+                    "⠀⠀        ⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢸⡇⠀⠀⣾⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀\n"
+                    "⠀        ⣤⣤⣤⣤⣤⣤⡤⠄⠀⠀⣀⡀⢸⡇⢠⣤⣁⣀⠀⠀⠠⢤⣤⣤⣤⣤⣤⣤⠀\n"
+                    "⠀⠀⠀⠀⠀        ⠀⣀⣤⣶⣾⣿⣿⣷⣤⣤⣾⣿⣿⣿⣿⣷⣶⣤⣀⠀⠀⠀⠀⠀⠀\n"
+                    "        ⠀⠀⠀⣠⣴⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣦⣄⠀⠀⠀\n"
+                    "⠀        ⠀⠼⠿⣿⣿⠿⠛⠉⠉⠉⠙⠛⠿⣿⣿⠿⠛⠛⠛⠛⠿⢿⣿⣿⠿⠿⠇⠀⠀\n"
+                    "⠀        ⢶⣤⣀⣀⣠⣴⠶⠛⠋⠙⠻⣦⣄⣀⣀⣠⣤⣴⠶⠶⣦⣄⣀⣀⣠⣤⣤⡶⠀\n"
+                    "        ⠀⠀⠈⠉⠉⠉⠀⠀⠀⠀⠀⠀⠀⠉⠉⠉⠉⠀⠀⠀⠀⠀⠉⠉⠉⠉⠀⠀⠀⠀\n"
+                )
 
         # Homogeneous case with equal island sizes (differences of +-1 possible due to load balancing).
         if island_sizes is None:

propulate/pollinator.py

@@ -2,18 +2,17 @@
 import logging
 import random
 import time
-from typing import Callable, Union, Tuple, List, Type
 from pathlib import Path
+from typing import Callable, Union, Tuple, List, Type
 
 import numpy as np
 from mpi4py import MPI
 
 from ._globals import MIGRATION_TAG, SYNCHRONIZATION_TAG
-from .propagators import Propagator, SelectMin, SelectMax
 from .population import Individual
+from .propagators import Propagator, SelectMin, SelectMax
 from .propulator import Propulator
 
-
 log = logging.getLogger(__name__)
 
 
@@ -327,9 +326,9 @@ def _check_for_duplicates(
 
         Returns
         -------
-        list[list[propulate.population.Individual | int]]
+        list[list[propulate.individual.Individual | int]]
             individuals and their occurrences
-        list[propulate.population.Individual]
+        list[propulate.individual.Individual]
             unique individuals in population
         """
         if active:

propulate/population.py

@@ -1,5 +1,7 @@
 from decimal import Decimal
 
+import numpy as np
+
 
 class Individual(dict):
     """
@@ -133,3 +135,34 @@ def equals(self, other) -> bool:
                 compare_traits = False
                 break
         return compare_traits and self.loss == other.loss
+
+
+class Particle(Individual):
+    """
+    Child class of ``Individual`` with additional properties required for PSO, i.e., an array-type velocity field and
+    a (redundant) array-type position field.
+
+    Note that Propulate relies on ``Individual``s being ``dict``s.
+
+    When defining new propagators, users of the ``Particle`` class thus need to ensure that a ``Particle``'s position
+    always matches its dict contents and vice versa.
+
+    This class also contains an attribute field called ``global_rank``. It contains the global rank of the propagator
+    that
+    created it.
+    This is for purposes of better (or at all) retrieval in multi swarm case.
+    """
+
+    def __init__(
+        self,
+        position: np.ndarray = None,
+        velocity: np.ndarray = None,
+        generation: int = -1,
+        rank: int = -1,
+    ):
+        super().__init__(generation=generation, rank=rank)
+        if position is not None and velocity is not None:
+            assert position.shape == velocity.shape
+        self.velocity = velocity
+        self.position = position
+        self.global_rank = rank  # The global rank of the creating propagator for later retrieval upon update.