From 8d67a003e2b1baf38cc2455363754e0d540a28df Mon Sep 17 00:00:00 2001
From: William Song <30965609+Freakwill@users.noreply.github.com>
Date: Thu, 14 Dec 2023 10:21:39 +0800
Subject: [PATCH] new example

---
 docs/source/Install.md  |  2 +-
 examples/comparison0.py |  1 -
 pyrimidine/base.py      | 46 +++++++++++++++++++++++++----------------
 pyrimidine/meta.py      |  4 ++--
 4 files changed, 31 insertions(+), 22 deletions(-)

diff --git a/docs/source/Install.md b/docs/source/Install.md
index ed2d625..0a1fbd4 100644
--- a/docs/source/Install.md
+++ b/docs/source/Install.md
@@ -8,7 +8,7 @@
 
 **Documentation as PDF**: download latest
 
-`pyrimidine` is a framework for genetic algorithm.
+`pyrimidine` stands as a versatile framework designed for GAs, offering exceptional extensibility for a wide array of evolutionary algorithms, including particle swarm optimization and difference evolution.
 
 ## Install pyrimidine
 
diff --git a/examples/comparison0.py b/examples/comparison0.py
index 70e358e..5960659 100644
--- a/examples/comparison0.py
+++ b/examples/comparison0.py
@@ -1,5 +1,4 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 
 
 """An easy knapsack problem
diff --git a/pyrimidine/base.py b/pyrimidine/base.py
index 84f2af3..c719c91 100755
--- a/pyrimidine/base.py
+++ b/pyrimidine/base.py
@@ -115,19 +115,31 @@ def __str__(self):
     def random(cls, size=None):
         raise NotImplementedError
 
+    def copy(self, *args, **kwargs):
+        raise NotImplementedError
+
+    def transition(self, *args, **kwargs):
+        self.mutate()
+
     def x(self, other):
         # alias for cross
         return self.cross(other)
 
     def cross(self, other):
+        # crossover operation
         raise NotImplementedError
 
-    def merge(self, *other):
-        raise NotImplementedError
-
+    @side_effect
     def mutate(self):
+        # mutation operation
         raise NotImplementedError
 
+    def replicate(self):
+        # Replication operation of a chromosome
+        ind = self.copy()
+        ind.mutate()
+        return ind
+
     def decode(self):
         """Decoding of the chromesome
         Translate the chromesome to (part of) solution, maybe a number.
@@ -142,15 +154,6 @@ def encode(cls, x):
     def equal(self, other):
         return np.array_equal(self, other)
 
-    def copy(self, *args, **kwargs):
-        raise NotImplementedError
-
-    def replicate(self):
-        # Replication operation of a chromosome
-        ind = self.copy()
-        ind.mutate()
-        return ind
-
 
 class BaseIndividual(FitnessMixin, metaclass=MetaContainer):
     """Base class of individuals
@@ -203,6 +206,9 @@ def copy(self, type_=None, *args, **kwargs):
         else:
             return type_([c.copy(type_=type_.element_class) for c in self])
 
+    def transition(self, *args, **kwargs):
+        self.mutate()
+
     def cross(self, other):
         # Cross operation of two individual
         return self.__class__([chromosome.cross(other_c) for chromosome, other_c in zip(self, other)])
@@ -258,6 +264,7 @@ def __sub__(self, other):
         return self.__class__([this - that for this, that in zip(self.chromosomes, other.chromosomes)])
 
     def __rmul__(self, other):
+        # assert isinstance(other, np.number)
         return self.__class__([other * this for this in self.chromosomes])
 
 
@@ -479,19 +486,22 @@ class BaseMultiPopulation(PopulationMixin, metaclass=MetaHighContainer):
     'best_population': 'best_element',
     'worst_population': 'worst_element',
     "get_best_population": "get_best_element",
-    "get_best_populations": "get_best_elements"}
+    "get_best_populations": "get_best_elements"
+    }
 
     def __str__(self):
         return '\n\n'.join(map(str, self))
 
-    def migrate(self, migrate_prob=None):
+    def migrate(self, migrate_prob=None, copy=True):
+        migrate_prob = migrate_prob or self.migrate_prob
         for population, other in zip(self[:-1], self[1:]):
-            if random() < (migrate_prob or self.migrate_prob):
-                other.append(population.get_best_individual(copy=True))
-                population.append(other.get_best_individual(copy=True))
+            if random() < migrate_prob:
+                other.append(population.get_best_individual(copy=copy))
+                population.append(other.get_best_individual(copy=copy))
 
     def transition(self, *args, **kwargs):
-        super().transition(*args, **kwargs)
+        for p in self:
+            p.transition(*args, **kwargs)
         self.migrate()
 
     def max_fitness(self):
diff --git a/pyrimidine/meta.py b/pyrimidine/meta.py
index 8a8820b..51d8eae 100755
--- a/pyrimidine/meta.py
+++ b/pyrimidine/meta.py
@@ -439,9 +439,9 @@ def __new__(cls, name, bases, attrs):
         if 'element_class' in attrs:
             element_class = attrs['element_class']
             if (not isinstance(element_class, MetaContainer)
-                and isinstance(element_class, tuple) and not isinstance(element_class[0], MetaContainer)
+                and isinstance(element_class, tuple) and not any(isinstance(ec, MetaContainer) for ec in element_class)
                 and not isinstance(element_class, ParamType)):
-                raise TypeError('`element_class` should be an instance of MetaContainer, or a list of such instances.')
+                raise TypeError('`element_class` should be an instance of `MetaContainer`, or a tuple where one element is an instance of `MetaContainer`.')
 
         def _flatten(self, type_):
             elms = []