paper

docs/source/Release History.md

@@ -6,6 +6,8 @@
 - define `get_worst_elements` method for `PopulationMixin` class
 - correct some code in examples and `IterativeMixin` class.
 - The argument `n_iter` is changed to `max_iter`
+- Debug for new version of `numpy`
+- move some optimization algo to the folder `misc`
 
 ## v1.5
 

paper/paper.md

@@ -122,7 +122,7 @@ There are three base classes in `pyrimidine`: `BaseChromosome`, `BaseIndividual`
 
 For convenience, `pyrimidine` provides some commonly used subclasses, where the genetic operations are implemented such as, `cross` and `mutate`, such as `BinaryChromosome` for the binary encoding as in the classical GA.
 
-Generally, the algorithm design starts as follows, where `MonoIndividual`, a subclass of `BaseIndividual`, enforces that the individuals can only have one chromosome.
+Generally, the algorithm design starts as follows, where `MonoIndividual` (a subclass of `BaseIndividual`) simply enforces that an individual can only have one chromosome.
 
 ```python
 class UserIndividual(MonoIndividual):
@@ -148,7 +148,7 @@ UserPopulation = StandardPopulation[UserIndividual] // 10
 
 Instead of overriding the `fitness` attribute, users are recommended to override the `_fitness` method, where the concrete fitness computation is defined. The operator `// 10` is equivalent to set `default_size = 10`.
 
-Algebraically, there is no difference between `MonoIndividual` and `Chromosome`. Meanwhile the population also can be treated as a container of chromosomes as follows. 
+Algebraically, there is no difference between `MonoIndividual` and `Chromosome`. Meanwhile the population also can be treated as a container of chromosomes as follows.
 
 ```python
 class UserChromosome(BaseChromosome):

pyrimidine/deco.py

@@ -6,6 +6,7 @@
 Two main kinds of decorators:
 1. cache decorator: store the information of previous computing, to seep up the algorithm.
          Should clear it to suppress the side effect. It is used with `@side-effect` decorator.
+         methods with `@side-effect` will clear the cache after executing.
 2. memory decorator: As cache, it record some information, but it will chage the behavior of the algorithms.
 """
 

pyrimidine/ep.py

@@ -1,6 +1,5 @@
 #!/usr/bin/env python3
 
-
 """Evolution Programming
 
 Invented by L. Fogel[1966] for designing FSM initially.

pyrimidine/gene.py

@@ -1,7 +1,9 @@
 #!/usr/bin/env python3
 
 """
-Gene classes
+Gene classes: as the elements in the chromosome.
+
+The wrapper of data type of `numpy`.
 """
 
 import numpy as np