Making progress. Slow but steady.

stepping_stone/range_expansion.pyx

@@ -12,48 +12,51 @@ __author__ = 'bryan'
 cimport cython
 import numpy as np
 cimport numpy as np
-import random
-import sys
 from libcpp cimport bool
 from matplotlib import animation
 import matplotlib.pyplot as plt
-import pandas as pd
 
 from cython_gsl cimport *
 from libc.stdlib cimport free
 
 cdef class Individual:
- '''We assume all individuals have the same mutation rate; this is implemented at the
- deme level, consequently. It is very annoying otherwise, as we have to worry about other scales...'''
+ """
+ Individuals are placed in demes.
+ """
 
  cdef:
- readonly long allele_id
  # Note that all rates should be non-dimensionalized in terms of generation time
- readonly double growth_rate
+ readonly long allele_id # Basically a marker for color
+ readonly double growth_rate # Growth rate is only used if we include selection, i.e. selection demes
 
  def __init__(Individual self, long allele_id = 0, growth_rate = 1.0):
  self.allele_id = allele_id
  self.growth_rate = growth_rate
 
 cdef class Deme:
- '''The neutral deme. Initiate selection deme or selection_mutation deme as appropriate.'''
- # Assumes population in each deme is fixed!
- # Otherwise random number generator breaks down.
- # Include selection too
+ """
+ The neutral deme. Individuals are placed in demes via the "members" memoryview. We currently
+ assume that the population size "num_individuals" is fixed.
+ """
 
  cdef:
- readonly Individual[:] members
- readonly long num_alleles
- readonly long[:] binned_alleles
- readonly long num_individuals
- readonly double fraction_swap
- public Deme[:] neighbors
- readonly double[:] growth_rate_list
- readonly int num_iterations
- readonly TIME_PER_ITERATION
-
- readonly int last_index_to_die
- readonly int last_index_to_reproduce
+ ##### Inputs ####
+ readonly long num_alleles # The number of alleles at the beginning of the simulation; assumes no creation of alleles
+ readonly Individual[:] members # A list of individuals currently in the deme
+ readonly double fraction_swap # The fraction of the individuals swapped with neighbors each generation
+ #################
+
+ #### Other Attributes ######
+ readonly long[:] binned_alleles # A count of each type of allele in the deme.
+ readonly long num_individuals # The number of individuals in the deme, N; assumes this is fixed
+ public Deme[:] neighbors # A list of neighboring demes. You have to initialize this.
+ readonly double[:] growth_rate_list # A list of growth rates in the deme. Important for dealing with selection
+ readonly int num_iterations # The number of iterations the deme has undergone
+ readonly TIME_PER_ITERATION # The time per generation is defined as 1/N; it is a constant, hence the capitals
+
+ readonly int last_index_to_die # The index of the last member to die in the members list. Important for subclassing
+ readonly int last_index_to_reproduce # The index of the last member to reproduce in the members list. Important for subclassing.
+ ############################
 
  def __init__(Deme self, long num_alleles, Individual[:] members not None, double fraction_swap = 0.0):
  self.members = members