Merge pull request #5 from mauriceling/master

1. Added "ragaraja_instructions" as simulation parameters. 2. Enabled users to define a set of Ragaraja instructions to be used. 3. Written function documentations for database loggers
Merge branch 'master' of https://github.com/mauriceling/dose
Changed simulation files ragaraja_version to 0 and added ragaraja_instructions key in parameters to avoid possible infinite loop in ragaraja interpreter
Removed printing of error message when ragaraja interpreter falls into an exception
Updated dose.py to copy the simulation file inside the simulation results directory
Fixed bug that increments generation_count twice during a single generation step
Updated bury_world() function to dump the object World instead of World's ecosystem dictionary
Implemented excavate_world in simulation_calls that returns a buried World file
Initial commit of revive_simulation function inside dose.py
Initial untested commit of 06_revive_simulation_01.py
Merge branch 'master' of https://github.com/clarencecastillo/dose

# By Clarence Castillo
# Via Clarence Castillo (2) and clarencecastillo (1)
* 'master' of https://github.com/clarencecastillo/dose:
  Initial untested commit of 06_revive_simulation_01.py
  Initial commit of revive_simulation function inside dose.py
  Implemented excavate_world in simulation_calls that returns a buried World file
  Updated bury_world() function to dump the object World instead of World's ecosystem dictionary
  Fixed bug that increments generation_count twice during a single generation step
  Updated dose.py to copy the simulation file inside the simulation results directory
  Removed printing of error message when ragaraja interpreter falls into an exception
  Changed simulation files ragaraja_version to 0 and added ragaraja_instructions key in parameters to avoid possible infinite loop in ragaraja interpreter

Conflicts:
	examples/00_test_simulation.py
	examples/01_basic_functions_one_cell_deployment.py
	examples/02_basic_functions_even_deployment.py
	examples/03_no_migration_isolated_mating.py
	examples/04_adjacent_migration_isolated_mating.py
	examples/05_long_migration_isolated_mating.py