Removed unused parameters from template_settings.yaml, have run_imaging_pipeline use num_cores from settings.yaml. Keeping the old template_settings file for now. Pipeline appears to run. For Ticket #130.
Actually added changes to run_imaging_pipeline mentioned in last commit. And removedmodule_name from the logging directory, so the pipeline log is actually written to the path specified in settings.yaml. For Ticket #130.
Removed old_template_settings.yaml file.
Added module_name back into the logging path. If the logging path does not exist, or if the module-specific logging folder does not exist, then either will be created and have their permissions set. For Tickets #130 and #132.
Merge pull request #132 from STScI-Citizen-Science/use_num_cores

Merging the use of num_cores in settings.yaml and logging now auto-creates the log/module folder.
In the process of removing redundant function definitions in run_trim. Currently, run_trim is broken. For Ticket #129.
Replaced subarrays as its own separate function, since it is sometimes called on arrays other than self.data. For Ticket #129.
Corrected mistake in PNGCreator.positive(), and updated run_trim_test's positive test to work on the class method.
Merge branch 'revise_PNG' of https://github.com/STScI-Citizen-Science/MTPipeline into revise_PNG

Rebasing revise_PNG off of master, now that master has been updated with use_num_cores.