fixed issue where %prog was not replaced with script name
Merge pull request #967 from gregcaporaso/updated-script-docs

fixed issue where %prog was not replaced with script name
Fixed RST sphinx errors
Merge pull request #968 from jrrideout/master

Fixed RST sphinx errors
Updated version strings from 1.7.0 to 1.7.0-dev.
Merge pull request #970 from jrrideout/170-post

Updated version strings from 1.7.0 to 1.7.0-dev.