This fixes #35. The default reaction firing output is now a JSON file and can be set with the argument -rxnlog reactions.json. Please note that there is no extension detection, the output will always be in JSON.
What is done
The file format is fully functional
A bug fix for reactions with deletion operations for the -connect argument
New test cases added and validation settings are updated to ensure consistent validation
What is left to do before merging:
Making sure that this file format is independent of the -connect argument
A new argument allowing for the buffering of multiple firings to allow the user to balance between memory usage and CPU usage for the file format
Add option for an infinite buffer size
Cleaning up code
Speed and memory tests to ensure no new major inefficiencies are introduced
This fixes #35. The default reaction firing output is now a JSON file and can be set with the argument
-rxnlog reactions.json. Please note that there is no extension detection, the output will always be in JSON.What is done
-connectargumentWhat is left to do before merging:
Making sure that this file format is independent of the-connectargumentA new argument allowing for the buffering of multiple firings to allow the user to balance between memory usage and CPU usage for the file formatAdd option for an infinite buffer sizeCleaning up codeSpeed and memory tests to ensure no new major inefficiencies are introducedFully documenting the file formatBonds in initial state blockCompress initial state molecule type arrayCheck compatibility with populations