Lots of different bug fixes. (#17)

* setting up setuptools to install subsbml package (not yet working)

* core working branch

* tutorial.py working - share, combine, connect. Initial amount volume mode does not work

* volume mode problems fixed for shareSpecies. Need to carry forward changes to others. Also not working for species not in list of shared resources. Also setting size using system size in volume mode amounts

* tutorial.py and iptg_transport.py both are working now. share, combine, and connect all working. Need to fix the volume mode and make it consistent all over.

* iptg graph temp

* setup working. imports fixed. consistent and correct importing of modules.

* simulatemultiplevariable method modified, compartment option added. IPTG_transport graph generate for multiple inputs

* combine/share etc. all working and updated for normal combine, not working yet in the new framework for combinations inside a System

* changed back to l3v2, because fast attribute is mandatory with l3v1, and it has been removed from the code. tutorial.py is working but combineSubsystem is not. minor fixes needed

* problem with combinesubsystems

* shareSubsystem working with volume mode

* subsystem.py modified

* combine working. share, connect, combine, all 3 working in all of the modes. Volume mode also works perfectly, virtual mode works too. combine does not depend on share now. All valid SBML models generated in SBML l3v2.

* removing trash files

* all of the core features in subsbml are working, generating and converting to latest SBML level and version (l3v2). IPTG transport example working with this commit

* jupyter notebooks edited, all 3 working now

* removed useless files and removed model reduction example since fast attribute was used which is obsolete in SBML L3v2

* added createBasicSubsystem to create one Subsystem with a SBMLDocument, SBML Model inside, and make all the basic settings using a standard set of preassigned values. An important bug fix in createSimpleReaction in SimpleModel class, to allow for reactions which create or degrade a particular species into nothing (when product/reactant missing).

* modified SimpleReaction.py to fix bug for creating simple reaction with numbers in species names/ids

* modified SimpleReaction.py to fix bug for creating simple reaction with numbers in species names/ids (#3)

* modified iptg transport circuit. Improved membrane model. simulateVariableInputs method modified and multiple bugs fixed. Accepts lists for compartments, plotting options in a single plot or a matrix using subplots (not yet working).

* added varying alhl and varying gfp dna plots to guide experiment on their concentrations. fixed minor bug in simulate variable inputs for compartment species in else loop set to species id, replaced now with blank string, so optional keywords arguments should work. also added **kwargs to this function argument

* iptg transport working with modifications to variable input simulations

* bug in create unit definition in simple model fixed

* added gitignore to remove temp files to go to github repo, bug fixes in SimpleModel class

* Simple model (#5)

* modified SimpleReaction.py to fix bug for creating simple reaction with numbers in species names/ids

* bug in create unit definition in simple model fixed

* added gitignore to remove temp files to go to github repo, bug fixes in SimpleModel class

* Transport - setMembrane etc. fixed.  (#4)

* modified SimpleReaction.py to fix bug for creating simple reaction with numbers in species names/ids

* modified iptg transport circuit. Improved membrane model. simulateVariableInputs method modified and multiple bugs fixed. Accepts lists for compartments, plotting options in a single plot or a matrix using subplots (not yet working).

* added varying alhl and varying gfp dna plots to guide experiment on their concentrations. fixed minor bug in simulate variable inputs for compartment species in else loop set to species id, replaced now with blank string, so optional keywords arguments should work. also added **kwargs to this function argument

* iptg transport working with modifications to variable input simulations

* all examples and tutorials running with the latest code. Need to create unit tests so that further code developments have backward compatibility. IPTG transport example renamed to main_IPTG_transport for better visibility.

* added debug option to system.getModel and kwargs options to some functions. Downgraded SBML output to L3V1

* minor bug fixed

* commiting changes from examples

* Core development (#6)

* new development branch

* code cleanup, verbose option added for warnings. old unused code removed. package dependencies cleanup and other general bug fixes

* added the overloaded functional operator to add subsystems and systems using + operator

* fixed deletion of multiple compartments. default suffixAllIds added using model ids.

* loads of bug fixes. major change to combineSystems function, core code remains mostly unchanged

* ready for upstream PR

* more fixes, be240 notebook runs

* fixed simple model functions and SBML level unified everywhere to be L3V2

* tutorial modeling working

* all examples and all tutorials working

* added BE240 lecture notebooks to examples

Co-authored-by: ayush-pandey <[email protected]>