Update Python installer; Minor bug fixes

Removed setup.py, fixed flake8-detected bugs, bumping to Python>=3.8.

Mayor Python>=3.7 code cleanup and speedups for some core functions.

1.1 -- Mayor Python>=3.7 code cleanup and speedups for some core functions.

• rewrite of all objects to use dsdobjects>=0.8 (an attempt to fix rare segfaults).
• moved ratemodel related functions to peppercornenumerator/ratemodel.py.
• renamed open to open1N in order to avoid name conflicts.
• default concentration unit for output is now 'nM' throughout the library.
• updating and extending unittests.
• some pythonification of old code.
• removing deprecated code and undocumented experimental features.
• updated files in case_study directory for compatibility with changes.

Stable release 1.0

Used for publication: https://doi.org/10.1098/rsif.2019.0866

Python 2.7 & 3.x compatible stable release

Used for publication: https://doi.org/10.1098/rsif.2019.0866

case study updates, revised library logging

• repository includes case studies from manuscript revision.
• update requirements of dsdobjects
• using logging module in a more standard way
• Python 3.x and Python 2.7 are still supported

Python 3.x support and case study notebooks

A major update of the code.

• Python 3.x and Python 2.7 are now supported
• repository includes case studies from manuscript submission.
• update requirements of dsdobjects and crnsimulator
• added seesaw parser

I/O pil interface

now write_pil can be used to write to a string instead of a filehandle.

setup.py now specifies exact versions

Previous versions of peppercorn may break, if the latest version of the dsdobjects changes.

Now this should work just fine.

changed max-helix, added peppercorn options, and more

• The max-helix notion is now consistent with explanations of the upcoming manuscript.
• Reject-remote 4-way mode requires now both sides to be remote.
• reactions.py: separated the max-helix function (zipper) from the find_on_loop function

peppercorn (executable)

• can specify composite-domains in PIL input
• Sequence information of domains and concentrations of complexes will be present in the output, if they were specified in the input.
• more commandline options
  Added "pilsimulator" (executable) for convenient ODE simulations of peppercorn results.

max helix "before-displacement" formulation including 4-way branch migration

• new max helix semantics including 4-way branch migration
• corrected calculation of condensed rates
• new input standard are PIL files in kernel notation
• using dsdobjects to define Domains, Complexes, Reactions and RestingSets