Improve adenine nucleotide balance and add assertions

[csmangum]

• Add assertions for initial and final metabolite levels
• Implement adenine nucleotide conservation in glycolysis and cellular respiration
• Adjust ATP production calculations to maintain balance
• Add logging for adenine nucleotide changes throughout simulation
• Implement checks for glucose consumption and ATP production
• Increase tolerance for adenine nucleotide conservation assertion

This pull request includes significant changes to the pyology package to improve the handling and tracking of adenine nucleotides during simulations. The changes introduce new assertions to ensure metabolite levels are non-negative, enhance the glycolysis and cellular respiration processes, and add detailed logging for adenine nucleotide balances.

Enhancements to Metabolite Handling:

• fun.py: Added assertions to ensure initial and final metabolite levels are non-negative and adjusted calculations for total adenine nucleotides. [1] [2]

Improvements in Glycolysis and Cellular Respiration:

• pyology/cytoplasm.py: Enhanced the glycolysis method to ensure ADP consumption when ATP is produced and introduced error handling for insufficient metabolites. [1] [2]
• pyology/mitochondrion.py: Improved the cellular_respiration method to ensure ADP consumption and added assertions for adenine nucleotide conservation. [1] [2]

Logging and Reporting Enhancements:

• pyology/simulation.py: Added detailed logging of adenine nucleotide changes and assertions to ensure non-negative quantities and proper glucose consumption during simulations. [1] [2] [3] [4] [5]

Minor Code Cleanups:

• pyology/glycolysis.py: Removed unused import and improved logging formatting in the perform, investment_phase, and yield_phase methods. [1] [2] [3] [4]