Parsing improvements - merge improve-parsing into master

[mopichalova]

This pull request closes #70 and represents an overhaul of the parsing module for eBCSgen. It integrates multiple smaller pull requests developed over an extended period, each addressing specific issues and introducing enhancements to ensure robust, flexible, and more efficient parsing capabilities.

Parsing corrections and features

• revised the logic of insert methods (insert_atomic_to_complex, insert_struct_to_complex, insert_atomic_to_struct) to enhance insertion validity and data integrity
  • issue insert_atomic_to_complex and insert_struct_to_complex do not check if the replaced agent is unspecified (i.e. atomic has '_' feature and structure has no atomics specified) #72
  • pr Insert parsing logic improved #91
• enabled the direct usage of complexes in abstract_sequence by modifying the grammar to support complex names as values
  • issue Use complexes directly in abstract_sequence #89
  • pr enable direct usage of complexes #92
• model syntax changes
  • introduced flexibility in the order of sections in BCSL files and
    • multiple definitions of the same sections are side effect turned into feature - contents of the section are merged
  • new lines are enforced and forbidden in specific places to prevent unclear model definition
  • issue Syntactic grammar improvements #93
  • pr Improve grammar syntax #94
• full support for bidirectional rules implemented
  • specifying distinct rates for each direction
  • issue Allow bidirectional rules #30
  • pr Bidirectional rules #96
• regulations
  • ensured that all referenced rule labels in regulation exist
    • regular regulations patterns are separated by semicolon ; to better check for existing labels
    • issue Check that rule labels used in regulations do actually exist #95
  • restricted regular regulations to accept only valid regular expressions, not expressions consisting of regex characters
    • issue Regular regulation - enable only regular expressions over rule labels #88
  • pr Rule labels in regulations and regular regulations #97
• expanded grammar to support rates as complex nested rational expression
  • issue Allow more robust rate expressions #87
  • pr Robust rate expressions #100
• zooming syntax aligned with original BCSL
  • zooming uses ::, same as compartment specification, instead of :
  • syntax ambiguity solved by switching to Earley parser from LALR(1)
  • issue Zooming in abstract syntax to original BCSL syntax #98
  • pr Reverting to BCSL Original Syntax: Implementing "::" #99
• added checks to ensure that all used complex aliases are defined before use, raising ComplexParsingError when mismatches are detected
  • issue raise error when an undefined complex alias is used in a rule #103
  • pr unique atomic agents #105
• checking for uniqueness of atomic agents within structure agents
  • issue structure agent can contain only unique atomic agents (w.r.t. names) in its composition #102
  • pr unique atomic agents #105
• defined replication rules
  • to avoid complex replication checks in every rule
  • issue replication rules #106
  • pr replication rules #107
• implemented parsing for observables
  • pools and basic arithmetic scaling based on the BNGL
  • issue define observables #108
  • pr Observables #109

Testing

• tests were extended to make sure any changes do not disrupt the existing functionalities of eBCSgen
• organized test cases for both existing parsing functionalities and feature tests
  • issue Separate all parsing tests to a separate file/folder #75
  • pr Extracting parsing tests #78
• added test cases for parsing
  • issue Write tests for all other classes that are omitted for now #79
  • pr 79 core tests #85
• moved testing objects to objects_testing.py to eliminate redundancy and text models shifted to .txt files
  • issue Testing: Clean up creation of objects #80
  • pr 80 testing objects #90
• changed tests for rules (replication and bidirectional), syntax for zooming ::, etc
• added parsing tests for new feature observables
  • pr Observables #109

All tests are passing, indicating that the updates are stable and maintain the integrity.