Updates to the MEW module and documentation

[cruz-f]

Updates to the MEW module

Features added to the MEW module:

• PROM implementation as phenotype simulation method (available at mewpy.mew.analysis and mewpy.omics)
• CoRegFlux implementation as phenotype simulation method (available at mewpy.mew.analysis and mewpy.omics)
• mewpy.mew.analysis.find_conflicts() implementation to search for conflicts between regulatory and metabolic states
• HTML representation for MEW algebra, models, variables, phenotype simulation methods, and solutions. MEW objects are now fully compatible with Jupyter Notebooks
• Example examples/mew_models.ipynb - How to use MEW models
• Example examples/mew_analysis.ipynb - How to perform phenotype simulations using MEW models
• Description of the integrated models used in the examples: E. coli core model; iMC1010 model; iNJ661 model; iMM904 model

Features removed, updated, or fixed in the MEW module:

• Simplification of LinearProblem and derived phenotype simulation methods
• Simplification of ModelSolution
• Improving RFBA implementation to use the following order: regulatory state -> metabolic state -> constraints
• Improving OptORF implementation to use the following order: regulatory state -> metabolic state -> constraints
• Removing the Coefficients object to simplify the variable's interface

Typing and Documentation

Documentation and typing added to the MEW module:

• All objects, methods, and functions have been typed using Python's typing module
• All objects, methods, and functions now have docstrings that can be consulted with the help method
• A new page with the documentation of MEW models and analysis

[codecov-commenter]

Codecov Report

Merging #32 (2c47139) into master (8b44bfd) will decrease coverage by 0.93%. The diff coverage is 56.52%.

@@            Coverage Diff             @@
##           master      #32      +/-   ##
==========================================
- Coverage   55.06%   54.13%   -0.94%     
==========================================
  Files         122      127       +5     
  Lines       15308    15209      -99     
  Branches     3406     3390      -16     
==========================================
- Hits         8430     8233     -197     
- Misses       6026     6145     +119     
+ Partials      852      831      -21     

Impacted Files	Coverage Δ
src/mewpy/io/gene_expression.py	0.00% <0.00%> (ø)
src/mewpy/mew/algebra/__init__.py	100.00% <ø> (ø)
src/mewpy/mew/algebra/algebra_constants.py	100.00% <ø> (ø)
src/mewpy/mew/models/metabolic.py	83.43% <ø> (ø)
src/mewpy/mew/models/model.py	81.53% <ø> (ø)
src/mewpy/mew/models/regulatory.py	87.37% <ø> (ø)
src/mewpy/mew/models/serialization.py	78.66% <ø> (ø)
src/mewpy/mew/solution/__init__.py	100.00% <ø> (ø)
src/mewpy/mew/solution/model_solution.py	31.93% <ø> (+2.62%)	:arrow_up:
src/mewpy/mew/solution/multi_solution.py	30.70% <ø> (+3.84%)	:arrow_up:
... and 83 more

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