Add comprehensive README with contributor onboarding guide

[Copilot]

The repository had a minimal 14-line README that only pointed to external directories. This adds comprehensive documentation covering the entire project for users and new contributors.

Sections Added

• Installation: Standard Python and Docker setup with Gurobi licensing instructions
• Usage: Working examples for FBA, FVA, E-Flux, GC-Flux, and visualization with correct API calls
• Project Structure: Directory layout and module organization
• Development: Environment setup, testing (make test), and linting (make lint)
• Contributing: Fork/PR workflow, code style expectations, and issue reporting guidelines
• Dependencies: Requirements with rationale (why Gurobi, Python 2.7 compatibility notes)

Example Usage

import pyabolism

# Load SBML model and run FBA
model = pyabolism.io.load_model('model.xml', filetype='sbml')
pyabolism.simulate.FBA(model, show=True)

# Run FVA maintaining 90% of optimal objective
pyabolism.simulate.FVA(model, obj_ratio=0.9)

# Access results
for reaction in model.reactions():
    print("{}: {}".format(reaction.id, reaction.flux_value))

All code examples use Python 2.7 compatible syntax (.format() not f-strings) and match actual implementation (e.g., obj_ratio parameter for FVA).

Original prompt

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This section details on the original issue you should resolve

<issue_title>Write a full-featured README</issue_title>
<issue_description>We need a readme that comprehensively covers the codebase, including onboarding new contributors.</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes Write a full-featured README #1

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