Fix Python 2/3 compatibility and modernize codebase #4
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This commit modernizes the Assembly Calculus codebase to work with Python 3:
## Python 2 to 3 Migration:
- Replace `xrange` with `range` in: project.py, overlap_sim.py, tests.py, brain_util.py
- Fix print statement syntax: `print "..."` → `print("...")` in overlap_sim.py
- Replace deprecated `dict.iteritems()` with `dict.items()` in simulations.py
## Bug Fixes:
- Fix undefined variable error in brain.py:289 (`from_area` → `from_area_name`)
- Add missing `DET_SIZE = 2` constant to parser.py and recursive_parser.py
## Code Quality:
- Standardize indentation in brain.py (convert tabs to spaces for consistency)
- Fix mixed indentation issues that could cause Python syntax errors
## Current State:
The repository now contains a fully functional Python 3 implementation of the
Assembly Calculus model for computational neuroscience research. All modules
execute without errors:
- brain.py: Core neural assembly simulation framework
- parser.py & recursive_parser.py: Brain-based language parsing models
- simulations.py: Comprehensive simulation library for assembly operations
- Tests and utilities: All supporting modules for research experiments
The codebase implements the theoretical framework from Papadimitriou et al.'s
research on biologically plausible neural computation and language processing.
🤖 Generated with [Claude Code](https://claude.ai/code)
Co-Authored-By: Claude <noreply@anthropic.com>
- Provide overview of assembly model of brain computation - Document all Python files and their purposes - Include getting started guide with prerequisites - Add example experiments for students to run - Explain key concepts: brain areas, projections, assembly formation - Include usage examples for simulations, language learning, and analysis - Add contribution guidelines and references 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <noreply@anthropic.com>
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Summary
This PR modernizes the Assembly Calculus codebase to work with Python 3 and fixes several code quality issues that were preventing execution.
Changes Made
Python 2 to 3 Migration
xrangewithrangein: project.py, overlap_sim.py, tests.py, brain_util.pyprint "..."→print("...")in overlap_sim.pydict.iteritems()withdict.items()in simulations.pyBug Fixes
from_area→from_area_name)DET_SIZE = 2constant to parser.py and recursive_parser.pyCode Quality
Testing
All Python modules now execute without errors:
Current State
The repository now contains a fully functional Python 3 implementation of the Assembly Calculus model for computational neuroscience research. The codebase successfully implements the theoretical framework from Papadimitriou et al.'s research on biologically plausible neural computation and language processing.
Example working output from parser:
Compatibility
🤖 Generated with Claude Code