Initialize biomimetic artificial-life package

[Spbd1]

Motivation

• Provide a minimal, research-oriented Python package that implements core primitives for biomimetic artificial-life experiments (compact genomes, genotype–phenotype mapping, inheritance/mutation, biome-specific fitness, and agent-based simulation).
• Keep the initial release conservative and extensible with explicit TODOs for empirical validation and literature linkage so model assumptions remain transparent.
• Enable reproducible CLI-driven experiments and programmatic usage with seeded randomness for deterministic smoke tests.

Description

• Add package layout and build metadata with pyproject.toml, a console entry point pishiegen, and top-level package pishiegen that re-exports key primitives.
• Implement genome primitives and operators: Gene and Genome dataclasses, Genome.compact_code()/parse(), random_genome(), mutate_gene(), and breed() with generation tracking and bounded numeric ranges.
• Implement genotype-to-phenotype expression, biome/environment primitives, and fitness scoring: express_genome() with bounded transform, Biome with normalization, and score_fitness() producing interpretable components and conservative distance-based scoring.
• Implement a small agent-based simulation engine (Organism, Simulation, SimulationResult), experiment presets (temperate_biome, create_seed_population), text visualization (summarize_fitness), a minimal CLI (generate-organism, decode-genome, breed, simulate-biome), README, docs (docs/model_assumptions.md), example script, and unit test placeholders under tests/.

Testing

• Ran the unit test suite with python -m pytest, which completed successfully (7 passed).
• Compiled packages and ran a runtime smoke example with python -m compileall -q pishiegen tests examples && python -m pishiegen.cli simulate-biome --seed 3 --population 5 --generations 2, which produced a valid fitness summary output.
• Performed an import audit by programmatically importing public modules (pishiegen, pishiegen.cli, pishiegen.genome, pishiegen.phenotype, pishiegen.environment, pishiegen.fitness, pishiegen.simulation, pishiegen.experiments, pishiegen.visualization) and observed success (import audit ok).

---

Codex Task