Troubleshooting¶

ImportError: No module named scipy or similar¶

Install runtime dependencies first:

uv sync

Plots are not being written¶

Check that the script can create the diagnostic_plots/ directory in the current working directory.

Also verify that your environment has a working Matplotlib backend for non-interactive figure saving.

Optimization returns unexpected values¶

Review the inputs first:

• very high toxicity_weight will strongly suppress abundance,
• essentiality_weight = 0 removes the robustness benefit,
• very low clone_fraction can collapse baseline abundance,
• high burstiness may push abundance optima upward.

A gene raises ValueError¶

GeneConfig.validate() rejects invalid parameter ranges. Check:

• positive transcription rate,
• positive translation efficiency,
• positive copy number,
• clone fraction within [0, 1],
• non-negative weights,
• positive burstiness.