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Fix hardcoded mamba path in environment runner and manager#3

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lucapinello wants to merge 1 commit intomainfrom
fix/use-conda-exe-path
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Fix hardcoded mamba path in environment runner and manager#3
lucapinello wants to merge 1 commit intomainfrom
fix/use-conda-exe-path

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Summary

  • Fix EnvironmentRunner.run_code_in_environment() and EnvironmentManager.install_chorus_primitive() which hardcoded mamba in subprocess calls
  • When mamba is not on PATH (e.g. only discoverable via MAMBA_EXE env var), model loading fails with FileNotFoundError: [Errno 2] No such file or directory: 'mamba'
  • Now uses the resolved conda_exe path from EnvironmentManager, which already handles discovery via MAMBA_EXE, CONDA_EXE, and common installation paths

Test plan

  • Verified fix on a system where mamba is only available via MAMBA_EXE env var
  • Successfully loaded and ran ChromBPNet ATAC predictions for K562, HepG2, and GM12878 after the fix

🤖 Generated with Claude Code

The EnvironmentRunner and EnvironmentManager were hardcoding 'mamba' in
subprocess calls, which fails when mamba is not on PATH (e.g. only
available via MAMBA_EXE env var). Use the resolved conda_exe path from
EnvironmentManager instead, which already handles discovery via
MAMBA_EXE, CONDA_EXE, and common installation paths.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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