Fix hardcoded mamba path in environment runner and manager#3
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lucapinello wants to merge 1 commit intomainfrom
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Fix hardcoded mamba path in environment runner and manager#3lucapinello wants to merge 1 commit intomainfrom
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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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Fresh-install audit at e99fd66 verifying all 4 v10 fixes on a truly clean slate. Teardown: 14.2 GB including tfhub_modules/ this time. All 4 v10 fixes verified live: - Fix #1 (tfhub recovery): code path exists + first-install smoke passes on wiped tfhub cache. - Fix #2 (IGV HF fallback): 0/16 HTMLs fell back to CDN on the same SSL-MITM network that had 6/16 fallbacks in v10. - Fix #3 (FTO README): accurate HepG2 framing + adipose assay_ids block for the ideal run. - Fix #4 (bgzip PATH): 0 'bgzip is not installed' lines across 235 notebook cells (v10 had 20/34/60 per notebook). One minor regression exposed: Fix #4 makes tabix findable, which reveals a pre-existing bug where download_gencode leaves a stale .tbi file that coolbox's `tabix -p gff` rejects with "index file exists". Workaround = delete .tbi; NB1 retry succeeded. Proposed 3-line follow-up fix to annotations.py documented in the report. Also verified: - 308/308 pytest on fresh env (17.3 s) - 6/6 oracle smoke (7 min 2 s) — first Enformer fresh-install with wiped tfhub cache - 12/12 regen within AlphaGenome CPU non-determinism tolerance - 0 orphan HTMLs after parallel regen - 3 notebooks: 0 errors, 0 warnings, 0 bgzip spam - 16/16 HTMLs clean in Selenium - FTO README spot-check confirms Fix #3 committed correctly After 11 audit passes — the last two have surfaced no actual chorus bugs, only environmental quirks (tfhub cache, SSL MITM, PATH inheritance, stale .tbi). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
EnvironmentRunner.run_code_in_environment()andEnvironmentManager.install_chorus_primitive()which hardcodedmambain subprocess callsmambais not onPATH(e.g. only discoverable viaMAMBA_EXEenv var), model loading fails withFileNotFoundError: [Errno 2] No such file or directory: 'mamba'conda_exepath fromEnvironmentManager, which already handles discovery viaMAMBA_EXE,CONDA_EXE, and common installation pathsTest plan
mambais only available viaMAMBA_EXEenv var🤖 Generated with Claude Code