audit(linux-cuda): v30 PR #60 spot-check — F1 fix holds, no findings

Cross-platform validation of the v30 macOS audit (PR #60: huggingface_hub
in chorus-chrombpnet env yaml + slim HF mirror). The macOS scorched-earth
audit flagged the env-yaml change as the kind of thing that can behave
differently across platforms; the v29 Linux/CUDA baseline predates the
slim-mirror feature so it's not a substitute. This audit pins parity on
Linux/CUDA.

Run on Linux ml008 (5.15.0-170-generic / 2× NVIDIA A100 80 GB PCIe).

Outcome: 0 new findings. Same fast-suite pass count + same integration
behaviour as macOS. The slim-mirror code path resolves under Linux
mamba just as it does on macOS.

Findings:
- mamba env create from the new chrombpnet.yml resolves clean on Linux
- huggingface_hub>=0.20.0 installs from conda-forge with no transitive
  dep mismatch
- F1 regression test passes inside the Linux-built chorus-chrombpnet env
- Fast pytest: 346 passed / 4 deselected (matches macOS)
- Integration pytest: 3 passed / 1 skipped (matches macOS)

Notes for future audits on this host:
- Lab shared NFS makes mamba env create and small-file ops slow
  (50+ min env build vs 40 s on local SSD)
- First fast-pytest run timed out on a transient do_poll syscall
  (52 s CPU in 30 min wall); kill + rerun completed in 10 min cleanly
- GPU contention on cuda:0 from another user at audit time; tests ran
  on cuda:1 / CPU — slim-mirror is HTTP-only so no GPU impact

Not in this audit (deferred to maintainer):
- Full chorus setup --oracle all reinstall on Linux
- Cherry-pick F1 lesson into docs/plans/sei-hf-mirror.md

Artifacts: report.md + chorus_fast_pytest.log + chorus_integration_pytest.log
+ chrombpnet_env_create.log + system_info.txt under
audits/2026-04-29_v30_linux_cuda_spotcheck/.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: lucapinello

audits/2026-04-29_v30_linux_cuda_spotcheck/chorus_fast_pytest.log

@@ -0,0 +1,34 @@
+........................................................................ [ 20%]
+........................................................................ [ 41%]
+........................................................................ [ 62%]
+........................................................................ [ 83%]
+..........................................................               [100%]
+=============================== warnings summary ===============================
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:88
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:88
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:88
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:88
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:88
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:88
+  /data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:88: PyparsingDeprecationWarning: 'parseString' deprecated - use 'parse_string'
+    parse = parser.parseString(pattern)
+
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:92
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:92
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:92
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:92
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:92
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:92
+  /data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:92: PyparsingDeprecationWarning: 'resetCache' deprecated - use 'reset_cache'
+    parser.resetCache()
+
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_mathtext.py:45
+  /data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_mathtext.py:45: PyparsingDeprecationWarning: 'enablePackrat' deprecated - use 'enable_packrat'
+    ParserElement.enablePackrat()
+
+tests/test_utils.py::TestNormalizationUtils::test_quantile_normalize
+  /data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/numpy/core/numeric.py:407: RuntimeWarning: invalid value encountered in cast
+    multiarray.copyto(res, fill_value, casting='unsafe')
+
+-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
+346 passed, 4 deselected, 14 warnings in 600.36s (0:10:00)

audits/2026-04-29_v30_linux_cuda_spotcheck/chorus_integration_pytest.log

@@ -0,0 +1,26 @@
+...s                                                                     [100%]
+=============================== warnings summary ===============================
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:88
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:88
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:88
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:88
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:88
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:88
+  /data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:88: PyparsingDeprecationWarning: 'parseString' deprecated - use 'parse_string'
+    parse = parser.parseString(pattern)
+
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:92
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:92
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:92
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:92
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:92
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:92
+  /data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_fontconfig_pattern.py:92: PyparsingDeprecationWarning: 'resetCache' deprecated - use 'reset_cache'
+    parser.resetCache()
+
+../../../data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_mathtext.py:45
+  /data/pinello/SHARED_SOFTWARE/envs/lab_envs/chorus/lib/python3.10/site-packages/matplotlib/_mathtext.py:45: PyparsingDeprecationWarning: 'enablePackrat' deprecated - use 'enable_packrat'
+    ParserElement.enablePackrat()
+
+-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
+3 passed, 1 skipped, 346 deselected, 13 warnings in 613.52s (0:10:13)