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feat: add whitelists for scipy import errors in Python 3.12.10-humanness builds#79

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May 28, 2026
Merged

feat: add whitelists for scipy import errors in Python 3.12.10-humanness builds#79
AStaroverov merged 2 commits into
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feat/add-promb

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@AStaroverov AStaroverov commented May 27, 2026

Greptile Summary

This PR adds scipy import error whitelists for the python-3.12.10-humanness build on linux-aarch64 and linux-x64, whitelisting the known scipy.linalg._matfuncs_sqrtm_triu circular-import failure.

  • Both new Linux files whitelist scipy.linalg._matfuncs_sqrtm_triu under scipy-1.*.whl, consistent with other builds.
  • Every other Linux build that includes scipy (e.g. sccoda, h5ad) also whitelists scipy.stats._unuran.unuran_wrapper for the 'SeedlessSequence' numpy compatibility error — and the macosx-aarch64.json for this same humanness build includes both entries. It's worth confirming whether the Linux humanness build uses a newer numpy that avoids this error, or whether the second entry is missing.

Confidence Score: 4/5

Safe to merge if the humanness Linux build intentionally uses a numpy version that avoids the unuran_wrapper error; otherwise the checker may silently miss a known failure.

The changes are minimal whitelist JSON additions. The only concern is that scipy.stats._unuran.unuran_wrapper is whitelisted in every other Linux scipy entry in the repo (and in the macOS counterpart for this very build), but is absent from the two new Linux files. If the humanness build's numpy version on Linux does exhibit this error, it would be treated as unexpected by the checker.

Both linux-aarch64.json and linux-x64.json — confirm whether the unuran_wrapper entry should be present, consistent with all other Linux scipy whitelists.

Important Files Changed

Filename Overview
checker/whitelists/python-3.12.10-humanness/linux-aarch64.json Adds scipy whitelist entry for linux-aarch64, but only includes one of the two scipy import errors seen in every other Linux scipy whitelist in the repo.
checker/whitelists/python-3.12.10-humanness/linux-x64.json Adds scipy whitelist entry for linux-x64, but only includes one of the two scipy import errors seen in every other Linux scipy whitelist in the repo.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[scipy-1.*.whl import check] --> B{Platform}
    B --> |linux-x64 / linux-aarch64| C[Whitelist lookup]
    B --> |macosx-aarch64| D[Whitelist lookup]
    C --> E[scipy.linalg._matfuncs_sqrtm_triu ✅ whitelisted]
    C --> F[scipy.stats._unuran.unuran_wrapper ❓ NOT whitelisted]
    D --> G[scipy.linalg._matfuncs_sqrtm_triu ✅ whitelisted]
    D --> H[scipy.stats._unuran.unuran_wrapper ✅ whitelisted]
    F --> I{Does error occur on Linux?}
    I -->|Yes - numpy older| J[Checker flags as unexpected failure]
    I -->|No - newer numpy| K[No issue]
Loading
Prompt To Fix All With AI
Fix the following 2 code review issues. Work through them one at a time, proposing concise fixes.

---

### Issue 1 of 2
checker/whitelists/python-3.12.10-humanness/linux-x64.json:1-5
Every other Linux build in this repo that whitelists scipy includes a second entry for `scipy.stats._unuran.unuran_wrapper` alongside `scipy.linalg._matfuncs_sqrtm_triu` (see `sccoda/linux-x64.json`, `h5ad/linux-x64.json`, `sccoda/linux-aarch64.json`). The `macosx-aarch64.json` for this same humanness build also includes both. If the humanness Linux build uses the same numpy version that triggers the `'SeedlessSequence'` error, this entry is missing and the checker will treat it as an unexpected failure.

```suggestion
{
  "scipy-1.*.whl": {
    "scipy.linalg._matfuncs_sqrtm_triu": "cannot import name 'within_block_loop' from partially initialized module",
    "scipy.stats._unuran.unuran_wrapper": "module 'numpy.random.bit_generator' has no attribute 'SeedlessSequence'"
  }
}
```

### Issue 2 of 2
checker/whitelists/python-3.12.10-humanness/linux-aarch64.json:1-5
Same pattern as `linux-x64.json` — every other Linux scipy whitelist in the repo (`sccoda/linux-aarch64.json`, `h5ad/linux-aarch64.json`) includes the `scipy.stats._unuran.unuran_wrapper` entry. If this error also occurs on Linux aarch64 for the humanness build, omitting it here would cause the checker to flag it as unexpected.

```suggestion
{
  "scipy-1.*.whl": {
    "scipy.linalg._matfuncs_sqrtm_triu": "cannot import name 'within_block_loop' from partially initialized module",
    "scipy.stats._unuran.unuran_wrapper": "module 'numpy.random.bit_generator' has no attribute 'SeedlessSequence'"
  }
}
```

Reviews (1): Last reviewed commit: "feat: add whitelists for scipy import er..." | Re-trigger Greptile

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Code Review

This pull request updates the humanness whitelists for Python 3.12.10 on both linux-aarch64 and linux-x64 platforms. Specifically, it adds an entry for scipy-1.*.whl to ignore a partial initialization import error in scipy.linalg._matfuncs_sqrtm_triu. There are no review comments, and I have no additional feedback to provide.

Comment thread checker/whitelists/python-3.12.10-humanness/linux-x64.json
Comment thread checker/whitelists/python-3.12.10-humanness/linux-aarch64.json
@AStaroverov AStaroverov merged commit 0e90292 into main May 28, 2026
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2 participants