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Merged
julenmendieta merged 3 commits into from
Jul 20, 2026
Merged

Julenmendieta/MILAB-6501_bigEmbeddings #99

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84f0241
Add hdbscan
julenmendieta Jul 8, 2026
a8fb7d8
Changeset
julenmendieta Jul 8, 2026
a5ca32e
Remove redundant changeset
julenmendieta Jul 19, 2026
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5 changes: 5 additions & 0 deletions .changeset/add-hdbscan-python-3-12-10.md
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---
"@platforma-open/milaboratories.runenv-python-3.12.10": patch
---

Add `hdbscan==0.8.44` (scikit-learn-contrib HDBSCAN) to the Python 3.12.10 runenv. Built from prebuilt wheels on linux-x64, macOS (universal2) and win-x64; compiled from the Cython sources on the native runner for linux-aarch64 (no ARM64 wheel on PyPI). Provides density-based clustering with out-of-sample assignment (`approximate_predict`), enabling the embedding-clustering block's large-dataset path.
7 changes: 7 additions & 0 deletions python-3.12.10/config.json
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Expand Up @@ -12,6 +12,7 @@
"parasail==1.3.4",
"numpy==2.2.6",
"umap-learn==0.5.7",
"hdbscan==0.8.44",

@greptile-apps greptile-apps Bot Jul 8, 2026

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P1 hdbscan 0.8.44 prebuilt wheels may be incompatible with NumPy 2.x

hdbscan==0.8.44 ships prebuilt cp312 wheels for linux-x64, macOS universal2, and win-x64. If those wheels were compiled against NumPy 1.x, they will fail to import at runtime against numpy==2.2.6 because NumPy 2.0 introduced ABI-breaking changes for Cython extensions that used the old C API. The linux-aarch64 path builds from source (fine — it will compile against the 2.2.6 headers), but the three prebuilt-wheel platforms are at risk. It is worth verifying that the PyPI wheels for hdbscan 0.8.44 were built with NPY_TARGET_VERSION targeting NumPy 2.x before merging.

Prompt To Fix With AI 
This is a comment left during a code review.
Path: python-3.12.10/config.json
Line: 15

Comment:
**hdbscan 0.8.44 prebuilt wheels may be incompatible with NumPy 2.x**

`hdbscan==0.8.44` ships prebuilt cp312 wheels for linux-x64, macOS universal2, and win-x64. If those wheels were compiled against NumPy 1.x, they will fail to import at runtime against `numpy==2.2.6` because NumPy 2.0 introduced ABI-breaking changes for Cython extensions that used the old C API. The linux-aarch64 path builds from source (fine — it will compile against the 2.2.6 headers), but the three prebuilt-wheel platforms are at risk. It is worth verifying that the PyPI wheels for hdbscan 0.8.44 were built with `NPY_TARGET_VERSION` targeting NumPy 2.x before merging.

How can I resolve this? If you propose a fix, please make it concise.

Note: If this suggestion doesn't match your team's coding style, reply to this and let me know. I'll remember it for next time!

Fix in Claude Code

"PyYAML==6.0.3",
"cudf-cu12==25.6.0",
"scanpy==1.10.1",
Expand Down Expand Up @@ -71,6 +72,12 @@
"reason": "No cp312 / Windows wheel; compile with MSVC. The shared runner workflow activates vcvars via milaboratory/github-ci/actions/setup-msvc-dev-cmd@v4 before this step runs, so the env (INCLUDE / LIB / LIBPATH / PATH plus DISTUTILS_USE_SDK) is in scope when pip wheel invokes setuptools.",
"buildRequires": ["setuptools", "wheel"]
}
},
"hdbscan": {
"linux-aarch64": {
"reason": "No cp312 / Linux ARM64 wheel on PyPI for hdbscan 0.8.44 (wheels exist for linux-x64, macOS universal2, and win-x64); compile the Cython sources on the native ARM runner.",
"buildRequires": ["setuptools", "wheel", "Cython", "numpy"]
}
}
}
}
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