Update code to support latest versions of pyhmmer and scikit-learn#105
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CedricHermansBIT wants to merge 1 commit into
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Update code to support latest versions of pyhmmer and scikit-learn#105CedricHermansBIT wants to merge 1 commit into
CedricHermansBIT wants to merge 1 commit into
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scikit-learn: Starting from version 1.3.0, copy is no longer a valid parameter in Birch clustering of scikit learn. pyhmmer: This property replaces the query_name, query_accession and query_length properties that were deprecated in *v0.10.15* and removed in *v0.11.0*. From 0.11 onwards you have to access the name, accession and length as a property of the query object.
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Pull request overview
Updates BigSlice’s integration points with upstream library changes so the project runs against newer scikit-learn and pyhmmer releases.
Changes:
- Removed the deprecated/removed
copy=parameter fromsklearn.cluster.Birchconstruction. - Updated
pyhmmerusage to access HMM query metadata viatop_hits.query.*instead of removedquery_*properties.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 5 comments.
| File | Description |
|---|---|
bigslice/modules/clustering/birch.py |
Removes the no-longer-supported copy argument when instantiating Birch. |
bigslice/bigslice |
Updates pyhmmer query metadata accessors (top_hits.query.name/accession) across multiple scanning paths. |
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Versions are not documented clearly for the libraries needed, as such things break in latest versions of the pip install and docker releases. I fixed the issues and the bigslice test case at least seams to work now with scikit-learn 1.8.0 and pyhmmer 0.12.0
scikit-learn: Starting from version 1.3.0, copy is no longer a valid parameter in Birch clustering of scikit learn.
pyhmmer: This property replaces the query_name, query_accession and query_length properties that were deprecated in v0.10.15 and removed in v0.11.0. From 0.11 onwards you have to access the name, accession and length as a property of the query object.