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upgrade to numpy2 and python3.12#115

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OleinikovasV merged 13 commits intomainfrom
use_numpy2
Feb 19, 2026
Merged

upgrade to numpy2 and python3.12#115
OleinikovasV merged 13 commits intomainfrom
use_numpy2

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@OleinikovasV OleinikovasV commented Feb 18, 2026

Relieving the pains of this issue #111 !

Undoing the damage of PR #98 that pinned numpy<2 due to issues with networkit=11.0.0. This has since been remedied.

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FileStatementsMissingCoverageCoverage
(new stmts)
Lines missing
  src/plinder
  __init__.py
  src/plinder/core/index
  system.py
  src/plinder/core/structure
  smallmols_similarity.py
  structure.py
  src/plinder/core/utils
  cpl.py
  src/plinder/data
  databases.py
  final_structure_qc.py
  splits.py
  src/plinder/data/pipeline
  utils.py
  src/plinder/data/utils/annotations
  get_similarity_scores.py
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LGTM!

@OleinikovasV OleinikovasV changed the title release numpy<2 pin; upgrade networkit upgrade to numpy2 and python3.12 Feb 19, 2026
@OleinikovasV OleinikovasV merged commit 85b3f1c into main Feb 19, 2026
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OleinikovasV added a commit that referenced this pull request Feb 19, 2026
* upgrade to numpy 2
* upgrade openstructure, networkit
* fix: python 3.12 support
* fix: force LD_LIBRARY_PATH to conda
* chore: update development.md
* Proxima (formerly VantAI)
* test: update tests for updated call signatures
* Update tests/core/test_core_system.py
* Update tests/test_annotations.py

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Co-authored-by: Thomas Duignan <thomas.j.duignan@gmail.com>
Co-authored-by: Tom Duignan <tjduigna@users.noreply.github.com>
@OleinikovasV OleinikovasV deleted the use_numpy2 branch February 20, 2026 19:56
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2 participants