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Commits on Mar 16, 2026

• Bump geekyeggo/delete-artifact from 5 to 6

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  dependabot[bot]

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  peterjc

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Commits on Mar 9, 2026

• Stress importance of the PR template

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  peterjc

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• Fix vector test for NumPy 2.4

  peterjc

  committed
  a6000cd

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• closes #5162

  

  manulera

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Commits on Feb 25, 2026

• Fix `Entrez.Parser.DataHandler` URL security check continuity (related to #5109 and #5114) (#5148)

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  hartwork

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  peterjc

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Commits on Feb 19, 2026

• Using np.sin or np.cos was generating return values which were not plain float.

  peterjc

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• Drop older commented code lines in PDB vector code

  peterjc

  committed
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• Use more typical double indexing with numpy arrays

  peterjc

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• Added PERMISSIVE argument to MMCIFParser as in PDBParser. (#5134)

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  piecole

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Commits on Feb 12, 2026

• Correctly clean up files generated by the Phylo tutorial.

  

  xelandernt

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  peterjc

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  f4d8ae4

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• Fix unstable doctest (key order random)

  peterjc

  committed
  f0973f6

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• Migrate to pyproject.toml

  

  xelandernt

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  peterjc

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Commits on Jan 26, 2026

• Add test for run_psea using a temporary directory

  

  kirandharmar867-maker

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  peterjc

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  f948a55

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• Format Bio/PDB/PSEA.py with black

  

  kirandharmar867-maker

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  peterjc

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  156e6b6

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• Run PSEA in a temporary directory to avoid leftover files

  

  kirandharmar867-maker

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  peterjc

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Commits on Jan 23, 2026

• Avoid http links in Bio.Entrez (#5114)

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  mdehoon

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• Remove code that was deprecated in 1.85 (#5144)

  mdehoon

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Commits on Jan 18, 2026

• Replace print statements with warnings/stderr in NCBIXML (#5140)

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  csbiy

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Commits on Jan 17, 2026

• Silence PDBConstructionWarning in test_PDB_StructureAlignment

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  csbiy

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• Replace Union and Optional with Python 3.10+ typing

  peterjc

  committed
  d952922

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• Stay on mypy 1.16.1 and older black

  peterjc

  committed
  c489daa

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• Ignore B905 in ruff command line too

  peterjc

  committed
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• Ignore B905

  peterjc

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• [pre-commit.ci] autoupdate

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  pre-commit-ci[bot]

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  peterjc

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• ruff v0.11.10 format then black 25.9.0

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  peterjc

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Commits on Dec 26, 2025

• Issue 5122 bug fix (#5126)

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  beneopp

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Commits on Dec 25, 2025

• DOC: Clarify Visual Studio Build Tools workload requirement for Windows (#5118)

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  suyash469

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  peterjc

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Commits on Dec 15, 2025

• use an existing pdb file for the test

  

  timjden

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  peterjc

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  fb2f3f0

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• test for fixed format string

  

  timjden

  authored and

  peterjc

  committed
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• add missing space in the format string

  

  timjden

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  peterjc

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• Bump actions/cache from 4 to 5

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  dependabot[bot]

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  peterjc

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Commits on Dec 6, 2025

• Fix parsing of snapgene features with linebreaks in qualifier values (#5117)

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  manulera

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Commits on Nov 28, 2025

• README.rst: Mass-replace http:// links with https://

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  hartwork

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  peterjc

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Commits on Nov 26, 2025

• Make pre-commit CI more helpful

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  hartwork

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  peterjc

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  b936f62

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• Fix typo/bug in biopython.Bio.PDB.vectors vector_to_axis (#5045)

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  Mikel-MG

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