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Commits on Nov 17, 2023

• update (#4495)

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  mdehoon

  and

  Michiel de Hoon

  authored
  3d541b6

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• removed deprecated modules and function in Bio.SeqUtils (#4493)

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  mdehoon

  and

  Michiel de Hoon

  authored
  960a5e2

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Commits on Nov 16, 2023

• Docs update, Bio.SearchIO is not experimental

  peterjc

  authored
  6eca7ef

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• SeqRecord does not check type of Seq argument (#4477)

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  netogallo

  authored
  5ab7317

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Commits on Nov 13, 2023

• MMCIFParser ignore '.' header values (#4399)

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  rob-miller

  authored
  1172195

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• Allow Entrez.parse("myfilename") (#4490)

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  mdehoon

  and

  Michiel de Hoon

  authored
  9e5ea1b

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Commits on Nov 7, 2023

• Remove the parser for plain text output from Blast (#4488)

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  mdehoon

  and

  Michiel de Hoon

  authored
  c1093ec

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• Catch non-UniProt-XML in SeqIO parser (#4486)

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  lurkingviolet

  authored
  b454dca

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Commits on Nov 6, 2023

• Check the contents of the Blast header in test_NCBIXML (#4487)

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  mdehoon

  and

  Michiel de Hoon

  authored
  f68dbb2

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• Note base class ``AbstractPosition`` was renamed to ``Position``

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  peterjc

  authored
  a847fe6

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Commits on Nov 3, 2023

• fix flake8-docstrings D202 No blank lines allowed after function docstring

  peterjc

  committed
  a0fd680

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• Ignore these W293 blank line contains whitespace

  peterjc

  committed
  ddc98c7

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• Ignore flake8 W291 trailing whitespace in tests

  peterjc

  committed
  bd07204

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• Remove no longer needed flake8 skip commands

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  peterjc

  committed
  107e308

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• Ignore flake8 E131,E122,E124,E126,E127,E128,E201,E241 - trust black

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  peterjc

  committed
  f4924d8

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• Fix alignment printing for frameshifts (#4485)

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  mdehoon

  authored
  86d24df

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Commits on Nov 2, 2023

• update substitution matrix reading to ensure files are closed (#4476)

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  byerlyj

  authored
  5b7f016

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• ruff fix most F401 unused imports in Tests

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  peterjc

  committed
  f40d6b7

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• ruff fix RUF010 Use explicit conversion flag (f-strings)

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  peterjc

  committed
  6b98447

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• ruff fix PLR1701 Merge isinstance calls

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  peterjc

  committed
  dc4357c

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• ruff fix PIE790 Unnecessary pass statement

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  peterjc

  committed
  68e3c98

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• ruff fix np.product is deprecated; use np.prod instead

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  peterjc

  committed
  c0663bd

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• ruff fix PIE808 Unnecessary start argument in range

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  peterjc

  committed
  a891abf

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• ruff fix UP024 Replace aliased errors with OSError

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  peterjc

  committed
  216913e

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• ruff UP032 Use f-string instead of format call

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  peterjc

  committed
  98372cd

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• ruff UP015 Unnecessary open mode parameters

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  peterjc

  committed
  9c952b9

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• ruff: UP021 universal_newlines is deprecated, use text

  peterjc

  committed
  3fb325c

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• ruff fix PYI032 Prefer object to Any for __eq__ and __nee__

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  peterjc

  committed
  6acd6b6

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• ruff fix PIE804 Unnecessary parentheses on raised exception

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  peterjc

  committed
  11bfa75

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• ruff: PIE810 multiple-starts-ends-with

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  peterjc

  committed
  a5dc004

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• Fix flake8-simplify SIM201

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  peterjc

  committed
  2021594

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• ruff format v1.0.3 then black v23.10.1

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  peterjc

  committed
  7073e53

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• Align codonaligner (#4479)

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  mdehoon

  authored
  e33876c

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• update (#4482)

  mdehoon

  authored
  8b1606a

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Commits on Nov 1, 2023

• Add missing molecule types in EMBL writer (#4480)

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  kimrutherford

  authored
  67dcf11

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