Sunbelt Computer Software

PL/B Language Development and Support

History for Bio - data2code/biopython · GitHub

Commits

History for

Commits on Sep 28, 2025

move terminal_columns into a class attribute
Yingyao Zhou
committed
9fba345

Commits on Sep 27, 2025

Add terminal_columns to the Alignment class as a new attribute
Yingyao Zhou
committed
63a6686
Move TestAlignmentFormat into Tests/test_Align_Alignment.py, fixed black style
Yingyao Zhou
committed
3a1f356

Commits on Sep 24, 2025

Improve test script to use unittest
Yingyao Zhou
committed
518de3c
check for if terminal_columns is defined in Bio/Align/__init__.py
Yingyao Zhou
committed
8374c81

Commits on Sep 19, 2025

Add support for terminal_columns in Alignment formatting, issue 5035
Yingyao Zhou
committed
4ae4b5a

Commits on Sep 16, 2025

Aligner default arguments (#5029)

authored
be97b2d

Commits on Sep 4, 2025

Align: add substitution matrix support to Alignment.format() (#5049)

authored
ad9456f

Commits on Sep 3, 2025

Fixes formatting for extremely high B-factor values in PDB files (#5047)
OWissett
authored
d3de878

Commits on Aug 19, 2025

pairwisealigner pickle fix (#5041)
amitschang
authored
d1c4b3d

Commits on Aug 12, 2025

typo (#5040)

mdehoon
and
Michiel de Hoon
authored
4ceee03

Commits on Aug 11, 2025

declare local functions as static (#5037)

mdehoon
and
Michiel Jan Laurens de Hoon
authored
ff4bed0

Commits on Jul 30, 2025

Update YN00 docstrings

twalsh-ebi
authored and
peterjc
committed
35bdb3f
Uppercase PAML software names except in run methods

twalsh-ebi
authored and
peterjc
committed
053bdc8
Update long docstrings in PAML class methods

twalsh-ebi
authored and
peterjc
committed
f6e56e5
Set PAML class names in CamelCase

twalsh-ebi
authored and
peterjc
committed
aceebef
Fixed flake8 rule D209 violations

Franziska Arndt
authored and
peterjc
committed
392ede4
Updated docstrings to use consistent capitalization. paml >> PAML etc.

funcylambda
authored and
peterjc
committed
727b505
Updated docstrings to include the output and mention any validation that occurs. Also, changed docstring so they have consistent capitalization. Baseml >> BASEML etc

funcylambda
authored and
peterjc
committed
95f8119

Commits on Jul 24, 2025

Prevent side-effect in SeqRecord._per_letter_annotations

Michael M
authored and
peterjc
committed
b027825

Commits on Jul 11, 2025

Extend the .counts method of an Alignment (#5011)

authored
66ad0a0
Drop trailing whitespace in some docstrings
peterjc
committed
116d92b
[pre-commit.ci] auto fixes from pre-commit.com hooks

pre-commit-ci[bot]
authored and
peterjc
committed
ed51b11

Commits on Jul 3, 2025

Add automatic alignment generation to StructureAlignment
dimi1729
authored
0969cc2

Commits on Jun 21, 2025

Style change only (#5019)

mdehoon
and
Michiel Jan Laurens de Hoon
authored
feeb728

Commits on Jun 20, 2025

follow recommended style for PyTypeObject (#5014)

mdehoon
and
Michiel Jan Laurens de Hoon
authored
b19a210

Commits on Jun 9, 2025

Fix QCPSuperimposer bug (#5005)
paajasan
authored
0b41684

Commits on May 30, 2025

Uniprotxml parse ligand tag (#5001)
irahorecka
authored
1172869

Commits on May 29, 2025

Remove unused f-string
peterjc
committed
91740a7
linting

lee-t
authored and
peterjc
committed
2cb91f3
improve coverage of tests

lee-t
authored and
peterjc
committed
28f18b2
remove urlerror and httperror

lee-t
authored and
peterjc
committed
377635e
format with black

lee-t
authored and
peterjc
committed
41fa46f
if error is caught should return None instead of final_file

lee-t
authored and
peterjc
committed
49a3981
fixed PDBlist.retrieve_pdb_file(); improved error handling, should not show misleading message

lee-t
authored and
peterjc
committed
a4b3afb