Sunbelt Computer Software

PL/B Language Development and Support

Commits · data2code/biopython · GitHub

Commits

Commits on Sep 28, 2025

set terminal_columns to 80 to ensure backward compatibility for other tests
Yingyao Zhou
committed
3dbba05
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 23, 2025

add spaces in Tests/test_Align_Alignment_format.py required by the style check
Yingyao Zhou
committed
a36be93

Commits on Sep 20, 2025

imporve Tests/test_Align_Alignment_format.py
Yingyao Zhou
committed
3e895ef

Commits on Sep 19, 2025

Update test_Align_Alignment_format.py
data2code
authored
b392e42
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 11, 2025

Bump actions/setup-python from 5 to 6

dependabot[bot]
authored and
peterjc
committed
b4d7c11

Commits on Sep 4, 2025

documentation tweaks (#5055)

mdehoon
and
Michiel de Hoon
authored
6e43775
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 17, 2025

Bump actions/checkout from 4 to 5

dependabot[bot]
authored and
peterjc
committed
a4f7ca0

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
Update CONTRIB.rst

funcylambda
authored and
peterjc
committed
b86d003
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

Drop comment
peterjc
committed
6851cd8
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
Stay at black 24.10.0 for trailing whitespace in doctests
peterjc
committed
1b5e9cc
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
[pre-commit.ci] autoupdate

pre-commit-ci[bot]
authored and
peterjc
committed
8aaa7ff

Commits on Jul 3, 2025

Add automatic alignment generation to StructureAlignment
dimi1729
authored
0969cc2