Dimitris Kalafatis 0969cc24fd Add automatic alignment generation to StructureAlignment

2025-07-03 09:33:06 -07:00

..

Affy

ruff format v0.3.1, black v24.2.0

2024-03-14 11:05:43 +00:00

Align

Style change only (#5019)

2025-06-21 10:16:04 +09:00

AlignIO

Changed several parsers avoid using next.

2025-02-24 14:16:22 +00:00

Alphabet

Misc spellings flagged by codespell (#4716)

2024-05-01 14:21:12 +01:00

Blast

update (#4975)

2025-03-21 11:50:50 +09:00

CAPS

ruff fix PIE790 Unnecessary pass statement

2023-11-02 09:34:48 +00:00

Cluster

use PyOS_double_to_string to prevent locale-specific behavior (#4982)

2025-03-26 17:58:08 +09:00

codonalign

Remove more unused imports (F401)

2024-06-27 09:55:07 +09:00

Compass

More f-strings using flynt 0.69

2021-09-17 09:04:20 +01:00

Data

Can drop Optional and Union in typing on Python 3.10 onwards

2025-01-16 00:24:37 +00:00

Emboss

commit

2025-01-16 10:45:19 +00:00

Entrez

Update esummary_clinvar.dtd for fda_recognized_database (#4852)

2024-09-22 09:05:09 +09:00

ExPASy

Move or remove import comments

2024-06-26 15:31:39 +09:00

GenBank

update

2025-03-01 00:54:49 +00:00

Geo

remove spurious print statements (#4198)

2022-12-13 18:22:11 +09:00

Graphics

update

2025-03-01 00:54:49 +00:00

HMM

Move or remove import comments

2024-06-26 15:31:39 +09:00

KEGG

Apply isort (forcing single lines, not sorting by type) via ruff

2024-06-26 15:31:39 +09:00

Medline

Handle all blank continuation lines in Medline (#4558)

2023-12-31 08:22:41 +09:00

motifs

remove deprecated code from Bio.motifs (#4915)

2025-01-17 10:48:06 +09:00

Nexus

update

2025-03-01 00:54:49 +00:00

NMR

ruff format v0.3.1, black v24.2.0

2024-03-14 11:05:43 +00:00

Pathway

More f-strings using flynt 0.69

2021-09-17 09:04:20 +01:00

PDB

Add automatic alignment generation to StructureAlignment

2025-07-03 09:33:06 -07:00

phenotype

Standardizing on import numpy as np

2024-09-03 12:30:49 +01:00

Phylo

update

2025-03-01 00:54:49 +00:00

PopGen

commit

2025-01-16 10:45:19 +00:00

Restriction

Update Restriction.py

2025-02-19 21:49:09 +00:00

SCOP

Apply isort (forcing single lines, not sorting by type) via ruff

2024-06-26 15:31:39 +09:00

SearchIO

Remove reference to the fmt override in the documentation

2025-03-22 06:59:36 +01:00

SeqIO

Uniprotxml parse ligand tag (#5001)

2025-05-31 00:09:26 +01:00

Sequencing

commit

2025-01-16 10:45:19 +00:00

SeqUtils

Deprecate ProteinAnalysis.get_amino_acids_percent() and create ProteinAnalysis.amino_acids_percent (#4783)

2024-07-31 14:48:47 +09:00

SVDSuperimposer

Apply isort (forcing single lines, not sorting by type) via ruff

2024-06-26 15:31:39 +09:00

SwissProt

Apply isort (forcing single lines, not sorting by type) via ruff

2024-06-26 15:31:39 +09:00

TogoWS

Remove now redundany typing imports

2024-06-27 09:55:07 +09:00

UniGene

More f-strings using flynt 0.69

2021-09-17 09:04:20 +01:00

UniProt

Can drop Optional and Union in typing on Python 3.10 onwards

2025-01-16 00:24:37 +00:00

__init__.py

Post release version bump, will be dropping Pyhton 3.9 now

2025-01-15 15:31:09 +00:00

_utils.py

Can drop Optional and Union in typing on Python 3.10 onwards

2025-01-16 00:24:37 +00:00

bgzf.py

Do not mention BAM when encountering an invalid bgzipped file

2024-12-31 18:31:50 +00:00

cpairwise2module.c

Address C compiler warnings (#4885)

2024-11-20 14:31:17 +09:00

File.py

Apply isort (forcing single lines, not sorting by type) via ruff

2024-06-26 15:31:39 +09:00

pairwise2.py

Apply isort (forcing single lines, not sorting by type) via ruff

2024-06-26 15:31:39 +09:00

py.typed

Include py.typed declaration files for type annotation

2023-08-11 15:57:43 +01:00

Seq.py

Can drop Optional and Union in typing on Python 3.10 onwards

2025-01-16 00:24:37 +00:00

SeqFeature.py

fix(SeqFeature): add missing decorator to Location.fromstring factory method

2025-03-28 14:47:27 +00:00

SeqRecord.py

Retain letter_annotation as None in upper and lower methods (#4966)

2025-03-10 14:01:25 +00:00