Peter J. A. Cock 4c8696aa82 Remove unused or read only globals (flake8 F824)

2025-10-15 14:49:15 +01:00

..

Affy

ruff format v0.3.1, black v24.2.0

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

Align

removing deprecated code

2025-09-21 10:07:53 +01:00

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

removing deprecated code

2025-09-21 10:07:53 +01:00

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

Handle possible non-existent attributes in clusterbuster.py (#5074)

2025-09-27 16:03:53 +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

make spheres nicer on first start

2025-10-10 13:20:13 +01:00

phenotype

Standardizing on import numpy as np

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

Phylo

Update YN00 docstrings

2025-07-30 16:28:38 +01:00

PopGen

commit

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

Restriction

Update Restriction.py

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

SCOP

removing deprecated code

2025-09-21 10:07:53 +01:00

SearchIO

Drop trailing whitespace in some docstrings

2025-07-11 10:26:05 +09:00

SeqIO

added test and docstring for #5053

2025-10-01 19:19:11 +01:00

Sequencing

commit

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

SeqUtils

[pre-commit.ci] auto fixes from pre-commit.com hooks

2025-07-11 10:26:05 +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 unused or read only globals (flake8 F824)

2025-10-15 14:49:15 +01:00

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

Prevent side-effect in SeqRecord._per_letter_annotations

2025-07-24 18:13:30 +01:00