34 Commits

Author SHA1 Message Date
d4fa446660 Remove defunct comment 2024-03-18 10:52:50 +00:00
79dbcf7bc4 pydocstyle is deprecated: use ruff instead of flake8-pydocstyle
We may want to move the ruff linter configuration into its own
file soon...
2024-03-14 11:05:43 +00:00
3bb7085448 Ignore E704 due to false positives
This might get fixed in flake8, but we can probably disable
this in favour of black style anyway.
2024-03-14 11:05:43 +00:00
bd07204359 Ignore flake8 W291 trailing whitespace in tests 2023-11-03 15:11:47 +00:00
f4924d8d31 Ignore flake8 E131,E122,E124,E126,E127,E128,E201,E241 - trust black
These would only get triggered in regions of the
code where we are explicitly disabling black.
i.e. Places where human judgment overrides.
2023-11-03 15:11:47 +00:00
6ee45129d2 Don't need to ignore flake8 W504 anymore
Also updated ignore counts, most have gone up sadly.

$ flake8 Bio --isolated --statistics \
         --select F401,F841,D105,B009,B010 --statistics
$ flake8 Tests --isolated --statistics \
         --select F401,F841,D101,D102,D103,W504,B009,B010,B015
2023-06-06 12:50:54 +01:00
6e5212bb29 Update .flake8 to ignore Bugbear's new B028 (#4253) 2023-03-03 17:24:41 +01:00
6fa067f0ab flake8 v6 onwards flags in-line comments in config as errors
See https://github.com/PyCQA/flake8/issues/1689
2023-01-12 09:17:25 +00:00
ca586f350c Can now enforce flake8-bugbear B011
Also ignore all the flake8-commas C8## codes, the
plugin is no longer maintained - just use black.
2022-11-18 12:30:10 +00:00
fb13d50aa8 Stop ignoring flake8 E741 ambiguous variable name 'l' 2022-11-15 14:49:30 +00:00
f12e4fb3b3 add sphinx directives to .flake8 file 2021-11-30 20:09:52 +00:00
5f2feee6e8 Ignore flake8-blind-except B902 except Exception:
This is new in flake8-blind-except v0.2.0 released 2021-01-07

We are checking this via pre-commit
2021-01-25 14:50:10 +00:00
25f5152f4a Ignore flake8-bugbear B015 in tests
These are superficially pointless expressions,
but are intended to trigger an exception.
2020-12-30 11:40:44 +00:00
5cc36bff6e update codonalign documentation rst (#3161)
* update codonalign documentation rst

* travis

* doc.rst is generated by pandoc

* This'll teach him

* This'll teach him
2020-07-28 11:55:57 +09:00
e0470e8c4a Remove ignore instruction for black in the pre-commit hook 2020-07-25 20:56:04 +01:00
ad36d2f714 Update flake8 config to stop ignoring black on tests 2020-07-25 20:56:04 +01:00
7cd91358ea Clarify flake8 configuration comments 2020-06-30 00:47:10 +01:00
caaa894ba5 Fixed typos in docstrings and docs (#3013)
Used https://github.com/erichurkman/misspellings to find common misspellings in the code.
2020-06-29 11:52:25 +01:00
d9b58e5054 No flake8 E123 left in Tests/ 2020-05-14 01:08:21 +01:00
1065fa9ada Ignore flake8 E741 ambiguous variable name 'l'
New in flake8 v3.8, we have lots of these.
Single letter variable names are frowned on
2020-05-13 10:12:01 +01:00
8f50dcb837 Update .flake8 comments 2020-02-19 09:38:44 +00:00
958b0d04af Update flake8 settings (#2696)
* Remove remaining 'line-break before binary operator' issues in MeltingTemp.py

* Update .flake8 file
2020-02-12 11:33:00 +01:00
35736323d7 If flake8-sfs installed, ignore percent & f-string formatting 2020-01-30 12:53:16 +00:00
79eb29ac25 flake8: enforce black on Bio/
Only ignoring black requirement on Tests/ now, that will
require a vast amount of changes to bring into compliance.

Note now including flake8-black in recommended plugins,
already being used on TravisCI via Tox.
2020-01-28 19:51:53 +00:00
dc9733116e Enforce black on BioSQL/ Scripts/ + Doc/ 2019-12-06 13:17:08 +00:00
1dc16ee0b6 Enforce double quotes via flake8-quotes 2019-09-12 09:35:32 +01:00
d4b782ceef Apply black to GenomeDiagram; update .flake8 &NEWS (#2251)
* Start ignoring flake8/pycodestyle E203 due to black false positives

Workaround for open pycodestyle issue giving a false positive on
the whitespace changes from the formatting tool black, which we
are starting to adaopt for Biopython.

* Run black (version 19.3b0) on GenomeDiagram

* Adjust a few comment placements

* Mention using black in NEWS.rst
2019-09-11 13:45:42 +02:00
475022bef5 Document where flake8 PIE781 comes from
[ci skip]
2019-08-22 13:39:25 +01:00
4202e6ee13 Fixed typo
[ci skip]
2019-08-22 13:37:05 +01:00
e217f4bcff Update settings if using flake-quote or flake8-pie locally 2019-08-02 14:44:04 +01:00
9499a73b92 Remove stlye issues E122 and E126 in Test folder (#2148)
* Remove E122 and E126 issues in Tests folder

* Update .flake8 file
2019-06-22 23:46:52 +02:00
f58b7bd8d0 Remove D101 and D102 from Bio flake8 ignores (#2108) 2019-06-06 00:00:07 +02:00
5613253cab Update .flake8 to ignore some folders (#2093)
Closes #2090.
2019-05-31 11:25:04 +01:00
da1259a29d Single .flake8 file for general and folder specific ignores (#2074)
* Towards a single .flake8 file

* Duplicated per-file-ignores with different paths

* Remove folder specific .flake8 files

* Changed .travis-tox.ini

* Expanded .flake8 file

* Alternative .flake8 'styles'

* Remove E731 from Bio

* Remove D103 from Bio
2019-05-23 16:38:10 +02:00