20 Commits

Author SHA1 Message Date
de0bb21fb3 Apply isort (forcing single lines, not sorting by type) via ruff
$ ruff check --fix --select=I \
  --config=lint.isort.force-single-line=true \
  --config=lint.isort.order-by-type=false \
  BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py

Using ruff version 0.4.10
2024-06-26 15:31:39 +09:00
e9496f5e88 Automatically remove redundant commas
Used this hack from https://github.com/psf/black/issues/1288

$ pip install black==19.3b0 && black . && pip install black==19.10b && black .

I then manually reverted changes to a handful of explicit data
structures where the magic trailing comma should be retained
(indicates to black not to squash into one line).

Doing this dramatically improves the changes from trying black
version 21.7b0 (right now just four minor changes).
2021-08-27 13:42:55 +01:00
7b5af2bf69 Apply black style to test_pro* files, version 19.10b0.
test_Probcons_tool.py
test_prodoc.py
test_prosite1.py
test_prosite2.py
test_ProtParam.py
2020-02-11 13:12:45 +00:00
1b9e569a7f Using tool unify to convert Tests/ to use double quotes
Using https://github.com/myint/unify for this:

$ unify --quote \" --in-place Tests/*.py Tests/*/*.py
2019-08-02 14:10:22 +01:00
8f29a851fc Docstring fixes for flake8 - D202, D300, D401 etc
Plus a few other related fixes like adding missing docstrings.
2019-04-19 14:02:58 +01:00
725e64a591 use with open 2016-05-23 16:44:06 +01:00
7e36d8ea08 PEP8 work on test_prodoc.py 2014-11-11 14:50:59 +09:00
b67cebf60e Fix common PEP8 violation in unittest verbosity argument 2014-11-11 14:38:37 +09:00
6db0745b7c Close handle in test_prodoc.py
Tested with:

$ python3.4 -W all test_prodoc.py
2014-04-30 16:47:07 +01:00
78c2b3d3ce Use built in next() function in misc test_*.py
Under Python 3 need to use next(iterator) rather than
iterator.next(), and this built in function is new in
Python 2.6 (so we couldn't use it until we dropped
support for Python 2.5).
2013-09-05 18:21:22 +01:00
fd82a0a7a7 Add blank lines where needed (PEP8 E302). 2012-12-06 10:43:43 +08:00
9c76921b91 Remove excessive blank lines (PEP8 E303). 2012-12-05 09:22:22 +00:00
b1c859788e Trim EOL whitespace (PEP8 W291, W293), batch 3. 2012-12-04 19:22:28 +08:00
dafdac3266 Updating the Prosite tests. 2009-03-15 10:06:09 +00:00
89d5901682 Some cleanup. 2007-12-12 00:35:59 +00:00
dc5f29c7d5 Using the new read() function in Bio.Prosite.Prodoc. 2007-12-11 10:25:07 +00:00
fe8a8bebb0 fixed a possible bug in test_prodoc.py where it was printing some
text based on the length of a string.  I suspect this may have different
counts because of line break differences between platforms, and may
be causing a test failure on windows.
2001-08-01 17:30:21 +00:00
b9d2988060 *** empty log message *** 2000-11-20 06:46:39 +00:00
60b53acab5 changed copyright notice to Cayte Lindner, since she wrote the files 2000-08-03 05:04:52 +00:00
f5ad5379b4 *** empty log message *** 2000-07-09 21:29:27 +00:00