Nicola Soranzo
64af46c4ae
Fix new B018 errors raised by ruff 0.0.260
2023-04-13 16:53:01 +01:00
Nicola Soranzo
30f60493c3
Format Python code with black 23.1.0
...
with manual fixes to 3 files to make them compatible with black 22.12.0 .
We need to keep black pinned at `<23` until we vendorise `packaging`, since
the new version of black depends on `packaging >=22.0` which is the version
where `LegacyVersion` (which we use for tool lineages) was removed.
2023-02-01 23:51:03 +00:00
Dannon Baker
623a5e165a
Apply black formatting.
...
Apply isort.
2022-02-03 07:42:20 -05:00
Nicola Soranzo
90a729e431
New pyupgrade fixes
...
Found by running `ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py36-plus`
2021-10-24 12:10:34 +01:00
Nicola Soranzo
452aba9ee3
Fix remaining issues reported by bugbear; add it to flake8 reqs
2021-01-16 05:58:15 +00:00
Nicola Soranzo
9d74bba7fb
Drop support for retired Python 3.5
...
Upgrade syntax using `pyupgrade --py36-plus` .
Manually drop several `six` imports.
Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
2020-10-07 11:52:13 +01:00
will
009611cf04
add .gitattributes file and normalize line endings to use LF instead of CLRF
2019-09-18 22:03:37 -04:00
Nicola Soranzo
0c931235af
Change all remaining old-style classes to new style
2018-09-17 12:26:07 +01:00
Nicola Soranzo
326a564eb9
Stop shipping old BeautifulSoup library
2018-03-07 01:19:55 +00:00
Nicola Soranzo
14259b11d9
Python3: finish first pass on whole codebase
2017-12-14 12:01:01 +00:00
Nicola Soranzo
48aca7dce8
Update to flake8-import-order 0.16
2017-12-01 11:09:57 +00:00
Nicola Soranzo
9b4de72ca6
Fix all E722 errors and ignore E741
...
Introduced in flake8 3.5.0
Fix import order.
2017-10-24 11:29:09 +01:00
Nicola Soranzo
b956406c4d
Fix Python3 compatibility and import order for 21 files
2017-10-16 19:43:01 +01:00
Nicola Soranzo
d1bc98dfcb
Python3: fix remaining print statements
...
Remove some debugging prints.
Fix import order.
Consolidate exception logging in ToolShed database migrations.
2017-10-12 18:34:29 +01:00
Nicola Soranzo
9b1832abb1
Fix import order for cron/, scripts/ and test/
2017-09-25 23:44:39 +01:00
E Rasche
290971ca7a
more review comments
2017-09-25 11:39:15 +02:00
E Rasche
9b8e76f9d9
Convert urllib to requests
...
Which has built-in protection against urls like "file:///tmp/a"
2017-09-25 11:39:13 +02:00
Nicola Soranzo
a8d7b2df8b
Fix more indentation errors
2017-08-17 11:35:39 +01:00
Nicola Soranzo
a353b2e88f
Fix E127 errors introduced by previous commit
...
using:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 .
```
2017-08-17 11:35:39 +01:00
Nicola Soranzo
21b44bf348
Fix all E201 and E202 style errors
...
using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
2017-08-17 11:35:39 +01:00
Nicola Soranzo
1d17a29c79
Fixes for pycodestyle 2.2.0
2016-11-15 16:56:50 +00:00
Nicola Soranzo
6ba6f798ec
Fix more E203 flake8 errors
2016-05-17 23:53:16 +01:00
Nicola Soranzo
8a43b2b492
Python 3: use "as" instead of comma in except clause
2016-05-17 23:53:16 +01:00
Nicola Soranzo
93348e7199
Fix the remaining 1334 flake8 errors in scripts/ . Close #391 .
2016-02-18 15:45:15 +00:00
Nicola Soranzo
cc9b0bed85
Fix all E712 errors. Standardize sqlalchemy imports.
2015-07-14 20:49:34 +01:00
Dannon Baker
dba89dff83
Convert everything from elementtree to stdlib xml module.
2015-01-29 16:10:56 -05:00
Greg Von Kuster
af3b0669aa
Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.
2008-03-28 15:24:50 +00:00
Daniel Blankenberg
254077c4e3
Add scripts required to fetch and process data for the Microbial Genome Datasource Tool.
2008-03-27 15:36:13 +00:00
Nicola Soranzo