Nicola Soranzo
00f7522e7e
Merge branch 'release_22.01' into dev
2022-03-19 01:57:33 +00:00
mvdbeek
4c7bfd1032
Fix tool shed bootstrapping script
2022-03-17 19:34:43 +01:00
Dannon Baker
623a5e165a
Apply black formatting.
...
Apply isort.
2022-02-03 07:42:20 -05:00
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
Nicola Soranzo
f5cd88465e
Make str.join()s more efficient
...
by using generator expressions and tuples instead of lists.
2020-01-23 11:06:32 +00:00
John Chilton
d4196b61a4
Remove tool shed API examples.
...
These aren't tested, bioblend likely has better documentation (https://bioblend.readthedocs.io/en/latest/api_docs/toolshed/all.html ), and we should be encouraging TS interactions to be done through Planemo and not raw API calls.
Excluding scripts used by bootstrap.
2019-11-11 02:55:26 -05:00
Nicola Soranzo
949dcfdbc3
Do not log exceptions twice
...
`logging.exception()` already adds the the exception information after
the supplied message.
Also: the `message` attribute of `Exception` class has been dropped in
Python 3, always use `str(e)`.
xref. https://github.com/galaxyproject/galaxy/issues/1715
2018-10-24 12:57:05 +01:00
Nicola Soranzo
14259b11d9
Python3: finish first pass on whole codebase
2017-12-14 12:01:01 +00:00
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
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
de3c50a5ef
Python3 support and import order fixes for lib/tool_shed/
2016-08-04 13:41:36 +01:00
Nicola Soranzo
8a43b2b492
Python 3: use "as" instead of comma in except clause
2016-05-17 23:53:16 +01:00
Dave Bouvier
fbf8cfce2a
Remove unused import.
2016-04-05 14:23:56 -04:00
Dave Bouvier
9bf3976e8a
Fix sys.path.insert
2016-04-05 13:50:51 -04:00
Dave Bouvier
77353902ee
Move scripts out of lib/tool_shed.
2016-04-05 13:04:44 -04:00
Nicola Soranzo