21 Commits

Include renames

Author	SHA1	Message	Date
Nicola Soranzo	7f04b5d698	Merge branch 'release_22.01' into dev	2022-03-02 20:08:55 +00:00
mvdbeek	034f518e43	Move init_models_from_config to galaxy.model.mapping	2022-03-01 16:50:06 +01:00
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	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
John Chilton	528497f7c4	Refactor galaxy.web.security into galaxy.security.idencoding. ... I want to be able to use this class in galaxy.model and it doesn't have any dependnecies on "web" stuff so I'd like to move it out of galaxy.model and into galaxy.security. galaxy.model shouldn't have dependencies on galaxy.web (and doesn't after the recent 976f5ad367), so this pre-emptively ensures it doesn't require these dependencies for https://github.com/galaxyproject/galaxy/pull/7367. This has the benefit of also eliminating any galaxy.web dependencies from the generic test base file (test/base/testcase.py) which has long been a goal of mine as well. There are places we legimately use ID encoding and decoding for security (i.e. job files API) but for the most part it doesn't provide security for API endpoints and this causes confusion repeatedly, so I've started the process of renaming the contained class SecurityHelper to something I feel makes it clearer this is just about encoding and decoding IDs.	2019-03-19 14:28:31 -04:00
John Chilton	5f3f792f6f	Unification of Galaxy configuration parsing for scripts/*	2018-03-23 16:14:49 -04:00
Nicola Soranzo	14259b11d9	Python3: finish first pass on whole codebase	2017-12-14 12:01:01 +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	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	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	d85db9daa6	Use __file__ when adding paths to sys.path instead of os.getcwd() . ... Also insert additional paths in position 1 unless strictly necessary.	2016-02-18 15:45:15 +00:00
Nicola Soranzo	34d9388456	Use os.pardir everywhere instead of '..' .	2015-07-14 16:20:29 +01:00
Nicola Soranzo	6569c2dcc3	Partially lint scripts/ .	2015-07-13 20:13:28 +01:00
Dannon Baker	c733ce370b	Fix path insertion vs appending of <galaxy>/lib for all scripts.	2015-02-12 10:34:51 -05:00
Nate Coraor	bc5ec4fec4	Bug fixes to scripts for config subdir.	2014-09-15 16:52:50 -04:00
Nate Coraor	8fadc6392b	Rename universe_wsgi.ini -> galaxy.ini everywhere.	2014-09-15 16:43:51 -04:00
John Duddy	a2c0328241	Merge	2011-10-07 13:25:19 -07:00
Nate Coraor	9126df9685	Make it easier to run helper.py from outside the galaxy-dist root directory.	2011-09-08 12:09:10 -04:00
Nate Coraor	83163908e8	Add helper.py (posted to the -dev list as "galaxythinger.py" in the past), a command line tool for performing a couple common operations like encoding/decoding IDs and getting the disk path of HDAs.	2011-08-22 10:45:22 -04:00