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
8a327db74d
Remove log_tempfile.
...
Simplify packaging - @natefoo said I could.
2019-07-08 14:52:13 +02:00
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
9b1832abb1
Fix import order for cron/, scripts/ and test/
2017-09-25 23:44:39 +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
Nate Coraor
0469ed29e0
Remove egg cruft from scripts/
2015-09-21 15:55:07 -04:00
Nicola Soranzo
6569c2dcc3
Partially lint scripts/ .
2015-07-13 20:13:28 +01:00
Nate Coraor
e64ab4c85c
There's no reliable way to use the Galaxy config file to control egg use/fetching since so many things use galaxy.eggs from outside of Galaxy, so drop the support for the config file options and rely on the environment variables only. Reverse the defaults so that eggs and fetching are enabled by default. I'll make sure that they properly get passed to the tool execution environments in the next commit.
2015-02-12 15:10:19 -05:00
Nate Coraor
1e07117791
Place the new egg config options into the environment at Galaxy startup since
...
eggs.require() has no access to the config file.
2015-02-12 14:27:37 -05:00
James Taylor
15ec130bfb
core: add PasteDeploy dependency back, used inside Paste#httpserver
2013-02-01 17:30:58 -05:00
James Taylor
f6629fd8c4
changeset: 8701:c3ac9849dd1b
...
branch: unstable
tag: tip
user: James Taylor <james@jamestaylor.org >
summary: core: pull the pieces of PasteScript we use into galaxy.util.pastescript. Remove all dependencies on PasteScript and PasteDeploy. Begin stripping down the serve command so we can start to enhance it for our needs.
2013-01-30 15:26:00 -05:00
Nate Coraor
006716f53a
Egg support overhaul, introduces a number of fixes to the ABI recognition, better build scripts, a rewrite of the eggs library and eliminition of the need for python -ES
2010-03-01 15:41:30 -05:00
Kanwei Li
e4a4889524
Fix run.sh --reload by requiring Paste before PasteScript
2009-11-23 17:20:01 -05:00
Nate Coraor
c9e0e1ea17
A get_platform() monkeypatch for fat versions of python on Mac. Also do more explicit version checking ( >= 2.4, <= 2.5 ) and provide helpful messages if the version is not supported.
2009-10-27 11:36:57 -04:00
Greg Von Kuster
354d0447df
Fixes for i18n support - all charsets set to utf-8, now able to paste multi-byte chars in upload form, templates use utf-8 as output_charset, other miscellaneous fixes.
2009-03-20 02:49:30 -04:00
Greg Von Kuster
69e383d6a8
Integrating i18n support provided by Mitsuteru Nakao, Takashi Hatakeyama, and Hideyuki Morita.
2009-03-17 22:46:47 -04:00
Nate Coraor
80f42e4199
Since tempfiles seem to occasionally be left behind, allow logging of
...
open tempfiles, including a traceback (to determine callers) if
LOG_TEMPFILES is set in the environment when Galaxy starts. This
should be considered temporary and will be removed when it's determined
where/how this happens.
2008-12-23 13:28:27 -05:00
Nate Coraor
7560751dc8
Separate framework and tool environments.
...
Whether running locally or via PBS, $PATH should now be handled in your
user's environment.
This also fixes problems like PYTHONPATH on the new blast nodes being
wrong (because they are x86_64 and the frontends are i686).
Note that you can actually start Galaxy without having an eggs dir now.
2008-04-11 20:11:21 +00:00
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
James Taylor
2c4c20436e
Cleaning up modules. Still a few stragglers that can't be easily eggified.
...
EVERYTHING we depend on should eventually be under the galaxy module or
packaged in eggs to avoid namespace problems.
2006-11-15 18:27:21 +00:00
Nicola Soranzo