Dannon Baker
1f62be4e1a
Fix lped converters and remove from flake8 blacklist
2015-07-13 14:44:47 -04:00
Dannon Baker
e1bbbe5ae8
Merge branch 'dev' into lint-additions
2015-07-13 14:20:24 -04:00
Dannon Baker
e0d38ae662
noqa removal in api/histories
2015-07-13 13:59:14 -04:00
Dannon Baker
b8b34cef60
noqa removal in api/groups
2015-07-13 13:59:01 -04:00
Dannon Baker
589dad6205
pep8'd and noqa removal of framework/webapp
2015-07-13 13:53:20 -04:00
Dannon Baker
e68e81dc67
sqlalchemy expressions in grids helper
2015-07-13 13:03:04 -04:00
Dannon Baker
8a031fb290
sqlalchemy expressions in admin controller
2015-07-13 12:54:27 -04:00
Dannon Baker
cb5593f840
Noqa sqlalchemy fix in base controller.
2015-07-13 12:50:25 -04:00
Dannon Baker
3df6daa52c
Various fixes and removal of noqas in security module
2015-07-13 12:47:12 -04:00
Dannon Baker
f623e28ae9
Fix alignment in model
2015-07-13 12:37:51 -04:00
Dannon Baker
2c100d715b
Remove noqas from model
2015-07-13 12:37:29 -04:00
Dannon Baker
db6786e413
Remove noqas from sharable manager
2015-07-13 12:32:44 -04:00
Dannon Baker
a34c5460a4
Remove noqas in library manager
2015-07-13 12:27:27 -04:00
carlfeberhard
4792825924
Merge pull request #446 from jgoecks/trackster-close-files
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Trackster fixes: (a) close data provider files after reading from the…
2015-07-13 11:36:02 -04:00
Dannon Baker
97ac587fed
One more sqlalchemy identity/value comparison fix.
2015-07-13 11:32:21 -04:00
Dannon Baker
2bf2844b21
Merge pull request #440 from dctrud/trackster_nowrap
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Stop trackster location wrap in chrome
2015-07-13 11:17:01 -04:00
Dannon Baker
f122c87ec4
Merge pull request #452 from natefoo/group_round
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Fixed: Return integer values when 'round to nearest integer' is selected in Group tool
2015-07-13 11:15:22 -04:00
Nate Coraor
d5b28bea6d
Merge pull request #443 from Christian-B/config_file_not_found
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Added log error for config file not found
2015-07-13 16:13:59 +01:00
Nate Coraor
647fcf1f60
Only make the Group tool's return value an integer if rounding is
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selected, as pointed out by @nsoranzo.
2015-07-13 11:01:55 -04:00
Nate Coraor
2a63b7b9b3
Merge branch 'group' of https://github.com/moskalenko/galaxy into group_round
2015-07-13 11:01:07 -04:00
Dannon Baker
ab45efaba9
Fix broken sqlalchemy identity logic. Example:
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```
In [3]:
sa_session.query(galaxy.model.User).filter(galaxy.model.User.deleted is
False).all()
Out[3]: []
In [4]:
sa_session.query(galaxy.model.User).filter(galaxy.model.User.deleted ==
False).all()
Out[4]: [<galaxy.model.User at 0x1094e1610>]
```
2015-07-13 11:00:57 -04:00
Martin Cech
e9aa6e843d
Merge pull request #426 from ericenns/feature/library_folder_export_to_history
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Feature/library folder export to history
2015-07-13 16:29:01 +02:00
Bjoern Gruening
5e149d01ba
Switch over to a blacklist for linting.
2015-07-13 00:13:21 +01:00
Nicola Soranzo
43aa5fa482
Lint various Python files.
2015-07-13 00:13:21 +01:00
Nicola Soranzo
2c61543d72
Lint cron/ .
2015-07-13 00:13:21 +01:00
Nicola Soranzo
626871c2b4
Fix for 6135cb5764 "linting lib/galaxy/webapps" .
2015-07-12 21:33:12 +01:00
Bjoern Gruening
1bbff415f2
lint fixes for test/functional/
2015-07-12 21:32:49 +01:00
Bjoern Gruening
f318379d67
add E402 to the exclude rules, until we can fix this
2015-07-12 21:32:14 +01:00
Bjoern Gruening
cdf089e322
remove unsued import
2015-07-12 21:31:47 +01:00
Bjoern Gruening
f1fa2ab316
additional linting of datatypes to make it more strict
2015-07-12 21:31:12 +01:00
Bjoern Gruening
1dab5f9384
revert changes to model/migrate/versions/
2015-07-12 21:30:43 +01:00
Nicola Soranzo
9805294f97
Revert "Revert "[WIP] Mega flake8 linting""
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This reverts commit 37f1976d38
2015-07-12 21:25:44 +01:00
John Chilton
25cb291b80
Merge pull request #449 from galaxyproject/revert-433-lint2
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Revert "[WIP] Mega flake8 linting"
2015-07-11 23:06:20 +01:00
John Chilton
df1b30ebd8
Merge pull request #433 from bgruening/lint2
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[WIP] Mega flake8 linting
2015-07-11 21:37:28 +01:00
Dannon Baker
37f1976d38
Revert "[WIP] Mega flake8 linting"
2015-07-11 13:17:38 -04:00
John Chilton
4dc96cc932
Merge pull request #5 from jmchilton/fix_datatypes_pep8
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Fix problematic PEP-8 fix.
2015-07-11 14:20:19 +01:00
John Chilton
cd0a122d4d
Fix https://github.com/bgruening/galaxy/commit/c691b9216031dce4a66251c83fbdf680cd5a411e#commitcomment-12038966 .
2015-07-11 14:17:16 +01:00
=
58e319d368
downgraded warning to debug as would happen on default
2015-07-09 14:04:17 +01:00
John Chilton
5c60fa6d21
Merge pull request #431 from carlfeberhard/fix.dcecollection-ids
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UI, collections: fix DatasetCollectionElement and DatasetAssociation …
2015-07-09 07:20:54 -04:00
Jeremy Goecks
75ab206ca5
Trackster fixes: (a) close data provider files after reading from them (but there are some data providers that currently lack close functions so those files will remain open); (b) fix running tools by correcting HDA manager function call; (c) remove use of underscore template because uglify does not handle it well.
2015-07-09 12:47:15 +02:00
Björn Grüning
d1e122d41d
Merge pull request #4 from dannon/bgruening-lint2
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Resolves the merge conflict, one minor whitespace fix.
2015-07-08 17:54:28 +02:00
Dannon Baker
432beb5782
Strip a trailing space from the merge.
2015-07-08 15:56:22 +01:00
Dannon Baker
def341b5c3
Merge to fix conflict.
2015-07-08 15:55:30 +01:00
Dannon Baker
6f475e9a5c
Merge branch 'yhoogstrate-dev' into dev
2015-07-08 12:31:10 +01:00
Dannon Baker
9b0ee0589a
Resolve sample merge conflict.
2015-07-08 12:30:39 +01:00
=
91bffc0e98
Added log error for config file not found
2015-07-08 12:24:15 +01:00
David Trudgian
b734aee99c
Stop trackster location wrap in chrome
2015-07-07 10:59:42 -05:00
youri
534d7b8b50
Added datatype definition for ConnectivityTable (*.ct) - RNA 2D structure file format
2015-07-07 17:30:54 +02:00
Dannon Baker
e5341ab020
Merge pull request #438 from peterjc/patch-3
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Fixed typo in docstring
2015-07-07 16:05:00 +01:00
Peter Cock
0a359add08
Fixed typo in docstring
2015-07-07 16:01:50 +01:00
Dannon Baker