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Author SHA1 Message Date
Carl Eberhard c91cabf2a4 Client build: add template task 2015-07-21 13:30:30 -04:00
John Chilton e9e34c9c5f Merge pull request #481 from dannon/flake8_contd 
Even more sqlalchemy/flake8 fixes.
 2015-07-21 14:59:04 +01:00
Dannon Baker e7d3cceb5e Another sqla comparison in the user controller. 2015-07-21 08:28:29 -04:00
Dannon Baker ed616f5575 sqlalchemy fixes in toolshed repository controller 2015-07-21 08:21:33 -04:00
Dannon Baker 01010d3a69 Another job handler comparison fix. 2015-07-21 08:19:11 -04:00
Dannon Baker 54368b185c Merge pull request #480 from nsoranzo/dev 
Fix last SQLAlchemy comparison broken during flake8'ing.
 2015-07-21 06:37:56 -04:00
Nicola Soranzo 4ba3cf2a13 Fix last SQLAlchemy comparison broken in 9805294f97 . 2015-07-21 02:48:43 +02:00
John Chilton 0a9a2f8ba5 Merge pull request #479 from dannon/more_sqla_flake8_fixes 
More sqla flake8 fixes
 2015-07-20 20:47:24 +01:00
Dannon Baker fed3bddc30 Import null, oops. 2015-07-20 15:38:36 -04:00
Dannon Baker b0c6512c5b Fix more sqlalchemy comparisons broken during flake8'ing. 2015-07-20 15:36:59 -04:00
Martin Cech 6d9ac63681 Merge pull request #370 from Airistotal/Reports_Paginate 
Reports pagination
 2015-07-20 13:31:26 +02:00
John Chilton 428705e7ec Merge pull request #478 from dannon/fix_flake8_breakage 
Fix for egg building broken by flake8'ing
 2015-07-18 19:24:54 +01:00
Dannon Baker 209ff0f6e6 Fix for egg building broken in flake8'ing 2015-07-18 08:49:18 -04:00
Airistotal 5710ee1458 Removed unused import 2015-07-17 14:43:33 -05:00
Airistotal 3811c43eb9 Fixed duplicate imports 2015-07-17 14:42:29 -05:00
Airistotal e7eb7686ac Fix imports 2015-07-17 14:30:43 -05:00
Airistotal 7e6198a8f7 Merge branch 'dev' of https://github.com/galaxyproject/galaxy into Reports_Paginate 
Conflicts:
	lib/galaxy/webapps/reports/controllers/jobs.py
 2015-07-17 14:28:23 -05:00
John Chilton ef55279d58 Merge pull request #473 from carlfeberhard/update.spritesmith-less 
Client build: update style tools: grunt-contrib-less to 1.0, grunt-sp…
 2015-07-17 19:24:16 +01:00
John Chilton be3bd7a296 Merge pull request #419 from kaktus42/error_specification 
add error message for bad dependency declaration
 2015-07-17 14:56:52 +01:00
John Chilton 70ef7e5561 Merge pull request #463 from carlfeberhard/fix.trackster-chrint 
Trackster, chromosome interaction: fix display of chrint files in tra…
 2015-07-17 14:50:32 +01:00
Carl Eberhard 9e2e909d3e Client build: update style tools: grunt-contrib-less to 1.0, grunt-spritesmith to 4.7, fixes NameError with grunt style on node > 0.10, update galaxy_bootstrap/variables for different(?) lighten/saturate 2015-07-17 09:18:04 -04:00
Dannon Baker 223583470b Merge pull request #454 from bgruening/lint-additions 
General cleanup, flake8 monster PR
 2015-07-17 08:30:55 -04:00
Dannon Baker c18887c0d1 Clean up pam auth helper. 2015-07-17 08:06:04 -04:00
Dannon Baker 345c86d8ef More fixes for toolshed step handler post-merge. 2015-07-17 08:04:19 -04:00
Dannon Baker 7019e32305 Merge with dev 2015-07-17 07:54:25 -04:00
Carl Eberhard d31822e6d4 Trackster, chromosome interaction: fix display of chrint files in trackster, do not apply config default_value if explicitly set to undefined, clean line endings 2015-07-15 12:45:19 -04:00
Nate Coraor 39f6730e5f Merge branch 'release_15.05' into release_15.07 2015-07-14 22:48:30 -04:00
John Chilton ddf4ce5680 Merge pull request #459 from natefoo/dev 
Lint fixes for #458
 2015-07-15 03:42:35 +01:00
Nate Coraor 37cf1af4df lint fixes for #458 2015-07-14 22:15:08 -04:00
Nate Coraor cb8f6354de Merge pull request #458 from pvanheus/auth_pam 
AuthProvider for PAM (Pluggable Authentication Modules)
 2015-07-14 22:12:17 -04:00
Peter van Heusden b9c9f11ce1 * New PAM AuthProvider for interfacing with the Pluggable Authentication Module system (http://www.linux-pam.org/) 
* Helper script to allow authenticating against modules as root
 2015-07-15 00:47:13 +02:00
Nicola Soranzo cc9b0bed85 Fix all E712 errors. Standardize sqlalchemy imports. 2015-07-14 20:49:34 +01:00
Nate Coraor 4fe2bd4798 Merge pull request #398 from abretaud/section 
Fix error when displaying job params for tools containing a section
 2015-07-14 14:48:29 -04:00
John Chilton 23209d5497 Merge pull request #441 from Christian-B/unlinked_dependencies 
Added unlinked dependency resolver
 2015-07-14 12:54:16 -04:00
John Chilton 141980451c Merge pull request #444 from yhoogstrate/dev 
Fix md5sum/sha256 in toolshed action
 2015-07-14 12:48:02 -04:00
Nate Coraor ac75e6ff8d Merge pull request #455 from jmchilton/output_collection_filter 
Implement <filter> tag for output collections.
 2015-07-14 11:34:13 -04:00
Nicola Soranzo 34d9388456 Use os.pardir everywhere instead of '..' . 2015-07-14 16:20:29 +01:00
yhoogstrate e1d53139a8 Merge pull request #4 from erasche/docs-fix 
Update docs, re-instate backwards compatability
 2015-07-14 13:06:45 +02:00
John Chilton 163b0e37ca Implement <filter> tag for output collections. 
Closes #445.
 2015-07-14 10:18:24 +01:00
Dannon Baker be6cce14dc Merge branch 'dev' into lint-additions 2015-07-13 15:24:01 -04:00
Dannon Baker ec36199a27 Merge pull request #453 from natefoo/group_round 
Remove superflous assignment left over from...
 2015-07-13 15:13:28 -04:00
Nicola Soranzo 6569c2dcc3 Partially lint scripts/ . 2015-07-13 20:13:28 +01:00
Dannon Baker 29c4f1ae85 Clean up model.mapping. TODO: this made it compliant, still needs a pass to make it consistent. 2015-07-13 15:12:04 -04:00
Nate Coraor 6eafa52f41 Remove superflous assignment left over from 
647fcf1f60, thanks @nsoranzo.
 2015-07-13 14:55:33 -04:00
Dannon Baker 1f62be4e1a Fix lped converters and remove from flake8 blacklist 2015-07-13 14:44:47 -04:00
Nate Coraor 37b231cb3d Verify MD5 and SHA256 sums on other types of actions. For all types of 
actions other than download_by_url, these must be specified as
attributes on the <action> tag, the old `#hash#` method in the URL is
not supported.
 2015-07-13 14:43:05 -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