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v16.04
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Author SHA1 Message Date
John Chilton 99c8f54a77 Update version to 16.04 v16.04 2016-05-18 07:43:10 -04:00
John Chilton 8195d81739 Merge pull request #2353 from martenson/16.04_release_notes 
[16.04] Release notes for 16.04
 2016-05-18 07:28:01 -04:00
John Chilton f887c059a2 Expand 16.04 highlights... 2016-05-18 07:26:25 -04:00
Martin Cech 9d5bf7b62d minor release notes touch 2016-05-17 15:56:50 -04:00
Martin Cech 50e596fb1b reorder sections, un-quote bitbucket paragraph 2016-05-17 15:51:23 -04:00
Martin Cech afb9027482 final touch of release notes from my side 2016-05-17 15:48:00 -04:00
Martin Cech cc86096c83 Merge pull request #2362 from dannon/slurm_complete_job_fix 
[16.04] Fix for slurm's complete_terminal_job where if unable to inspect the …
 2016-05-16 18:26:46 -04:00
Martin Cech 62b6eaa92a Merge branch '16.04_release_notes' of https://github.com/martenson/galaxy into 16.04_release_notes 2016-05-16 17:08:32 -04:00
Martin Cech 3b7f6cb777 add some highlights, seems tough for this release 2016-05-16 17:07:32 -04:00
Dannon Baker 2390da54ae Fix for slurm's complete_terminal_job where if unable to inspect the failed job with scontrol drmaajobrunner's _complete_terminal_job was called twice. 2016-05-16 11:48:33 -04:00
John Chilton 38209bbbac Merge pull request #2350 from natefoo/fix-ajs-red-herring 
[16.04] Properly handle AsynchronousJobState objects in the job runner work queue
 2016-05-14 15:30:38 -04:00
Nicola Soranzo 76fb9b72c3 Add some missing PRs and merge some entries 2016-05-13 16:12:15 +01:00
Nate Coraor dc5a5eb2eb Add Bitbucket deprecation details 2016-05-13 10:30:52 -04:00
Nicola Soranzo c516c9fd45 Fix truncated PR titles and some acknowledgements 2016-05-13 12:34:12 +01:00
Nicola Soranzo b85d604e30 Move some PRs that were merged in 16.01 before its release 
Galaxy 16.01 was officially released on 2016/02/24.
 2016-05-13 12:11:30 +01:00
Martin Cech db5c0d95f6 reorde notes a bit more based on impact/importance 2016-05-12 17:43:14 -04:00
Martin Cech 65e1d68efd typo 2016-05-12 17:37:08 -04:00
Martin Cech 633162c7f5 fix wrong merge 2016-05-12 17:31:22 -04:00
Martin Cech edbc82c215 Merge branch '16.04_release_notes' of https://github.com/martenson/galaxy into 16.04_release_notes 
Conflicts:
	doc/source/releases/16.04_announce.rst
 2016-05-12 17:28:00 -04:00
Martin Cech e0a9efc307 include security note for hg upgrade; some reordering 2016-05-12 17:25:07 -04:00
carlfeberhard 86127cdfdd Update 16.04_announce.rst 
Fix my rst syntax.
 2016-05-12 17:20:06 -04:00
carlfeberhard 40e596f264 Update 16.04_announce.rst 
Added more deprecations from #1757
 2016-05-12 17:12:45 -04:00
Martin Cech 93d1d5611e add deprecation notices 2016-05-12 16:40:01 -04:00
Martin Cech d8430e5c4b generated notes with basic manual curation 2016-05-12 16:22:56 -04:00
Daniel Blankenberg e28d305f3c Merge pull request #2345 from nsoranzo/release_16.04_fix_for_2029 
[16.04] Do not pollute param_dict with a non JSONifiable dict
 2016-05-12 14:01:45 -04:00
Nate Coraor 35a716b854 Not all objects added to the runner work queue are 
JobWrappers/TaskWrappers as claimed in the comment.
AsynchronousJobStates could also be added, and if the fail method was
called this would result in the AttributeError of attempting to access
an AJS' non-existent `get_id_tag` being logged in job.exeception as a
red herring.
 2016-05-12 10:43:48 -04:00
Nicola Soranzo 8255e722cd Do not pollute param_dict with a non JSONifiable dict 
When running a data manager with a dataset parameter, the job fails
with the following backtrace:

Traceback (most recent call last):
  File "/opt/galaxy/lib/galaxy/jobs/runners/__init__.py", line 166, in prepare_job
    job_wrapper.prepare()
  File "/opt/galaxy/lib/galaxy/jobs/__init__.py", line 885, in prepare
    tool_evaluator.set_compute_environment( compute_environment, get_special=get_special )
  File "/opt/galaxy/lib/galaxy/tools/evaluation.py", line 107, in set_compute_environment
    self.tool.exec_before_job( self.app, inp_data, out_data, param_dict )
  File "/opt/galaxy/lib/galaxy/tools/__init__.py", line 1956, in exec_before_job
    out.write( json.dumps( (json_params) ).encode('utf8') )
  File "/usr/lib/python2.7/json/__init__.py", line 243, in dumps
    return _default_encoder.encode(obj)
  File "/usr/lib/python2.7/json/encoder.py", line 207, in encode
    chunks = self.iterencode(o, _one_shot=True)
  File "/usr/lib/python2.7/json/encoder.py", line 270, in iterencode
    return _iterencode(o, 0)
TypeError: keys must be a string

The bug was introduced in PR #2029.
 2016-05-11 17:28:07 +01:00
Dannon Baker 013813691a Merge pull request #2339 from natefoo/gie-proxy-path 
[16.04] Re-fix the bug with multiple preceding '/' characters in the GIE proxy prefix
 2016-05-11 11:06:13 -04:00
Nate Coraor bd25ae95f9 Re-fix the bug with multiple preceding '/' characters in the GIE proxy 
prefix
 2016-05-10 14:24:17 -04:00
Eric Rasche d0830e0c22 Merge pull request #2333 from bgruening/proxy_fix 
Fixes the proxy naming
 2016-05-10 13:20:55 +00:00
Bjoern Gruening 443a9e281c fix proxy name 2016-05-10 13:26:52 +02:00
John Chilton 8ee9ad2937 Merge pull request #2316 from guerler/fix_accept_000 
[16.04] Relax default value acceptance condition
 2016-05-09 14:37:42 -04:00
Nicola Soranzo 5710506229 Merge branch 'release_16.01' into release_16.04 
Conflicts:
	templates/show_params.mako
 2016-05-09 10:48:17 +01:00
Dannon Baker 79dd8c82f0 Merge pull request #2312 from nsoranzo/release_16.01_fix_makos 
[16.01] Unicodify pretty datetimes which can contain non-ASCII chars
 2016-05-07 18:11:24 -04:00
Björn Grüning 5bb7c1d448 Merge pull request #2317 from nsoranzo/release_16.04_tsv_fix 
[16.04] Do not sniff one-line files as CSV/TSV
 2016-05-07 17:52:07 +02:00
Nicola Soranzo 427804ff82 Do not sniff one-line files as CSV/TSV 2016-05-05 18:21:16 +01:00
Nicola Soranzo ff903ac684 Merge branch 'release_16.01' into release_16.04 2016-05-05 18:16:12 +01:00
guerler 37c50d0768 Relax default value acceptance condition 2016-05-05 13:12:34 -04:00
John Chilton 41e6f22f33 Merge pull request #2309 from nsoranzo/release_16.01_slurm_mem_limit 
[16.01] Remove SLURM memory limit warning from stderr if the job was successful
 2016-05-05 12:47:20 -04:00
John Chilton ce8fa33d54 Merge pull request #2311 from natefoo/drmaa-failed 
[16.04] If a Slurm post-mortem determines that a job is in a non-terminal state, return the job to the monitor queue
 2016-05-05 12:45:56 -04:00
Nicola Soranzo 0f984d3bfd Unicodify pretty datetimes which can contain non-ASCII chars 2016-05-05 11:49:05 +01:00
Nicola Soranzo ad0647d677 Change elif to if because drmaa_state can be changed inside the if 2016-05-04 20:12:03 +01:00
Nicola Soranzo 338d254031 Use partial messages to match SLURM memory warnings 2016-05-04 19:56:48 +01:00
Nate Coraor d40c237102 If a Slurm post-mortem determines that a job is in a non-terminal state, 
return the job to the monitor queue.
 2016-05-04 14:55:14 -04:00
Lance Parsons 3005bba5e3 Remove SLURM memory limit warning from stderr if the job was successful 2016-05-04 16:20:39 +01:00
Dannon Baker a54a618970 Merge branch 'release_16.01' into release_16.04 2016-05-03 18:18:20 -04:00
Dannon Baker 063b25f660 Merge pull request #2260 from jmchilton/fix_burst_background_workflows 
[16.01] Fix running workflows in the background when tool bursting is enabled.
 2016-05-03 18:18:00 -04:00
Dannon Baker 56bd4ada04 Merge pull request #2265 from jmchilton/pbs_pro_name_fix 
[16.04] Truncate job name in DRMAA runner by default for PBSPro.
 2016-05-03 08:38:35 -04:00
Dannon Baker d282ed9ce3 Merge branch 'release_16.01' into release_16.04 2016-05-02 14:14:57 -04:00
Nitesh Turaga cdea922890 Merge pull request #2195 from dannon/remoteuser_work 
[16.01] Prepass on remote user header based on maildomain and normalize confi…
 2016-05-02 14:12:33 -04:00