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633 Commits
Author SHA1 Message Date
John Chilton bbef5ed737 Improvements to release notes generation. 
- Add last commit for 15.10 (need to automate finding that).
- Generate next release annoucement.
- Generate annoucement for this release.
- Respect the minor tag.
 2015-10-14 17:04:49 +01:00
Dannon Baker 7f3ee5b167 Merge pull request #612 from lparsons/manual_builds 
Move manual_builds.txt to manual_builds.txt.sample
 2015-09-24 17:10:49 -04:00
Nate Coraor 150c17b9e8 Do not explicitly require pexpect. If anyone wants to use the old and 
mostly unused features that depend on it (namely remote sequencer
transfers via scp) they can pip install pexpect.
 2015-09-17 13:56:44 -04:00
John Chilton bd55650f06 Add testing environment variable GALAXY_TEST_LOGGING_CONFIG. 
Unifies logging through the testing process. Requires adding a Galaxy option to disable its own attempts to configure a different root logger.
 2015-09-16 16:24:53 +01:00
Nicola Soranzo cd456e186d Print to stderr when calling sys.exit(1) 2015-09-11 19:05:37 +01:00
Nicola Soranzo 2625bc4bc0 Fix flake8 broken when merging 041c94bf78 from release_15.07 . 2015-09-02 16:30:50 +01:00
Nicola Soranzo bcbeb75a68 Merge branch 'master' into dev 
Conflicts:
	lib/tool_shed/dependencies/tool/tag_attribute_handler.py
 2015-09-02 16:10:03 +01:00
John Chilton 4a05c07aa5 Fixup end of release items for release notes. 2015-08-27 13:04:17 +01:00
John Chilton 041c94bf78 Release notes for 15.07. 
This includes a script to boot strap the notes for future releases, updated announcement page for 15.07, and new announcement page for 15.10.
 2015-08-27 12:00:18 +01:00
Nicola Soranzo 0f883ef776 Merge branch 'release_15.07' into dev 
Conflicts:
	lib/galaxy/model/__init__.py
 2015-08-20 14:12:27 +01:00
Nicola Soranzo a34f13a9f6 Merge branch 'release_15.05' into release_15.07 2015-08-20 14:07:09 +01:00
Nicola Soranzo 238d908cce Fix purging datasets whose total_size is None. 
Fix the error:

Removing disk, file  /opt/galaxy/database/files/000/dataset_192.dat
Error attempting to purge data file:  /opt/galaxy/database/files/000/dataset_192.dat  error:  unsupported operand type(s) for -=: 'Decimal' and 'NoneType'

when running:

python scripts/cleanup_datasets/cleanup_datasets.py config/galaxy.ini -d 10 -3 -r
 2015-08-19 15:33:54 +01:00
Lance Parsons 5810a853b0 Move manual_builds.txt to manual_builds.txt.sample to allow for customization 2015-08-18 14:00:30 -04:00
Martin Cech 7a39867933 Merge branch 'release_15.07' into dev 2015-08-06 11:29:18 -04:00
Martin Cech 4d697b7b50 fix overriding the name variable 2015-08-06 10:38:12 -04:00
Martin Cech 871e253015 merge 15.07 into dev 2015-08-06 09:33:44 -04:00
Martin Cech d583c376a5 flake8 spotted by @nsoranzo 2015-08-05 14:27:25 -04:00
Martin Cech 0ad5c8a1a8 fix TS search index building script to properly visit subdirectories 2015-08-05 13:55:01 -04:00
Dannon Baker c18887c0d1 Clean up pam auth helper. 2015-07-17 08:06:04 -04:00
Dannon Baker 7019e32305 Merge with dev 2015-07-17 07:54:25 -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
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
Martin Cech eb54b1d854 expose searching full TS toolset over a separate index 
the index is created by the same script (build_ts_whoosh_index.py)
 2015-06-19 16:24:27 -04:00
John Chilton 4e82c80293 Fix for 38679a0d32. 
Reported by @golharam.
 2015-06-18 15:57:49 -04:00
Martin Cech 508b685c70 fix common API scripts so they dont fail when response has no url param 2015-06-15 16:12:21 -04:00
John Chilton 374795f631 Only cleanup successful jobs when testing. 
As per the recommendation of Ryan G. at http://dev.list.galaxyproject.org/keep-job-output-and-scripts-on-failed-tests-td4667327.html.

I considered making this 'never' - since those files will get cleaned up at the end anyway. This would actually reduce our test coverage related to job cleanup logic - so I have decided this is a fine a middle ground.
 2015-06-15 09:53:59 -04:00
John Chilton 584f673f8d Merge remote-tracking branch 'jmchilton/dev' into ts-search-expansion 
Conflicts:
	lib/galaxy/webapps/tool_shed/buildapp.py
 2015-06-15 09:43:59 -04:00
John Chilton 732abcc0db Merge remote-tracking branch 'jmchilton/release_15.05' into dev 2015-06-08 14:04:28 -04:00
Nicola Soranzo 292d16a593 Mark also HDAs as purged when purging datasets via cleanup script. 
This will make purged datasets be shown as purged in histories,
preventing them to be undeleted through the UI.
This will not fix datasets previously purged through this script,
scripts/cleanup_datasets/pgcleanup.py may be used for that.
 2015-06-04 18:06:01 +01:00
Dannon Baker e56b2a3433 Merge pull request #274 from dpryan79/dev 
Add usage information to python cleanup scripts
 2015-06-02 07:57:02 -04:00
John Chilton 3946ff50bb Merge pull request #80 from erasche/jbrowse-ie 
Add EDAM IDs to datatypes
 2015-05-22 09:42:59 -05:00
dpryan79 00eb96923f Add a missing period in populate_uuid.py 2015-05-20 13:01:40 +02:00
dpryan79 0ff5a050d5 Indentation fix 2015-05-19 21:55:36 +02:00
dpryan79 0763cab37a Update the remainder of the python cleanup scripts 2015-05-19 21:53:45 +02:00
John Chilton 98d8c2cc2e Allow config of shed tool conf used with `run_tests.sh -installed`. 
Set with GALAXY_TEST_SHED_TOOL_CONF.

This is required to implement galaxyproject/planemo#176.
 2015-05-18 02:07:36 -04:00
John Chilton 08e2c351d9 Add edam formats to most Galaxy datatypes and a script for producing a mapping. 
See notes in scripts/edam_mapping.py for more information on mapping.

This is based on mapping of terms done by Eric Rasche (@erasche) (in galaxyproject/galaxy#80) and by the team at Pasteur including @hmenager, @fmareuil, and @odoppelt (in https://docs.google.com/spreadsheets/d/1vptTpJvQfb5FOtRJOajjftUkL9aZ0eeVdhUPvd9h5wY/edit#gid=0).

Current mapping at time of commit is https://gist.github.com/jmchilton/73cd540d7a08488843d7.
 2015-05-16 16:47:39 -04:00
Nate Coraor 656d9bef50 Merge remote-tracking branch 'upstream/release_15.05' into dev 
Conflicts:
	lib/galaxy/version.py
 2015-05-14 11:11:46 -04:00
dpryan79 4c20494011 Make python scripts executable. Tweak remove_renamed_datasets_from_disk.py. 2015-05-12 18:25:32 +02:00
John Chilton 4e1324e432 Add PR7 to release notes (caught by @bgruening). 
... small updates to bootstrap history script for reuse in planemo.
 2015-05-12 12:15:56 -04:00
dpryan79 a092aa2f59 Start providing usage information for the various cleanup scripts 2015-05-12 17:53:18 +02:00
John Chilton bb7fb089fe First crack at release notes for 15.05. 2015-05-11 23:05:56 -04:00
Martin Cech e0c7e02e40 do not require option that is actualy in the config 2015-05-07 16:50:27 -04:00
John Chilton 0aabdd4048 Merge remote-tracking branch 'jmchilton/release_15.05' into dev 2015-05-06 20:56:43 -04:00
John Chilton 5d31ce641a Fix problem with twill's custom subprocess module. 
There has been for some time a scary warning when testing (http://dev.list.galaxyproject.org/run-test-sh-ImportError-cannot-import-name-args-from-interpreter-flags-td4666277.html) that I now understand is the result of Twill being packaged with its own custom subprocess module that conflicts with modules using multiprocessing (e.g. kombu).

After the #198 this scary warning has become an exception that prevents exception of tests (see https://travis-ci.org/galaxyproject/planemo/jobs/61547827 for instance). Importing subprocess seems to force Python to use the system module instead of twills - which seems to prevent these problems.

There have been other reports of this problem with Twill in other projects and removing the subprocess module didn't seem to break anything for them either.
 2015-05-06 20:24:50 -04:00
John Chilton 6e71a90cdd Merge pull request #151 from natefoo/runtime_stats 
A command line script for collecting stats on job runtimes
 2015-04-28 13:11:33 -05:00
Marek Vavrusa 43cd2083f6 runners/drmaa: set 'workingDirectory' correctly 
this fixes an issue with when the Galaxy lib (and therefore working
directory) is not shared with the compute nodes
 2015-04-24 16:12:33 +02:00
Nate Coraor 73dd0b1a6f Add some additional documentation/usage in the doc string 2015-04-23 16:03:58 -04:00