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Author SHA1 Message Date
Gildas Le Corguillé 4e64c23f46 Update datatypes_conf.xml.sample 
Add the sniffer in the sniffers
 2016-08-03 12:13:13 +02:00
Gildas Le Corguillé ad8483a7db Update binary.py 2016-08-03 10:47:16 +02:00
lecorguille b16356e490 add a netcdf datatype for metabolomics spectre data 2016-08-03 10:32:15 +02:00
Dannon Baker 7389b93bd6 Merge pull request #2703 from sszakony/dev 
Fixing button width on Composite upload dialog #2591
 2016-08-02 22:28:05 -04:00
galaxy 2b7fc3d377 Fixing button width on Composite upload dialog 2016-08-02 16:02:49 -04:00
Dannon Baker d8c22b70e8 Merge branch 'PasswordStrengthBar' into dev 2016-08-01 16:49:35 -04:00
Dannon Baker dd4eabb484 Merge pull request #2654 from carlfeberhard/history.delete_current-id 
History, UI: use id of displayed history in delete
 2016-08-01 14:09:18 -04:00
Martin Cech 6db43585c1 Merge pull request #2695 from dannon/sed_compat 
sed bsd compatibility for release versioning in Makefile
 2016-08-01 11:50:52 -04:00
Dannon Baker ef0d27d677 Change extension of the file that gets immediately deleted to address nsoranzo's concern about bsd utilities. 2016-08-01 11:19:22 -04:00
Dannon Baker 00e41385d7 The previous approach to sed worked great on bsd sed, but gnu sed 
doesn't understand an empty '' in-place extension the same way.  So,
fixed one, broke the other.

This approach with the -e argument feels like a total hack since it
explits the fact that bsd sed consumes the -e as the argument to -i, but
it still has the command interpreted correctly.
 2016-08-01 09:11:49 -04:00
Dannon Baker 2c75551a02 Fix sed usage in Makefile to be compatible with both gnu and bsd sed. -i's argument is not optional for bsd, but an empty string (no backup extension) works fine and has the same behavior as gnu sed. 2016-08-01 07:48:50 -04:00
John Chilton 3fd0e405fd Merge pull request #2690 from nsoranzo/datatypes_fixes 
Misc datatypes fixes and enhancements
 2016-07-29 19:34:20 -04:00
Daniel Blankenberg 9aac1569f4 Merge pull request #2688 from dannon/makefile_updates 
Makefile updates for compatibility with OSX
 2016-07-29 16:17:03 -04:00
Dannon Baker e291012afd Merge branch 'release_16.07' into dev 2016-07-29 15:35:29 -04:00
Dannon Baker 62815aff39 Merge pull request #2691 from nsoranzo/release_16.07_fix_tests 
[16.07] Fix unit tests
 2016-07-29 15:25:49 -04:00
Nicola Soranzo 5e7f0c4b18 Fix unit tests exit status 
Broken in https://github.com/galaxyproject/galaxy/pull/2564
Also update scripts/nosetests.py
 2016-07-29 19:47:08 +01:00
Nicola Soranzo f06c895d61 Update INDETERMINATE_DEPENDENCY to NullDependency 
Fix unit test broken in https://github.com/galaxyproject/galaxy/pull/2554
 2016-07-29 19:38:06 +01:00
Nicola Soranzo 5b52b73fbb Datatype classes fixes: wrong file_ext, import order, Python3 
- Specify some classes are abstracts
- Use super() to call superclass methods
- Various simplifications
 2016-07-29 19:29:27 +01:00
Nicola Soranzo af3f8cf846 Redefine svg datatype as subclass of GenericXml 
SVG is XML-based and Python Pillow does not support it.
 2016-07-29 19:29:27 +01:00
Eric Rasche c9a5d29134 Merge pull request #2689 from martenson/add_p4_bootstrap 
mention need to update P4's conf when freezing
 2016-07-29 18:19:41 +00:00
Martin Cech 09aef7eda5 mention need to update P4's conf when freezing 2016-07-29 14:16:58 -04:00
Dannon Baker dc668a0bf3 Checkout dev again prior to version branch deletion. This prevents 
error: Cannot delete the branch 'blah' which you are currently on
 2016-07-29 12:56:39 -04:00
Dannon Baker 6be8d6356d Remove unused def 2016-07-29 12:40:34 -04:00
Dannon Baker 820d545d3a Roll the check into the rule so it gets reevaluated 2016-07-29 12:40:00 -04:00
Dannon Baker 5c38221971 A different form of upstream check that works on osx (and hopefully 
still other locations).
 2016-07-29 12:30:37 -04:00
Ben Fulton bb209c6e59 Add a password strength evaluation bar 
Modify the register and change_password pages to show a bar
evaluating the strength of the password. Bar displays in red
for passwords < 6 chars or below a certain minimum complexity;
green otherwise. Adds a dependency on Complexify, a password
evaluator written by Dan Palmer.
 2016-07-29 11:14:02 -04:00
carlfeberhard cdab64820c Merge remote-tracking branch 'upstream/dev' into history.delete_current-id 2016-07-29 11:08:45 -04:00
Nicola Soranzo b2fbfcd6ac Merge pull request #2686 from dannon/version-16.10.dev 
Version 16.10.dev
 2016-07-29 11:15:04 +01:00
Nicola Soranzo 1a0052aa71 Merge pull request #2685 from dannon/version-16.07 
Update version to 16.07.rc1
 2016-07-29 08:46:01 +01:00
Dannon Baker 7893f1a571 Merge branch 'version-16.07' into version-16.10.dev 2016-07-28 22:55:39 -04:00
Dannon Baker 19b363cdcd Update version to 16.07.rc1 2016-07-28 22:55:39 -04:00
Dannon Baker 9789c116e6 Update version to 16.10.dev 2016-07-28 22:55:39 -04:00
John Chilton 05c537e384 Merge pull request #2678 from dannon/azure_followup 
Fix an error with getting the size of an object from Azure.  Attempte…
 2016-07-28 19:49:52 -04:00
Nicola Soranzo 0066847e0a Merge pull request #2684 from dannon/remote_auth_many_histories 
Limit creation of multitudes of default, empty histories.
 2016-07-28 17:49:33 +01:00
Dannon Baker 5c2402f837 Merge pull request #2682 from nsoranzo/flake8-import-order 
Extend the list of files tested with flake8-import-order to all files already passing
 2016-07-28 12:25:25 -04:00
Dannon Baker 4f12282138 Limit creation of multitudes of default, empty histories. This was happening for every new session using remote auth 2016-07-28 11:46:43 -04:00
Martin Cech e8f2a74f21 Merge pull request #2681 from guerler/help_word_break 
Break tool parameter help words if necessary
 2016-07-28 10:49:52 -04:00
Nicola Soranzo ec6e6255c1 Extend the list to all files already passing 
Generated with:

find . -path ./.venv -prune -o -path ./.tox -prune -o -path ./eggs -prune -o -path ./database -prune -o -name '*.py' -print0 | sort -z | xargs -0 -L 1 -I '{}' sh -c 'flake8 -qq {} && echo {}' | sed 's|^\./||' > .ci/flake8_lint_include_list.txt

followed by some manual editing.
 2016-07-28 15:26:28 +01:00
Nicola Soranzo 5c79e27436 Unpin flake8 in py27-lint-imports* test environments 
flake8-import-order 0.9 has been released
 2016-07-28 15:26:28 +01:00
guerler addc151797 Use word-wrap instead of word-break to apply break-word due to better browser support 2016-07-28 09:33:58 -04:00
guerler 4978173e4e Break tool parameter help words if necessary 2016-07-28 09:27:36 -04:00
Dannon Baker c096be04bd Merge branch 'release_16.04' into dev 2016-07-28 09:06:34 -04:00
Enis Afgan e4ca3bf80f Merge pull request #2673 from blankenberg/ucsc-hg38-display-16.04 
[16.04] Add hg38 to main for ucsc_build_sites.txt.sample
 2016-07-28 08:38:37 -04:00
Dannon Baker fdbaf437c9 Merge pull request #2672 from guerler/fix_populating_collections 
Properly populate collections regardless of context values
 2016-07-28 08:32:13 -04:00
Dannon Baker fed3665fcf Merge pull request #2680 from mvdbeek/toolshed_test_fixes 
Fix broken toolshed tests with #2554
 2016-07-28 07:44:21 -04:00
Marius van den Beek 12a789f3e1 Adjust tests for 8cca7be 2016-07-28 14:05:09 +03:00
Dannon Baker fcbaf8d17a Fix an error with getting the size of an object from Azure. Attempted to future-proof it if the library is fixed. 2016-07-27 23:07:29 -04:00
Dannon Baker c7caeb3c39 Merge branch 'azure-blob-objectstore' into dev 2016-07-27 23:06:18 -04:00
Dannon Baker c4841b3521 Merge pull request #2677 from guerler/update_select 
Fix dataset selector update when deleting history items
 2016-07-27 18:05:54 -04:00
Eric Rasche d7a1776a91 Merge pull request #2610 from thobalose/dev 
Added Neo4j IE
 2016-07-27 21:36:53 +00:00