Merge pull request #92 from jmchilton/master

Update travis to reflect latest galaxy config reorganization
Add a method for retrieving Tool Shed repositories
Handle data_type changes in forthcoming Galaxy release.

Updated commit with fix from @nsoranzo.

The forthcoming release of Galaxy makes breaking change to history contents API - data_type will no longer represent the short format/file extension of the history dataset - it will now represent the Python module and class.

This commit attempts to use the new file_ext attribute when it can and falls back to the old data_type attribute for older releases that don't include file_ext. This change should make the various methods that consume data_type within bioblend backward compatible but clients should be made aware that show_dataset is going to return different values as of the October release.

For more information on the Galaxy API changes see https://bitbucket.org/galaxy/galaxy-central/commits/9d152ed#chg-lib/galaxy/model/__init__.py.
Fix libraries.get_folders() documentation. Fix afgane/bioblend#91.
Add 'deleted' attribute to DatasetContainer.
Add extra parameters to histories.update_history() and History.update() .

Add test_update_history to TestGalaxyHistories.py .
Fix some typos.
Merge pull request #95 from nsoranzo/misc_fixes

Misc enhancements
Fix 2 method docstrings.
Add more attributes to HistoryDatasetAssociation and HistoryContentInfo objects.
Add delete() method to HistoryDatasetAssociation and LibraryDataset classes.

Add corresponding tests.
Update the payload field when installing Tool Shed repos to match the expected one in current Galaxy
Merge
Fix for objects library dataset downloads.

My best guess is there was a subtle bug in this code - because it was passing library dataset ids to an API endpoint that was expecting LDDA ids. LDDA ids would match LD ids in all the tests I guess because an LD never has its LDDA replaced I don't think.

Regardless - the API endpoint has changed so that now it does infact expect an LD id - but the parameter name has changed as well so I have fixed this here. More information on the Galaxy change can be found here - https://bitbucket.org/galaxy/galaxy-central/commits/c0c00d69cae3966a5c1e67abc3ba7aa67a735a64.

But this is definitely breaking - the new object library client will not work on older versions of Galaxy anymore and the older version of the client will not work with Galaxy after the October release. @simleo @nsoranzo is this acceptable - should we revisit the Galaxy API and make it more backward compatible to still allow LDDA IDs (I don't think it is worth it because of the bug mentioned above - but maybe I am wrong about the bug or maybe it is common to never replace a dataset so LD ids always match LDDA ids). Pinging @martenson on this as well.
dataset: get_stream: backward compatibility fixes
Merge pull request #96 from nsoranzo/misc_fixes

BioBlend.objects: delete history and library datasets
Implement tool shed tar ball uploads.
Refactor email/password auth to allow use with tool shed API as well.