Bioblend

* BioBlend.objects: enabled import of workflows containing dataset collection
inputs.

* Implemented APIs for a modern Galaxy workflow APIs (i.e. delayed scheduling).

* Implemented APIs to search Tool Shed repositories and tools.

* Added support for uploading (importing) from FTP (thanks to
[Helena Rasche](https://github.com/erasche)).

* Added ``to_posix_lines`` and ``space_to_tab`` params to ``upload_file()``,
``upload_from_ftp()`` and ``paste_content()`` methods of ``ToolClient``.

* BioBlend.objects: added ``upload_from_ftp()`` method to ``History``.

* Updated the testing framework to work with Galaxy wheels; use TravisCI's
container infrastructure; test Galaxy release 15.07.

* Updated CloudmanLauncher's ``launch`` method to accept ``subnet_id``
parameter, for VPC support (thanks to Matthew Ralston).

* Properly pass extra arguments to cloud instance userdata.

* Updated placement finding methods and `get_clusters_pd` method to return a
dict vs. lists so error messages can be included.

* A numer of documentation improvements and minor updates/fixes (see individual
commits).

* BioBlend.objects: renamed ``ObjDatasetClient`` abstract class to
``ObjDatasetContainerClient``.

* BioBlend.objects: added ``ABCMeta`` metaclass and ``list()`` method to
``ObjClient``.

* BioBlend.objects: added ``io_details`` and ``link_details`` parameters to
``ObjToolClient.get()`` method.

* Open port 8800 when launching cloud instances for use by NodeJS proxy for
Galaxy IPython Interactive Environments.

* When launching cloud instances, propagate error messages back to the called.
The return types for methods ``create_cm_security_group``, ``create_key_pair``
in ``CloudManLauncher`` class have changed as a result of this.

* Added support for Python >= 3.3.

* Added ``get_library_permissions()`` method to ``LibraryClient``.

* Added ``update_group()``, ``get_group_users()``, ``get_group_roles()``,
``add_group_user()``, ``add_group_role()``, ``delete_group_user()`` and
``delete_group_role()`` methods to ``GroupsClient``.

* Added ``full_details`` parameter to ``JobsClient.show_job()`` (thanks to
Rossano Atzeni).

* BioBlend.objects: added ``ObjJobClient`` and ``Job`` wrapper (thanks to
Rossano Atzeni).

* BioBlend.objects: added check to verify that all tools in a workflow are
installed on the Galaxy instance (thanks to
[Gianmauro Cuccuru](https://github.com/gmauro)).

* Removed several deprecated parameters: see commits [19e168f](https://github.com/galaxyproject/bioblend/commit/19e168f5342f4c791d37694d7039a85f2669df71)
and [442ae98](https://github.com/galaxyproject/bioblend/commit/442ae98037be7455d57be15542553dc848d99431).

* Verify SSL certificates by default.

* Added documentation about the Tool Shed and properly link all the docs on
ReadTheDocs.

* Solidified automated testing by using [tox](https://tox.readthedocs.org/) and
[flake8](https://gitlab.com/pycqa/flake8).

* Project source moved to new URL - https://github.com/galaxyproject/bioblend

* Huge improvements to automated testing, tests now run against Galaxy

* BioBlend.objects: enabled email&password auth

* Enabled Tool Shed tar ball uploads

* BioBlend.objects: implemented deletion of history and library datasets

* BioBlend.objects: fixed library dataset downloads

* Fixed the Tool Shed tool installation method

* Added 'deleted' attribute to DatasetContainer

* Handle `data_type` changes in the Oct 2014 Galaxy release

* Renamed `get_current_history()` to `get_most_recently_used_history()`

* A number of documentation improvements and other small fixes (see
the commit messages for more details)

* Fixed url joining problem described in issue 82

* Enabled Travis Continuous Inetgration testing

* Added script to create a user and get its API key

* Deprecated ``create_user()`` method in favor of clearer
``create_remote_user()``. Added ``create_local_user()``.

* Skip instead of fail tests when ``BIOBLEND_GALAXY_URL`` and
``BIOBLEND_GALAXY_API_KEY`` environment variables are not defined.

* Added export and download to objects API

* Added export/download history

* GalaxyClient: changed ``make_put_request()`` to return whole ``requests``
response object

* Added Tool wrapper to *BioBlend.objects* plus methods to list tools and get
one.

* Added ``show_tool()`` method to ``ToolClient`` class

* Added ``name``, ``in_panel`` and ``trackster`` filters to ``get_tools()``

* Added ``upload_dataset()`` method to ``History`` class.

* Removed ``DataInput`` and ``Tool`` classes for workflow steps. ``Tool`` is to
be used for running single tools.