diff --git a/CHANGELOG.md b/CHANGELOG.md index 19852983d..3b9270be7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,12 +1,49 @@ -### BioBlend v - unreleased +### BioBlend v0.15.0 - 2021-02-10 * Dropped support for Python 3.5. Added support for Python 3.9. Added support for Galaxy releases 20.09 and 21.01. + * Changed the return value of ``RolesClient.create_role()`` method from a 1-element list containing a dict to a dict. + +* Removed deprecated ``download_dataset()`` and ``get_current_history`` + methods of ``HistoryClient``. + +* Removed deprecated ``export_workflow_json()`` and ``import_workflow_json`` + methods of ``WorkflowClient``. + +* Added ``copy_content()``, ``get_published_histories()`` and ``open_history()`` + methods to ``HistoryClient``. + +* Added ``rerun_job()`` method to ``JobsClient``. + +* Added ``requirements()`` method to ``ToolClient`` (thanks to + [cat-bro](https://github.com/cat-bro)). + +* Added ``published`` and ``slug`` parameters to + ``HistoryClient.get_histories()``. + +* Added ``require_state_ok`` parameter to ``DatasetClient.download_dataset()``. + +* Added ``input_format`` parameter to ``ToolClient.run_tool()``. + +* Deprecated ``history_id`` parameter of ``HistoryClient.get_histories()`` + method. + +* BioBlend.objects: Added ``owner`` property to all objects. Added + ``annotation``, ``published`` and ``purged`` properties to ``HistoryPreview`` + objects. + +* Fixed issue where specifying the Galaxy URL with "http://" instead of + "https://" when creating a ``GalaxyInstance`` made the subsequent non-GET + requests to silently fail. + * Moved the Continuous Integration (CI) from TravisCI to GitHub workflows (thanks to [Oleg Zharkov](https://github.com/OlegZharkov)). +* Improvements to tests and documentation (thanks to + [Gianmauro Cuccuru](https://github.com/gmauro)). + ### BioBlend v0.14.0 - 2020-07-04 * Dropped support for Python 2.7. Dropped support for Galaxy releases diff --git a/bioblend/__init__.py b/bioblend/__init__.py index 93c0927fd..9f69baf25 100644 --- a/bioblend/__init__.py +++ b/bioblend/__init__.py @@ -7,7 +7,7 @@ ) # Current version of the library -__version__ = '0.14.0' +__version__ = '0.15.0' # default chunk size (in bytes) for reading remote data try: diff --git a/bioblend/galaxy/histories/__init__.py b/bioblend/galaxy/histories/__init__.py index 5bab9a740..083f7bc72 100644 --- a/bioblend/galaxy/histories/__init__.py +++ b/bioblend/galaxy/histories/__init__.py @@ -2,7 +2,6 @@ Contains possible interactions with the Galaxy Histories """ import logging -import os import re import sys import time @@ -513,22 +512,6 @@ def create_dataset_collection(self, history_id, collection_description): ) return self._post(payload, id=history_id, contents=True) - def download_dataset(self, history_id, dataset_id, file_path, - use_default_filename=True): - """ - .. deprecated:: 0.8.0 - Use :meth:`~bioblend.galaxy.datasets.DatasetClient.download_dataset` - instead. - """ - meta = self.show_dataset(history_id, dataset_id) - if use_default_filename: - file_local_path = os.path.join(file_path, meta['name']) - else: - file_local_path = file_path - return self.gi.datasets.download_dataset(dataset_id, - file_path=file_local_path, - use_default_filename=False) - def delete_history(self, history_id, purge=False): """ Delete a history. @@ -593,13 +576,6 @@ def get_status(self, history_id): state['percent_complete'] = 0 return state - def get_current_history(self): - """ - .. deprecated:: 0.5.2 - Use :meth:`get_most_recently_used_history` instead. - """ - return self.get_most_recently_used_history() - def get_most_recently_used_history(self): """ Returns the current user's most recently used history (not deleted). diff --git a/bioblend/galaxy/workflows/__init__.py b/bioblend/galaxy/workflows/__init__.py index 60fbd26cd..9f18d7e21 100644 --- a/bioblend/galaxy/workflows/__init__.py +++ b/bioblend/galaxy/workflows/__init__.py @@ -127,16 +127,6 @@ def import_workflow_dict(self, workflow_dict, publish=False): url = self._make_url() + "/upload" return self._post(url=url, payload=payload) - def import_workflow_json(self, workflow_json): - """ - .. deprecated:: 0.9.0 - Use :meth:`import_workflow_dict` instead. - - :type workflow_json: dict - :param workflow_json: dictionary representing the workflow to be imported - """ - return self.import_workflow_dict(workflow_json) - def import_workflow_from_local_path(self, file_local_path, publish=False): """ Imports a new workflow given the path to a file containing a previously @@ -212,13 +202,6 @@ def export_workflow_dict(self, workflow_id, version=None): url = '/'.join((self._make_url(), 'download', workflow_id)) return self._get(url=url, params=params) - def export_workflow_json(self, workflow_id): - """ - .. deprecated:: 0.9.0 - Use :meth:`export_workflow_dict` instead. - """ - return self.export_workflow_dict(workflow_id) - def export_workflow_to_local_path(self, workflow_id, file_local_path, use_default_filename=True): """ Exports a workflow in JSON format to a given local path.