diff --git a/CHANGELOG.md b/CHANGELOG.md index bc2ac3a77..01b493588 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,8 +1,11 @@ -### BioBlend v +### BioBlend v1.0.0 - 2022-10-13 * Drop support for deprecated CloudMan, see https://galaxyproject.org/blog/2021-10-sunsetting-cloudlaunch/ +* Added dependency on ``typing-extensions`` package, removed dependencies on + ``boto`` and ``pyyaml``. + * Deprecated ``max_get_retries()``, ``set_max_get_retries()``, ``get_retry_delay()`` and ``set_get_retry_delay()`` methods of ``Client``. @@ -12,6 +15,9 @@ * Added ``get_or_create_user_apikey()`` method to ``UserClient``. +* Added ``all`` parameter to ``HistoryClient.get_histories()`` method (thanks to + [Paprikant](https://github.com/Paprikant)). + * Added ``require_exact_tool_versions`` parameter to ``WorkflowClient.invoke_workflow()`` method (thanks to [cat-bro](https://github.com/cat-bro)). @@ -26,8 +32,11 @@ support history purging via Celery (thanks to [Nolan Woods](https://github.com/innovate-invent)). +* Fixed bug in ``FormsClient.create_form()`` where the ``form_xml_text`` + argument was not passed correctly to the Galaxy API. + * Fixed bug in ``HistoryClient.show_dataset_provenance()`` where the ``follow`` - parameter was not passed to the Galaxy API. + argument was not passed to the Galaxy API. * BioBlend.objects: Added ``delete()`` abstract method to ``DatasetContainer`` class. @@ -125,9 +134,9 @@ * Pass the API key for all requests as the ``x-api-key`` header instead of as a parameter (thanks to [rikeshi](https://github.com/rikeshi)). -* Try prepending https:// and http:// if the scheme is missing in the ``url`` - parameter of ``GalaxyClient``, i.e. when initialising a Galaxy or ToolShed - instance. +* Try prepending "https://" and "http://" if the scheme is missing in the + ``url`` argument passed to ``GalaxyClient``, i.e. when initialising a Galaxy + or ToolShed instance. * Added a new ``dataset_collections`` attribute to ``GalaxyInstance`` objects, which is an instance of the new ``DatasetCollectionClient``. This new module @@ -341,15 +350,15 @@ * Added ``maxwait`` parameter to ``HistoryClient.export_history()`` and ``History.export()`` methods. -* Fixed handling of ``type`` parameter in ``HistoryClient.show_history()`` +* Fixed handling of ``type`` argument in ``HistoryClient.show_history()`` (thanks to [Marius van den Beek](https://github.com/mvdbeek)). -* Fixed handling of ``deleted`` parameter in ``LibraryClient.get_libraries()`` +* Fixed handling of ``deleted`` argument in ``LibraryClient.get_libraries()`` (thanks to [Luke Sargent](https://github.com/luke-c-sargent), reported by [Katie](https://github.com/emartchenko)). * Fixed ``LibraryClient.wait_for_dataset()`` when ``maxwait`` or ``interval`` - parameters are of type ``float``. + arguments are of type ``float``. * Unify JSON-encoding of non-file parameters of POST requests inside ``GalaxyClient.make_post_request()``. @@ -483,7 +492,7 @@ Galaxy API request (thanks to @DamCorreia). * Fixed ``HistoryClient.update_history()`` and ``History.update()`` methods - when ``name`` parameter is not specified. + when ``name`` argument is not specified. * Added warning if content size differs from content-length header in ``DatasetClient.download_dataset()``. @@ -571,7 +580,7 @@ * Updated CloudmanLauncher's ``launch`` method to accept ``subnet_id`` parameter, for VPC support (thanks to Matthew Ralston). -* Properly pass extra parameters to cloud instance userdata. +* 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. diff --git a/bioblend/__init__.py b/bioblend/__init__.py index 840100616..93b576472 100644 --- a/bioblend/__init__.py +++ b/bioblend/__init__.py @@ -13,7 +13,7 @@ ) # Current version of the library -__version__ = "0.18.0" +__version__ = "1.0.0" # 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 32430d1ba..0812211ea 100644 --- a/bioblend/galaxy/histories/__init__.py +++ b/bioblend/galaxy/histories/__init__.py @@ -383,10 +383,9 @@ def show_matching_datasets( """ if isinstance(name_filter, str): name_filter = re.compile(name_filter + "$") - history_content = self.show_history(history_id, contents=True) return [ self.show_dataset(history_id, h["id"]) - for h in history_content + for h in self.show_history(history_id, contents=True) if name_filter is None or name_filter.match(h["name"]) ] diff --git a/bioblend/galaxy/objects/wrappers.py b/bioblend/galaxy/objects/wrappers.py index 9c07dccac..3fbdd3f77 100644 --- a/bioblend/galaxy/objects/wrappers.py +++ b/bioblend/galaxy/objects/wrappers.py @@ -386,8 +386,7 @@ def sorted_step_ids(self) -> List[str]: while source_ids: head = source_ids.pop() ids.append(head) - tails: Set[str] = self.dag[head] if head in self.dag else set() - for tail in tails: + for tail in self.dag.get(head, set()): incoming = inv_dag[tail] incoming.remove(head) if not incoming: