From 2ddf410cd1adfd6026f0d81f9b5751fc0b5160e7 Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Fri, 9 Aug 2019 17:55:22 +0100 Subject: [PATCH] Release 0.13.0 --- CHANGELOG.md | 80 +++++++++++++++++++++++++++++++++----------- bioblend/__init__.py | 2 +- 2 files changed, 61 insertions(+), 21 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 918901727..5d577ec9a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,8 +1,39 @@ -### BioBlend v - unreleased +### BioBlend v0.13.0 - 2019-08-09 * Dropped support for Python 3.4. Added support for Galaxy releases 19.01 and 19.05. +* Updated ``requests-toolbelt`` requirement to ``>=0.5.1`` to prevent failing of + uploads to Galaxy (reported by [m93](https://github.com/mmeier93)). + +* Added ``toolshed`` attribute to ``GalaxyInstance`` and made ``toolShed`` an + alias to it (reported by [Miriam Payá](https://github.com/mpaya)). + +* Added ``uninstall_repository_revision()`` method to ``ToolShedClient`` (thanks + to [Helena Rasche](https://github.com/erasche), reported by + [Alexander Lenail](https://github.com/alexlenail)). + +* Added ``maxwait`` parameter to ``HistoryClient.export_history()`` and + ``History.export()`` methods. + +* Fixed handling of ``type`` parameter in ``HistoryClient.show_history()`` + (thanks to [Marius van den Beek](https://github.com/mvdbeek)). + +* Fixed handling of ``deleted`` parameter 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``. + +* Unify JSON-encoding of non-file parameters of POST requests inside + ``GalaxyClient.make_post_request()``. + +* Improvements to tests and documentation (thanks to + [Helena Rasche](https://github.com/erasche), + [selten](https://github.com/selten) and + [Pablo Moreno](https://github.com/pcm32)). + ### BioBlend v0.12.0 - 2018-12-17 * Added support for Python 3.7. Added support for Galaxy releases 18.05 and @@ -38,8 +69,8 @@ * Deprecated ``wait_for_completion`` parameter of ``DatasetClient.download_dataset()`` method. -* Fixed downloading of datasets receiving a HTTP 500 status code (thanks to Eric - Rasche). +* Fixed downloading of datasets receiving a HTTP 500 status code (thanks to + [Helena Rasche](https://github.com/erasche)). * Added ``wait_for_dataset()`` method to ``LibraryClient``. @@ -53,7 +84,7 @@ * Dropped support for Python 2.6. Added support for Galaxy release 17.09. * Added ``contents`` parameter to ``FoldersClient.show_folder()`` method - (thanks to Eric Rasche). + (thanks to [Helena Rasche](https://github.com/erasche)). * Exposed the `verify` attribute of `GalaxyInstance` and `ToolShedInstance` objects as `__init__()` parameter. @@ -73,11 +104,12 @@ * Do not check for mismatching content size when streaming a dataset to file (reported by Jorrit Boekel). -* Fixed delete requests when Galaxy uses external authentication (thanks to Eric - Rasche). +* Fixed delete requests when Galaxy uses external authentication (thanks to + [Helena Rasche](https://github.com/erasche)). * Fixed retrieval of the API key when a ``GalaxyClient`` object is initialised - with email and password on Python 3 (thanks to Marius van den Beek). + with email and password on Python 3 (thanks to + [Marius van den Beek](https://github.com/mvdbeek)). * Documentation improvements. @@ -95,26 +127,31 @@ ``DatasetClient`` in favour of ``JobsClient.show_job()`` with ``full_details=True``. -* Added ``install_dependencies()`` method to ``ToolClient`` (thanks to Marius - van den Beek). +* Added ``install_dependencies()`` method to ``ToolClient`` (thanks to + [Marius van den Beek](https://github.com/mvdbeek)). -* Added ``reload_data_table()`` method to ``ToolDataClient`` (thanks to Marius - van den Beek). +* Added ``reload_data_table()`` method to ``ToolDataClient`` (thanks to + [Marius van den Beek](https://github.com/mvdbeek)). * Added ``create_folder()``, ``update_folder()``, ``get_permissions()``, - ``set_permissions()`` methods to ``FoldersClient`` (thanks to Eric Rasche). + ``set_permissions()`` methods to ``FoldersClient`` (thanks to + [Helena Rasche](https://github.com/erasche)). -* Added ``get_version()`` method to ``ConfigClient`` (thanks to Eric Rasche). +* Added ``get_version()`` method to ``ConfigClient`` (thanks to + [Helena Rasche](https://github.com/erasche)). -* Added ``get_user_apikey()`` method to ``UserClient`` (thanks to Eric Rasche). +* Added ``get_user_apikey()`` method to ``UserClient`` (thanks to + [Helena Rasche](https://github.com/erasche)). * Added ``create_quota()``, ``update_quota()``, ``delete_quota()`` and - ``undelete_quota()`` methods to ``QuotaClient`` (thanks to Eric Rasche). + ``undelete_quota()`` methods to ``QuotaClient`` (thanks to + [Helena Rasche](https://github.com/erasche)). * Added ``purge`` parameter to ``HistoryClient.delete_dataset()`` method. * Added ``f_email``, ``f_name``, and ``f_any`` parameters to - ``UserClient.get_users()`` method (thanks to Eric Rasche). + ``UserClient.get_users()`` method (thanks to + [Helena Rasche](https://github.com/erasche)). * Updated ``WorkflowClient.import_shared_workflow()`` method to use the newer Galaxy API request (thanks to @DamCorreia). @@ -154,7 +191,8 @@ * Added ``install_resolver_dependencies`` parameter to ``ToolShedClient.install_repository_revision()``, applicable for Galaxy - release_16.07 and later (thanks to Marius van den Beek). + release_16.07 and later (thanks to + [Marius van den Beek](https://github.com/mvdbeek)). * Improve ``DatasetClient.download_dataset()`` by downloading the dataset in chunks when saving to file (thanks to Jorrit Boekel). @@ -193,7 +231,8 @@ * Implemented APIs to search Tool Shed repositories and tools. -* Added support for uploading (importing) from FTP (thanks to Eric Rasche). +* 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``. @@ -270,7 +309,8 @@ release_14.02 and all later versions to ensure backward compatibility (see `.travis.yml` for details). -* Many documentation improvements (thanks to Eric Rasche). +* Many documentation improvements (thanks to + [Helena Rasche](https://github.com/erasche)). * Added Galaxy clients for the tool data tables, the roles, and library folders (thanks to Anthony Bretaudeau). @@ -283,7 +323,7 @@ * Added ``copy_from_dataset()`` method to ``LibraryClient``. * Added ``create_repository()`` method to ``ToolShedRepositoryClient`` (thanks - to Eric Rasche). + to [Helena Rasche](https://github.com/erasche)). * Fixed ``DatasetClient.download_dataset()`` for certain proxied Galaxy deployments. diff --git a/bioblend/__init__.py b/bioblend/__init__.py index 9b95430c5..4d3df1564 100644 --- a/bioblend/__init__.py +++ b/bioblend/__init__.py @@ -4,7 +4,7 @@ from bioblend.config import BioBlendConfigLocations, Config # Current version of the library -__version__ = '0.12.0' +__version__ = '0.13.0' # default chunk size (in bytes) for reading remote data try: