diff --git a/doc/source/releases/20.05.rst b/doc/source/releases/20.05.rst index 9a2031412d6..226acc2097e 100644 --- a/doc/source/releases/20.05.rst +++ b/doc/source/releases/20.05.rst @@ -62,7 +62,7 @@ Enhancements (thanks to `@OlegZharkov `__). `Pull Request 9562`_ * Datasource tool for SRA manifest - `Pull Request 9613`_ + `Pull Request 9613`_, `Pull Request 9892`_ .. enhancement_tag_viz * Skip visualization build, if no changes were registered @@ -175,7 +175,7 @@ Enhancements `Pull Request 9186`_ * Full Python dependencies update (thanks to `@nsoranzo `__). - `Pull Request 9188`_ + `Pull Request 9188`_, `Pull Request 9402`_, `Pull Request 9529`_, `Pull Request 9697`_ * Allow mixed store_by objectstore configurations. `Pull Request 9197`_ * implement workflow bookmark selenium test @@ -217,9 +217,6 @@ Enhancements `Pull Request 9390`_ * Replace editor grid image with css, add editor client unit tests `Pull Request 9392`_ -* Full Python dependencies update - (thanks to `@nsoranzo `__). - `Pull Request 9402`_ * Vuefy interactive tools (thanks to `@OlegZharkov `__). `Pull Request 9409`_ @@ -254,9 +251,6 @@ Enhancements `Pull Request 9521`_ * Rename and modify current_history_contents method `Pull Request 9526`_ -* Full Python dependencies update - (thanks to `@nsoranzo `__). - `Pull Request 9529`_ * Improvement to the selenium test to change password from user preferences (thanks to `@Realjuan `__). `Pull Request 9545`_ @@ -306,14 +300,11 @@ Enhancements * Feature/3937 advanced search tooltip (thanks to `@assuntad23 `__). `Pull Request 9696`_ -* Full Python dependencies update - (thanks to `@nsoranzo `__). - `Pull Request 9697`_ .. small_enhancement * Rename function, params in ConfigSerializer `Pull Request 9247`_ -* Make `str.join()`s more efficient +* Make ``str.join()``s more efficient (thanks to `@nsoranzo `__). `Pull Request 9258`_ * Faster and cleaner set creation @@ -338,7 +329,7 @@ Enhancements `Pull Request 9443`_ * Move sanitize_whitelist into mutable_config_dir `Pull Request 9455`_ -* Use auto_create functionality of `get_private_user_role()` +* Use auto_create functionality of ``get_private_user_role()`` (thanks to `@nsoranzo `__). `Pull Request 9509`_ * Combine selenium tests for creating and switching histories @@ -401,6 +392,9 @@ Fixes * extract_genomic_dna.py: import Comment, Header from bx.tabular.io instead of bx.intervals.io (thanks to `@cat-bro `__). `Pull Request 9748`_ +* Move some tools that no longer need galaxy on the PATH + (thanks to `@bernt-matthias `__). + `Pull Request 9850`_ .. bug_tag_workflows * Fix workflow list filtering dropdown @@ -411,6 +405,8 @@ Fixes `Pull Request 9676`_ * Trigger onchange event, fixes tool version changes being lost `Pull Request 9695`_ +* Input dataset module format filtering fix; + `Pull Request 9884`_ .. bug_tag_ui * fix for python3 and GEDA, was getting "Connection closed at byte 0" @@ -451,6 +447,8 @@ Fixes * Migrate condor runner to jwd for job-files (thanks to `@bgruening `__). `Pull Request 9833`_ +* Fix incorrect variable assignment + `Pull Request 9907`_ .. bug_tag_admin * Fix vue helper in admin router, fixes toolshed installation, avoids console errors @@ -514,7 +512,7 @@ Fixes * Use a Galaxy root path with a space for converters and mulled tests (thanks to `@nsoranzo `__). `Pull Request 9429`_ -* Fix `test_run_simple()` test broken on Python 2 by virtualenv 20.0.5 +* Fix ``test_run_simple()`` test broken on Python 2 by virtualenv 20.0.5 (thanks to `@nsoranzo `__). `Pull Request 9458`_ * Use browser locale over global default @@ -575,8 +573,8 @@ Fixes * Fix indexing script `Pull Request 9565`_ * Assign random password in user manager if none specified - (thanks to `@nuwang `__). - `Pull Request 9587`_ + (thanks to `@nuwang `__, `@nsoranzo `__). + `Pull Request 9587`_, `Pull Request 9851`_ * Fix removal of workflow outputs from workflow nodes in editor `Pull Request 9606`_ * Fix ELIXIR AAI @@ -587,7 +585,7 @@ Fixes `Pull Request 9622`_ * Change session timeout redirect URL to login entrypoint. `Pull Request 9626`_ -* Changed CSS overflow property from scroll to hidden to make table scr… +* Changed CSS overflow property from scroll to hidden to make table scrollable (thanks to `@assuntad23 `__). `Pull Request 9627`_ * fix links in Galaxy xsd docs @@ -601,7 +599,7 @@ Fixes * Hide "python: not found" error when Python 2 is not installed (thanks to `@nsoranzo `__). `Pull Request 9657`_ -* Fix for `time.clock()` removal in Python 3.8 +* Fix for ``time.clock()`` removal in Python 3.8 (thanks to `@nsoranzo `__). `Pull Request 9666`_ * Fixed an issue in object store integration tests @@ -622,6 +620,8 @@ Fixes `Pull Request 9724`_ * Fix custos credential fetching in python3 `Pull Request 9726`_ +* oidc-based authnz provider overhaul; breaking changes for keycloak + `Pull Request 9730`_ * Sort Workflow list by last updated time instead of created time `Pull Request 9740`_ * Remove dummy tool sequence @@ -648,6 +648,31 @@ Fixes `Pull Request 9821`_ * Tolerate exception in container resolution `Pull Request 9824`_ +* Invalidate tool cache when tool modified outside of Galaxy + `Pull Request 9866`_ +* Custos spec fixes + `Pull Request 9889`_ +* Fixes for flake8 3.8 and bugbear + (thanks to `@nsoranzo `__). + `Pull Request 9896`_ +* Fix webpack import proxy prefix + `Pull Request 9898`_ +* Fix extra preference values leaking between requests + (thanks to `@nuwang `__). + `Pull Request 9913`_ +* Rewrite ``check_html()`` and ``Text.count_data_lines()`` to read a chunk of each line + (thanks to `@nsoranzo `__). + `Pull Request 9920`_ +* Make cookie handling more robust + `Pull Request 9921`_ +* Enable regex validator to validate lists of values. + `Pull Request 9925`_ +* oidc: fix dict_keys does not support indexing + (thanks to `@almahmoud `__). + `Pull Request 9931`_ +* Move the ``--debug`` flag after the conda subcommand + (thanks to `@nsoranzo `__). + `Pull Request 9932`_ .. include:: 20.05_prs.rst diff --git a/doc/source/releases/20.05_prs.rst b/doc/source/releases/20.05_prs.rst index da0105d63ed..eee1092d8cc 100644 --- a/doc/source/releases/20.05_prs.rst +++ b/doc/source/releases/20.05_prs.rst @@ -226,6 +226,7 @@ .. _Pull Request 9719: https://github.com/galaxyproject/galaxy/pull/9719 .. _Pull Request 9724: https://github.com/galaxyproject/galaxy/pull/9724 .. _Pull Request 9726: https://github.com/galaxyproject/galaxy/pull/9726 +.. _Pull Request 9730: https://github.com/galaxyproject/galaxy/pull/9730 .. _Pull Request 9731: https://github.com/galaxyproject/galaxy/pull/9731 .. _Pull Request 9733: https://github.com/galaxyproject/galaxy/pull/9733 .. _Pull Request 9734: https://github.com/galaxyproject/galaxy/pull/9734 @@ -250,3 +251,22 @@ .. _Pull Request 9824: https://github.com/galaxyproject/galaxy/pull/9824 .. _Pull Request 9833: https://github.com/galaxyproject/galaxy/pull/9833 .. _Pull Request 9835: https://github.com/galaxyproject/galaxy/pull/9835 +.. _Pull Request 9838: https://github.com/galaxyproject/galaxy/pull/9838 +.. _Pull Request 9850: https://github.com/galaxyproject/galaxy/pull/9850 +.. _Pull Request 9851: https://github.com/galaxyproject/galaxy/pull/9851 +.. _Pull Request 9866: https://github.com/galaxyproject/galaxy/pull/9866 +.. _Pull Request 9870: https://github.com/galaxyproject/galaxy/pull/9870 +.. _Pull Request 9878: https://github.com/galaxyproject/galaxy/pull/9878 +.. _Pull Request 9884: https://github.com/galaxyproject/galaxy/pull/9884 +.. _Pull Request 9889: https://github.com/galaxyproject/galaxy/pull/9889 +.. _Pull Request 9892: https://github.com/galaxyproject/galaxy/pull/9892 +.. _Pull Request 9894: https://github.com/galaxyproject/galaxy/pull/9894 +.. _Pull Request 9896: https://github.com/galaxyproject/galaxy/pull/9896 +.. _Pull Request 9898: https://github.com/galaxyproject/galaxy/pull/9898 +.. _Pull Request 9907: https://github.com/galaxyproject/galaxy/pull/9907 +.. _Pull Request 9913: https://github.com/galaxyproject/galaxy/pull/9913 +.. _Pull Request 9920: https://github.com/galaxyproject/galaxy/pull/9920 +.. _Pull Request 9921: https://github.com/galaxyproject/galaxy/pull/9921 +.. _Pull Request 9925: https://github.com/galaxyproject/galaxy/pull/9925 +.. _Pull Request 9931: https://github.com/galaxyproject/galaxy/pull/9931 +.. _Pull Request 9932: https://github.com/galaxyproject/galaxy/pull/9932