Merge pull request #17610 from jdavcs/24.0_release_notes

[24.0] 24.0 release notes

doc/source/releases/24.0_announce.rst

@@ -1,12 +1,102 @@
 
-:orphan:
+===========================================================
+24.0 Galaxy Release (March 2024)
+===========================================================
+
+.. include:: _header.rst
+
+Highlights
+===========================================================
+
+**New Workflow List and Card View.** As part of our ongoing efforts to enhance user experience, we are proud to announce several new improvements to the workflows user interface, including workflow list view, workflow card view and workflow quick view. These improvements also include new tabs for "My workflows" (owned by the user), "Shared with me" (shared by other users) and "Published workflows" (publicly accessible workflows).
+
+**New select component for selecting a large amount of options.** This new tool form component improves selecting many options at once. The elements interface features a table based layout which can be filtered using plain-text or regular expressions. Options can be added individually, in bulk via the filter value, or by highlighting a range. It appears when there are many options available in a multi-select field, but can also be switched to/from and can be set as a default directly from within the tool form.
+
+**Multiple item drag and drop and keyboard navigation.** This new feature allows users to select multiple history items and drag and drop them into other histories or even tool forms! Users can also navigate their history using the arrow keys; multiple history items can be selected with the Shift + ArrowUp/ArrowDown key combination.
+
+**image_diff.** For tool developers, image_diff, a new comparison method for test output verification using images has been added. Unlike previously used comparison methods, image_diff is specifically tailored for single-channel and multi-channel image data (e.g. RGB). The difference of a pair of images is quantified as the pixel-wise distance between the images, for which different metrics can be used. A pair of images is considered to be equal in terms of the specified metric, if the distance between the images computed with respect to the metric is not above a given threshold. For more details, see `the original pull request <https://github.com/galaxyproject/galaxy/pull/17556>`__).
+
+Other notable improvements include consolidating resource grids for histories, visualizations and pages into tab views; the addition of a new UI feature for "relocating" a dataset to a new object store; and, for tool developers, a new comparison method for test output verification using images. Check out the `24.0 user release notes <24.0_announce_user.html>`__ for all the details.
+
+Are you an admin? See the Administration Notes below, and check out `some admin relevant PRs <https://github.com/galaxyproject/galaxy/pulls?q=label%3Ahighlight%2Fadmin+milestone%3A24.0+is%3Aclosed+is%3Apr>`__.
+
+Get Galaxy
+===========================================================
+
+The code lives at `GitHub <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
+
+To get a new Galaxy repository run:
+  .. code-block:: shell
+
+      $ git clone -b release_24.0 https://github.com/galaxyproject/galaxy.git
+
+To update an existing Galaxy repository run:
+  .. code-block:: shell
+
+      $ git fetch origin && git checkout release_24.0 && git pull --ff-only origin release_24.0
 
+See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details on source code locations.
+
+Administration Notes
 ===========================================================
-24.0 Galaxy Release (Early 2024)
+
+* A new built-in tool has been added: "Harmonize two collections". It takes two collections as input. Outputs are two collections with the same identifiers, with identifiers that are specific to one or the other removed. The tool creates new history datasets from the collection, but the user's quota usage does not increase. ( #16662)
+* A new object store plugin for the Rucio data management system has been added. (#17156)
+* The wig_to_bigWig tool removed; replaced by Wigbigwig. (#17328)
+* Notification Broadcasts Admin Panel has been enhanced. (#17090)
+* Setting dataset permissions for typical users has been simplified. (#17166)
+* When a user is deleted, all active user jobs will be canceled. (#17390)
+* Job resubmissions have been enabled in the k8s runner. (#17324)
+* Documentation has been added for tool panel and panel view administration. (#17078)
+* Documentation has been added on how to use vault keys in file sources. (#17498)
+* The release notes webhook has been dropped in favor of utilizing the notification system. (#17675)
+* Python 3.8 is now a minimum requirement. (#16954)
+* Python 3.12 is now supported. (#16796)
+
+Configuration Changes
 ===========================================================
 
+Added
+-----
+
+The following configuration options are new
+
+config/galaxy.yml.sample:galaxy
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+-  mapping.galaxy.mapping.object_store_config
+-  mapping.galaxy.mapping.oidc_scope_prefix
+-  mapping.galaxy.mapping.tus_upload_store_job_files
+
+
+Changed
+-------
+
+The following configuration options have been changed
 
-Schedule
+config/galaxy.yml.sample:galaxy
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+-  mapping.galaxy.mapping.tus_upload_store.desc has changed from
+
+   ::
+
+    The upload store is a temporary directory in which files uploaded by the
+    tus middleware or server will be placed.
+    Defaults to new_file_path if not set.
+
+   to
+
+   ::
+
+    The upload store is a temporary directory in which files uploaded by the
+    tus middleware or server for user uploads will be placed.
+    Defaults to new_file_path if not set.
+
+Release Notes
 ===========================================================
- * Planned Freeze Date: 2024-02-05
- * Planned Release Date: 2024-02-26
+
+.. include:: 24.0.rst
+   :start-after: announce_start
+
+.. include:: _thanks.rst

doc/source/releases/24.0_announce_user.rst

@@ -0,0 +1,191 @@
+
+===========================================================
+24.0 Galaxy Release (March 2024)
+===========================================================
+
+.. include:: _header.rst
+
+Highlights
+===========================================================
+
+New Workflow List and Card View
+-----------------------------------------------------------
+
+As part of our ongoing efforts to enhance user experience, we are proud to announce several new improvements to the workflows user interface, including workflow list view, workflow card view and workflow quick view. These improvements also include new tabs for "My workflows" (owned by the user), "Shared with me" (shared by other users) and "Published workflows" (publicly accessible workflows).
+
+.. raw:: html
+
+   <iframe width="560" height="315" src="https://youtu.be/YKTiTIBCi1E?si=tRGyurzIMxeAfL9-" title="Galaxy 24.0 - Workflow cards" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+My workflows: card view
+
+.. figure:: images/24.0-wf-cardview.png
+   :alt: Workflow card view.
+
+My workflows: list view
+
+.. figure:: images/24.0-wf-listview.png
+   :alt: Workflow list view.
+
+New select component for selecting a large amount of options
+-----------------------------------------------------------
+
+This new component addresses the need of selecting a very large number of options at once. The component features a list based layout which can be filtered using plain-text or a regular expression. Options can be added individually, in bulk via the filter value, or by first highlighting a range. 
+
+The component is fully keyboard accessible. All methods of selection and highlighting work via keyboard. The options are not selectable individually with tab, but can be scrolled through using the arrow-keys. The hover hint adapts when a keyboard is used. 
+
+The size of the table can be increased to allow for seeing more options at once.The options in the list are limited to 1000 for performance reasons, but this can be temporarily increased in steps of 500, when reaching the end of a list.
+
+.. figure:: images/24.0-selectview.png
+   :alt: Using the new select component.
+
+The component can be chosen when multiple options are available; a local preference for which component to choose can be set. If no preference is set, the component will be used if there are more than 15 options selected, or more than 500 options are available.
+
+.. figure:: images/24.0-selectdropdown.png
+   :alt: Choosing the new select component.
+
+Multiple item drag and drop and keyboard navigation
+-----------------------------------------------------------
+
+This new feature allows users to select multiple history items and drag and drop them into other histories or even tool forms! Users can also navigate their history using the arrow keys; multiple history items can be selected with the <kbd>Shift + ArrowUp/ArrowDown</kbd> key combination. 
+
+Drag and drop:
+
+.. raw:: html
+
+   <iframe width="560" height="315" src="https://youtu.be/CL6AJkSmkf4?si=pV1U404pP4HkTjwt" title="Galaxy 24.0 - Multiselect / drag and drop enhancements" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+Keyboard navigation and selection:
+
+.. raw:: html
+
+   <iframe width="560" height="315" src="https://youtu.be/tzTxmPzl6qU?si=J4Ge1KDinjEwbOcR" title="Galaxy 24.0 - Multiselect / keyboard navigation" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+Resource grids have been consolidated into tab views
+-----------------------------------------------------------
+
+Your histories, visualisations, and pages are now consolidated into an easier to use interface. Switch between your results and published results easily.
+
+.. raw:: html
+
+   <iframe width="560" height="315" src="https://youtu.be/mkwLAYdncRs?si=dmZmM9TmBMIW_dE0" title="Galaxy 24.0 - Resource grids" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+Move datasets between storage locations
+-----------------------------------------------------------
+
+Relocate a dataset to a new object store with ease using this new UI feature! The example below uses an instance with four object stores defined, but only three of them declaring the same "device" ID. Clicking on the dataset information and scrolling to storage details has a "Relocate" option if the dataset is "safe" to relocate and there are valid targets to relocate it to. The UI utilizes the same visual language used for describing attributes of the storage and exposing admin provided details. This example also shows what the buttons look like with quota enabled object stores and object stores without quota enabled.
+
+.. raw:: html
+
+   <iframe width="560" height="315" src="https://youtu.be/uas3zdg-Ea0?si=5GS2tQhWQuIZQfHx" title="Galaxy 24.0 - Moving datasets between storage locations" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+Visualizations
+===========================================================
+
+.. visualizations
+* Fix for fits_image_viewer visualization plugin
+  (thanks to `@francoismg <https://github.com/francoismg>`__).
+  `Pull Request 17002`_
+* Replaces Trackster Grids with Data Dialog, Removes Phyloviz, Circster and Sweepster
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 17415`_
+* Add basic TIFF Image visualization
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 17553`_
+* Enhance Avivator display app to support regular Tiffs
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 17554`_
+* Remove legacy phyloviz, circster and sweepster artifacts
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 17573`_
+
+Datatypes
+===========================================================
+
+.. datatypes
+* Make columns types an empty list for empty tabular data
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 13918`_
+* Python 3.8 as minimum
+  (thanks to `@mr-c <https://github.com/mr-c>`__).
+  `Pull Request 16954`_
+* Add support for (fast5.tar).xz binary compressed files
+  (thanks to `@tuncK <https://github.com/tuncK>`__).
+  `Pull Request 17106`_
+* Fix for converter tests
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 17188`_
+* correct dbkey for minerva display app
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
+  `Pull Request 17196`_
+* Add a3m datatype
+  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
+  `Pull Request 17217`_
+* Add binary datatypes for intermediate output of fastk tools
+  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
+  `Pull Request 17265`_
+* Enable ``warn_unreachable`` mypy option
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 17365`_
+* Fix type annotation of code using XML etree
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 17367`_
+* Update to black 2024 stable style
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 17391`_
+* Allow using tool data bundles as inputs to reference data select parameters
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 17435`_
+* Faster FASTA and FASTQ metadata setting
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 17462`_
+* Feature SBOL datatypes
+  (thanks to `@guillaume-gricourt <https://github.com/guillaume-gricourt>`__).
+  `Pull Request 17482`_
+* Better display of estimated line numbers and add number of columns for tabular
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 17492`_
+* Add magres datatype
+  (thanks to `@martenson <https://github.com/martenson>`__).
+  `Pull Request 17499`_
+* Add npy datatype
+  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
+  `Pull Request 17517`_
+
+Builtin Tool Updates
+===========================================================
+
+.. tools
+* Qiskit in galaxy
+  (thanks to `@thepineapplepirate <https://github.com/thepineapplepirate>`__).
+  `Pull Request 17170`_
+* Hide wig_to_bigWig tool
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 17328`_
+* Update to black 2024 stable style
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 17391`_
+* Update RStudio GxIT to use the reworked 23.1 image
+  (thanks to `@natefoo <https://github.com/natefoo>`__).
+  `Pull Request 17533`_
+
+Release Testing Team
+===========================================================
+
+A special thanks to the release testing team:
+
+* `Ahmed Awan <https://github.com/ahmedhamidawan>`__
+* `Amirhossein Naghsh Nilchi <https://github.com/nilchia>`__
+* `David López <https://github.com/davelopez>`__
+* `Jennifer Hillman-Jackson <https://github.com/jennaj>`__
+* `John Davis <https://github.com/jdavcs>`__
+* `Tyler Collins <https://github.com/tcollins2011>`__
+
+Release Notes
+===========================================================
+
+Please see the :doc:`full release notes <24.0_announce>` for more details.
+
+.. include:: 24.0_prs.rst
+
+.. include:: _thanks.rst