[24.2] Release notes

doc/source/releases/24.2_announce_user.rst

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+
+===========================================================
+24.2 Galaxy Release (January 2025)
+===========================================================
+
+.. include:: _header.rst
+
+Please see the full :doc:`24.2 release notes <24.2_announce>` for more details.
+
+Highlights
+===========================================================
+
+A Wizard-like Export View for Workflow Invocations
+-----------------------------------------------------------
+
+The workflow invocation export process has been enhanced with a new wizard-like interface,
+making it more guided and user-friendly. This interface simplifies complex processes with many
+options, providing a step-by-step approach to exporting workflow invocations.
+
+- **Select export format**. Choose from various formats such as RO Crate, BioCompute Object,
+  or Compressed File.
+- **Choose export destination**. Options include temporary direct download, remote file source,
+  or RDM repository.
+- **Export**! Finalize and complete the export process with ease.
+
+This new interface aims to improve the user experience and may be extended to other complex
+processes in Galaxy in the future.
+[`#18796 <https://github.com/galaxyproject/galaxy/pull/18796>`__]
+
+.. figure:: images/24.2-export-invocation-wizard.gif
+   :alt: Export invocation wizard.
+
+Workflow Editor Enhancements: Activity Bar and Undo Stack UI
+-----------------------------------------------------------
+
+The Activity Bar is now present in the Workflow Editor along side multiple interface
+improvements.
+[`#18729 <https://github.com/galaxyproject/galaxy/pull/18729>`__]
+[`#18548 <https://github.com/galaxyproject/galaxy/pull/18548>`__]
+
+- **No more double side bars**. Inspecting a step now has it's own floating window,
+  which can be easily expanded and remembers it's size. All other features were moved to the
+  left side-bar.
+- **Undo redo UI**. A new interactive way of viewing recent changes. Click a change to scroll
+  backwards and forwards in time.
+- **Layout anything with ease**. The auto-layout feature was moved to the Editor Tool Bar. It
+  now aligns to the grid, untangles connections, and sorts Workflow Comments along with steps.
+- **Find your workflows**. Workflows now have their own dedicated interface, from which you can
+  find, copy into, and inserts Sub-Workflows into your Workflow.
+- **Inputs** are not tools, and are now no longer treated as such. Find inputs in their own
+  interface, and easily add input sub-types directly.
+
+.. raw:: html
+
+   <iframe width="560" height="315" src="https://www.youtube.com/embed/42HZQkC7PHY" title="Galaxy 24.2 - Workflow Editor Enhancements: Activity Bar and Undo Stack UI" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+Masthead Revision and Activity Bar Improvements
+-----------------------------------------------------------
+
+The Galaxy masthead has been revised to achieve consistency and reduce redundancy, aligning its
+functionality with the Activity Bar.
+
+- **New "More" activity**. Hidden and less frequently used activities are now accessible through
+  a new "More" activity, allowing users to add or remove items from the activity bar and navigate
+  directly to any activity.
+- **Username visible in masthead**. The username is now visible in the masthead, with user
+  preferences and logout options accessible through the user dropdown.
+- **A compact masthead**. The masthead has been streamlined, removing redundant links and only
+  displaying essential items such as storage and the username on the right end.
+
+These changes enhance the user experience by making the interface more intuitive and reducing
+clutter.
+[`#17927 <https://github.com/galaxyproject/galaxy/pull/17927>`__]
+
+.. raw:: html
+
+   <iframe width="560" height="315" src="https://www.youtube.com/embed/5NMkcpj-1w8" title="Galaxy 24.2 - Masthead Revision and Activity Bar Improvements" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+Improved Navigation and Usability of Collection Builders
+-----------------------------------------------------------
+
+To guide users towards creating collections of the correct type, Galaxy now provides
+better navigation via buttons directly on data collection parameters. Users can create a
+collection with the required structure for the input, with pre-filtered items from their
+current history, also ensuring compatibility with required file extensions. Additionally, users
+can upload datasets directly to the collection builder. These updates will improve the user
+experience of opening a workflow run form, creating appropriate collection(s) for its inputs
+and running the workflow in one seamless iteration.
+[`#18857 <https://github.com/galaxyproject/galaxy/pull/18857>`__]
+
+.. raw:: html
+
+   <iframe width="560" height="315" src="https://www.youtube.com/embed/y4gNThU_BZE" title="Galaxy 24.2 - Improved Navigation and Usability of Collection Builders" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+Enhanced Workflow Invocation View
+-----------------------------------------------------------
+
+The Workflow Invocation View, introduced in the `previous release <24.1_announce_user.html>`__
+has been significantly refined to improve the usability and visualization of workflow runs.
+[`#18615 <https://github.com/galaxyproject/galaxy/pull/18615>`__]
+
+Updates include:
+
+- **Workflow steps moved to a separate tab**, allocating maximum space for the graph.
+- **Progress bars relocated to the header** for a cleaner layout.
+- **Workflow inputs displayed directly on the graph**, eliminating the need for clicking
+  and investigating each input.
+- **The Invocations panel also toggles out on mouse leave**, providing an uncluttered view when
+  exploring runs.
+
+.. list-table::
+   :header-rows: 1
+
+   * - Before
+     - After
+   * - .. image:: images/24.2-invocation-view-improvements-before.png
+          :alt: Invocation view improvements before
+          :width: 100%
+     - .. image:: images/24.2-invocation-view-improvements-after.png
+          :alt: Invocation view improvements after
+          :width: 100%
+   * - Steps show on the right, the progress bars are within the `Overview` tab
+     - Only the currently active step shows below, leaving full width for graph, progress
+       bars in the Header
+
+Display Metrics for Workflow Invocations
+-----------------------------------------------------------
+
+Galaxy now provides a Metrics tab in the Workflow Invocation View, allowing users to quickly
+summarize runtime, memory usage, and core allocation per invocation. This enhancement helps users
+better understand the resource usage of their workflows. The Metrics tab displays runtime in
+seconds and core allocation for each step and tool in the workflow.
+[`#19048 <https://github.com/galaxyproject/galaxy/pull/19048>`__]
+
+.. figure:: images/24.2-workflow-invocation-metrics.png
+   :alt: Metrics tab in the Workflow Invocation View.
+
+Libraries Modernization: Directory Dataset Picker
+-----------------------------------------------------------
+
+The dataset picker for user and import directories has been modernized, providing a more
+intuitive and user-friendly interface. Users can now easily import files or folders from their
+user directory or import directory into a library. Admins can also import datasets from a
+specified path. Additionally, the new History Dataset Picker allows users to explore their
+histories and select datasets to add to the library, streamlining the dataset management process.
+[`#18638 <https://github.com/galaxyproject/galaxy/pull/18638>`__]
+
+.. raw:: html
+
+   <iframe width="560" height="315" src="https://www.youtube.com/embed/i8AHdv5sU5A" title="Galaxy 24.2 - Libraries Modernization: Directory Dataset Picker" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+Live Reporting of Job Console Outputs
+-----------------------------------------------------------
+
+If enabled by the Galaxy administrators, it will now be possible to view live console output
+for running jobs. The job output will be available on the Job Information page where these
+logs have always been available for completed jobs. The job information view has also been
+updated with scrollable code blocks, a more intuitive expand/collapse feature,
+and an auto-scroll function for seamless log viewing. This should allow you to debug issues with
+running jobs faster and track the progress of running jobs in realtime in a way that has never
+been an option in Galaxy. A huge thanks to Gregory Cage at Oak Ridge National Laboratory for
+this valuable contribution!
+[`#16975 <https://github.com/galaxyproject/galaxy/pull/16975>`__]
+
+Visualizations
+===========================================================
+
+.. visualizations
+* Update visualizations package versions
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19232`_
+* Fix MSA viz, new dependency specification options
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 18760`_
+* Parse stored config details to script-based visualizations
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 18651`_
+* Install npm-package viz to the package prefix explicitly
+  (thanks to `@dannon <https://github.com/dannon>`__).
+  `Pull Request 18950`_
+* Migrate NGL viewer to npm package
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 18946`_
+* Support deferred datasets in visualizations
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 19097`_
+* Openlayer update to npm package
+  (thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
+  `Pull Request 19134`_
+* Replace static Cytoscape plugin with npm package
+  (thanks to `@itisAliRH <https://github.com/itisAliRH>`__).
+  `Pull Request 19127`_
+* Update tiff viewer to use script entry_point
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19151`_
+* Migrate Venn Diagram to Script-Tag
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19153`_
+* FITS file table graph visualization plugin
+  (thanks to `@francoismg <https://github.com/francoismg>`__).
+  `Pull Request 19003`_
+* Restore access to saved visualizations
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19136`_
+* Remove OpenLayers legacy files and add SVG logo
+  (thanks to `@guerler <https://github.com/guerler>`__).
+  `Pull Request 19135`_
+
+Datatypes
+===========================================================
+
+.. datatypes
+* Add pod5 datatype
+  (thanks to `@TomHarrop <https://github.com/TomHarrop>`__).
+  `Pull Request 18419`_
+* Handle compressed content in dataset preview for all sequence classes
+  (thanks to `@PlushZ <https://github.com/PlushZ>`__).
+  `Pull Request 18776`_
+* Type annotations and fixes
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18911`_
+* Improve usability of Directory datatype
+  (thanks to `@wm75 <https://github.com/wm75>`__).
+  `Pull Request 17614`_
+* Add some Zarr-based datatypes
+  (thanks to `@davelopez <https://github.com/davelopez>`__).
+  `Pull Request 19040`_
+* Add XML based `vtk` datatype
+  (thanks to `@tStehling <https://github.com/tStehling>`__).
+  `Pull Request 19104`_
+* Add gtf to auto_compressed_types
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 19175`_
+
+Builtin Tool Updates
+===========================================================
+
+.. tools
+* Drop "Send to cloud" tool and associated cloudauthz code
+  (thanks to `@jdavcs <https://github.com/jdavcs>`__).
+  `Pull Request 18196`_
+* Update GPU JupyterLab tool
+  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
+  `Pull Request 18220`_
+* Improvements to Tool Test Parsing
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18560`_
+* Add Tool-Centric APIs to the Tool Shed 2.0
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18524`_
+* Add BlobToolkit to the list of interactive tools
+  (thanks to `@Delphine-L <https://github.com/Delphine-L>`__).
+  `Pull Request 18630`_
+* Enable ``ignore-without-code`` mypy error code
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18898`_
+* Remove some unused dynamic drill down options
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18892`_
+* Fix commas that shouldn't be in biotools_mappings.tsv
+  (thanks to `@jmchilton <https://github.com/jmchilton>`__).
+  `Pull Request 18919`_
+* Add filter null collection operation tool
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 18928`_
+* Remove outdated fimo wrapper and galaxy-sequence-utils dependency
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 18937`_
+* Jupyter Interactive Tool 1.0.1/24.07
+  (thanks to `@natefoo <https://github.com/natefoo>`__).
+  `Pull Request 18861`_
+* Add Interactive Tool Ilastik
+  (thanks to `@lldelisle <https://github.com/lldelisle>`__).
+  `Pull Request 16837`_
+
+Please see the full :doc:`24.2 release notes <24.2_announce>` for more details.
+
+.. include:: 24.2_prs.rst
+
+----
+
+.. include:: _thanks.rst