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starting user facing notes
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@@ -8,32 +8,81 @@ January 2021 Galaxy Release (v 21.01)
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Highlights
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===========================================================
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**Feature1**
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Feature description.
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* Galaxy Markdown enhancements including integration of visualizations - allow embedding
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visualizations in Galaxy Markdown (workflow invocation reports and pages) with
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Markdown editor support and allow exporting workflow reports directly to Galaxy Pages.
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`Pull Request 10241`_, `Pull Request 10288`_, `Pull Request 10404`_
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**Feature2**
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Feature description.
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* History panel rewrite (available in the UI as a beta option).
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`Pull Request 8441`_, `Pull Request 11071`_, `Pull Request 10971`_
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* Allow organizing the panel via EDAM ontology annotations.
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(thanks to `@hexylena <https://github.com/hexylena>`__).
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`Pull Request 10592`_
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* Large overhaul over history import and export - including improved user experience, APIs, and allowing importing and exporting
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to file sources plugins (including FTP).
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`Pull Request 11054`_, `Pull Request 10993`_
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* Various substantial improvements to data library user interface and performance
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(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
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`Pull Request 10204`_, `Pull Request 11099`_,
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`Pull Request 10557`_, `Pull Request 10558`_,
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`Pull Request 10807`_
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* UI & API for Supporting Best Practice Workflows
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`Pull Request 10988`_, `Pull Request 11025`_
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* Add author and license metadata and corresponding web microdata annotations for tools
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and workflows.
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`Pull Request 10408`_
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* Implement edit & upgrade subworkflow buttons in workflow editor.
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`Pull Request 11032`_
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* Allow the "Apply Rules" tool to attach tags to output datasets.
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`Pull Request 10382`_
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* Add S3 plugin for remote files browser.
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`Pull Request 10523`_
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* Support stopping Interactive Tools without deleting their outputs
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`Pull Request 10497`_
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* Allow InteractiveTools to use path-based proxying when ``requires_domain=False``.
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`Pull Request 8596`_
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* Auto-focus upload name in upload dialog.
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`Pull Request 10487`_
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* Add update time to workflow version selector in workflow editor.
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`Pull Request 10492`_
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* Use dataset selector in rules input dialog.
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`Pull Request 10505`_
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* Make primary extract workflow action button more visible
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(thanks to `@hexylena <https://github.com/hexylena>`__).
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`Pull Request 10583`_
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* Revision of sharing component, adds url copy to clipboard feature
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`Pull Request 10754`_
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* Persist scroll/url information for GTN webhook
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(thanks to `@hexylena <https://github.com/hexylena>`__).
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`Pull Request 11290`_
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**Feature3**
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Feature description.
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New Visualizations
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===========================================================
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.. visualizations
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* hide purged datasets from visualizations
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(thanks to `@OlegZharkov <https://github.com/OlegZharkov>`__).
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`Pull Request 10483`_
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* Integrate NORA's image viewer - a medical image viewer and annotation tool.
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(thanks to `@bgruening <https://github.com/bgruening>`__).
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`Pull Request 11035`_
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* Add the OpenSeadragon viewer for deep zoom images
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(thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
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`Pull Request 10756`_
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* Fix reference error
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(thanks to `@tmcgowan <https://github.com/tmcgowan>`__).
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`Pull Request 10782`_
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* Expand image formats for viewing in OpenSeadragon
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(thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
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`Pull Request 11017`_
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New Datatypes
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===========================================================
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@@ -42,34 +91,15 @@ New Datatypes
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* initial commit for gfa2
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(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
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`Pull Request 10270`_
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* Datatypes refactoring
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(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
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`Pull Request 10279`_
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* Drop unnecessary list casting in Anndata datatype
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`Pull Request 10296`_
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* add ome.tiff datatype
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(thanks to `@qiagu <https://github.com/qiagu>`__).
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`Pull Request 10349`_
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* Add support for the dzi (Deep Zoom Image) data format
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(thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
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`Pull Request 10546`_
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* GTF Sniffer Fix
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(thanks to `@mtekman <https://github.com/mtekman>`__).
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`Pull Request 10588`_
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* Add datatype converters for various MD filetypes
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(thanks to `@simonbray <https://github.com/simonbray>`__).
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`Pull Request 10757`_
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* AnnData Peek Fix
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(thanks to `@mtekman <https://github.com/mtekman>`__).
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`Pull Request 10986`_
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* remove mutatable arguments from function calls
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(thanks to `@bgruening <https://github.com/bgruening>`__).
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`Pull Request 10998`_
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* More mutable fixes
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(thanks to `@bgruening <https://github.com/bgruening>`__).
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`Pull Request 11003`_
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* mypy type checking for more Galaxy packages
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`Pull Request 11009`_
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* Add nifti1 and nifti2 datatype
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(thanks to `@bgruening <https://github.com/bgruening>`__).
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`Pull Request 11020`_
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@@ -84,8 +114,6 @@ New Datatypes
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* Add minimal `msf` datatype
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(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
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`Pull Request 11084`_
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* Allow setting filename_pattern by client
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`Pull Request 11108`_
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Builtin Tool Updates
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===========================================================
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@@ -93,22 +121,6 @@ Builtin Tool Updates
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.. tools
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* Allow the Apply Rules tool to attach tags to output datasets.
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`Pull Request 10382`_
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* EDAM tool panel
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(thanks to `@hexylena <https://github.com/hexylena>`__).
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`Pull Request 10592`_
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* Enhancements for galaxy-tool-test script.
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`Pull Request 10620`_
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* Speedup xml replacement
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`Pull Request 10804`_
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* Disable tool cache if there is a problem
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`Pull Request 10808`_
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* Update askomics IT to 4.1.1
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(thanks to `@abretaud <https://github.com/abretaud>`__).
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`Pull Request 10878`_
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* Use "email_from" value from schema for tool error report email
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`Pull Request 10956`_
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* Put new toolshed tools in existing tool panel sections if the ID matches
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`Pull Request 10984`_
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* allow empty file uploads
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(thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
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`Pull Request 11079`_
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