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Reformat
Fix wording
Drop irrelevant PRs from user-facing notes
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@jdavcs
jdavcs committed Jan 11, 2024
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84 changes: 42 additions & 42 deletions doc/source/releases/23.2.rst
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Expand Up @@ -29,7 +29,7 @@ Enhancements
* Add Invenio RDM repository integration
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 16381`_
* add new tabular file formats cns,cnr and cnn to datatypes_conf.xml.sample file as they are neaded for cnvkit galaxy tools
* Add new cns, cnr and cnn datatypes (cnvkit tools)
(thanks to `@khaled196 <https://github.com/khaled196>`__).
`Pull Request 16503`_
* Create reusable `FilterMenu` with advanced options
Expand Down Expand Up @@ -73,19 +73,19 @@ Enhancements
.. enhancement_tag_datatypes
* implement display function for all datatypes
* Implement display function for all datatypes
(thanks to `@SergeyYakubov <https://github.com/SergeyYakubov>`__).
`Pull Request 15447`_
* Add new datatype: STL
* Add stl datatype
(thanks to `@TanguyGen <https://github.com/TanguyGen>`__).
`Pull Request 16478`_
* Bump samtools converters
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 16668`_
* Update datatypes_conf.xml.sample with docx type
* Add docx datatype
(thanks to `@yvanlebras <https://github.com/yvanlebras>`__).
`Pull Request 16713`_
* optimize object store cache operations
* Optimize object store cache operations
(thanks to `@SergeyYakubov <https://github.com/SergeyYakubov>`__).
`Pull Request 17025`_
.. enhancement_tag_tools
Expand Down Expand Up @@ -135,7 +135,7 @@ Enhancements
`Pull Request 16345`_
.. enhancement_tag_jobs
* Towards SQLAlchemy 2.0 (upgrades to SA Core usage)
* Towards SQLAlchemy 2.0 (upgrades to SQLAlchemy Core usage)
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 16264`_
* Add HEAD route to job_files endpoint
Expand Down Expand Up @@ -172,7 +172,7 @@ Enhancements
* Add Python string formatting best practices
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 16312`_
* Migrate a part of the users API to Fast API
* Migrate a part of the users API to FastAPI
(thanks to `@heisner-tillman <https://github.com/heisner-tillman>`__).
`Pull Request 16341`_
* Update Python dependencies
Expand All @@ -184,7 +184,7 @@ Enhancements
* Update Python dependencies
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
`Pull Request 16389`_
* Update carbon emissions methodology page to match current feature spe…
* Update carbon emissions methodology page to match current feature specifications
(thanks to `@Renni771 <https://github.com/Renni771>`__).
`Pull Request 16392`_
* Update Python dependencies
Expand All @@ -202,7 +202,7 @@ Enhancements
* Add support for CILogon deployments in different regions than the US
(thanks to `@uwwint <https://github.com/uwwint>`__).
`Pull Request 16490`_
* Published Workflow Sharing Page Overhaul
* Published Workflow Sharing page overhaul
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
`Pull Request 16510`_
* Update Python dependencies
Expand Down Expand Up @@ -253,7 +253,7 @@ Enhancements
* Change Sentry error reporting plug-in
(thanks to `@kysrpex <https://github.com/kysrpex>`__).
`Pull Request 16686`_
* Use fs.onedatarestfs for Onedata files source plugin implementation
* Use fs.onedatarestfs for Onedata files source plugin implementation
(thanks to `@lopiola <https://github.com/lopiola>`__).
`Pull Request 16690`_
* Skip node installation for ``check_indexes`` tests
Expand All @@ -274,13 +274,13 @@ Enhancements
* Selective bold text
(thanks to `@hujambo-dunia <https://github.com/hujambo-dunia>`__).
`Pull Request 16748`_
* WF Report Enhancement: Adding Time Format to Time the Workflow Report was Generated
* Workflow report enhancement: add time format to generated text
(thanks to `@assuntad23 <https://github.com/assuntad23>`__).
`Pull Request 16757`_
* WF Report Enhancement: Converting ISO to UTC for Invocation Date/Time
* Workflow report enhancement: convert ISO to UTC for invocation date/time
(thanks to `@assuntad23 <https://github.com/assuntad23>`__).
`Pull Request 16758`_
* WF Report Enhancement: Exposing Workflow Version as Workflow Checkpoint
* Workflow report enhancement: expose workflow version as workflow checkpoint
(thanks to `@assuntad23 <https://github.com/assuntad23>`__).
`Pull Request 16760`_
* Replace ELIXIR AAI button with Life Science login
Expand All @@ -289,7 +289,7 @@ Enhancements
* Update Python dependencies
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
`Pull Request 16770`_
* Add ClientSearchMiss Sentry Capture
* Add ClientSearchMiss Sentry capture
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 16789`_
* Update Python dependencies
Expand All @@ -304,7 +304,7 @@ Enhancements
* Allow partial matches in workflow name tag search and search all tags for unquoted query
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
`Pull Request 16860`_
* Vueify Visualizations Grid
* Vueify visualizations grid
(thanks to `@guerler <https://github.com/guerler>`__).
`Pull Request 16892`_
* Update Python dependencies
Expand All @@ -316,7 +316,7 @@ Enhancements
* Test link data with extended metadata
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16921`_
* Publish tool shed frontend to npm
* Publish Tool Shed frontend to npm
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 16924`_
* Update Python dependencies
Expand All @@ -343,13 +343,13 @@ Enhancements
* Update Python dependencies
(thanks to `@galaxybot <https://github.com/galaxybot>`__).
`Pull Request 17011`_
* Restyle Vue Multiselect and Adapt Option Order
* Restyle Vue multiselect and adapt option order
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
`Pull Request 17015`_
* Show current tool panel view name on top of tool panel
(thanks to `@ahmedhamidawan <https://github.com/ahmedhamidawan>`__).
`Pull Request 17021`_
* Change Broadcast Notifications Style
* Change broadcast notifications style
(thanks to `@ElectronicBlueberry <https://github.com/ElectronicBlueberry>`__).
`Pull Request 17032`_
* Open `HistoryStorageOverview` in center panel from `HistoryPanel`
Expand All @@ -361,18 +361,18 @@ Enhancements
* Enhance xsd schema and allow simpler assertion lists
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 17134`_
* Disable Workflow Report and Generate PDF buttons unless workflow is successful
* Disable workflow report and generate PDF buttons unless workflow is successful
(thanks to `@assuntad23 <https://github.com/assuntad23>`__).
`Pull Request 17149`_
* Add rerun and show details buttons in expanded collection
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 17182`_
.. small_enhancement
* Toolshed client build separation
* Tool Shed client build separation
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 15000`_
* Migrate cloud API to Fast API
* Migrate cloud API to FastAPI
(thanks to `@heisner-tillman <https://github.com/heisner-tillman>`__).
`Pull Request 16296`_
* Drop (admin only) userskeys controller
Expand All @@ -390,7 +390,7 @@ Enhancements
* Refactor FilesDialog + Remote Files API schema improvements
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 16420`_
* Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test)
* Towards SQLAlchemy 2.0 (upgrades to SQLAlchemy ORM usage in /test)
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 16431`_
* SQLAlchemy 2.0 upgrades to ORM usage in /lib
Expand Down Expand Up @@ -450,22 +450,22 @@ Enhancements
* Optimize iteration in DatasetInstance model + SA2.0 fix
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 16776`_
* Migrate a part of the jobs API to Fast API
* Migrate a part of the jobs API to FastAPI
(thanks to `@heisner-tillman <https://github.com/heisner-tillman>`__).
`Pull Request 16778`_
* Replace file_name property with get_file_name function
(thanks to `@SergeyYakubov <https://github.com/SergeyYakubov>`__).
`Pull Request 16783`_
* SA2.0 fixes for TS2.0
* SQLAlchemy 2.0 fixes for TS2.0
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 16791`_
* Another batch of SA2.0 edits in TS 2.0
* Another batch of SQLAlchemy 2.0 edits in TS 2.0
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 16799`_
* Use vue modal instead of global backbone modal in user preferences
(thanks to `@guerler <https://github.com/guerler>`__).
`Pull Request 16830`_
* Another batch of SA2.0 edits in TS2.0 (part 3)
* Another batch of SQLAlchemy 2.0 edits in TS 2.0 (part 3)
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 16833`_
* Remove remaining legacy backbone form input elements
Expand Down Expand Up @@ -537,16 +537,16 @@ Fixes
`Pull Request 16593`_
.. bug_tag_datatypes
* MINERVA display application: enable cors, add for tabular
* MINERVA display application: enable cors, add for tabular datasets
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 16737`_
* prep for updated h5py and typos
* Prep for updated h5py
(thanks to `@mr-c <https://github.com/mr-c>`__).
`Pull Request 16963`_
* Update tar_to_directory dependency
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 17009`_
* Fix Display Application link generation
* Fix display application link generation
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 17227`_
* Display application fixes and tests
Expand All @@ -557,7 +557,7 @@ Fixes
* Add missing requirements to perl tools
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16763`_
* chore: fix typos
* Fix typos across code base
(thanks to `@afuetterer <https://github.com/afuetterer>`__).
`Pull Request 16851`_
* Fix missing grep input in sort1 tool
Expand Down Expand Up @@ -624,12 +624,12 @@ Fixes
* Upgrade axios to 1.6.2
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 17053`_
* Ensure that plugin build hash actually has a git hash to compare with…
* Ensure that plugin build hash actually has a git hash to compare with otherwise force rebuild
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 17104`_
.. bug_tag_jobs
* Ensure Job belongs to current SA session
* Ensure Job belongs to current SQLAlchemy session
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 16647`_
* Fix and prevent persisting null file_size
Expand Down Expand Up @@ -669,10 +669,10 @@ Fixes
* Disable verbose parso logging in db_shell.py
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16410`_
* Fix SA2.0 syntax in scripts/helper.py, fix ancient bug
* Fix SQLAlchemy 2.0 syntax in scripts/helper.py, fix ancient bug
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 16425`_
* pin fs.dropboxfs to >=1
* Pin fs.dropboxfs to >=1
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 16451`_
* Fix labeler for UI UX labels
Expand Down Expand Up @@ -726,13 +726,13 @@ Fixes
* Fix public archived histories not importable
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 16766`_
* provide specific example for API docs - tags
* Provide specific example for API docs - tags
(thanks to `@martenson <https://github.com/martenson>`__).
`Pull Request 16769`_
* Fix ItemOwnerShipException in tag removal
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16773`_
* Initial bug fixes for tool shed 2
* Initial bug fixes for Tool Shed 2.0
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 16787`_
* Fix short ids in tool panel views.
Expand All @@ -741,10 +741,10 @@ Fixes
* Use AlignedSegment.to_string
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16803`_
* move the email and username redacting from the role loop
* Move the email and username redacting from the role loop
(thanks to `@martenson <https://github.com/martenson>`__).
`Pull Request 16805`_
* move history and tool panel tooltips out of the way
* Move history and tool panel tooltips out of the way
(thanks to `@martenson <https://github.com/martenson>`__).
`Pull Request 16808`_
* Fix tool panel views for versionless tool ids
Expand Down Expand Up @@ -789,19 +789,19 @@ Fixes
* Fix bug in SQLAlchemy statement
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 16881`_
* Fix bug in SA statement: desc() applied to column, not statement
* Fix bug in SQLAlchemy statement: desc() applied to column, not statement
(thanks to `@jdavcs <https://github.com/jdavcs>`__).
`Pull Request 16887`_
* Update help in relabel_from_file.xml
(thanks to `@lldelisle <https://github.com/lldelisle>`__).
`Pull Request 16891`_
* Fix link to mercurial tip in tool shed 2.0
* Fix link to mercurial tip in Tool Shed 2.0
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 16895`_
* Fix type annotation of ``lib/tool_shed/test/functional/``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 16901`_
* Fix navigation error in tool shed tests
* Fix navigation error in Tool Shed tests
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 16902`_
* Fix subtle bug in listify function + simplify list munging
Expand All @@ -813,7 +813,7 @@ Fixes
* Fix selenium selector for Workflow Run warnings
(thanks to `@davelopez <https://github.com/davelopez>`__).
`Pull Request 16908`_
* Fix GQL infinite scrolling in tool shed
* Fix GQL infinite scrolling in Tool Shed
(thanks to `@jmchilton <https://github.com/jmchilton>`__).
`Pull Request 16914`_
* Fix library import from path linking files
Expand Down
25 changes: 8 additions & 17 deletions doc/source/releases/23.2_announce_user.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -24,17 +24,17 @@ Feature3
Feature description.


New Datatypes
Datatypes
===========================================================

.. datatypes
* implement display function for all datatypes
* Implement display function for all datatypes
(thanks to `@SergeyYakubov <https://github.com/SergeyYakubov>`__).
`Pull Request 15447`_
* Add new datatype: STL
* Add stl datatype
(thanks to `@TanguyGen <https://github.com/TanguyGen>`__).
`Pull Request 16478`_
* add new tabular file formats cns,cnr and cnn to datatypes_conf.xml.sample file as they are neaded for cnvkit galaxy tools
* Add new cns, cnr and cnn datatypes (cnvkit tools)
(thanks to `@khaled196 <https://github.com/khaled196>`__).
`Pull Request 16503`_
* Support new genome browser chain file format
Expand All @@ -43,30 +43,24 @@ New Datatypes
* Bump samtools converters
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 16668`_
* Update datatypes_conf.xml.sample with docx type
* Add docx datatype
(thanks to `@yvanlebras <https://github.com/yvanlebras>`__).
`Pull Request 16713`_
* MINERVA display application: enable cors, add for tabular
* MINERVA display application: enable cors, add for tabular datasets
(thanks to `@hexylena <https://github.com/hexylena>`__).
`Pull Request 16737`_
* prep for updated h5py and typos
* Prep for updated h5py
(thanks to `@mr-c <https://github.com/mr-c>`__).
`Pull Request 16963`_
* Minor clarification/typo fix in datatypes.data
(thanks to `@dannon <https://github.com/dannon>`__).
`Pull Request 16993`_
* Update tar_to_directory dependency
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 17009`_
* optimize object store cache operations
* Optimize object store cache operations
(thanks to `@SergeyYakubov <https://github.com/SergeyYakubov>`__).
`Pull Request 17025`_
* Add support for larch datatypes
(thanks to `@patrick-austin <https://github.com/patrick-austin>`__).
`Pull Request 17080`_
* Fix `.file_name` access in merge forward
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 17097`_
* Fix Display Application link generation
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 17227`_
Expand Down Expand Up @@ -94,9 +88,6 @@ Builtin Tool Updates
Podman job_conf
(thanks to `@sveinugu <https://github.com/sveinugu>`__).
`Pull Request 16795`_
* chore: fix typos
(thanks to `@afuetterer <https://github.com/afuetterer>`__).
`Pull Request 16851`_
* Fix missing grep input in sort1 tool
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 16910`_
Expand Down

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