diff --git a/doc/source/releases/23.2.rst b/doc/source/releases/23.2.rst index bdd93656ab17..f41241e07df2 100644 --- a/doc/source/releases/23.2.rst +++ b/doc/source/releases/23.2.rst @@ -29,7 +29,7 @@ Enhancements * Add Invenio RDM repository integration (thanks to `@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 `__). `Pull Request 16503`_ * Create reusable `FilterMenu` with advanced options @@ -73,19 +73,19 @@ Enhancements .. enhancement_tag_datatypes -* implement display function for all datatypes +* Implement display function for all datatypes (thanks to `@SergeyYakubov `__). `Pull Request 15447`_ -* Add new datatype: STL +* Add stl datatype (thanks to `@TanguyGen `__). `Pull Request 16478`_ * Bump samtools converters (thanks to `@bernt-matthias `__). `Pull Request 16668`_ -* Update datatypes_conf.xml.sample with docx type +* Add docx datatype (thanks to `@yvanlebras `__). `Pull Request 16713`_ -* optimize object store cache operations +* Optimize object store cache operations (thanks to `@SergeyYakubov `__). `Pull Request 17025`_ .. enhancement_tag_tools @@ -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 `__). `Pull Request 16264`_ * Add HEAD route to job_files endpoint @@ -172,7 +172,7 @@ Enhancements * Add Python string formatting best practices (thanks to `@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 `__). `Pull Request 16341`_ * Update Python dependencies @@ -184,7 +184,7 @@ Enhancements * Update Python dependencies (thanks to `@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 `__). `Pull Request 16392`_ * Update Python dependencies @@ -202,7 +202,7 @@ Enhancements * Add support for CILogon deployments in different regions than the US (thanks to `@uwwint `__). `Pull Request 16490`_ -* Published Workflow Sharing Page Overhaul +* Published Workflow Sharing page overhaul (thanks to `@ElectronicBlueberry `__). `Pull Request 16510`_ * Update Python dependencies @@ -253,7 +253,7 @@ Enhancements * Change Sentry error reporting plug-in (thanks to `@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 `__). `Pull Request 16690`_ * Skip node installation for ``check_indexes`` tests @@ -274,13 +274,13 @@ Enhancements * Selective bold text (thanks to `@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 `__). `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 `__). `Pull Request 16758`_ -* WF Report Enhancement: Exposing Workflow Version as Workflow Checkpoint +* Workflow report enhancement: expose workflow version as workflow checkpoint (thanks to `@assuntad23 `__). `Pull Request 16760`_ * Replace ELIXIR AAI button with Life Science login @@ -289,7 +289,7 @@ Enhancements * Update Python dependencies (thanks to `@galaxybot `__). `Pull Request 16770`_ -* Add ClientSearchMiss Sentry Capture +* Add ClientSearchMiss Sentry capture (thanks to `@dannon `__). `Pull Request 16789`_ * Update Python dependencies @@ -304,7 +304,7 @@ Enhancements * Allow partial matches in workflow name tag search and search all tags for unquoted query (thanks to `@ahmedhamidawan `__). `Pull Request 16860`_ -* Vueify Visualizations Grid +* Vueify visualizations grid (thanks to `@guerler `__). `Pull Request 16892`_ * Update Python dependencies @@ -316,7 +316,7 @@ Enhancements * Test link data with extended metadata (thanks to `@mvdbeek `__). `Pull Request 16921`_ -* Publish tool shed frontend to npm +* Publish Tool Shed frontend to npm (thanks to `@jmchilton `__). `Pull Request 16924`_ * Update Python dependencies @@ -343,13 +343,13 @@ Enhancements * Update Python dependencies (thanks to `@galaxybot `__). `Pull Request 17011`_ -* Restyle Vue Multiselect and Adapt Option Order +* Restyle Vue multiselect and adapt option order (thanks to `@ElectronicBlueberry `__). `Pull Request 17015`_ * Show current tool panel view name on top of tool panel (thanks to `@ahmedhamidawan `__). `Pull Request 17021`_ -* Change Broadcast Notifications Style +* Change broadcast notifications style (thanks to `@ElectronicBlueberry `__). `Pull Request 17032`_ * Open `HistoryStorageOverview` in center panel from `HistoryPanel` @@ -361,7 +361,7 @@ Enhancements * Enhance xsd schema and allow simpler assertion lists (thanks to `@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 `__). `Pull Request 17149`_ * Add rerun and show details buttons in expanded collection @@ -369,10 +369,10 @@ Enhancements `Pull Request 17182`_ .. small_enhancement -* Toolshed client build separation +* Tool Shed client build separation (thanks to `@dannon `__). `Pull Request 15000`_ -* Migrate cloud API to Fast API +* Migrate cloud API to FastAPI (thanks to `@heisner-tillman `__). `Pull Request 16296`_ * Drop (admin only) userskeys controller @@ -390,7 +390,7 @@ Enhancements * Refactor FilesDialog + Remote Files API schema improvements (thanks to `@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 `__). `Pull Request 16431`_ * SQLAlchemy 2.0 upgrades to ORM usage in /lib @@ -450,22 +450,22 @@ Enhancements * Optimize iteration in DatasetInstance model + SA2.0 fix (thanks to `@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 `__). `Pull Request 16778`_ * Replace file_name property with get_file_name function (thanks to `@SergeyYakubov `__). `Pull Request 16783`_ -* SA2.0 fixes for TS2.0 +* SQLAlchemy 2.0 fixes for TS2.0 (thanks to `@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 `__). `Pull Request 16799`_ * Use vue modal instead of global backbone modal in user preferences (thanks to `@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 `__). `Pull Request 16833`_ * Remove remaining legacy backbone form input elements @@ -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 `__). `Pull Request 16737`_ -* prep for updated h5py and typos +* Prep for updated h5py (thanks to `@mr-c `__). `Pull Request 16963`_ * Update tar_to_directory dependency (thanks to `@mvdbeek `__). `Pull Request 17009`_ -* Fix Display Application link generation +* Fix display application link generation (thanks to `@mvdbeek `__). `Pull Request 17227`_ * Display application fixes and tests @@ -557,7 +557,7 @@ Fixes * Add missing requirements to perl tools (thanks to `@mvdbeek `__). `Pull Request 16763`_ -* chore: fix typos +* Fix typos across code base (thanks to `@afuetterer `__). `Pull Request 16851`_ * Fix missing grep input in sort1 tool @@ -624,12 +624,12 @@ Fixes * Upgrade axios to 1.6.2 (thanks to `@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 `__). `Pull Request 17104`_ .. bug_tag_jobs -* Ensure Job belongs to current SA session +* Ensure Job belongs to current SQLAlchemy session (thanks to `@jdavcs `__). `Pull Request 16647`_ * Fix and prevent persisting null file_size @@ -669,10 +669,10 @@ Fixes * Disable verbose parso logging in db_shell.py (thanks to `@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 `__). `Pull Request 16425`_ -* pin fs.dropboxfs to >=1 +* Pin fs.dropboxfs to >=1 (thanks to `@bernt-matthias `__). `Pull Request 16451`_ * Fix labeler for UI UX labels @@ -726,13 +726,13 @@ Fixes * Fix public archived histories not importable (thanks to `@davelopez `__). `Pull Request 16766`_ -* provide specific example for API docs - tags +* Provide specific example for API docs - tags (thanks to `@martenson `__). `Pull Request 16769`_ * Fix ItemOwnerShipException in tag removal (thanks to `@mvdbeek `__). `Pull Request 16773`_ -* Initial bug fixes for tool shed 2 +* Initial bug fixes for Tool Shed 2.0 (thanks to `@jmchilton `__). `Pull Request 16787`_ * Fix short ids in tool panel views. @@ -741,10 +741,10 @@ Fixes * Use AlignedSegment.to_string (thanks to `@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 `__). `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 `__). `Pull Request 16808`_ * Fix tool panel views for versionless tool ids @@ -789,19 +789,19 @@ Fixes * Fix bug in SQLAlchemy statement (thanks to `@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 `__). `Pull Request 16887`_ * Update help in relabel_from_file.xml (thanks to `@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 `__). `Pull Request 16895`_ * Fix type annotation of ``lib/tool_shed/test/functional/`` (thanks to `@nsoranzo `__). `Pull Request 16901`_ -* Fix navigation error in tool shed tests +* Fix navigation error in Tool Shed tests (thanks to `@jmchilton `__). `Pull Request 16902`_ * Fix subtle bug in listify function + simplify list munging @@ -813,7 +813,7 @@ Fixes * Fix selenium selector for Workflow Run warnings (thanks to `@davelopez `__). `Pull Request 16908`_ -* Fix GQL infinite scrolling in tool shed +* Fix GQL infinite scrolling in Tool Shed (thanks to `@jmchilton `__). `Pull Request 16914`_ * Fix library import from path linking files diff --git a/doc/source/releases/23.2_announce_user.rst b/doc/source/releases/23.2_announce_user.rst index e20d03e65898..7b4cf6084dbc 100644 --- a/doc/source/releases/23.2_announce_user.rst +++ b/doc/source/releases/23.2_announce_user.rst @@ -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 `__). `Pull Request 15447`_ -* Add new datatype: STL +* Add stl datatype (thanks to `@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 `__). `Pull Request 16503`_ * Support new genome browser chain file format @@ -43,30 +43,24 @@ New Datatypes * Bump samtools converters (thanks to `@bernt-matthias `__). `Pull Request 16668`_ -* Update datatypes_conf.xml.sample with docx type +* Add docx datatype (thanks to `@yvanlebras `__). `Pull Request 16713`_ -* MINERVA display application: enable cors, add for tabular +* MINERVA display application: enable cors, add for tabular datasets (thanks to `@hexylena `__). `Pull Request 16737`_ -* prep for updated h5py and typos +* Prep for updated h5py (thanks to `@mr-c `__). `Pull Request 16963`_ -* Minor clarification/typo fix in datatypes.data - (thanks to `@dannon `__). - `Pull Request 16993`_ * Update tar_to_directory dependency (thanks to `@mvdbeek `__). `Pull Request 17009`_ -* optimize object store cache operations +* Optimize object store cache operations (thanks to `@SergeyYakubov `__). `Pull Request 17025`_ * Add support for larch datatypes (thanks to `@patrick-austin `__). `Pull Request 17080`_ -* Fix `.file_name` access in merge forward - (thanks to `@mvdbeek `__). - `Pull Request 17097`_ * Fix Display Application link generation (thanks to `@mvdbeek `__). `Pull Request 17227`_ @@ -94,9 +88,6 @@ Builtin Tool Updates Podman job_conf (thanks to `@sveinugu `__). `Pull Request 16795`_ -* chore: fix typos - (thanks to `@afuetterer `__). - `Pull Request 16851`_ * Fix missing grep input in sort1 tool (thanks to `@mvdbeek `__). `Pull Request 16910`_