From d80bf6bb007cb775cb41524bdc80505c5dad6fb7 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 16 Feb 2021 11:44:33 -0500 Subject: [PATCH] More progress on release notes for 21.01. --- doc/source/releases/21.01.rst | 130 +++++++++++++++------------------- 1 file changed, 57 insertions(+), 73 deletions(-) diff --git a/doc/source/releases/21.01.rst b/doc/source/releases/21.01.rst index 9a612599e9e..4dfa17f4cb5 100644 --- a/doc/source/releases/21.01.rst +++ b/doc/source/releases/21.01.rst @@ -16,10 +16,13 @@ Enhancements * Add workflow invocation detail component. `Pull Request 10976`_ * History panel rewrite (available in the UI as a beta option). - `Pull Request 8441`_ + `Pull Request 8441`_, `Pull Request 11071`_, `Pull Request 10971`_ * Allow organizing the panel via EDAM ontology annotations. (thanks to `@hexylena `__). `Pull Request 10592`_ +* Large overhaul over history import and export - including improved user experience, APIs, and allowing importing and exporting + to file sources plugins (including FTP). + `Pull Request 11054`_, `Pull Request 10993`_ * Various substantial improvements to data library user interface (thanks to `@OlegZharkov `__). `Pull Request 10204`_, `Pull Request 11099`_, @@ -74,7 +77,7 @@ Enhancements * Implement mypy type checking for the Galaxy Python backend. `Pull Request 11009`_, `Pull Request 11037`_, `Pull Request 11022`_, `Pull Request 11007`_, - `Pull Request 11027`_ + `Pull Request 11027`_, `Pull Request 11039`_ * Allow setting file download filename_pattern by client. `Pull Request 11108`_ * Add FastAPI migration of licenses endpoints @@ -83,8 +86,10 @@ Enhancements * Improvements to workflow imports from GA4GH TRS servers (thanks to `@OlegZharkov `__). `Pull Request 10805`_, `Pull Request 10619`_ -* Enhancements for galaxy-tool-test script. - `Pull Request 10620`_, `Pull Request 10779`_ +* Major enhancements for the ``galaxy-tool-test`` script (installed as part of the PyPI + package ``galaxy-tool-util``). + `Pull Request 10620`_, `Pull Request 10779`_, + `Pull Request 10908`_, `Pull Request 10879`_ * Speedup xml replacement when loading tools. `Pull Request 10804`_ * Update askomics interactive tool to 4.1.1 @@ -99,10 +104,6 @@ Enhancements * Implement expression tool for picking non-null values for CWL-style merging of conditional branches in native Galaxy workflows. `Pull Request 10712`_ -* Add workflow tests for some newer workflow features. - `Pull Request 10478`_, `Pull Request 10669`_ -* wait_for_invocation should take in an assert_ok flag like other wait methods. - `Pull Request 10668`_ * Add and document API for publishing and tagging workflows (thanks to `@simonbray `__). `Pull Request 10748`_ @@ -112,7 +113,8 @@ Enhancements * Various small cleanups and improvements to the workflow editor and migrations toward Vue. `Pull Request 10999`_, `Pull Request 11001`_, `Pull Request 11024`_, - `Pull Request 10769`_, `Pull Request 11036`_, `Pull Request 11042`_ + `Pull Request 10769`_, `Pull Request 11036`_, `Pull Request 11042`_, + `Pull Request 11041`_, `Pull Request 10580`_ * Replace StreamBall, replace tarballs with zip `Pull Request 10919`_ * Simplify JobInformation and DatasetInformation components @@ -143,14 +145,14 @@ Enhancements `Pull Request 11078`_ * Implement backend quota interface - with better logic isolation and unit tests. `Pull Request 10212`_ -* When compiling dynamic installation confs, ensure location is actually writeable +* When compiling dynamic installation tool conf files, ensure location is actually writeable. `Pull Request 10387`_ * Display minutes in admin jobs cutoff (thanks to `@OlegZharkov `__). `Pull Request 10493`_ -* Display user disk usage in admin user panel +* Display user disk usage in admin user panel. `Pull Request 10666`_ -* Allow TRS servers to not be defined +* Allow GA4GH TRS servers configuration to not be undefined/empty (thanks to `@selten `__). `Pull Request 10817`_ * Drop ``legacy_eager_objectstore_initialization`` config option. @@ -160,7 +162,7 @@ Enhancements `Pull Request 11067` * Allow InteractiveTools to use path-based proxying when ``requires_domain=False``. `Pull Request 8596`_ -* Add warning for non-existing tool version +* Add warning for non-existing tool versions on tool form (thanks to `@OlegZharkov `__). `Pull Request 10139`_ * Set up confirmation page for new Custos/oidc users. @@ -206,56 +208,56 @@ Enhancements `Pull Request 10499`_ * Use dataset selector in rules input dialog. `Pull Request 10505`_ -* Add enumeration restriction to detect_errors +* Add enumeration restriction to ``detect_errors`` in tool XML schema (thanks to `@davelopez `__). `Pull Request 10510`_ * Simpler API for getting user API key. `Pull Request 10522`_ * Add S3 plugin for remote files browser. `Pull Request 10523`_ -* informative error message on /api/authenticate/baseauth +* More informative error message for ``/api/authenticate/baseauth`` (thanks to `@OlegZharkov `__). `Pull Request 10524`_ * Add more tags to Github. `Pull Request 10525`_ -* More comments for rapid testing optional galaxy.files stuff. +* More comments for rapid testing optional ``galaxy.files`` stuff. `Pull Request 10526`_ -* 'copy to clipboard' button on datasets +* add ``copy to clipboard`` button to datasets (thanks to `@OlegZharkov `__). `Pull Request 10529`_ * Add awesome-galaxy repo link to docs (thanks to `@innovate-invent `__). `Pull Request 10530`_ -* Generate path resolution note for sample file, docs +* Generate path resolution note for sample file, docs. `Pull Request 10537`_ * Allow admins to add an additional custom logo to the masthead `Pull Request 10540`_ -* Improve performance of copying HDAs and HDCAs +* Improve performance of copying HDAs and HDCAs. `Pull Request 10549`_ -* Update to new LTS nodejs version +* Update to new LTS nodejs version. `Pull Request 10565`_ * Document data manager repository layout - (thanks to `@brinkmanlab `__). + (thanks to `@innovate-invent `__). `Pull Request 10573`_ -* Set uwsgi's honour-stdin option when in debug mode +* Set uwsgi's honour-stdin option when in debug mode. `Pull Request 10577`_ -* Make extract wf action more visible +* Make primary extract workflow action button more visible (thanks to `@hexylena `__). `Pull Request 10583`_ -* pgcleanup can redirect logging to stdout +* Allow ``pgcleanup`` to redirect logging to stdout (thanks to `@gmauro `__). `Pull Request 10594`_ * Remove IUC conda channel from default configuration (thanks to `@bernt-matthias `__). `Pull Request 10608`_ * Document toolshed repository response object - (thanks to `@brinkmanlab `__). + (thanks to `@innovate-invent `__). `Pull Request 10633`_ -* Rev cwltool to 3.0.20201109103151 - `Pull Request 10658`_ * Full Python dependencies update (thanks to `@nsoranzo `__). `Pull Request 10660`_ +* Rev Python cwltool dependency to ``3.0.20201109103151``. + `Pull Request 10658`_ * Migrate API tests to GitHub workflow (thanks to `@nsoranzo `__). `Pull Request 10674`_ @@ -322,23 +324,17 @@ Enhancements (thanks to `@nsoranzo `__). `Pull Request 10861`_ * Allow build_list inputs to be optional - (thanks to `@brinkmanlab `__). + (thanks to `@innovate-invent `__). `Pull Request 10863`_ -* Report galaxy URL in tool test script, optionally publish history - `Pull Request 10879`_ * Dynamic select parameters: also allow to choose legal options by name (thanks to `@bernt-matthias `__). `Pull Request 10880`_ -* More improvements to tool test scripting. - `Pull Request 10908`_ * Add screenshot decorators to selenium tests (thanks to `@OlegZharkov `__). `Pull Request 10911`_ * Add version tab which links to release notes to help tab (thanks to `@astrovsky01 `__). `Pull Request 10960`_ -* API support for history import/export from/to galaxy.files plugins - `Pull Request 10993`_ * Check Python typing for galaxy-containers and galaxy-tool-util during CI. `Pull Request 11000`_ * Update locale.js @@ -354,44 +350,36 @@ Enhancements `Pull Request 11030`_ * Remove migration logic that will never be used now. `Pull Request 11038`_ -* More type annotation fixes. - `Pull Request 11039`_ -* Support complex markers in `run_tests.sh` +* Support complex markers in ``run_tests.sh`` (thanks to `@nsoranzo `__). `Pull Request 11045`_ * Optimized binary datatype sniffing for various binary datatypes. `Pull Request 11049`_ -* Revise user experience for history import and export. - `Pull Request 11054`_ * Move framework tests to GitHub workflows + lint test tools (thanks to `@nsoranzo `__). `Pull Request 11055`_ -* add validation for collection parameters +* Add validation for tool ``data_collection`` parameters (thanks to `@bernt-matthias `__). `Pull Request 11063`_ -* Verify behavior of non-existent from_work_dir outputs. +* Verify behavior of non-existent ``from_work_dir`` outputs. `Pull Request 11073`_ * Show OpenAPI documentation for API tags (thanks to `@davelopez `__). `Pull Request 11083`_ -* Documentation for Writing Tests - `Pull Request 11088`_ -* Update coverage documentation in run_tests.sh - `Pull Request 11102`_ -* Make minor improvements, add ToC - `Pull Request 11104`_ -* Persist scroll/url information, in chrome, firefox +* Major overhaul and expansion of documentation for writing tests in Galaxy. + `Pull Request 11088`_, `Pull Request 11102`_, `Pull Request 11104`_ +* Persist scroll/url information for GTN webhook (thanks to `@hexylena `__). `Pull Request 11290`_ -* Improve API test for datatype change +* Improve API test for datatype changing (thanks to `@simonbray `__). `Pull Request 10272`_ -* Datatypes refactoring +* Various datatype code structure improvements (thanks to `@nsoranzo `__). `Pull Request 10279`_ -* Drop unnecessary list casting in Anndata datatype +* Drop unnecessary list casting in ``Anndata`` datatype. `Pull Request 10296`_ -* Drop unused helpers in web.framework.helpers +* Drop unused helpers in ``web.framework.helpers`` `Pull Request 10345`_ * Drop support for retired Python 3.5 (thanks to `@nsoranzo `__). @@ -402,48 +390,44 @@ Enhancements * Typos and semantic fixes for iRODS object store (thanks to `@trel `__). `Pull Request 10423`_ -* K8s runner typo: job_destinantion->job_destination +* Fix K8s job runner typo (thanks to `@almahmoud `__). `Pull Request 10501`_ -* Drop communication server +* Drop communication server. `Pull Request 10514`_ -* Worfklow typo fix in styling - `Pull Request 10580`_ -* Refactor logic for workflow_step.input_type into model. +* Add workflow tests for some newer workflow features. + `Pull Request 10478`_, `Pull Request 10669`_ +* Improve helper code ``wait_for_invocation``. + `Pull Request 10668`_ +* Refactor logic for ``workflow_step.input_type`` into model. `Pull Request 10657`_ -* Rename flake8 ignorelist +* Rename flake8 ignorelist. `Pull Request 10702`_ * Refactor more generally useful Selenium code into reusable library code. `Pull Request 10783`_ * Rely on emails to determine GitLab users (thanks to `@selten `__). `Pull Request 10830`_ -* Convert datasets.set_edit to modern decorator, reuse manager. +* Convert ``datasets.set_edit`` to modern decorator, reuse manager. `Pull Request 10854`_ -* Make model somewhat compatible with sqlalchemy-1.4 +* Make model somewhat compatible with sqlalchemy-1.4. `Pull Request 10856`_ * Run maintenance bot only once (thanks to `@OlegZharkov `__). `Pull Request 10858`_ -* Replace usage of mkstemp with NamedTemporaryFile +* Replace usage of ``mkstemp`` with ``NamedTemporaryFile``. `Pull Request 10862`_ * Small edits objectstore code. `Pull Request 10867`_ * Remove trans from stream_dataset_collection() `Pull Request 10907`_ -* Use "email_from" value from schema for tool error report email +* Use ``email_from`` value from schema for tool error report email. `Pull Request 10956`_ -* Beta History initial load optimization (a.k.a. Added many data providers) - `Pull Request 10971`_ -* drop migration hack from htcondor +* Drop migration hack for htcondor (thanks to `@bgruening `__). `Pull Request 10991`_ -* Remove unused tag_outputs workflow controller action. +* Remove unused ``tag_outputs`` workflow controller action. `Pull Request 11040`_ -* Drop 'unreachable'-ish showWarnings method in workflow editor. - `Pull Request 11041`_ -* Sync vuex to galaxy - `Pull Request 11071`_ * Build FastAPI app in a single location `Pull Request 11074`_ @@ -496,11 +480,11 @@ Fixes `Pull Request 11029`_ * Maintain expanded state of JobStep during polling `Pull Request 11144`_ -* Fix tool version switch in workflow editor +* Fix tool version switch in workflow editor. `Pull Request 11257`_ -* Fix populated state for empty collections +* Fix populated state for empty collections. `Pull Request 11312`_ -* Fix Workflow report markdown lost upon renaming the workflow +* Fix Workflow report markdown lost upon renaming the workflow. (thanks to `@davelopez `__). `Pull Request 11317`_ * Bump client axios dependency from 0.19.2 to 0.21.1.