From a48233493aeefb00a835b09f8316f09bcef14df9 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 5 May 2021 22:12:25 +0200 Subject: [PATCH] Release notes for 21.05 --- doc/source/releases/21.05.rst | 803 ++++++++++++++++++++ doc/source/releases/21.05_announce.rst | 12 + doc/source/releases/21.05_announce_user.rst | 129 ++++ doc/source/releases/21.05_prs.rst | 319 ++++++++ 4 files changed, 1263 insertions(+) create mode 100644 doc/source/releases/21.05.rst create mode 100644 doc/source/releases/21.05_announce.rst create mode 100644 doc/source/releases/21.05_announce_user.rst create mode 100644 doc/source/releases/21.05_prs.rst diff --git a/doc/source/releases/21.05.rst b/doc/source/releases/21.05.rst new file mode 100644 index 00000000000..7240a2b75a6 --- /dev/null +++ b/doc/source/releases/21.05.rst @@ -0,0 +1,803 @@ + +.. to_doc + +21.05 +=============================== + +.. announce_start + +Enhancements +------------------------------- + +.. major_feature + +* Beta History scrolling behavior and polling efficiency tuning + `Pull Request 11693`_ + +.. feature + +* Add FastAPI routes for tours + `Pull Request 11089`_ +* Add FastAPI routes for datatypes + (thanks to `@davelopez `__). + `Pull Request 11098`_ +* Add cache_dir to schema + `Pull Request 11202`_ +* Allow requesting extra scopes + (thanks to `@hexylena `__). + `Pull Request 11561`_ +* Github workflow for updating dependencies + `Pull Request 11570`_ +* Allow line break html tag in markdown pages + `Pull Request 11592`_ +* Allow workflow imports in pages + `Pull Request 11607`_ +* Add option to download collections in markdown pages + `Pull Request 11676`_ +* Add the SimText shiny app as Interactive Tool + (thanks to `@dlal-group `__). + `Pull Request 11680`_ +* Replace sqlalchemy-utilities with local implementation + `Pull Request 11696`_ +* Circus + Celery - MVP + `Pull Request 11720`_ +* Support role and group permissions in file sources plugins + (thanks to `@davelopez `__). + `Pull Request 11769`_ +* Add circus + gunicorn option when using run.sh + `Pull Request 11772`_ +* Run history export setup via celery, if configured + `Pull Request 11789`_ +* Allow importing histories through pages / reports + `Pull Request 11863`_ +.. enhancement_tag_viz + +* Migrate api/genomes to fastapi + `Pull Request 11241`_ +.. enhancement_tag_datatypes + +* Add FlowCytometry and MetaCyto datatypes + (thanks to `@pcm32 `__). + `Pull Request 9807`_ +* Add mrc datatype (and Python dependency) + (thanks to `@gregvonkuster `__). + `Pull Request 11220`_ +* Add HHR datatype + (thanks to `@bgruening `__). + `Pull Request 11661`_ +* add meryldb datatype + (thanks to `@bgruening `__). + `Pull Request 11694`_ +* Add datatype for PretextMap output + `Pull Request 11747`_ +* add new datatype class for meryldb + (thanks to `@bgruening `__). + `Pull Request 11758`_ +* Make Avivator GEDA and sniffer for ome.tiff datatype + (thanks to `@qiagu `__). + `Pull Request 11801`_ +* jellyfish db datatype + (thanks to `@astrovsky01 `__). + `Pull Request 11802`_ +* add new datatype JPEG 2000 in Galaxy + (thanks to `@annefou `__). + `Pull Request 11812`_ +* Make datatype h5_model for machine leaning models + (thanks to `@qiagu `__). + `Pull Request 11825`_ +* Add support for the Relion STAR data format + (thanks to `@gregvonkuster `__). + `Pull Request 11831`_ +* add minerva display app for covid + (thanks to `@hexylena `__). + `Pull Request 11880`_ +* Add toml datatype + (thanks to `@jj-umn `__). + `Pull Request 11909`_ +.. enhancement_tag_tools + +* grep, tail, head: add option to keep header + (thanks to `@bernt-matthias `__). + `Pull Request 11859`_ +* add a bit of docs to the add tags tool + (thanks to `@bernt-matthias `__). + `Pull Request 11874`_ +.. enhancement_tag_workflows + +* Selenium test case for invocation grid + display. + `Pull Request 11160`_ +* be more verbose on output filter errors + (thanks to `@bernt-matthias `__). + `Pull Request 11197`_ +* Add UpgradeAllSteps workflow refactor action + (thanks to `@simonbray `__). + `Pull Request 11429`_ +* Guess tool name when extracting workflows with imported datasets + (thanks to `@davelopez `__). + `Pull Request 11483`_ +* Avoid appending imported source on workflow name multiple times. + (thanks to `@davelopez `__). + `Pull Request 11671`_ +* Switch default handler assignment to skip locked or transaction isolation if possible + `Pull Request 11792`_ +.. enhancement_tag_ui + +* Client testing/linting updates and followup + `Pull Request 11121`_ +* replaced global vue with test vue in unit tests + `Pull Request 11138`_ +* Manage folder rewrite in Vue & VueRouter + (thanks to `@OlegZharkov `__). + `Pull Request 11259`_ +* Copy to Clipboard button next to the tool id in job information + (thanks to `@OlegZharkov `__). + `Pull Request 11478`_ +* Better webpack-dev-server handling. + `Pull Request 11566`_ +* Speed up get history list + `Pull Request 11883`_ +* Implement switch to history modal for beta history panel + `Pull Request 11895`_ +.. enhancement_tag_jobs + +* Store job_id on Dataset table. + `Pull Request 10222`_ +* Handle unschedulable jobs in k8s runner + (thanks to `@almahmoud `__). + `Pull Request 10496`_ +* Establish a best practice for trans dependency management. + `Pull Request 11113`_ +* Adding GALAXY_MEMORY_MB_PER_SLOT to k8s runner + (thanks to `@almahmoud `__). + `Pull Request 11227`_ +* add reworked chronos job runner + (thanks to `@mtangaro `__). + `Pull Request 11228`_ +* Generalise rule helper to detect whether tools can use any container + (thanks to `@pcm32 `__). + `Pull Request 11274`_ +* Only return a subset of jobs ready to run per user when querying for jobs ready to run + `Pull Request 11358`_ +* ITs on Kubernetes + (thanks to `@almahmoud `__). + `Pull Request 11383`_ +* Read cgroups from cgroup filesystem mount rather than cgget, which is not always installed + `Pull Request 11393`_ +* SLURM: stop editing job stderr file + (thanks to `@bernt-matthias `__). + `Pull Request 11575`_ +* Fixes for extended metadata working with Pulsar. + `Pull Request 11788`_ +* Fix collection state updates by setting collection update time + `Pull Request 11849`_ +* Test a better Pulsar configuration for extended metadata. + `Pull Request 11852`_ +* Add handler column in admin jobs, remove webcontroller + `Pull Request 11868`_ +* improve three debug messages + (thanks to `@bernt-matthias `__). + `Pull Request 11908`_ +.. enhancement_tag_admin + +* Add documentation on how to setup Pulsar's two-container job runner + `Pull Request 11557`_ +* sortable columns in Admin->Users + (thanks to `@OlegZharkov `__). + `Pull Request 11665`_ +* Create install database with create_db.sh + `Pull Request 11753`_ +.. enhancement + +* Performance testing infrastructure. + `Pull Request 10117`_ +* Stub MQ docs + (thanks to `@brinkmanlab `__). + `Pull Request 10347`_ +* Implement read-only conda resolver. + `Pull Request 10810`_ +* really test variables in conditionals + (thanks to `@bernt-matthias `__). + `Pull Request 11111`_ +* Updated API Design Guidelines + `Pull Request 11115`_ +* uvicorn-compatible factory function for fastapi. + `Pull Request 11116`_ +* Dynamic discovery of FastAPI routers. + `Pull Request 11124`_ +* FastAPI routes for configuration + `Pull Request 11126`_ +* Start type signature for UniverseApplication. + `Pull Request 11142`_ +* Various testing framework cleanups. + `Pull Request 11156`_ +* FastAPI routes for tool data tables + (thanks to `@davelopez `__). + `Pull Request 11167`_ +* Recommend 2FA and commit signing + (thanks to `@nsoranzo `__). + `Pull Request 11173`_ +* Warns that build_mulled_singularity requires docker + (thanks to `@pcm32 `__). + `Pull Request 11176`_ +* Documentation and helpers for using galaxy-selenium package within Jupyter + `Pull Request 11177`_ +* History beta poll decay time reset + `Pull Request 11178`_ +* Holistic approach to dependency injection. + `Pull Request 11180`_ +* Selenium test for ``library_import_dir`` + (thanks to `@OlegZharkov `__). + `Pull Request 11188`_ +* Replace pipenv with poetry. Update all dependencies + (thanks to `@nsoranzo `__). + `Pull Request 11192`_ +* Add missing xml:lang attribute to documentation annotations + (thanks to `@davelopez `__). + `Pull Request 11198`_ +* Selenium tests for user library import dir + (thanks to `@OlegZharkov `__). + `Pull Request 11203`_ +* FastAPI route for remote files + (thanks to `@davelopez `__). + `Pull Request 11211`_ +* More debug info for failed integration selenium tests during CI. + `Pull Request 11217`_ +* Implement abstraction around InferringApiRouter tailored to typical Galaxy usage. + `Pull Request 11219`_ +* FastAPI route for tags (Disabled) + (thanks to `@davelopez `__). + `Pull Request 11224`_ +* Remove `folder_up` button from data folder + (thanks to `@OlegZharkov `__). + `Pull Request 11230`_ +* add ActionChains example in documentation of galaxy-selenium package within Jupyter + (thanks to `@OlegZharkov `__). + `Pull Request 11232`_ +* Sync x-frame-options handling across frameworks and test. + `Pull Request 11235`_ +* FastAPI/ASGI CORS handling. + `Pull Request 11240`_ +* FastAPI routes for Pages (Disabled) + (thanks to `@davelopez `__). + `Pull Request 11262`_ +* Don't fail silently in `User.system_user_pwent()` + (thanks to `@nsoranzo `__). + `Pull Request 11272`_ +* Move docstring linting to GitHub workflows + (thanks to `@nsoranzo `__). + `Pull Request 11300`_ +* Add Nuwan Goonasekera to the committers group + `Pull Request 11304`_ +* ignore subdirectories if recurse is false + (thanks to `@bernt-matthias `__). + `Pull Request 11307`_ +* Fix transiently failing roles API test. + `Pull Request 11319`_ +* Allow `GET /api/dataset_collections/{hdca_id}` without specifying `instance_type` + (thanks to `@nsoranzo `__). + `Pull Request 11346`_ +* Add support for Plausible analytics and Matomo analytics + (thanks to `@selten `__). + `Pull Request 11351`_ +* Lint for optional or multiple selects with radio display + (thanks to `@bernt-matthias `__). + `Pull Request 11385`_ +* Test library dataset permissions + (thanks to `@OlegZharkov `__). + `Pull Request 11402`_ +* Use request id middleware to scope session + `Pull Request 11411`_ +* Move unit tests to GitHub workflows, test also under Python 3.9 + (thanks to `@nsoranzo `__). + `Pull Request 11452`_ +* Allow anonymous access to S3 buckets via file sources plugins. + `Pull Request 11458`_ +* add copy tooldID btn + (thanks to `@OlegZharkov `__). + `Pull Request 11477`_ +* Libraries rewrite + (thanks to `@OlegZharkov `__). + `Pull Request 11485`_ +* adding nameSuggestion to PairCollectionCreator + (thanks to `@assuntad23 `__). + `Pull Request 11489`_ +* xsd: use validator as child of param + (thanks to `@bernt-matthias `__). + `Pull Request 11497`_ +* add sshfs plugin to the new file infrastructure + (thanks to `@bgruening `__). + `Pull Request 11507`_ +* add ftp files.plugin + (thanks to `@bgruening `__). + `Pull Request 11508`_ +* Add ready-to-go gitpod config + `Pull Request 11509`_ +* Create pull_request_template.md + (thanks to `@assuntad23 `__). + `Pull Request 11530`_ +* Add more filtering options to api/jobs endpoint + (thanks to `@rikeshi `__). + `Pull Request 11560`_ +* Migrate metrics API to FastAPI + (thanks to `@davelopez `__). + `Pull Request 11568`_ +* Sample conf for dropbox and owncloud file sources + (thanks to `@abretaud `__). + `Pull Request 11580`_ +* An attempt to improve dependency management + `Pull Request 11619`_ +* Overhaul make-based release process + `Pull Request 11641`_ +* Pin fs.webdavfs requirement to latest version + (thanks to `@abretaud `__). + `Pull Request 11648`_ +* Update all Python dependencies + (thanks to `@nsoranzo `__). + `Pull Request 11649`_ +* update to cope with impending changes to cwltool internals + (thanks to `@rupertnash `__). + `Pull Request 11655`_ +* Lint for duplicated options + (thanks to `@bernt-matthias `__). + `Pull Request 11662`_ +* Single User Mode - Disable irrelevant and broken options + `Pull Request 11669`_ +* Swap 'Analyze Data' to home icon + `Pull Request 11674`_ +* Bugfix/11476/disabled upload button explanation + (thanks to `@assuntad23 `__). + `Pull Request 11682`_ +* Break up dynamic dataset collection into chunks + `Pull Request 11697`_ +* enable the S3 plugin to use non-AWS resrouces + (thanks to `@bgruening `__). + `Pull Request 11703`_ +* Implement selenium tests for exporting library datasets to history collections. + (thanks to `@OlegZharkov `__). + `Pull Request 11716`_ +* lint for checkboxes select + (thanks to `@bernt-matthias `__). + `Pull Request 11727`_ +* Refactor stdout/stderr in Job Information + (thanks to `@OlegZharkov `__). + `Pull Request 11731`_ +* Copy collections dbkey + (thanks to `@assuntad23 `__). + `Pull Request 11732`_ +* Fix CI docs build for feature branches + (thanks to `@nsoranzo `__). + `Pull Request 11740`_ +* Updated Code of Conduct to point to the exact copy of this CoC on the hub. + `Pull Request 11750`_ +* Allow AWS s3 access for ec2 instances without hardcoding credentials + (thanks to `@crashGoBoom `__). + `Pull Request 11757`_ +* Add an explicit statement of assent to licensing to the pull request template + `Pull Request 11777`_ +* Fixes for installed Galaxy + `Pull Request 11779`_ +* Update Python dependencies + `Pull Request 11782`_ +* Handle deprecated postgresql db urls; update postgres version in ci + `Pull Request 11790`_ +* Update localisation options to include Español + (thanks to `@hexylena `__). + `Pull Request 11791`_ +* Open update deps PRs from galaxybot's fork + (thanks to `@nsoranzo `__). + `Pull Request 11795`_ +* Make k8s container 39 MB smaller by using vim-tiny + (thanks to `@rhpvorderman `__). + `Pull Request 11826`_ +* Make tool parameter options capable of referring to metadata file + (thanks to `@qiagu `__). + `Pull Request 11832`_ +* Restore triggers dropped in `#10821 `__ + (thanks to `@nsoranzo `__). + `Pull Request 11843`_ +* Do not invoke workflow if not all tools are available + (thanks to `@simonbray `__). + `Pull Request 11844`_ +* Improve error handling when creating a new History with the master API key + (thanks to `@davelopez `__). + `Pull Request 11846`_ +* Expose StoredWorkflowId in invocation API + (thanks to `@simonbray `__). + `Pull Request 11871`_ +* Create FastAPI entry points for Tool Shed and Reports + (thanks to `@davelopez `__). + `Pull Request 11872`_ +* Rev mypy. + `Pull Request 11877`_ +* Backport `#11871 `__ + (thanks to `@scholtalbers `__). + `Pull Request 11881`_ +* Allow to filter /api/invocations by job_id + (thanks to `@scholtalbers `__). + `Pull Request 11882`_ +* Complete Spanish language version + (thanks to `@nomadscientist `__). + `Pull Request 11891`_ +* Add subpathing to k8s_persistent_volume_claims + (thanks to `@anvilproject `__). + `Pull Request 11899`_ +* Make _metadata regular JSONType field + `Pull Request 11902`_ +* Abstraction for fetching qualified app URL across webapp types + `Pull Request 11904`_ +* Add ``delete account`` selenium test + (thanks to `@OlegZharkov `__). + `Pull Request 11905`_ +* Update framework dependencies + `Pull Request 11907`_ +* expose copied_from_ldda_id on dataset api endpoint + (thanks to `@scholtalbers `__). + `Pull Request 11922`_ +.. small_enhancement + +* Fix remaining issues reported by bugbear; add it to flake8 reqs + (thanks to `@nsoranzo `__). + `Pull Request 11153`_ +* Fix all E203, E741 and W504 flake8 errors + (thanks to `@nsoranzo `__). + `Pull Request 11155`_ +* Remove unused TS methods. + `Pull Request 11179`_ +* Remove some seemingly unused cruft in GalaxyWebTransaction + `Pull Request 11234`_ +* Drop unused transfer_manager.py + `Pull Request 11238`_ +* Get rid of legacy decorator in api/tours + `Pull Request 11253`_ +* Update vscode dev instructions, drop helper script + `Pull Request 11258`_ +* Replace $.isArray with Array prototype check + `Pull Request 11264`_ +* Drop docker testing image + `Pull Request 11329`_ +* Renamed virtualscroller since it is no longer virtual + `Pull Request 11331`_ +* Dataset lib permissions Vue rewrite + (thanks to `@OlegZharkov `__). + `Pull Request 11347`_ +* Refactor libraries API logic into LibrariesManager + (thanks to `@davelopez `__). + `Pull Request 11359`_ +* Refactor display_applications API logic into DisplayApplicationsManager + (thanks to `@davelopez `__). + `Pull Request 11386`_ +* Repair styleguide + `Pull Request 11404`_ +* Refactor groups API logic into GroupsManager + (thanks to `@davelopez `__). + `Pull Request 11412`_ +* Refactor group_roles API logic into GroupRolesManager + (thanks to `@davelopez `__). + `Pull Request 11417`_ +* Refactor group_users API logic into GroupUsersManager + (thanks to `@davelopez `__). + `Pull Request 11418`_ +* Pin mypy to 0.790 to prevent linting errors when running v 0.8 + `Pull Request 11422`_ +* Use galaxy Router instead of InferringRouter + (thanks to `@davelopez `__). + `Pull Request 11591`_ +* Front-end Library Routing refactor + (thanks to `@OlegZharkov `__). + `Pull Request 11614`_ +* Remove unused `TraceLogger` class + (thanks to `@nsoranzo `__). + `Pull Request 11616`_ +* Refactor library folder API logic into FoldersService + (thanks to `@davelopez `__). + `Pull Request 11631`_ +* Rewrite Library Permissions + (thanks to `@OlegZharkov `__). + `Pull Request 11637`_ +* Fix prop mutation in FolderTopBar + (thanks to `@OlegZharkov `__). + `Pull Request 11638`_ +* Refactor library folder contents api + (thanks to `@davelopez `__). + `Pull Request 11686`_ +* Update Python dependencies + `Pull Request 11702`_ +* Partial refactor ShareableMixin into ShareableService + (thanks to `@davelopez `__). + `Pull Request 11712`_ +* Incorporate changes from Pulsar's copy of galaxy.jobs.runners.util + `Pull Request 11810`_ +* Separate tests for "remote" and "remote + extended" metadata. + `Pull Request 11840`_ +* Unify security decode id exceptions + (thanks to `@davelopez `__). + `Pull Request 11856`_ +* Optimized beta history polling by leveraging history.update_time + loading behavior bug fixes + `Pull Request 11884`_ +* Eslint tweaks + `Pull Request 11925`_ + + +Fixes +------------------------------- + +.. major_bug + + +.. bug_tag_viz + +* Shared visualization display fix + `Pull Request 11906`_ +.. bug_tag_datatypes + +* remove duplicated qcml from datatypes_conf sample + (thanks to `@bernt-matthias `__). + `Pull Request 11378`_ +* Limit max column in tabular dataset preview + `Pull Request 11901`_ +* Use keep_original in pysam.tabix_index to not remove original data + `Pull Request 11913`_ +.. bug_tag_tools + +* Resolve session problems, enabled pages and tags fastAPI routes + `Pull Request 11342`_ +* Make filter work with file containing header + (thanks to `@bernt-matthias `__). + `Pull Request 11365`_ +.. bug_tag_workflows + +* Workflow editor null/zero fixes + `Pull Request 11265`_ +* Fix reconnecting terminals + `Pull Request 11660`_ +* Fix tags not included when importing shared workflow + (thanks to `@davelopez `__). + `Pull Request 11663`_ +* Fix workflow rename dropping metadata. + `Pull Request 11670`_ +* Use Modal to show wrong RuntimeValue + `Pull Request 11678`_ +* Ensure new outputs have correct mapOver state + `Pull Request 11683`_ +* Redraw connections when adding or removing inputs + `Pull Request 11684`_ +* Fix displaying data column parameters in workflow editor + `Pull Request 11692`_ +* Fix workflow refactor schema parsing for pydantic 1.8. + `Pull Request 11778`_ +.. bug_tag_ui + +* Remove filter from list:paired element names when filter is not _1 + `Pull Request 11486`_ +* Beta history current history mismatch with legacy code. + `Pull Request 11850`_ +* Reposition history scroller during new updates + `Pull Request 11879`_ +.. bug_tag_jobs + +* Fix mule job messaging + `Pull Request 11148`_ +* Deal with empty claim names in k8s runner + (thanks to `@nuwang `__). + `Pull Request 11223`_ +* Fix SLURM runner for real user setups and avoid uneccesary chowns + (thanks to `@bernt-matthias `__). + `Pull Request 11403`_ +* Prevent endless fail_job cycles + `Pull Request 11673`_ +* Fix value of 'unknown_error' resubmit condition variable + (thanks to `@brinkmanlab `__). + `Pull Request 11749`_ +* Pulsar: mark cancelled jobs as finished + (thanks to `@abretaud `__). + `Pull Request 11763`_ +* Lower tool id case while populating resource params + (thanks to `@eancelet `__). + `Pull Request 11793`_ +* Don't overwrite $GALAXY_MEMORY_MB if it's already set + `Pull Request 11808`_ +* Transfer fewer unneeded files back to Galaxy when using remote extended metadata with Pulsar. + `Pull Request 11814`_ +* Don't write job and job-related attributes when creating export model + `Pull Request 11815`_ +* Handle resubmission before changing job state in CLI runner + (thanks to `@pcm32 `__). + `Pull Request 11886`_ +.. bug_tag_admin + +* fix broken docs links + `Pull Request 11384`_ +* Add missing ssl keyword in nginx example [docs] + (thanks to `@rhpvorderman `__). + `Pull Request 11633`_ +.. bug + +* Beta History: implement missing advanced search filters + `Pull Request 10972`_ +* Fix mypy error with Union in response_model + (thanks to `@davelopez `__). + `Pull Request 11132`_ +* Minor spelling error fix + (thanks to `@selten `__). + `Pull Request 11135`_ +* Fix permission in user dir library import + (thanks to `@OlegZharkov `__). + `Pull Request 11137`_ +* fix error message + (thanks to `@bernt-matthias `__). + `Pull Request 11157`_ +* changing tooltip to match functionality + (thanks to `@assuntad23 `__). + `Pull Request 11204`_ +* Copy only dataset tags in Extract Dataset tool + (thanks to `@pvanheus `__). + `Pull Request 11206`_ +* Fix regression of 'disabled' masthead items. + `Pull Request 11215`_ +* fix `test_user_library_import_dir_warning` + (thanks to `@OlegZharkov `__). + `Pull Request 11226`_ +* Make OIDC email matching case-insensitive + (thanks to `@selten `__). + `Pull Request 11251`_ +* Tool XML container requirements: fix example + (thanks to `@selten `__). + `Pull Request 11271`_ +* Bugfix/8488/rule builder fails for one bad url + (thanks to `@assuntad23 `__). + `Pull Request 11276`_ +* Fix printing non-dict output in api/display script + `Pull Request 11278`_ +* Fix images in workflow PDF report + (thanks to `@OlegZharkov `__). + `Pull Request 11296`_ +* consider collections in all tests + (thanks to `@bernt-matthias `__). + `Pull Request 11313`_ +* Replace Query with Path + `Pull Request 11320`_ +* Custos `aud` handling fix + `Pull Request 11322`_ +* Get latest pull request labels in maintenance bot + (thanks to `@nsoranzo `__). + `Pull Request 11326`_ +* Update OIDC links + (thanks to `@selten `__). + `Pull Request 11362`_ +* fix profile logic for configfile generation + (thanks to `@bernt-matthias `__). + `Pull Request 11380`_ +* Standardise tool param attribute docs + (thanks to `@nsoranzo `__). + `Pull Request 11390`_ +* Run maintainance bot on ready_for_review and edit + `Pull Request 11400`_ +* Decrease verbosity of messages in poetry + `Pull Request 11405`_ +* Rename fixtures to fix test database object name conflict + `Pull Request 11424`_ +* Check for binary files at the middle of the file instead of at the beginning + (thanks to `@pcm32 `__). + `Pull Request 11425`_ +* Set default USE_UVICORN to true only on python >= 3.7 + `Pull Request 11454`_ +* Fix galaxy.files.sources plugin unit tests being missed by CI. + `Pull Request 11469`_ +* Fix exception handling in datasets display API. + `Pull Request 11482`_ +* Mark some tool reload tests as expected to fail + (thanks to `@davelopez `__). + `Pull Request 11496`_ +* Fix clearing of search inputs + `Pull Request 11526`_ +* Fix bug with Pulsar and $__tool_directory__ + (thanks to `@abretaud `__). + `Pull Request 11599`_ +* Allow any extra field in Pages API + (thanks to `@davelopez `__). + `Pull Request 11600`_ +* Fix workflow labelling + `Pull Request 11604`_ +* Pin refgenconf to <0.10.0 + (thanks to `@nsoranzo `__). + `Pull Request 11627`_ +* Pin SQAlchemy to <1.4.0 + `Pull Request 11629`_ +* Change Upload button tooltip position + (thanks to `@OlegZharkov `__). + `Pull Request 11634`_ +* Set minimum requirements for starlette-context and fastapi + `Pull Request 11643`_ +* Match environment variable set up by doc building workflow + `Pull Request 11646`_ +* Don't check for missing `kind/` label for `minor` merged PRs + (thanks to `@nsoranzo `__). + `Pull Request 11647`_ +* Library folder_contents API tests + small fixes + (thanks to `@davelopez `__). + `Pull Request 11650`_ +* Refactor default mounting of $tmp_directory in containers + (thanks to `@brinkmanlab `__). + `Pull Request 11654`_ +* Fix datatype defined column name display + `Pull Request 11664`_ +* Expose command line if expose_dataset_path is set + `Pull Request 11687`_ +* Hotfix/paired list builder from data library + (thanks to `@assuntad23 `__). + `Pull Request 11700`_ +* Make extra user preferences behave like defaultdict + `Pull Request 11708`_ +* Fix importing collections to new history and import correct elements + `Pull Request 11718`_ +* Removedreference to remove-extensions + (thanks to `@assuntad23 `__). + `Pull Request 11724`_ +* Refgenie table del + (thanks to `@abretaud `__). + `Pull Request 11728`_ +* Fix job filtering by `date_range_max` / `date_range_mix` + (thanks to `@nsoranzo `__). + `Pull Request 11736`_ +* Fix a bug when unzipping collections with nametags. + `Pull Request 11741`_ +* Fix API job filtering by workflow or invocation + (thanks to `@nsoranzo `__). + `Pull Request 11751`_ +* Assorted tool shed fixes + `Pull Request 11762`_ +* Fix format="input" with implicit conversions + `Pull Request 11764`_ +* galaxy.webapps.tool_shed to webapp.tool_shed + (thanks to `@almahmoud `__). + `Pull Request 11765`_ +* Fix auto-pair naming in list paired creator. + `Pull Request 11773`_ +* Fix library scrolling + `Pull Request 11776`_ +* Use `assertRaisesRegex()` to fix new B017 linting errors + (thanks to `@nsoranzo `__). + `Pull Request 11783`_ +* Fix typo in `upstream_mod_zip` admin docs + (thanks to `@nsoranzo `__). + `Pull Request 11794`_ +* Fix tool profile details in schema docs + (thanks to `@nsoranzo `__). + `Pull Request 11798`_ +* Activate virtualenv in `updateucsc.sh.sample` + (thanks to `@nsoranzo `__). + `Pull Request 11800`_ +* Backport `#11815 `__: Don't write job and job-related attributes when creating export model + `Pull Request 11816`_ +* do not chown pasted urls + (thanks to `@bernt-matthias `__). + `Pull Request 11818`_ +* Fixed uploader link on tool list and legacy empty history message + `Pull Request 11830`_ +* Join QueueWorker thread + `Pull Request 11835`_ +* Patch to click the button which should be more stable + (thanks to `@hexylena `__). + `Pull Request 11838`_ +* fix data stickiness on folder change + (thanks to `@OlegZharkov `__). + `Pull Request 11845`_ +* BUGFIX: Also check for boolean True, not just string 'True' when evaluating conditional dependencies. + (thanks to `@rhpvorderman `__). + `Pull Request 11861`_ +* Fix ``Delete account`` visibility + `Pull Request 11897`_ +* Fix S3 backend support in iRODS object store + (thanks to `@kxk302 `__). + `Pull Request 11910`_ +* fix GalaxyInteractorApi get_tool_tests + (thanks to `@cat-bro `__). + `Pull Request 11911`_ +* Stabilize test_history_options selenium test + `Pull Request 11918`_ +* update legacy_framework.grids.StateColumn (bug fix) + (thanks to `@cat-bro `__). + `Pull Request 11923`_ + +.. include:: 21.05_prs.rst + diff --git a/doc/source/releases/21.05_announce.rst b/doc/source/releases/21.05_announce.rst new file mode 100644 index 00000000000..a8bb6e8d3e3 --- /dev/null +++ b/doc/source/releases/21.05_announce.rst @@ -0,0 +1,12 @@ + +:orphan: + +=========================================================== +May 2021 Galaxy Release (v 21.05) +=========================================================== + + +Schedule +=========================================================== + * Planned Freeze Date: 2021-05-03 + * Planned Release Date: 2021-05-24 diff --git a/doc/source/releases/21.05_announce_user.rst b/doc/source/releases/21.05_announce_user.rst new file mode 100644 index 00000000000..17b615e140a --- /dev/null +++ b/doc/source/releases/21.05_announce_user.rst @@ -0,0 +1,129 @@ + +=========================================================== +May 2021 Galaxy Release (v 21.05) +=========================================================== + +.. include:: _header.rst + +Highlights +=========================================================== + +**Feature1** + Feature description. + +**Feature2** + Feature description. + +**Feature3** + Feature description. + + +New Visualizations +=========================================================== + +.. visualizations +* Migrate api/genomes to fastapi + `Pull Request 11241`_ +* Shared visualization display fix + `Pull Request 11906`_ + +New Datatypes +=========================================================== + +.. datatypes +* Add FlowCytometry and MetaCyto datatypes + (thanks to `@pcm32 `__). + `Pull Request 9807`_ +* Add FastAPI routes for datatypes + (thanks to `@davelopez `__). + `Pull Request 11098`_ +* Fix remaining issues reported by bugbear; add it to flake8 reqs + (thanks to `@nsoranzo `__). + `Pull Request 11153`_ +* Add mrc datatype (and Python dependency) + (thanks to `@gregvonkuster `__). + `Pull Request 11220`_ +* remove duplicated qcml from datatypes_conf sample + (thanks to `@bernt-matthias `__). + `Pull Request 11378`_ +* Refactor display_applications API logic into DisplayApplicationsManager + (thanks to `@davelopez `__). + `Pull Request 11386`_ +* Merge release_21.01 -> dev + `Pull Request 11394`_ +* Add HHR datatype + (thanks to `@bgruening `__). + `Pull Request 11661`_ +* add meryldb datatype + (thanks to `@bgruening `__). + `Pull Request 11694`_ +* Merge 20.09 into dev + `Pull Request 11711`_ +* Add datatype for PretextMap output + `Pull Request 11747`_ +* add new datatype class for meryldb + (thanks to `@bgruening `__). + `Pull Request 11758`_ +* Make Avivator GEDA and sniffer for ome.tiff datatype + (thanks to `@qiagu `__). + `Pull Request 11801`_ +* jellyfish db datatype + (thanks to `@astrovsky01 `__). + `Pull Request 11802`_ +* add new datatype JPEG 2000 in Galaxy + (thanks to `@annefou `__). + `Pull Request 11812`_ +* Make datatype h5_model for machine leaning models + (thanks to `@qiagu `__). + `Pull Request 11825`_ +* Add support for the Relion STAR data format + (thanks to `@gregvonkuster `__). + `Pull Request 11831`_ +* add minerva display app for covid + (thanks to `@hexylena `__). + `Pull Request 11880`_ +* Limit max column in tabular dataset preview + `Pull Request 11901`_ +* Add toml datatype + (thanks to `@jj-umn `__). + `Pull Request 11909`_ +* Use keep_original in pysam.tabix_index to not remove original data + `Pull Request 11913`_ + +Builtin Tool Updates +=========================================================== + +.. tools +* Fix remaining issues reported by bugbear; add it to flake8 reqs + (thanks to `@nsoranzo `__). + `Pull Request 11153`_ +* Resolve session problems, enabled pages and tags fastAPI routes + `Pull Request 11342`_ +* Make filter work with file containing header + (thanks to `@bernt-matthias `__). + `Pull Request 11365`_ +* Add the SimText shiny app as Interactive Tool + (thanks to `@dlal-group `__). + `Pull Request 11680`_ +* grep, tail, head: add option to keep header + (thanks to `@bernt-matthias `__). + `Pull Request 11859`_ +* add a bit of docs to the add tags tool + (thanks to `@bernt-matthias `__). + `Pull Request 11874`_ + +Release Testing Team +=========================================================== + +A special thanks to the release testing team for testing many of the new features and reporting many bugs: + + + +Release Notes +=========================================================== + +Please see the `full release notes <21.05_announce.html>`_ for more details. + +.. include:: 21.05_prs.rst + +.. include:: _thanks.rst diff --git a/doc/source/releases/21.05_prs.rst b/doc/source/releases/21.05_prs.rst new file mode 100644 index 00000000000..52657e8df23 --- /dev/null +++ b/doc/source/releases/21.05_prs.rst @@ -0,0 +1,319 @@ + +.. github_links +.. _Pull Request 9807: https://github.com/galaxyproject/galaxy/pull/9807 +.. _Pull Request 10117: https://github.com/galaxyproject/galaxy/pull/10117 +.. _Pull Request 10222: https://github.com/galaxyproject/galaxy/pull/10222 +.. _Pull Request 10347: https://github.com/galaxyproject/galaxy/pull/10347 +.. _Pull Request 10496: https://github.com/galaxyproject/galaxy/pull/10496 +.. _Pull Request 10810: https://github.com/galaxyproject/galaxy/pull/10810 +.. _Pull Request 10972: https://github.com/galaxyproject/galaxy/pull/10972 +.. _Pull Request 11089: https://github.com/galaxyproject/galaxy/pull/11089 +.. _Pull Request 11098: https://github.com/galaxyproject/galaxy/pull/11098 +.. _Pull Request 11107: https://github.com/galaxyproject/galaxy/pull/11107 +.. _Pull Request 11111: https://github.com/galaxyproject/galaxy/pull/11111 +.. _Pull Request 11113: https://github.com/galaxyproject/galaxy/pull/11113 +.. _Pull Request 11115: https://github.com/galaxyproject/galaxy/pull/11115 +.. _Pull Request 11116: https://github.com/galaxyproject/galaxy/pull/11116 +.. _Pull Request 11121: https://github.com/galaxyproject/galaxy/pull/11121 +.. _Pull Request 11122: https://github.com/galaxyproject/galaxy/pull/11122 +.. _Pull Request 11124: https://github.com/galaxyproject/galaxy/pull/11124 +.. _Pull Request 11126: https://github.com/galaxyproject/galaxy/pull/11126 +.. _Pull Request 11128: https://github.com/galaxyproject/galaxy/pull/11128 +.. _Pull Request 11132: https://github.com/galaxyproject/galaxy/pull/11132 +.. _Pull Request 11135: https://github.com/galaxyproject/galaxy/pull/11135 +.. _Pull Request 11137: https://github.com/galaxyproject/galaxy/pull/11137 +.. _Pull Request 11138: https://github.com/galaxyproject/galaxy/pull/11138 +.. _Pull Request 11142: https://github.com/galaxyproject/galaxy/pull/11142 +.. _Pull Request 11148: https://github.com/galaxyproject/galaxy/pull/11148 +.. _Pull Request 11153: https://github.com/galaxyproject/galaxy/pull/11153 +.. _Pull Request 11155: https://github.com/galaxyproject/galaxy/pull/11155 +.. _Pull Request 11156: https://github.com/galaxyproject/galaxy/pull/11156 +.. _Pull Request 11157: https://github.com/galaxyproject/galaxy/pull/11157 +.. _Pull Request 11160: https://github.com/galaxyproject/galaxy/pull/11160 +.. _Pull Request 11167: https://github.com/galaxyproject/galaxy/pull/11167 +.. _Pull Request 11173: https://github.com/galaxyproject/galaxy/pull/11173 +.. _Pull Request 11176: https://github.com/galaxyproject/galaxy/pull/11176 +.. _Pull Request 11177: https://github.com/galaxyproject/galaxy/pull/11177 +.. _Pull Request 11178: https://github.com/galaxyproject/galaxy/pull/11178 +.. _Pull Request 11179: https://github.com/galaxyproject/galaxy/pull/11179 +.. _Pull Request 11180: https://github.com/galaxyproject/galaxy/pull/11180 +.. _Pull Request 11188: https://github.com/galaxyproject/galaxy/pull/11188 +.. _Pull Request 11192: https://github.com/galaxyproject/galaxy/pull/11192 +.. _Pull Request 11197: https://github.com/galaxyproject/galaxy/pull/11197 +.. _Pull Request 11198: https://github.com/galaxyproject/galaxy/pull/11198 +.. _Pull Request 11202: https://github.com/galaxyproject/galaxy/pull/11202 +.. _Pull Request 11203: https://github.com/galaxyproject/galaxy/pull/11203 +.. _Pull Request 11204: https://github.com/galaxyproject/galaxy/pull/11204 +.. _Pull Request 11206: https://github.com/galaxyproject/galaxy/pull/11206 +.. _Pull Request 11211: https://github.com/galaxyproject/galaxy/pull/11211 +.. _Pull Request 11214: https://github.com/galaxyproject/galaxy/pull/11214 +.. _Pull Request 11215: https://github.com/galaxyproject/galaxy/pull/11215 +.. _Pull Request 11217: https://github.com/galaxyproject/galaxy/pull/11217 +.. _Pull Request 11219: https://github.com/galaxyproject/galaxy/pull/11219 +.. _Pull Request 11220: https://github.com/galaxyproject/galaxy/pull/11220 +.. _Pull Request 11223: https://github.com/galaxyproject/galaxy/pull/11223 +.. _Pull Request 11224: https://github.com/galaxyproject/galaxy/pull/11224 +.. _Pull Request 11226: https://github.com/galaxyproject/galaxy/pull/11226 +.. _Pull Request 11227: https://github.com/galaxyproject/galaxy/pull/11227 +.. _Pull Request 11228: https://github.com/galaxyproject/galaxy/pull/11228 +.. _Pull Request 11230: https://github.com/galaxyproject/galaxy/pull/11230 +.. _Pull Request 11232: https://github.com/galaxyproject/galaxy/pull/11232 +.. _Pull Request 11234: https://github.com/galaxyproject/galaxy/pull/11234 +.. _Pull Request 11235: https://github.com/galaxyproject/galaxy/pull/11235 +.. _Pull Request 11238: https://github.com/galaxyproject/galaxy/pull/11238 +.. _Pull Request 11240: https://github.com/galaxyproject/galaxy/pull/11240 +.. _Pull Request 11241: https://github.com/galaxyproject/galaxy/pull/11241 +.. _Pull Request 11251: https://github.com/galaxyproject/galaxy/pull/11251 +.. _Pull Request 11253: https://github.com/galaxyproject/galaxy/pull/11253 +.. _Pull Request 11258: https://github.com/galaxyproject/galaxy/pull/11258 +.. _Pull Request 11259: https://github.com/galaxyproject/galaxy/pull/11259 +.. _Pull Request 11262: https://github.com/galaxyproject/galaxy/pull/11262 +.. _Pull Request 11264: https://github.com/galaxyproject/galaxy/pull/11264 +.. _Pull Request 11265: https://github.com/galaxyproject/galaxy/pull/11265 +.. _Pull Request 11267: https://github.com/galaxyproject/galaxy/pull/11267 +.. _Pull Request 11271: https://github.com/galaxyproject/galaxy/pull/11271 +.. _Pull Request 11272: https://github.com/galaxyproject/galaxy/pull/11272 +.. _Pull Request 11274: https://github.com/galaxyproject/galaxy/pull/11274 +.. _Pull Request 11276: https://github.com/galaxyproject/galaxy/pull/11276 +.. _Pull Request 11278: https://github.com/galaxyproject/galaxy/pull/11278 +.. _Pull Request 11292: https://github.com/galaxyproject/galaxy/pull/11292 +.. _Pull Request 11296: https://github.com/galaxyproject/galaxy/pull/11296 +.. _Pull Request 11300: https://github.com/galaxyproject/galaxy/pull/11300 +.. _Pull Request 11304: https://github.com/galaxyproject/galaxy/pull/11304 +.. _Pull Request 11307: https://github.com/galaxyproject/galaxy/pull/11307 +.. _Pull Request 11313: https://github.com/galaxyproject/galaxy/pull/11313 +.. _Pull Request 11319: https://github.com/galaxyproject/galaxy/pull/11319 +.. _Pull Request 11320: https://github.com/galaxyproject/galaxy/pull/11320 +.. _Pull Request 11322: https://github.com/galaxyproject/galaxy/pull/11322 +.. _Pull Request 11326: https://github.com/galaxyproject/galaxy/pull/11326 +.. _Pull Request 11329: https://github.com/galaxyproject/galaxy/pull/11329 +.. _Pull Request 11331: https://github.com/galaxyproject/galaxy/pull/11331 +.. _Pull Request 11342: https://github.com/galaxyproject/galaxy/pull/11342 +.. _Pull Request 11346: https://github.com/galaxyproject/galaxy/pull/11346 +.. _Pull Request 11347: https://github.com/galaxyproject/galaxy/pull/11347 +.. _Pull Request 11351: https://github.com/galaxyproject/galaxy/pull/11351 +.. _Pull Request 11358: https://github.com/galaxyproject/galaxy/pull/11358 +.. _Pull Request 11359: https://github.com/galaxyproject/galaxy/pull/11359 +.. _Pull Request 11362: https://github.com/galaxyproject/galaxy/pull/11362 +.. _Pull Request 11365: https://github.com/galaxyproject/galaxy/pull/11365 +.. _Pull Request 11378: https://github.com/galaxyproject/galaxy/pull/11378 +.. _Pull Request 11380: https://github.com/galaxyproject/galaxy/pull/11380 +.. _Pull Request 11383: https://github.com/galaxyproject/galaxy/pull/11383 +.. _Pull Request 11384: https://github.com/galaxyproject/galaxy/pull/11384 +.. _Pull Request 11385: https://github.com/galaxyproject/galaxy/pull/11385 +.. _Pull Request 11386: https://github.com/galaxyproject/galaxy/pull/11386 +.. _Pull Request 11390: https://github.com/galaxyproject/galaxy/pull/11390 +.. _Pull Request 11393: https://github.com/galaxyproject/galaxy/pull/11393 +.. _Pull Request 11394: https://github.com/galaxyproject/galaxy/pull/11394 +.. _Pull Request 11400: https://github.com/galaxyproject/galaxy/pull/11400 +.. _Pull Request 11402: https://github.com/galaxyproject/galaxy/pull/11402 +.. _Pull Request 11403: https://github.com/galaxyproject/galaxy/pull/11403 +.. _Pull Request 11404: https://github.com/galaxyproject/galaxy/pull/11404 +.. _Pull Request 11405: https://github.com/galaxyproject/galaxy/pull/11405 +.. _Pull Request 11411: https://github.com/galaxyproject/galaxy/pull/11411 +.. _Pull Request 11412: https://github.com/galaxyproject/galaxy/pull/11412 +.. _Pull Request 11417: https://github.com/galaxyproject/galaxy/pull/11417 +.. _Pull Request 11418: https://github.com/galaxyproject/galaxy/pull/11418 +.. _Pull Request 11422: https://github.com/galaxyproject/galaxy/pull/11422 +.. _Pull Request 11424: https://github.com/galaxyproject/galaxy/pull/11424 +.. _Pull Request 11425: https://github.com/galaxyproject/galaxy/pull/11425 +.. _Pull Request 11429: https://github.com/galaxyproject/galaxy/pull/11429 +.. _Pull Request 11452: https://github.com/galaxyproject/galaxy/pull/11452 +.. _Pull Request 11454: https://github.com/galaxyproject/galaxy/pull/11454 +.. _Pull Request 11458: https://github.com/galaxyproject/galaxy/pull/11458 +.. _Pull Request 11467: https://github.com/galaxyproject/galaxy/pull/11467 +.. _Pull Request 11469: https://github.com/galaxyproject/galaxy/pull/11469 +.. _Pull Request 11477: https://github.com/galaxyproject/galaxy/pull/11477 +.. _Pull Request 11478: https://github.com/galaxyproject/galaxy/pull/11478 +.. _Pull Request 11482: https://github.com/galaxyproject/galaxy/pull/11482 +.. _Pull Request 11483: https://github.com/galaxyproject/galaxy/pull/11483 +.. _Pull Request 11485: https://github.com/galaxyproject/galaxy/pull/11485 +.. _Pull Request 11486: https://github.com/galaxyproject/galaxy/pull/11486 +.. _Pull Request 11489: https://github.com/galaxyproject/galaxy/pull/11489 +.. _Pull Request 11496: https://github.com/galaxyproject/galaxy/pull/11496 +.. _Pull Request 11497: https://github.com/galaxyproject/galaxy/pull/11497 +.. _Pull Request 11507: https://github.com/galaxyproject/galaxy/pull/11507 +.. _Pull Request 11508: https://github.com/galaxyproject/galaxy/pull/11508 +.. _Pull Request 11509: https://github.com/galaxyproject/galaxy/pull/11509 +.. _Pull Request 11526: https://github.com/galaxyproject/galaxy/pull/11526 +.. _Pull Request 11530: https://github.com/galaxyproject/galaxy/pull/11530 +.. _Pull Request 11539: https://github.com/galaxyproject/galaxy/pull/11539 +.. _Pull Request 11552: https://github.com/galaxyproject/galaxy/pull/11552 +.. _Pull Request 11557: https://github.com/galaxyproject/galaxy/pull/11557 +.. _Pull Request 11560: https://github.com/galaxyproject/galaxy/pull/11560 +.. _Pull Request 11561: https://github.com/galaxyproject/galaxy/pull/11561 +.. _Pull Request 11566: https://github.com/galaxyproject/galaxy/pull/11566 +.. _Pull Request 11568: https://github.com/galaxyproject/galaxy/pull/11568 +.. _Pull Request 11570: https://github.com/galaxyproject/galaxy/pull/11570 +.. _Pull Request 11575: https://github.com/galaxyproject/galaxy/pull/11575 +.. _Pull Request 11580: https://github.com/galaxyproject/galaxy/pull/11580 +.. _Pull Request 11588: https://github.com/galaxyproject/galaxy/pull/11588 +.. _Pull Request 11589: https://github.com/galaxyproject/galaxy/pull/11589 +.. _Pull Request 11590: https://github.com/galaxyproject/galaxy/pull/11590 +.. _Pull Request 11591: https://github.com/galaxyproject/galaxy/pull/11591 +.. _Pull Request 11592: https://github.com/galaxyproject/galaxy/pull/11592 +.. _Pull Request 11599: https://github.com/galaxyproject/galaxy/pull/11599 +.. _Pull Request 11600: https://github.com/galaxyproject/galaxy/pull/11600 +.. _Pull Request 11604: https://github.com/galaxyproject/galaxy/pull/11604 +.. _Pull Request 11607: https://github.com/galaxyproject/galaxy/pull/11607 +.. _Pull Request 11614: https://github.com/galaxyproject/galaxy/pull/11614 +.. _Pull Request 11616: https://github.com/galaxyproject/galaxy/pull/11616 +.. _Pull Request 11619: https://github.com/galaxyproject/galaxy/pull/11619 +.. _Pull Request 11627: https://github.com/galaxyproject/galaxy/pull/11627 +.. _Pull Request 11629: https://github.com/galaxyproject/galaxy/pull/11629 +.. _Pull Request 11631: https://github.com/galaxyproject/galaxy/pull/11631 +.. _Pull Request 11633: https://github.com/galaxyproject/galaxy/pull/11633 +.. _Pull Request 11634: https://github.com/galaxyproject/galaxy/pull/11634 +.. _Pull Request 11637: https://github.com/galaxyproject/galaxy/pull/11637 +.. _Pull Request 11638: https://github.com/galaxyproject/galaxy/pull/11638 +.. _Pull Request 11639: https://github.com/galaxyproject/galaxy/pull/11639 +.. _Pull Request 11640: https://github.com/galaxyproject/galaxy/pull/11640 +.. _Pull Request 11641: https://github.com/galaxyproject/galaxy/pull/11641 +.. _Pull Request 11643: https://github.com/galaxyproject/galaxy/pull/11643 +.. _Pull Request 11646: https://github.com/galaxyproject/galaxy/pull/11646 +.. _Pull Request 11647: https://github.com/galaxyproject/galaxy/pull/11647 +.. _Pull Request 11648: https://github.com/galaxyproject/galaxy/pull/11648 +.. _Pull Request 11649: https://github.com/galaxyproject/galaxy/pull/11649 +.. _Pull Request 11650: https://github.com/galaxyproject/galaxy/pull/11650 +.. _Pull Request 11654: https://github.com/galaxyproject/galaxy/pull/11654 +.. _Pull Request 11655: https://github.com/galaxyproject/galaxy/pull/11655 +.. _Pull Request 11660: https://github.com/galaxyproject/galaxy/pull/11660 +.. _Pull Request 11661: https://github.com/galaxyproject/galaxy/pull/11661 +.. _Pull Request 11662: https://github.com/galaxyproject/galaxy/pull/11662 +.. _Pull Request 11663: https://github.com/galaxyproject/galaxy/pull/11663 +.. _Pull Request 11664: https://github.com/galaxyproject/galaxy/pull/11664 +.. _Pull Request 11665: https://github.com/galaxyproject/galaxy/pull/11665 +.. _Pull Request 11669: https://github.com/galaxyproject/galaxy/pull/11669 +.. _Pull Request 11670: https://github.com/galaxyproject/galaxy/pull/11670 +.. _Pull Request 11671: https://github.com/galaxyproject/galaxy/pull/11671 +.. _Pull Request 11673: https://github.com/galaxyproject/galaxy/pull/11673 +.. _Pull Request 11674: https://github.com/galaxyproject/galaxy/pull/11674 +.. _Pull Request 11676: https://github.com/galaxyproject/galaxy/pull/11676 +.. _Pull Request 11678: https://github.com/galaxyproject/galaxy/pull/11678 +.. _Pull Request 11680: https://github.com/galaxyproject/galaxy/pull/11680 +.. _Pull Request 11682: https://github.com/galaxyproject/galaxy/pull/11682 +.. _Pull Request 11683: https://github.com/galaxyproject/galaxy/pull/11683 +.. _Pull Request 11684: https://github.com/galaxyproject/galaxy/pull/11684 +.. _Pull Request 11686: https://github.com/galaxyproject/galaxy/pull/11686 +.. _Pull Request 11687: https://github.com/galaxyproject/galaxy/pull/11687 +.. _Pull Request 11692: https://github.com/galaxyproject/galaxy/pull/11692 +.. _Pull Request 11693: https://github.com/galaxyproject/galaxy/pull/11693 +.. _Pull Request 11694: https://github.com/galaxyproject/galaxy/pull/11694 +.. _Pull Request 11696: https://github.com/galaxyproject/galaxy/pull/11696 +.. _Pull Request 11697: https://github.com/galaxyproject/galaxy/pull/11697 +.. _Pull Request 11700: https://github.com/galaxyproject/galaxy/pull/11700 +.. _Pull Request 11702: https://github.com/galaxyproject/galaxy/pull/11702 +.. _Pull Request 11703: https://github.com/galaxyproject/galaxy/pull/11703 +.. _Pull Request 11708: https://github.com/galaxyproject/galaxy/pull/11708 +.. _Pull Request 11711: https://github.com/galaxyproject/galaxy/pull/11711 +.. _Pull Request 11712: https://github.com/galaxyproject/galaxy/pull/11712 +.. _Pull Request 11716: https://github.com/galaxyproject/galaxy/pull/11716 +.. _Pull Request 11718: https://github.com/galaxyproject/galaxy/pull/11718 +.. _Pull Request 11720: https://github.com/galaxyproject/galaxy/pull/11720 +.. _Pull Request 11724: https://github.com/galaxyproject/galaxy/pull/11724 +.. _Pull Request 11727: https://github.com/galaxyproject/galaxy/pull/11727 +.. _Pull Request 11728: https://github.com/galaxyproject/galaxy/pull/11728 +.. _Pull Request 11731: https://github.com/galaxyproject/galaxy/pull/11731 +.. _Pull Request 11732: https://github.com/galaxyproject/galaxy/pull/11732 +.. _Pull Request 11736: https://github.com/galaxyproject/galaxy/pull/11736 +.. _Pull Request 11740: https://github.com/galaxyproject/galaxy/pull/11740 +.. _Pull Request 11741: https://github.com/galaxyproject/galaxy/pull/11741 +.. _Pull Request 11747: https://github.com/galaxyproject/galaxy/pull/11747 +.. _Pull Request 11749: https://github.com/galaxyproject/galaxy/pull/11749 +.. _Pull Request 11750: https://github.com/galaxyproject/galaxy/pull/11750 +.. _Pull Request 11751: https://github.com/galaxyproject/galaxy/pull/11751 +.. _Pull Request 11753: https://github.com/galaxyproject/galaxy/pull/11753 +.. _Pull Request 11757: https://github.com/galaxyproject/galaxy/pull/11757 +.. _Pull Request 11758: https://github.com/galaxyproject/galaxy/pull/11758 +.. _Pull Request 11761: https://github.com/galaxyproject/galaxy/pull/11761 +.. _Pull Request 11762: https://github.com/galaxyproject/galaxy/pull/11762 +.. _Pull Request 11763: https://github.com/galaxyproject/galaxy/pull/11763 +.. _Pull Request 11764: https://github.com/galaxyproject/galaxy/pull/11764 +.. _Pull Request 11765: https://github.com/galaxyproject/galaxy/pull/11765 +.. _Pull Request 11769: https://github.com/galaxyproject/galaxy/pull/11769 +.. _Pull Request 11772: https://github.com/galaxyproject/galaxy/pull/11772 +.. _Pull Request 11773: https://github.com/galaxyproject/galaxy/pull/11773 +.. _Pull Request 11776: https://github.com/galaxyproject/galaxy/pull/11776 +.. _Pull Request 11777: https://github.com/galaxyproject/galaxy/pull/11777 +.. _Pull Request 11778: https://github.com/galaxyproject/galaxy/pull/11778 +.. _Pull Request 11779: https://github.com/galaxyproject/galaxy/pull/11779 +.. _Pull Request 11782: https://github.com/galaxyproject/galaxy/pull/11782 +.. _Pull Request 11783: https://github.com/galaxyproject/galaxy/pull/11783 +.. _Pull Request 11788: https://github.com/galaxyproject/galaxy/pull/11788 +.. _Pull Request 11789: https://github.com/galaxyproject/galaxy/pull/11789 +.. _Pull Request 11790: https://github.com/galaxyproject/galaxy/pull/11790 +.. _Pull Request 11791: https://github.com/galaxyproject/galaxy/pull/11791 +.. _Pull Request 11792: https://github.com/galaxyproject/galaxy/pull/11792 +.. _Pull Request 11793: https://github.com/galaxyproject/galaxy/pull/11793 +.. _Pull Request 11794: https://github.com/galaxyproject/galaxy/pull/11794 +.. _Pull Request 11795: https://github.com/galaxyproject/galaxy/pull/11795 +.. _Pull Request 11798: https://github.com/galaxyproject/galaxy/pull/11798 +.. _Pull Request 11800: https://github.com/galaxyproject/galaxy/pull/11800 +.. _Pull Request 11801: https://github.com/galaxyproject/galaxy/pull/11801 +.. _Pull Request 11802: https://github.com/galaxyproject/galaxy/pull/11802 +.. _Pull Request 11808: https://github.com/galaxyproject/galaxy/pull/11808 +.. _Pull Request 11810: https://github.com/galaxyproject/galaxy/pull/11810 +.. _Pull Request 11811: https://github.com/galaxyproject/galaxy/pull/11811 +.. _Pull Request 11812: https://github.com/galaxyproject/galaxy/pull/11812 +.. _Pull Request 11814: https://github.com/galaxyproject/galaxy/pull/11814 +.. _Pull Request 11815: https://github.com/galaxyproject/galaxy/pull/11815 +.. _Pull Request 11816: https://github.com/galaxyproject/galaxy/pull/11816 +.. _Pull Request 11818: https://github.com/galaxyproject/galaxy/pull/11818 +.. _Pull Request 11825: https://github.com/galaxyproject/galaxy/pull/11825 +.. _Pull Request 11826: https://github.com/galaxyproject/galaxy/pull/11826 +.. _Pull Request 11830: https://github.com/galaxyproject/galaxy/pull/11830 +.. _Pull Request 11831: https://github.com/galaxyproject/galaxy/pull/11831 +.. _Pull Request 11832: https://github.com/galaxyproject/galaxy/pull/11832 +.. _Pull Request 11835: https://github.com/galaxyproject/galaxy/pull/11835 +.. _Pull Request 11838: https://github.com/galaxyproject/galaxy/pull/11838 +.. _Pull Request 11839: https://github.com/galaxyproject/galaxy/pull/11839 +.. _Pull Request 11840: https://github.com/galaxyproject/galaxy/pull/11840 +.. _Pull Request 11843: https://github.com/galaxyproject/galaxy/pull/11843 +.. _Pull Request 11844: https://github.com/galaxyproject/galaxy/pull/11844 +.. _Pull Request 11845: https://github.com/galaxyproject/galaxy/pull/11845 +.. _Pull Request 11846: https://github.com/galaxyproject/galaxy/pull/11846 +.. _Pull Request 11847: https://github.com/galaxyproject/galaxy/pull/11847 +.. _Pull Request 11849: https://github.com/galaxyproject/galaxy/pull/11849 +.. _Pull Request 11850: https://github.com/galaxyproject/galaxy/pull/11850 +.. _Pull Request 11852: https://github.com/galaxyproject/galaxy/pull/11852 +.. _Pull Request 11856: https://github.com/galaxyproject/galaxy/pull/11856 +.. _Pull Request 11859: https://github.com/galaxyproject/galaxy/pull/11859 +.. _Pull Request 11861: https://github.com/galaxyproject/galaxy/pull/11861 +.. _Pull Request 11863: https://github.com/galaxyproject/galaxy/pull/11863 +.. _Pull Request 11868: https://github.com/galaxyproject/galaxy/pull/11868 +.. _Pull Request 11871: https://github.com/galaxyproject/galaxy/pull/11871 +.. _Pull Request 11872: https://github.com/galaxyproject/galaxy/pull/11872 +.. _Pull Request 11873: https://github.com/galaxyproject/galaxy/pull/11873 +.. _Pull Request 11874: https://github.com/galaxyproject/galaxy/pull/11874 +.. _Pull Request 11877: https://github.com/galaxyproject/galaxy/pull/11877 +.. _Pull Request 11878: https://github.com/galaxyproject/galaxy/pull/11878 +.. _Pull Request 11879: https://github.com/galaxyproject/galaxy/pull/11879 +.. _Pull Request 11880: https://github.com/galaxyproject/galaxy/pull/11880 +.. _Pull Request 11881: https://github.com/galaxyproject/galaxy/pull/11881 +.. _Pull Request 11882: https://github.com/galaxyproject/galaxy/pull/11882 +.. _Pull Request 11883: https://github.com/galaxyproject/galaxy/pull/11883 +.. _Pull Request 11884: https://github.com/galaxyproject/galaxy/pull/11884 +.. _Pull Request 11886: https://github.com/galaxyproject/galaxy/pull/11886 +.. _Pull Request 11891: https://github.com/galaxyproject/galaxy/pull/11891 +.. _Pull Request 11895: https://github.com/galaxyproject/galaxy/pull/11895 +.. _Pull Request 11897: https://github.com/galaxyproject/galaxy/pull/11897 +.. _Pull Request 11899: https://github.com/galaxyproject/galaxy/pull/11899 +.. _Pull Request 11900: https://github.com/galaxyproject/galaxy/pull/11900 +.. _Pull Request 11901: https://github.com/galaxyproject/galaxy/pull/11901 +.. _Pull Request 11902: https://github.com/galaxyproject/galaxy/pull/11902 +.. _Pull Request 11904: https://github.com/galaxyproject/galaxy/pull/11904 +.. _Pull Request 11905: https://github.com/galaxyproject/galaxy/pull/11905 +.. _Pull Request 11906: https://github.com/galaxyproject/galaxy/pull/11906 +.. _Pull Request 11907: https://github.com/galaxyproject/galaxy/pull/11907 +.. _Pull Request 11908: https://github.com/galaxyproject/galaxy/pull/11908 +.. _Pull Request 11909: https://github.com/galaxyproject/galaxy/pull/11909 +.. _Pull Request 11910: https://github.com/galaxyproject/galaxy/pull/11910 +.. _Pull Request 11911: https://github.com/galaxyproject/galaxy/pull/11911 +.. _Pull Request 11912: https://github.com/galaxyproject/galaxy/pull/11912 +.. _Pull Request 11913: https://github.com/galaxyproject/galaxy/pull/11913 +.. _Pull Request 11918: https://github.com/galaxyproject/galaxy/pull/11918 +.. _Pull Request 11922: https://github.com/galaxyproject/galaxy/pull/11922 +.. _Pull Request 11923: https://github.com/galaxyproject/galaxy/pull/11923 +.. _Pull Request 11925: https://github.com/galaxyproject/galaxy/pull/11925 +.. _Pull Request 11928: https://github.com/galaxyproject/galaxy/pull/11928 +.. _Pull Request 11929: https://github.com/galaxyproject/galaxy/pull/11929