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galaxy/doc/source/releases/19.09.rst
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Nicola Soranzo 35fd602f87 Release notes fixes
2019-10-09 10:30:01 +01:00

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.. to_doc
19.09
===============================
.. announce_start
Enhancements
-------------------------------
* Add InteractiveTools.
`Pull Request 7494`_, `Pull Request 8506`_, `Pull Request 8574`_,
`Pull Request 8589`_
* Implement workflow invocation reports.
`Pull Request 8543`_, `Pull Request 8664`_, `Pull Request 8683`_
* VueJS rewrite of Toolshed install interface - with substantial API extensions to enable this.
`Pull Request 7402`_, `Pull Request 8090`_, `Pull Request 8621`_,
`Pull Request 8635`_, `Pull Request 8681`_, `Pull Request 7825`_
`Pull Request 8638`_, `Pull Request 8035`_, `Pull Request 8076`_,
`Pull Request 8585`_, `Pull Request 8622`_
* VueJS rewrite of admin jobs page
(thanks to `@scrathat <https://github.com/scrathat>`__).
`Pull Request 7790`_
* VueJS rewrite of tools panel (resolves `#8262
<https://github.com/galaxyproject/galaxy/issues/8262>`__)
(thanks to `@inkuzmin <https://github.com/inkuzmin>`__).
`Pull Request 8368`_
* VueJS rewrite of dataset job properties tables - with API extensions to enable this.
`Pull Request 8022`_, `Pull Request 8044`_
* VueJS rewrite of Page management components - with API extensions to enable this.
`Pull Request 8047`_
* New visualization - free style image annotation
(thanks to `@anuprulez <https://github.com/anuprulez>`__).
`Pull Request 6891`_
* New visualization - OpenLayers maps.
(thanks to `@anuprulez <https://github.com/anuprulez>`__).
`Pull Request 7888`_
* New visualization - hyphy-vision
(thanks to `@veg <https://github.com/veg>`__).
`Pull Request 8227`_
* Implement frameworks for datatype validation and tool-based QC.
`Pull Request 7913`_
* New Pulsar runner for Kubernetes allowing file staging with Kubernetes.
`Pull Request 7835`_, `Pull Request 8195`_
* Implement option to delete or preserve Kubernetes pods after completion
(thanks to `@nuwang <https://github.com/nuwang>`__).
`Pull Request 8091`_
* Implement ``walltime_limit`` option for the Kuberentes jobs
(thanks to `@telukir <https://github.com/telukir>`__).
`Pull Request 8311`_
* Implement UI for Authnz API.
`Pull Request 7665`_
* Extend dataset search and add search API endpoint
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 7745`_
* Add Matthias Bernt to the committers group.
`Pull Request 8446`_
* Add filtering and sorting for folders in data libraries
(with help from `@bwlang <https://github.com/bwlang>`__).
`Pull Request 8281`_, `Pull Request 8287`_, `Pull Request 8277`_
* Implement ``xref`` tag on the tool structure (with visualization)
(thanks to `@ValentinMarcon <https://github.com/ValentinMarcon>`__).
`Pull Request 7905`_
* Substantial progress toward refactoring and decomposing Galaxy into properly
installable packages.
(with help from `@dglaetzer <https://github.com/dglaetzer>`__,
`@nsoranzo <https://github.com/nsoranzo>`__ and `@gmauro <https://github.com/gmauro>`__).
`Pull Request 921`_, `Pull Request 7992`_, `Pull Request 8114`_,
`Pull Request 8234`_, `Pull Request 8241`_, `Pull Request 8266`_,
`Pull Request 8276`_, `Pull Request 8284`_, `Pull Request 8293`_,
`Pull Request 8306`_, `Pull Request 8305`_, `Pull Request 8307`_,
`Pull Request 8308`_, `Pull Request 7971`_, `Pull Request 8051`_,
`Pull Request 8062`_, `Pull Request 8280`_, `Pull Request 8310`_,
`Pull Request 8302`_, `Pull Request 8298`_, `Pull Request 8098`_,
`Pull Request 8208`_, `Pull Request 8235`_, `Pull Request 8365`_,
`Pull Request 8357`_, `Pull Request 8342`_, `Pull Request 8345`_,
`Pull Request 8431`_, `Pull Request 8269`_, `Pull Request 8314`_,
`Pull Request 8687`_, `Pull Request 8702`_, `Pull Request 8610`_,
`Pull Request 8315`_
* Enable dynamic reloading of select config options.
`Pull Request 8475`_
* Improved architecture for Galaxy's configuration object
`Pull Request 8502`_, `Pull Request 8526`_,
`Pull Request 8462`_, `Pull Request 8433`_,
`Pull Request 8545`_
* Allow YAML/JSON job configuration - including embedding right in Galaxy config, validation, better defaults,
and better section naming.
`Pull Request 7854`_, `Pull Request 8616`_, `Pull Request 7882`_
`Pull Request 8609`_
* Allow declaring dependency resolvers right in Galaxy config, validation, and serialization.
`Pull Request 8118`_, `Pull Request 8152`_
* Add external display application plugin for iCn3D.
`Pull Request 8347`_
* Enable external display application plugin parameters to declare ``allow_cors="true"``.
`Pull Request 8539`_
* Add XML Schema Definition (XSD) for Galaxy External Dispaly Applications (GEDAs).
`Pull Request 8461`_
* Adding Shapefile composite datatype
(thanks to `@Alanamosse <https://github.com/Alanamosse>`__).
`Pull Request 7615`_
* Add mcool datatype and extend h5 tool output testing
(thanks to `@msauria <https://github.com/msauria>`__).
`Pull Request 7993`_
* Add hyphy_results.json datatype
(thanks to `@veg <https://github.com/veg>`__).
`Pull Request 8186`_
* Add pgp and osw datatypes as used in OpenSWATH experiments
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 8458`_
* Add ckpt datatype
(thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
`Pull Request 8086`_
* Add dada2 datatypes
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 7895`_
* Add rDock active site datatype
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 8727`_
* Add Kallistobus datatypes
(thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
`Pull Request 8229`_
* Sniff fastqsanger more aggressively
(thanks to `@wm75 <https://github.com/wm75>`__).
`Pull Request 8322`_
* Various collection operation tool improvements
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8038`_
* Enhance unzip/zip collection collection operation to annotate output format properly
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 8239`_
* Implement option to strip whitespace from tool ``environment_variables``.
`Pull Request 8296`_
* Add tool output test assertion for ``n_lines``
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 8440`_
* Add zoom reset feature for workflows
(thanks to `@juleengraham <https://github.com/juleengraham>`__).
`Pull Request 8301`_
* Fix tool run output to display more data.
`Pull Request 8018`_
* Track basename at the time of creation for datasets.
`Pull Request 7670`_
* Remove GFF headers during conversion (backported to 19.05).
`Pull Request 7808`_
* Enable mulled containers by default for 19.09.
`Pull Request 8569`_
* Enhanced GitLab integration
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 8455`_, `Issue #8183 <https://github.com/galaxyproject/galaxy/issues/8183>`__
* Make admin users grid filter on purged
`Pull Request 8303`_
* Add links to admin entry page.
`Pull Request 8351`_
* Add ELIXIR OIDC backend, upgrade social-auth-core requirement version
(thanks to `@kidanem <https://github.com/kidanem>`__).
`Pull Request 7852`_
* Run futurize for python2 cheetah templates, fix scope issue for Python 3
comprehensions
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 7867`_
* Improve look and feel for data libraries
(thanks to `@inkuzmin <https://github.com/inkuzmin>`__).
`Pull Request 7878`_
* Raise detailed exception for broken citation
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 7891`_
* Remove ``file`` attribute of bibtex citation
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 7911`_
* Use transparent background in default welcome page.
`Pull Request 7929`_
* Cellxgene GIE - use API to get datasets.
`Pull Request 7945`_
* Change "username" to "public name" throughout the user interface.
`Pull Request 8009`_
* History menu (cog) UI updates.
`Pull Request 8024`_
* Delegate config file watching to single handler
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8078`_
* Allow admins to disable the visualizations tab in the masthead.
`Pull Request 8450`_
* Update all Python dependencies
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8120`_, `Pull Request 8126`_
* Enable authorization to Google Cloud Platform
`Pull Request 8123`_
* Update requirements and use pyuwsgi
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8489`_
* Update ``cloudauthz`` dependency to v0.4.0.
`Pull Request 8155`_
* Improve accessibility of certain UI elements.
`Pull Request 8133`_
* Round-off the time taken for CPU execution
(thanks to `@janani-prasad <https://github.com/janani-prasad>`__).
`Pull Request 8144`_
* Add API to tag library datasets
(thanks to `@abretaud <https://github.com/abretaud>`__).
`Pull Request 8530`_
* Improve API docs.
`Pull Request 8541`_
* Update repository issue handling text in docs.
`Pull Request 8542`_
* Improved tool parameter error reporting
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 8163`_
* Configuration API cleanup.
`Pull Request 8206`_
* New regular expression filter, and efficient sort filter
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 8211`_
* Data managers - allow removal of entries
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 8250`_, `Pull Request 8503`_
* Adjust minimum tag length.
`Pull Request 8256`_
* Some improvements to tool menu styles.
`Pull Request 8285`_
* Make styleguide work for VueJS components.
`Pull Request 8291`_
* Library date propagate
(thanks to `@bwlang <https://github.com/bwlang>`__).
`Pull Request 8294`_
* Skip database migrations on entirely clean new databases
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8300`_
* Implement undelete and purge API for users
(thanks to `@cganote <https://github.com/cganote>`__).
`Pull Request 8309`_
* Use lowercase true/false in config_schema.yml
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8319`_
* Check correct permission for allowing a user to modify lib folder
(thanks to `@scholtalbers <https://github.com/scholtalbers>`__).
`Pull Request 8326`_
* Issue`#8105 <https://github.com/galaxyproject/galaxy/issues/8105>`__: Make
tool favourite query a toggle
(thanks to `@janani-prasad <https://github.com/janani-prasad>`__).
`Pull Request 8331`_
* Update anchor tags and enhance navigation cues for screen readers
`Pull Request 8334`_
* Better config isolation for integration tests.
`Pull Request 8355`_
* catch exceptions occuring in expression validators
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 8359`_
* Update RST files to reflect code structure changes.
`Pull Request 8363`_
* make cleanup script use logging instead of print
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 8394`_
* Mention IGB in the docs
`Pull Request 8404`_
* Automatically replace dashes by underscores for ``argument`` attribute on tool parameters.
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 8409`_
* Add basic unit test for lint_inputs
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8410`_
* Various improvements designed to optimize ToolBox loading time.
`Pull Request 8421`_, `Pull Request 8422`_, `Pull Request 8426`_
* Fix authentication provider exception not logged
(thanks to `@BioinformaticsPlatformWIV-ISP <https://github.com
/BioinformaticsPlatformWIV-ISP>`__).
`Pull Request 8424`_
* Optimize unrestricted library dataset permission checks.
`Pull Request 8430`_
* Change 'a when tag has not been defined for' level to debug
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8439`_
* Fix database migrations for MySQL but mention it is unsupported in the docs
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8407`_, `Pull Request 8640`_, `Pull Request 8473`_
* Auto convert python 2 code files using 2to3
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8499`_
* Update sass version to support node 12.
`Pull Request 8507`_
* Integration test for ``outputs_to_working_directory`` with Pulsar.
`Pull Request 8335`_
* Fix 'postgres' dialect name has been renamed to 'postgresql' deprecat…
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 7804`_
* Use ``markupsafe.escape`` instead of ``cgi.escape``
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 7837`_
* Use ``getfullargspec`` on Python 3
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 7838`_
* Align popup/dropdown menu templating.
`Pull Request 7871`_
* Change keyboard input for floats and switch to ES6 features
`Pull Request 7927`_
* Tool output_checker - fix superficial condition
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 7980`_
* Enhance ``galaxy.js`` and entry folder for ES6.
`Pull Request 8025`_, `Pull Request 8034`_
* Switch ``var`` to ``let`` and ``const`` for VueJS components
`Pull Request 8028`_, `Pull Request 8036`_
* es6 upgrades in entry folder
* Remove unresolved function causing console error.
`Pull Request 8101`_
* Swap out ``galaxy.util.odict`` for core python ``collections.OrderedDict`` objects.
`Pull Request 8104`_
* Enhance ``make config-rebuild`` to update config/docs.
`Pull Request 8220`_
* Refactor ``setup_user_get_key`` method to return the created test user and its
API key.
`Pull Request 8233`_
* Fix various small UI issues.
`Pull Request 8275`_
* Replace in-python quota calc with a SQL query
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 8452`_
* Remove deprecated scripts
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 8465`_
* Fix markup in ToolEntryPoints, format client
`Pull Request 8549`_
* Allow specifying ``maxseconds`` in ``verify_tool``
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 7828`_
* Call tool_script.sh with shell
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8077`_
* Drop "Manage" from admin workflow Invocation link.
`Pull Request 8693`_
* Record Galaxy version a job is created with.
`Pull Request 8414`_
* Git ignore files in ``database/shed_tools`` directory
(thanks to `@ashvark <https://github.com/ashvark>`__).
`Pull Request 8268`_
* Added unit testing section to the client README
`Pull Request 7890`_
* Update Sphinx RST files for ``lib/``.
`Pull Request 8270`_
* Allow re-populating objectstore from ``to_dict`` form.
`Pull Request 8213`_
* Testing framework fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8147`_
* Extend ObjectStore integration tests.
`Pull Request 8042`_
* Fix link formats for mulled_containers.rst, minor rewording.
`Pull Request 8075`_
* Add missing files from galaxy-lib
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8113`_
Fixes
-------------------------------
* Add file extensions when downloading from data libraries
(thanks to `@selten <https://github.com/selten>`__).
`Pull Request 8456`_
* Fix tool ``assert_command`` tag test not executed
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 7730`_
* Fix inconsistent defaults for cleanup scripts - fixing `#975 <https://github.com/galaxyproject/galaxy/issues/975>`__
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 8470`_
* Allow missing H5 groups in Loom files
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8560`_
* Document undocumented ``workflow_schedulers_config_file``
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 8437`_
* Use bootstrap classes to fix form css issue.
`Pull Request 8371`_
* Fix Pulsar job files API to allow transferring directory content.
`Pull Request 8124`_
* Fix gops_intersect_1 importing galaxy
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 7805`_
* Quit gsummary script with non-zero exit code upon error
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8214`_
* Sort Collection - add missing when tags
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 8366`_
* Remove gops from venv list
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 8492`_
* Don't let ``parameter_input`` steps be workflow outputs
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 7799`_
* Fix column assign bug
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8023`_
* Quick hack to allow delayed invocations followed by step that consumes an
input parameter
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8249`_
* Expression tool fix - include workdir path when reading env var from file
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8253`_
* Fix workflow tags lost on save
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8398`_
* Fix failure in resubmitting job more than once
(thanks to `@pcm32 <https://github.com/pcm32>`__).
`Pull Request 7832`_
* Add file missing from `#7694
<https://github.com/galaxyproject/galaxy/issues/7694>`__
`Pull Request 7873`_
* Strip unicode control characters from TEXT before entering the database
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 7889`_
* Fix Kubernetes test for job I/O separation.
`Pull Request 7892`_
* In output_checker, fixed wrong comparison.
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 7966`_
* Fix typo grap -> grab.
`Pull Request 8061`_
* Fix wording for pod retries while maintaining backward compatibility
(thanks to `@nuwang <https://github.com/nuwang>`__).
`Pull Request 8082`_
* Kubernetes / CLI runner integration test fixes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8154`_
* Fail job if queueing job fails
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8161`_
* Fix job wrapper fail for queued jobs
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8179`_
* Fix failure to fail job when tool is unavailable
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8181`_
* Fix external_metadata_set_successfully when metadata file doesn't exist
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8182`_
* Fix portable metadata datatypes config.
`Pull Request 8207`_
* Fix cancelling jobs with a message from the admin panel
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8231`_
* Fix Kubernetes runner on Python 3
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8321`_
* Fix univa runner check for drmaa python module
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 8385`_
* Fix memory statement for drmaa (SGE/UNIVA)
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 8451`_
* Fix setting metadata externally
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8497`_
* Fix Pulsar version checking logic.
`Pull Request 8524`_
* Hack to fix Pulsar for containerized jobs.
`Pull Request 8533`_
* Improve and refactor process group handling in the local job runners
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8538`_
* Fix container property parsing for Singularity.
`Pull Request 8614`_
* Data Manager interface - fix to use standard card header styles without extra
markup.
`Pull Request 7811`_
* Allow looking up tool section using label
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8225`_
* Backport tool shed and data manager fixes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
* Create repository clone path if it doesn't exist.
`Pull Request 7770`_
* Remove unused requirejs imports from templates.
`Pull Request 7810`_
* Small bugfix to GRT for ancient data, deprecated params table
(thanks to `@erasche <https://github.com/erasche>`__).
`Pull Request 7830`_
* Fix help text in ftp-uploader dialog.
`Pull Request 7908`_
* Update instructions on conda upgrade
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 7918`_
* Remove view button, fix library flag in data dialog.
`Pull Request 7935`_
* Fix non-eager object store with nested object stores
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 7939`_
* Fix extra newlines in peek code.
`Pull Request 7952`_
* Fix populators.py workflow testing for non-text inputs.
`Pull Request 7953`_
* Only show colon when a port exists in URL.
`Pull Request 7985`_
* Remove href from a tag to prevent backbone page reload and change sometimes.
`Pull Request 7991`_
* Various datatype I/O fixes
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 7995`_
* Don't close popup menu if header item is clicked.
`Pull Request 8001`_
* Refactor comments in sample object stores to remove nested comments.
(thanks to `@simpsonw <https://github.com/simpsonw>`__).
`Pull Request 8016`_
* Fix Selenium DatasetPopulator for more interesting uploads.
`Pull Request 8046`_
* Fix ``stream_to_open_named_file`` for non-utf8 text (backported to 19.05)
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8050`_
* Small testing Dockerfile fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8094`_
* Report a lint error if a citation is empty
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8112`_
* Ensure ``DEFAULT_TOOL_TEST_WAIT`` is an integer
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8136`_
* Fix for tool test data in sub directories
(thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
`Pull Request 8162`_
* Increase default font size to 0.85rem. Unify default welcome page fonts.
`Pull Request 8168`_
* Use ``IdEncodingHelper`` to encode/decode user ids
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8201`_
* Fix prefix usage in history copy dialog.
`Pull Request 8205`_
* Fix UnicodeEncodeError when verifying test results
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8221`_
* Fix migration if ``WorkflowStepConnection`` index not present
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8247`_
* Fix regex rule count
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8254`_
* Fix and unify search bar handling.
`Pull Request 8257`_
* Typo fix comunity -> community
(thanks to `@yochannah <https://github.com/yochannah>`__).
`Pull Request 8267`_
* Fix typo in run_tests.sh help text.
`Pull Request 8289`_
* Don't show the pip progress bar when installing under CI
`Pull Request 8290`_
* Use temporary file for sniff tests
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8304`_
* Adjustments for panel spacing changes
`Pull Request 8316`_
* Restore docs building
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8323`_
* Updates interactor to not ignore numbers in user email address
`Pull Request 8324`_
* Test removing uwsgi weird python package from circleci
`Pull Request 8337`_
* Fix use of ``PIP_PROGRESS_BAR`` env variable
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8343`_
* Startup fixes
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8346`_
* Fix default involucro path
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8360`_
* Fix autodetection of zip file format (including xlsx)
(thanks to `@wm75 <https://github.com/wm75>`__).
`Pull Request 8362`_
* Hide references card if array is empty.
`Pull Request 8373`_
* Fix exception thrown with invalid session key
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8377`_
* Better isolation of embedded Pulsar tests.
`Pull Request 8386`_
* Fix absolutely positioned elements and children from displaying off-screen.
`Pull Request 8466`_
* Don't cleanup integration tests twice.
`Pull Request 8468`_
* Try separate amqp connection from database for integration testing.
`Pull Request 8469`_
* Fix for NodeJS executable being called ``nodejs`` in Conda.
(thanks to `@bgruening <https://github.com/bgruening>`__).
`Pull Request 8474`_
* Fix startup checks when using a Conda env
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8477`_
* Use default backdrop color for modals.
`Pull Request 8479`_
* Fix shed_tool_conf isolated tool (not in section) removal
`Pull Request 8485`_
* Do not warn for not configured ``user_preferences_extra_conf_path``
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8494`_
* Use default background for scratchbook.
`Pull Request 8527`_
* Explicitly declare ``expression`` as ``sql.text``.
`Pull Request 8544`_
* Update ``calculate_or_set_disk_usage`` to support sqlite
(thanks to `@qiagu <https://github.com/qiagu>`__).
`Pull Request 8552`_
* Fix menu option classes (and thus event bindings) for histories in th…
`Pull Request 8575`_
* Modify tool panel section text color, size and margin to improve readability.
`Pull Request 8579`_
* Replaces tabs with spaces in apache.md
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8590`_
* Capture missing log messages
`Pull Request 8605`_
* Regenerate ts search indexes in tmp directory.
`Pull Request 8611`_
* Only schedule file watching if an observer exists
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8629`_
* Fix issue with xml comment handling on python 3
(thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
`Pull Request 8643`_
* Fix tool JSON wrapper fail to wrap paths
(thanks to `@qiagu <https://github.com/qiagu>`__).
`Pull Request 8647`_
* Bugfix - kill testing container when test script is killed.
`Pull Request 8679`_
* Build dependency manager only for galaxy app
(thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
`Pull Request 8696`_
.. include:: 19.09_prs.rst
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