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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>`__ and
+  `@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`_
+* Pin SQLAlchemy to ``<1.3`` and update all dependencies
+  `Pull Request 8120`_
+* Enable authorization to Google Cloud Platform
+  `Pull Request 8123`_
+* Update Python dependencies, unpin SQLAlchemy
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8126`_
+* 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 8640`_,  `Pull Request 8407`_, `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
diff --git a/doc/source/releases/19.09_announce.rst b/doc/source/releases/19.09_announce.rst
index 7a051006b08..8588eaf3c7d 100644
--- a/doc/source/releases/19.09_announce.rst
+++ b/doc/source/releases/19.09_announce.rst
@@ -3,8 +3,60 @@
 September 2019 Galaxy Release (v 19.09)
 ===========================================================
 
+.. include:: _header.rst
 
-Schedule
+Highlights
 ===========================================================
- * Planned Freeze Date: 2019-09-02
- * Planned Release Date: 2019-09-23
+
+**Interactive Tools**
+  A new type of Galaxy tool has been implemented that allow interactive experiences like
+  Galaxy Interactive Environments (via a proxy and Docker containers) but using plugins defined with
+  Galaxy's XML tool syntax. Dan Blankenberg's slides on these new features from Galaxy
+  Community Conference can be found `here <https://static.sched.com/hosted_files/gcc2019/c1/S8A-4__Dan_Blankenberg_Tools.pdf>`__.
+  More information can be found in the original pull request including interactive tool
+  versions of all of Galaxy's bundled interactive environments `Pull Request 7494`_.
+
+**Workflow Invocation Reports**
+  Workflows may now define Markdown templates with Galaxy specific embedded syntax extensions
+  that can tie together workflow inputs, outputs, jobs, and metadata into rich reports.
+  More information on the motivation for these reports can be found in `these slides <bit.ly/gxreports19>`__,
+  implementation details and GUI enhancements are described in the original pull request
+  (`#8030 <https://github.com/galaxyproject/galaxy/pull/8030>`__), and details on the final
+  syntax selected for embedded Galaxy objects can be found in the pull request that was ultimately
+  merged (`#8543 <https://github.com/galaxyproject/galaxy/pull/8543>`__).  
+
+**New Toolshed Client Interface**
+  The march toward replacing templated backend generated HTML with modern, reactive
+  components continued in Galaxy 19.09. Galaxy's tool panel, job properties tables,
+  job management controls, and "Pages" infrastructure were all replaced with VueJS
+  components (with huge help from `@scrathat <https://github.com/scrathat>`__
+  and `@inkuzmin <https://github.com/inkuzmin>`__). Most notably, Galaxy's interface
+  to the Toolshed was also rewritten in VueJS and is now completely API driven.
+  This project drove numerous enhancements to the Toolshed API including vastly improved
+  search functionality. This interface has been completely re-imagined and feels much
+  more interactive.
+
+Get Galaxy
+==========
+
+The code lives at `GitHub <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
+
+To get a new Galaxy repository run:
+  .. code-block:: shell
+
+      $ git clone -b release_19.09 https://github.com/galaxyproject/galaxy.git
+
+To update an existing Galaxy repository run:
+  .. code-block:: shell
+
+      $ git fetch origin && git checkout release_19.09 && git pull --ff-only origin release_19.09
+
+See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
+
+Release Notes
+===========================================================
+
+.. include:: 19.09.rst
+   :start-after: announce_start
+
+.. include:: _thanks.rst
diff --git a/doc/source/releases/19.09_announce_user.rst b/doc/source/releases/19.09_announce_user.rst
new file mode 100644
index 00000000000..f57864f3b9e
--- /dev/null
+++ b/doc/source/releases/19.09_announce_user.rst
@@ -0,0 +1,86 @@
+
+===========================================================
+September 2019 Galaxy Release (v 19.09)
+===========================================================
+
+.. include:: _header.rst
+
+Highlights
+===========================================================
+
+**Feature1**
+  Feature description.
+
+**Feature2**
+  Feature description.
+
+**Feature3**
+  Feature description.
+
+
+New Visualizations
+===========================================================
+
+.. visualizations
+* 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`_
+* Add external display application plugin for iCn3D.
+  `Pull Request 8347`_
+
+New Datatypes
+===========================================================
+
+.. datatypes
+
+* 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`_
+
+Builtin Tool Updates
+===========================================================
+
+.. tools
+
+* 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`_
+
+Release Notes
+===========================================================
+
+Please see the `full release notes <19.09_announce.html>`_ for more details.
+
+.. include:: 19.09_prs.rst
+
+.. include:: _thanks.rst
diff --git a/doc/source/releases/19.09_prs.rst b/doc/source/releases/19.09_prs.rst
new file mode 100644
index 00000000000..346fa6ef373
--- /dev/null
+++ b/doc/source/releases/19.09_prs.rst
@@ -0,0 +1,334 @@
+
+.. github_links
+.. _Pull Request 921: https://github.com/galaxyproject/galaxy/pull/921
+.. _Pull Request 6891: https://github.com/galaxyproject/galaxy/pull/6891
+.. _Pull Request 7402: https://github.com/galaxyproject/galaxy/pull/7402
+.. _Pull Request 7494: https://github.com/galaxyproject/galaxy/pull/7494
+.. _Pull Request 7615: https://github.com/galaxyproject/galaxy/pull/7615
+.. _Pull Request 7665: https://github.com/galaxyproject/galaxy/pull/7665
+.. _Pull Request 7670: https://github.com/galaxyproject/galaxy/pull/7670
+.. _Pull Request 7730: https://github.com/galaxyproject/galaxy/pull/7730
+.. _Pull Request 7745: https://github.com/galaxyproject/galaxy/pull/7745
+.. _Pull Request 7770: https://github.com/galaxyproject/galaxy/pull/7770
+.. _Pull Request 7772: https://github.com/galaxyproject/galaxy/pull/7772
+.. _Pull Request 7790: https://github.com/galaxyproject/galaxy/pull/7790
+.. _Pull Request 7799: https://github.com/galaxyproject/galaxy/pull/7799
+.. _Pull Request 7804: https://github.com/galaxyproject/galaxy/pull/7804
+.. _Pull Request 7805: https://github.com/galaxyproject/galaxy/pull/7805
+.. _Pull Request 7808: https://github.com/galaxyproject/galaxy/pull/7808
+.. _Pull Request 7810: https://github.com/galaxyproject/galaxy/pull/7810
+.. _Pull Request 7811: https://github.com/galaxyproject/galaxy/pull/7811
+.. _Pull Request 7825: https://github.com/galaxyproject/galaxy/pull/7825
+.. _Pull Request 7828: https://github.com/galaxyproject/galaxy/pull/7828
+.. _Pull Request 7829: https://github.com/galaxyproject/galaxy/pull/7829
+.. _Pull Request 7830: https://github.com/galaxyproject/galaxy/pull/7830
+.. _Pull Request 7832: https://github.com/galaxyproject/galaxy/pull/7832
+.. _Pull Request 7835: https://github.com/galaxyproject/galaxy/pull/7835
+.. _Pull Request 7837: https://github.com/galaxyproject/galaxy/pull/7837
+.. _Pull Request 7838: https://github.com/galaxyproject/galaxy/pull/7838
+.. _Pull Request 7843: https://github.com/galaxyproject/galaxy/pull/7843
+.. _Pull Request 7852: https://github.com/galaxyproject/galaxy/pull/7852
+.. _Pull Request 7854: https://github.com/galaxyproject/galaxy/pull/7854
+.. _Pull Request 7867: https://github.com/galaxyproject/galaxy/pull/7867
+.. _Pull Request 7871: https://github.com/galaxyproject/galaxy/pull/7871
+.. _Pull Request 7873: https://github.com/galaxyproject/galaxy/pull/7873
+.. _Pull Request 7878: https://github.com/galaxyproject/galaxy/pull/7878
+.. _Pull Request 7882: https://github.com/galaxyproject/galaxy/pull/7882
+.. _Pull Request 7885: https://github.com/galaxyproject/galaxy/pull/7885
+.. _Pull Request 7888: https://github.com/galaxyproject/galaxy/pull/7888
+.. _Pull Request 7889: https://github.com/galaxyproject/galaxy/pull/7889
+.. _Pull Request 7890: https://github.com/galaxyproject/galaxy/pull/7890
+.. _Pull Request 7891: https://github.com/galaxyproject/galaxy/pull/7891
+.. _Pull Request 7892: https://github.com/galaxyproject/galaxy/pull/7892
+.. _Pull Request 7895: https://github.com/galaxyproject/galaxy/pull/7895
+.. _Pull Request 7897: https://github.com/galaxyproject/galaxy/pull/7897
+.. _Pull Request 7905: https://github.com/galaxyproject/galaxy/pull/7905
+.. _Pull Request 7908: https://github.com/galaxyproject/galaxy/pull/7908
+.. _Pull Request 7911: https://github.com/galaxyproject/galaxy/pull/7911
+.. _Pull Request 7913: https://github.com/galaxyproject/galaxy/pull/7913
+.. _Pull Request 7918: https://github.com/galaxyproject/galaxy/pull/7918
+.. _Pull Request 7927: https://github.com/galaxyproject/galaxy/pull/7927
+.. _Pull Request 7929: https://github.com/galaxyproject/galaxy/pull/7929
+.. _Pull Request 7935: https://github.com/galaxyproject/galaxy/pull/7935
+.. _Pull Request 7939: https://github.com/galaxyproject/galaxy/pull/7939
+.. _Pull Request 7945: https://github.com/galaxyproject/galaxy/pull/7945
+.. _Pull Request 7952: https://github.com/galaxyproject/galaxy/pull/7952
+.. _Pull Request 7953: https://github.com/galaxyproject/galaxy/pull/7953
+.. _Pull Request 7966: https://github.com/galaxyproject/galaxy/pull/7966
+.. _Pull Request 7971: https://github.com/galaxyproject/galaxy/pull/7971
+.. _Pull Request 7980: https://github.com/galaxyproject/galaxy/pull/7980
+.. _Pull Request 7985: https://github.com/galaxyproject/galaxy/pull/7985
+.. _Pull Request 7986: https://github.com/galaxyproject/galaxy/pull/7986
+.. _Pull Request 7991: https://github.com/galaxyproject/galaxy/pull/7991
+.. _Pull Request 7992: https://github.com/galaxyproject/galaxy/pull/7992
+.. _Pull Request 7993: https://github.com/galaxyproject/galaxy/pull/7993
+.. _Pull Request 7995: https://github.com/galaxyproject/galaxy/pull/7995
+.. _Pull Request 8001: https://github.com/galaxyproject/galaxy/pull/8001
+.. _Pull Request 8009: https://github.com/galaxyproject/galaxy/pull/8009
+.. _Pull Request 8016: https://github.com/galaxyproject/galaxy/pull/8016
+.. _Pull Request 8018: https://github.com/galaxyproject/galaxy/pull/8018
+.. _Pull Request 8022: https://github.com/galaxyproject/galaxy/pull/8022
+.. _Pull Request 8023: https://github.com/galaxyproject/galaxy/pull/8023
+.. _Pull Request 8024: https://github.com/galaxyproject/galaxy/pull/8024
+.. _Pull Request 8025: https://github.com/galaxyproject/galaxy/pull/8025
+.. _Pull Request 8028: https://github.com/galaxyproject/galaxy/pull/8028
+.. _Pull Request 8034: https://github.com/galaxyproject/galaxy/pull/8034
+.. _Pull Request 8035: https://github.com/galaxyproject/galaxy/pull/8035
+.. _Pull Request 8036: https://github.com/galaxyproject/galaxy/pull/8036
+.. _Pull Request 8038: https://github.com/galaxyproject/galaxy/pull/8038
+.. _Pull Request 8042: https://github.com/galaxyproject/galaxy/pull/8042
+.. _Pull Request 8044: https://github.com/galaxyproject/galaxy/pull/8044
+.. _Pull Request 8045: https://github.com/galaxyproject/galaxy/pull/8045
+.. _Pull Request 8046: https://github.com/galaxyproject/galaxy/pull/8046
+.. _Pull Request 8047: https://github.com/galaxyproject/galaxy/pull/8047
+.. _Pull Request 8050: https://github.com/galaxyproject/galaxy/pull/8050
+.. _Pull Request 8051: https://github.com/galaxyproject/galaxy/pull/8051
+.. _Pull Request 8061: https://github.com/galaxyproject/galaxy/pull/8061
+.. _Pull Request 8062: https://github.com/galaxyproject/galaxy/pull/8062
+.. _Pull Request 8070: https://github.com/galaxyproject/galaxy/pull/8070
+.. _Pull Request 8075: https://github.com/galaxyproject/galaxy/pull/8075
+.. _Pull Request 8076: https://github.com/galaxyproject/galaxy/pull/8076
+.. _Pull Request 8077: https://github.com/galaxyproject/galaxy/pull/8077
+.. _Pull Request 8078: https://github.com/galaxyproject/galaxy/pull/8078
+.. _Pull Request 8082: https://github.com/galaxyproject/galaxy/pull/8082
+.. _Pull Request 8086: https://github.com/galaxyproject/galaxy/pull/8086
+.. _Pull Request 8090: https://github.com/galaxyproject/galaxy/pull/8090
+.. _Pull Request 8091: https://github.com/galaxyproject/galaxy/pull/8091
+.. _Pull Request 8094: https://github.com/galaxyproject/galaxy/pull/8094
+.. _Pull Request 8098: https://github.com/galaxyproject/galaxy/pull/8098
+.. _Pull Request 8101: https://github.com/galaxyproject/galaxy/pull/8101
+.. _Pull Request 8104: https://github.com/galaxyproject/galaxy/pull/8104
+.. _Pull Request 8112: https://github.com/galaxyproject/galaxy/pull/8112
+.. _Pull Request 8113: https://github.com/galaxyproject/galaxy/pull/8113
+.. _Pull Request 8114: https://github.com/galaxyproject/galaxy/pull/8114
+.. _Pull Request 8118: https://github.com/galaxyproject/galaxy/pull/8118
+.. _Pull Request 8120: https://github.com/galaxyproject/galaxy/pull/8120
+.. _Pull Request 8123: https://github.com/galaxyproject/galaxy/pull/8123
+.. _Pull Request 8124: https://github.com/galaxyproject/galaxy/pull/8124
+.. _Pull Request 8126: https://github.com/galaxyproject/galaxy/pull/8126
+.. _Pull Request 8133: https://github.com/galaxyproject/galaxy/pull/8133
+.. _Pull Request 8136: https://github.com/galaxyproject/galaxy/pull/8136
+.. _Pull Request 8137: https://github.com/galaxyproject/galaxy/pull/8137
+.. _Pull Request 8138: https://github.com/galaxyproject/galaxy/pull/8138
+.. _Pull Request 8144: https://github.com/galaxyproject/galaxy/pull/8144
+.. _Pull Request 8147: https://github.com/galaxyproject/galaxy/pull/8147
+.. _Pull Request 8152: https://github.com/galaxyproject/galaxy/pull/8152
+.. _Pull Request 8154: https://github.com/galaxyproject/galaxy/pull/8154
+.. _Pull Request 8155: https://github.com/galaxyproject/galaxy/pull/8155
+.. _Pull Request 8161: https://github.com/galaxyproject/galaxy/pull/8161
+.. _Pull Request 8162: https://github.com/galaxyproject/galaxy/pull/8162
+.. _Pull Request 8163: https://github.com/galaxyproject/galaxy/pull/8163
+.. _Pull Request 8168: https://github.com/galaxyproject/galaxy/pull/8168
+.. _Pull Request 8179: https://github.com/galaxyproject/galaxy/pull/8179
+.. _Pull Request 8181: https://github.com/galaxyproject/galaxy/pull/8181
+.. _Pull Request 8182: https://github.com/galaxyproject/galaxy/pull/8182
+.. _Pull Request 8186: https://github.com/galaxyproject/galaxy/pull/8186
+.. _Pull Request 8195: https://github.com/galaxyproject/galaxy/pull/8195
+.. _Pull Request 8201: https://github.com/galaxyproject/galaxy/pull/8201
+.. _Pull Request 8205: https://github.com/galaxyproject/galaxy/pull/8205
+.. _Pull Request 8206: https://github.com/galaxyproject/galaxy/pull/8206
+.. _Pull Request 8207: https://github.com/galaxyproject/galaxy/pull/8207
+.. _Pull Request 8208: https://github.com/galaxyproject/galaxy/pull/8208
+.. _Pull Request 8211: https://github.com/galaxyproject/galaxy/pull/8211
+.. _Pull Request 8212: https://github.com/galaxyproject/galaxy/pull/8212
+.. _Pull Request 8213: https://github.com/galaxyproject/galaxy/pull/8213
+.. _Pull Request 8214: https://github.com/galaxyproject/galaxy/pull/8214
+.. _Pull Request 8220: https://github.com/galaxyproject/galaxy/pull/8220
+.. _Pull Request 8221: https://github.com/galaxyproject/galaxy/pull/8221
+.. _Pull Request 8225: https://github.com/galaxyproject/galaxy/pull/8225
+.. _Pull Request 8227: https://github.com/galaxyproject/galaxy/pull/8227
+.. _Pull Request 8229: https://github.com/galaxyproject/galaxy/pull/8229
+.. _Pull Request 8231: https://github.com/galaxyproject/galaxy/pull/8231
+.. _Pull Request 8233: https://github.com/galaxyproject/galaxy/pull/8233
+.. _Pull Request 8234: https://github.com/galaxyproject/galaxy/pull/8234
+.. _Pull Request 8235: https://github.com/galaxyproject/galaxy/pull/8235
+.. _Pull Request 8239: https://github.com/galaxyproject/galaxy/pull/8239
+.. _Pull Request 8241: https://github.com/galaxyproject/galaxy/pull/8241
+.. _Pull Request 8246: https://github.com/galaxyproject/galaxy/pull/8246
+.. _Pull Request 8247: https://github.com/galaxyproject/galaxy/pull/8247
+.. _Pull Request 8249: https://github.com/galaxyproject/galaxy/pull/8249
+.. _Pull Request 8250: https://github.com/galaxyproject/galaxy/pull/8250
+.. _Pull Request 8253: https://github.com/galaxyproject/galaxy/pull/8253
+.. _Pull Request 8254: https://github.com/galaxyproject/galaxy/pull/8254
+.. _Pull Request 8256: https://github.com/galaxyproject/galaxy/pull/8256
+.. _Pull Request 8257: https://github.com/galaxyproject/galaxy/pull/8257
+.. _Pull Request 8266: https://github.com/galaxyproject/galaxy/pull/8266
+.. _Pull Request 8267: https://github.com/galaxyproject/galaxy/pull/8267
+.. _Pull Request 8268: https://github.com/galaxyproject/galaxy/pull/8268
+.. _Pull Request 8269: https://github.com/galaxyproject/galaxy/pull/8269
+.. _Pull Request 8270: https://github.com/galaxyproject/galaxy/pull/8270
+.. _Pull Request 8275: https://github.com/galaxyproject/galaxy/pull/8275
+.. _Pull Request 8276: https://github.com/galaxyproject/galaxy/pull/8276
+.. _Pull Request 8277: https://github.com/galaxyproject/galaxy/pull/8277
+.. _Pull Request 8280: https://github.com/galaxyproject/galaxy/pull/8280
+.. _Pull Request 8281: https://github.com/galaxyproject/galaxy/pull/8281
+.. _Pull Request 8284: https://github.com/galaxyproject/galaxy/pull/8284
+.. _Pull Request 8285: https://github.com/galaxyproject/galaxy/pull/8285
+.. _Pull Request 8287: https://github.com/galaxyproject/galaxy/pull/8287
+.. _Pull Request 8289: https://github.com/galaxyproject/galaxy/pull/8289
+.. _Pull Request 8290: https://github.com/galaxyproject/galaxy/pull/8290
+.. _Pull Request 8291: https://github.com/galaxyproject/galaxy/pull/8291
+.. _Pull Request 8293: https://github.com/galaxyproject/galaxy/pull/8293
+.. _Pull Request 8294: https://github.com/galaxyproject/galaxy/pull/8294
+.. _Pull Request 8296: https://github.com/galaxyproject/galaxy/pull/8296
+.. _Pull Request 8298: https://github.com/galaxyproject/galaxy/pull/8298
+.. _Pull Request 8300: https://github.com/galaxyproject/galaxy/pull/8300
+.. _Pull Request 8301: https://github.com/galaxyproject/galaxy/pull/8301
+.. _Pull Request 8302: https://github.com/galaxyproject/galaxy/pull/8302
+.. _Pull Request 8303: https://github.com/galaxyproject/galaxy/pull/8303
+.. _Pull Request 8304: https://github.com/galaxyproject/galaxy/pull/8304
+.. _Pull Request 8305: https://github.com/galaxyproject/galaxy/pull/8305
+.. _Pull Request 8306: https://github.com/galaxyproject/galaxy/pull/8306
+.. _Pull Request 8307: https://github.com/galaxyproject/galaxy/pull/8307
+.. _Pull Request 8308: https://github.com/galaxyproject/galaxy/pull/8308
+.. _Pull Request 8309: https://github.com/galaxyproject/galaxy/pull/8309
+.. _Pull Request 8310: https://github.com/galaxyproject/galaxy/pull/8310
+.. _Pull Request 8311: https://github.com/galaxyproject/galaxy/pull/8311
+.. _Pull Request 8314: https://github.com/galaxyproject/galaxy/pull/8314
+.. _Pull Request 8315: https://github.com/galaxyproject/galaxy/pull/8315
+.. _Pull Request 8316: https://github.com/galaxyproject/galaxy/pull/8316
+.. _Pull Request 8319: https://github.com/galaxyproject/galaxy/pull/8319
+.. _Pull Request 8320: https://github.com/galaxyproject/galaxy/pull/8320
+.. _Pull Request 8321: https://github.com/galaxyproject/galaxy/pull/8321
+.. _Pull Request 8322: https://github.com/galaxyproject/galaxy/pull/8322
+.. _Pull Request 8323: https://github.com/galaxyproject/galaxy/pull/8323
+.. _Pull Request 8324: https://github.com/galaxyproject/galaxy/pull/8324
+.. _Pull Request 8326: https://github.com/galaxyproject/galaxy/pull/8326
+.. _Pull Request 8329: https://github.com/galaxyproject/galaxy/pull/8329
+.. _Pull Request 8331: https://github.com/galaxyproject/galaxy/pull/8331
+.. _Pull Request 8334: https://github.com/galaxyproject/galaxy/pull/8334
+.. _Pull Request 8335: https://github.com/galaxyproject/galaxy/pull/8335
+.. _Pull Request 8337: https://github.com/galaxyproject/galaxy/pull/8337
+.. _Pull Request 8342: https://github.com/galaxyproject/galaxy/pull/8342
+.. _Pull Request 8343: https://github.com/galaxyproject/galaxy/pull/8343
+.. _Pull Request 8345: https://github.com/galaxyproject/galaxy/pull/8345
+.. _Pull Request 8346: https://github.com/galaxyproject/galaxy/pull/8346
+.. _Pull Request 8347: https://github.com/galaxyproject/galaxy/pull/8347
+.. _Pull Request 8351: https://github.com/galaxyproject/galaxy/pull/8351
+.. _Pull Request 8355: https://github.com/galaxyproject/galaxy/pull/8355
+.. _Pull Request 8357: https://github.com/galaxyproject/galaxy/pull/8357
+.. _Pull Request 8359: https://github.com/galaxyproject/galaxy/pull/8359
+.. _Pull Request 8360: https://github.com/galaxyproject/galaxy/pull/8360
+.. _Pull Request 8362: https://github.com/galaxyproject/galaxy/pull/8362
+.. _Pull Request 8363: https://github.com/galaxyproject/galaxy/pull/8363
+.. _Pull Request 8365: https://github.com/galaxyproject/galaxy/pull/8365
+.. _Pull Request 8366: https://github.com/galaxyproject/galaxy/pull/8366
+.. _Pull Request 8368: https://github.com/galaxyproject/galaxy/pull/8368
+.. _Pull Request 8371: https://github.com/galaxyproject/galaxy/pull/8371
+.. _Pull Request 8373: https://github.com/galaxyproject/galaxy/pull/8373
+.. _Pull Request 8377: https://github.com/galaxyproject/galaxy/pull/8377
+.. _Pull Request 8385: https://github.com/galaxyproject/galaxy/pull/8385
+.. _Pull Request 8386: https://github.com/galaxyproject/galaxy/pull/8386
+.. _Pull Request 8394: https://github.com/galaxyproject/galaxy/pull/8394
+.. _Pull Request 8398: https://github.com/galaxyproject/galaxy/pull/8398
+.. _Pull Request 8404: https://github.com/galaxyproject/galaxy/pull/8404
+.. _Pull Request 8405: https://github.com/galaxyproject/galaxy/pull/8405
+.. _Pull Request 8407: https://github.com/galaxyproject/galaxy/pull/8407
+.. _Pull Request 8409: https://github.com/galaxyproject/galaxy/pull/8409
+.. _Pull Request 8410: https://github.com/galaxyproject/galaxy/pull/8410
+.. _Pull Request 8414: https://github.com/galaxyproject/galaxy/pull/8414
+.. _Pull Request 8421: https://github.com/galaxyproject/galaxy/pull/8421
+.. _Pull Request 8422: https://github.com/galaxyproject/galaxy/pull/8422
+.. _Pull Request 8424: https://github.com/galaxyproject/galaxy/pull/8424
+.. _Pull Request 8426: https://github.com/galaxyproject/galaxy/pull/8426
+.. _Pull Request 8430: https://github.com/galaxyproject/galaxy/pull/8430
+.. _Pull Request 8431: https://github.com/galaxyproject/galaxy/pull/8431
+.. _Pull Request 8433: https://github.com/galaxyproject/galaxy/pull/8433
+.. _Pull Request 8437: https://github.com/galaxyproject/galaxy/pull/8437
+.. _Pull Request 8439: https://github.com/galaxyproject/galaxy/pull/8439
+.. _Pull Request 8440: https://github.com/galaxyproject/galaxy/pull/8440
+.. _Pull Request 8446: https://github.com/galaxyproject/galaxy/pull/8446
+.. _Pull Request 8450: https://github.com/galaxyproject/galaxy/pull/8450
+.. _Pull Request 8451: https://github.com/galaxyproject/galaxy/pull/8451
+.. _Pull Request 8452: https://github.com/galaxyproject/galaxy/pull/8452
+.. _Pull Request 8455: https://github.com/galaxyproject/galaxy/pull/8455
+.. _Pull Request 8456: https://github.com/galaxyproject/galaxy/pull/8456
+.. _Pull Request 8457: https://github.com/galaxyproject/galaxy/pull/8457
+.. _Pull Request 8458: https://github.com/galaxyproject/galaxy/pull/8458
+.. _Pull Request 8461: https://github.com/galaxyproject/galaxy/pull/8461
+.. _Pull Request 8462: https://github.com/galaxyproject/galaxy/pull/8462
+.. _Pull Request 8465: https://github.com/galaxyproject/galaxy/pull/8465
+.. _Pull Request 8466: https://github.com/galaxyproject/galaxy/pull/8466
+.. _Pull Request 8468: https://github.com/galaxyproject/galaxy/pull/8468
+.. _Pull Request 8469: https://github.com/galaxyproject/galaxy/pull/8469
+.. _Pull Request 8470: https://github.com/galaxyproject/galaxy/pull/8470
+.. _Pull Request 8473: https://github.com/galaxyproject/galaxy/pull/8473
+.. _Pull Request 8474: https://github.com/galaxyproject/galaxy/pull/8474
+.. _Pull Request 8475: https://github.com/galaxyproject/galaxy/pull/8475
+.. _Pull Request 8477: https://github.com/galaxyproject/galaxy/pull/8477
+.. _Pull Request 8479: https://github.com/galaxyproject/galaxy/pull/8479
+.. _Pull Request 8485: https://github.com/galaxyproject/galaxy/pull/8485
+.. _Pull Request 8489: https://github.com/galaxyproject/galaxy/pull/8489
+.. _Pull Request 8490: https://github.com/galaxyproject/galaxy/pull/8490
+.. _Pull Request 8492: https://github.com/galaxyproject/galaxy/pull/8492
+.. _Pull Request 8494: https://github.com/galaxyproject/galaxy/pull/8494
+.. _Pull Request 8495: https://github.com/galaxyproject/galaxy/pull/8495
+.. _Pull Request 8497: https://github.com/galaxyproject/galaxy/pull/8497
+.. _Pull Request 8499: https://github.com/galaxyproject/galaxy/pull/8499
+.. _Pull Request 8502: https://github.com/galaxyproject/galaxy/pull/8502
+.. _Pull Request 8503: https://github.com/galaxyproject/galaxy/pull/8503
+.. _Pull Request 8506: https://github.com/galaxyproject/galaxy/pull/8506
+.. _Pull Request 8507: https://github.com/galaxyproject/galaxy/pull/8507
+.. _Pull Request 8510: https://github.com/galaxyproject/galaxy/pull/8510
+.. _Pull Request 8521: https://github.com/galaxyproject/galaxy/pull/8521
+.. _Pull Request 8524: https://github.com/galaxyproject/galaxy/pull/8524
+.. _Pull Request 8526: https://github.com/galaxyproject/galaxy/pull/8526
+.. _Pull Request 8527: https://github.com/galaxyproject/galaxy/pull/8527
+.. _Pull Request 8530: https://github.com/galaxyproject/galaxy/pull/8530
+.. _Pull Request 8532: https://github.com/galaxyproject/galaxy/pull/8532
+.. _Pull Request 8533: https://github.com/galaxyproject/galaxy/pull/8533
+.. _Pull Request 8536: https://github.com/galaxyproject/galaxy/pull/8536
+.. _Pull Request 8537: https://github.com/galaxyproject/galaxy/pull/8537
+.. _Pull Request 8538: https://github.com/galaxyproject/galaxy/pull/8538
+.. _Pull Request 8539: https://github.com/galaxyproject/galaxy/pull/8539
+.. _Pull Request 8541: https://github.com/galaxyproject/galaxy/pull/8541
+.. _Pull Request 8542: https://github.com/galaxyproject/galaxy/pull/8542
+.. _Pull Request 8543: https://github.com/galaxyproject/galaxy/pull/8543
+.. _Pull Request 8544: https://github.com/galaxyproject/galaxy/pull/8544
+.. _Pull Request 8545: https://github.com/galaxyproject/galaxy/pull/8545
+.. _Pull Request 8549: https://github.com/galaxyproject/galaxy/pull/8549
+.. _Pull Request 8552: https://github.com/galaxyproject/galaxy/pull/8552
+.. _Pull Request 8560: https://github.com/galaxyproject/galaxy/pull/8560
+.. _Pull Request 8561: https://github.com/galaxyproject/galaxy/pull/8561
+.. _Pull Request 8569: https://github.com/galaxyproject/galaxy/pull/8569
+.. _Pull Request 8574: https://github.com/galaxyproject/galaxy/pull/8574
+.. _Pull Request 8575: https://github.com/galaxyproject/galaxy/pull/8575
+.. _Pull Request 8579: https://github.com/galaxyproject/galaxy/pull/8579
+.. _Pull Request 8585: https://github.com/galaxyproject/galaxy/pull/8585
+.. _Pull Request 8589: https://github.com/galaxyproject/galaxy/pull/8589
+.. _Pull Request 8590: https://github.com/galaxyproject/galaxy/pull/8590
+.. _Pull Request 8605: https://github.com/galaxyproject/galaxy/pull/8605
+.. _Pull Request 8608: https://github.com/galaxyproject/galaxy/pull/8608
+.. _Pull Request 8609: https://github.com/galaxyproject/galaxy/pull/8609
+.. _Pull Request 8610: https://github.com/galaxyproject/galaxy/pull/8610
+.. _Pull Request 8611: https://github.com/galaxyproject/galaxy/pull/8611
+.. _Pull Request 8613: https://github.com/galaxyproject/galaxy/pull/8613
+.. _Pull Request 8614: https://github.com/galaxyproject/galaxy/pull/8614
+.. _Pull Request 8616: https://github.com/galaxyproject/galaxy/pull/8616
+.. _Pull Request 8621: https://github.com/galaxyproject/galaxy/pull/8621
+.. _Pull Request 8622: https://github.com/galaxyproject/galaxy/pull/8622
+.. _Pull Request 8623: https://github.com/galaxyproject/galaxy/pull/8623
+.. _Pull Request 8629: https://github.com/galaxyproject/galaxy/pull/8629
+.. _Pull Request 8630: https://github.com/galaxyproject/galaxy/pull/8630
+.. _Pull Request 8635: https://github.com/galaxyproject/galaxy/pull/8635
+.. _Pull Request 8638: https://github.com/galaxyproject/galaxy/pull/8638
+.. _Pull Request 8640: https://github.com/galaxyproject/galaxy/pull/8640
+.. _Pull Request 8643: https://github.com/galaxyproject/galaxy/pull/8643
+.. _Pull Request 8647: https://github.com/galaxyproject/galaxy/pull/8647
+.. _Pull Request 8650: https://github.com/galaxyproject/galaxy/pull/8650
+.. _Pull Request 8654: https://github.com/galaxyproject/galaxy/pull/8654
+.. _Pull Request 8658: https://github.com/galaxyproject/galaxy/pull/8658
+.. _Pull Request 8663: https://github.com/galaxyproject/galaxy/pull/8663
+.. _Pull Request 8664: https://github.com/galaxyproject/galaxy/pull/8664
+.. _Pull Request 8679: https://github.com/galaxyproject/galaxy/pull/8679
+.. _Pull Request 8681: https://github.com/galaxyproject/galaxy/pull/8681
+.. _Pull Request 8683: https://github.com/galaxyproject/galaxy/pull/8683
+.. _Pull Request 8687: https://github.com/galaxyproject/galaxy/pull/8687
+.. _Pull Request 8693: https://github.com/galaxyproject/galaxy/pull/8693
+.. _Pull Request 8696: https://github.com/galaxyproject/galaxy/pull/8696
+.. _Pull Request 8698: https://github.com/galaxyproject/galaxy/pull/8698
+.. _Pull Request 8702: https://github.com/galaxyproject/galaxy/pull/8702
+.. _Pull Request 8703: https://github.com/galaxyproject/galaxy/pull/8703
+.. _Pull Request 8719: https://github.com/galaxyproject/galaxy/pull/8719
+.. _Pull Request 8721: https://github.com/galaxyproject/galaxy/pull/8721
+.. _Pull Request 8727: https://github.com/galaxyproject/galaxy/pull/8727
diff --git a/doc/source/releases/20.01_announce.rst b/doc/source/releases/20.01_announce.rst
new file mode 100644
index 00000000000..2c7a6a98ff5
--- /dev/null
+++ b/doc/source/releases/20.01_announce.rst
@@ -0,0 +1,10 @@
+
+===========================================================
+January 2020 Galaxy Release (v 20.01)
+===========================================================
+
+
+Schedule
+===========================================================
+ * Planned Freeze Date: 2020-01-06
+ * Planned Release Date: 2020-01-27
diff --git a/doc/source/releases/index.rst b/doc/source/releases/index.rst
index edc8647c307..98c88cbf52a 100644
--- a/doc/source/releases/index.rst
+++ b/doc/source/releases/index.rst
@@ -4,6 +4,7 @@ Releases
 .. toctree::
    :maxdepth: 1
 
+   19.09_announce
    19.05_announce
    19.01_announce
    18.09_announce
diff --git a/lib/galaxy/config/config_manage.py b/lib/galaxy/config/config_manage.py
index dce8e5ecc39..ec3dab803f3 100644
--- a/lib/galaxy/config/config_manage.py
+++ b/lib/galaxy/config/config_manage.py
@@ -295,6 +295,7 @@ OPTION_ACTIONS = {
     'allow_library_path_paste': _RenameAction("allow_path_paste"),
     'trust_ipython_notebook_conversion': _RenameAction("trust_jupyter_notebook_conversion"),
     'enable_beta_tool_command_isolation': _DeprecatedAndDroppedAction(),
+    'enable_beta_ts_api_install': _DeprecatedAndDroppedAction(),
     'single_user': _ProductionUnsafe(True),
     'tool_submission_burst_threads': _DeprecatedAndDroppedAction(),
     'tool_submission_burst_at': _DeprecatedAndDroppedAction(),
diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py
index 154b4e34de5..216595bc6ff 100644
--- a/scripts/bootstrap_history.py
+++ b/scripts/bootstrap_history.py
@@ -11,6 +11,7 @@ import re
 import string
 import sys
 import textwrap
+from collections import OrderedDict
 
 try:
     import requests
@@ -38,10 +39,11 @@ DEVTEAM = [
     "davebx", "martenson", "jmchilton",
     "tnabtaf", "natefoo", "jgoecks",
     "guerler", "jennaj", "nekrut", "jxtx",
-    "VJalili", "WilliamHolden", "Nerdinacan"
+    "VJalili", "WilliamHolden", "Nerdinacan",
+    "ic4f",
 ]
 
-TEMPLATE = string.Template("""
+TEMPLATE = """
 .. to_doc
 
 ${release}
@@ -57,10 +59,8 @@ Enhancements
 
 .. feature
 
-
 .. enhancement
 
-
 .. small_enhancement
 
 
@@ -76,7 +76,7 @@ Fixes
 
 .. include:: ${release}_prs.rst
 
-""")
+"""
 
 ANNOUNCE_TEMPLATE = string.Template("""
 ===========================================================
@@ -286,6 +286,16 @@ RELEASE_ISSUE_TEMPLATE = string.Template("""
     - [ ] Close this issue.
 """)
 
+GROUPPED_TAGS = OrderedDict([
+    ('area/visualizations', 'viz'),
+    ('area/datatypes', 'datatypes'),
+    ('area/tools', 'tools'),
+    ('area/workflows', 'workflows'),
+    ('area/client', 'ui'),
+    ('area/jobs', 'jobs'),
+    ('area/admin', 'admin'),
+])
+
 # https://api.github.com/repos/galaxyproject/galaxy/pulls?base=dev&state=closed
 # https://api.github.com/repos/galaxyproject/galaxy/pulls?base=release_15.07&state=closed
 # https://api.github.com/repos/galaxyproject/galaxy/compare/release_15.05...dev
@@ -334,7 +344,12 @@ def release_issue(argv):
 def do_release(argv):
     release_name = argv[2]
     release_file = _release_file(release_name + ".rst")
-    release_info = TEMPLATE.safe_substitute(release=release_name)
+    enhancement_targets = "\n\n".join([".. enhancement_tag_%s" % a for a in GROUPPED_TAGS.values()])
+    bug_targets = "\n\n".join([".. bug_tag_%s" % a for a in GROUPPED_TAGS.values()])
+    template = TEMPLATE
+    template = template.replace(".. enhancement", "%s\n\n.. enhancement" % enhancement_targets)
+    template = template.replace(".. bug", "%s\n\n.. bug" % bug_targets)
+    release_info = string.Template(template).safe_substitute(release=release_name)
     open(release_file, "w").write(release_info.encode("utf-8"))
     month = int(release_name.split(".")[1])
     month_name = calendar.month_name[month]
@@ -533,6 +548,8 @@ def main(argv):
 
     def extend_target(target, line, source=history):
         from_str = ".. %s\n" % target
+        if target not in source:
+            raise Exception("Failed to find target [%s] in source [%s]" % (target, source))
         return source.replace(from_str, from_str + line + "\n")
 
     ident = argv[1]
@@ -596,7 +613,8 @@ def main(argv):
         to_doc += "{0}_".format(short_rev)
 
     to_doc = wrap(to_doc)
-    history = extend_target(text_target, to_doc, history)
+    if text_target is not None:
+        history = extend_target(text_target, to_doc, history)
     if req and 'labels' in req:
         labels = req['labels']
         if 'area/datatypes' in labels:
@@ -671,13 +689,23 @@ def _text_target(github, pull_request, labels=None):
     elif is_feature:
         text_target = "feature"
     elif is_enhancement:
-        text_target = "enhancement"
+        for group_name in GROUPPED_TAGS.keys():
+            if group_name in labels:
+                text_target = "enhancement_tag_%s" % GROUPPED_TAGS[group_name]
+                break
+        else:
+            text_target = "enhancement"
     elif is_some_kind_of_enhancement:
         text_target = "small_enhancement"
     elif is_major:
         text_target = "major_bug"
     elif is_bug:
-        text_target = "bug"
+        for group_name in GROUPPED_TAGS.keys():
+            if group_name in labels:
+                text_target = "bug_tag_%s" % GROUPPED_TAGS[group_name]
+                break
+        else:
+            text_target = "bug"
     else:
         print("Logic problem, cannot determine section for %s" % _pr_to_str(pull_request))
         text_target = None