From 6233a408cc93152a379651db3cc143d368f78dda Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 18 Sep 2018 09:34:53 -0400
Subject: [PATCH 01/24] Release notes templated; still needs manual curation

---
 doc/source/releases/18.09.rst          | 1029 ++++++++++++++++++++++++
 doc/source/releases/18.09_announce.rst |   43 +
 doc/source/releases/19.01_announce.rst |   10 +
 3 files changed, 1082 insertions(+)
 create mode 100644 doc/source/releases/18.09.rst
 create mode 100644 doc/source/releases/18.09_announce.rst
 create mode 100644 doc/source/releases/19.01_announce.rst

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
new file mode 100644
index 00000000000..5ae74596ccc
--- /dev/null
+++ b/doc/source/releases/18.09.rst
@@ -0,0 +1,1029 @@
+
+.. to_doc
+
+18.09
+===============================
+
+.. announce_start
+
+Enhancements
+-------------------------------
+
+.. major_feature
+
+
+.. feature
+
+* Allow selecting subset of collection by group tag
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5457`_
+* Copy data from a cloud-based storage to a Galaxy history
+  (thanks to `@VJalili <https://github.com/VJalili>`__).
+  `Pull Request 5835`_
+* Upload data to a cloud-based storage
+  (thanks to `@VJalili <https://github.com/VJalili>`__).
+  `Pull Request 6078`_
+* New datatype: SBML
+  (thanks to `@cmonjeau <https://github.com/cmonjeau>`__).
+  `Pull Request 6201`_
+* Enable automatic reload of dynamic job rules on change
+  `Pull Request 6215`_
+* added daa (diamond alignment) datatype
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 6313`_
+* Allows DatasetMatcher to use multiple filters
+  (thanks to `@ebolyen <https://github.com/ebolyen>`__).
+  `Pull Request 6443`_
+* Adding 4 new GROMACS datatypes: cpt, xtc, top, and gro
+  (thanks to `@simonbray <https://github.com/simonbray>`__).
+  `Pull Request 6655`_
+* Implement runtime parameters for subworkflows.
+  `Pull Request 6664`_
+* Expose workflow versions
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6683`_
+
+.. enhancement
+
+* Add a FilterEmptyDatasetsTool and allow filtering tools to apply to
+  arbitrary collection structures
+  (thanks to `@Mataivic <https://github.com/Mataivic>`__).
+  `Pull Request 5640`_
+* Minor enhancements for cgroup metrics
+  `Pull Request 5993`_
+* Optimize safe_walk to call realpath a lot less for typical calls...
+  `Pull Request 5995`_
+* Documentation and typo fixes
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6013`_
+* Add hostname metric
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 6021`_
+* Pause jobs with invalid inputs
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6036`_
+* Replace sharing mako with vue component
+  `Pull Request 6048`_
+* Rules - test case for apply rules tutorial.
+  `Pull Request 6066`_
+* Add resume job api
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6072`_
+* Add blib datatype for Mass Spectrometry spectral library
+  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
+  `Pull Request 6092`_
+* Remove duplicate visualization list entries from masthead
+  `Pull Request 6110`_
+* Make cache_directory configurable in mulled Singularity resolvers.
+  `Pull Request 6122`_
+* Sharing.vue bootstrapping and a bugfix
+  `Pull Request 6132`_
+* Use from_work_dir in CONVERTER_fasta_to_fai
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6135`_
+* Make workflow editor toolTitle link include the tools description
+  (thanks to `@scrathat <https://github.com/scrathat>`__).
+  `Pull Request 6142`_
+* Small fixes and small refactorings toward reuse in CWL branch (retry)
+  `Pull Request 6148`_
+* Add impersonate to main user grid when it's enabled
+  `Pull Request 6176`_
+* Common dataset selector
+  `Pull Request 6195`_
+* Permit numeric values of GRT instance ID in config
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 6200`_
+* Add the newick extension for the Newick datatype,
+  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
+  `Pull Request 6206`_
+* Some more upload/sniff tests.
+  `Pull Request 6212`_
+* Test element_identifier usage with single data parameters, in repeat/cond.
+  `Pull Request 6213`_
+* Charts filename download fix
+  `Pull Request 6216`_
+* Wrap inputs in labels
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 6221`_
+* Workflow submit text links
+  `Pull Request 6240`_
+* Password encoding improvements
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6242`_
+* Align input element update mechanism
+  `Pull Request 6248`_
+* Fix collection mapping to allow subcollection mapping over multi-data
+  inputs.
+  `Pull Request 6255`_
+*  Use Mercurial CLI instead of API for archive_repository_revision()
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6273`_
+* Consolidate use of get_repo_for_repository() and clone_repository()
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6277`_
+* Index select2 field values
+  `Pull Request 6286`_
+* Job success message revision
+  `Pull Request 6288`_
+* To clear workflow tool search field press ESC or click the X button
+  (thanks to `@scrathat <https://github.com/scrathat>`__).
+  `Pull Request 6290`_
+* Upload collections directly for tests.
+  `Pull Request 6294`_
+* Add specific datatype for CuffDiff SQLite database.
+  `Pull Request 6302`_
+* Fix default job script by moving env setup
+  (thanks to `@rhpvorderman <https://github.com/rhpvorderman>`__).
+  `Pull Request 6305`_
+* More use of Mercurial CLI instead of API
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6307`_
+* Lists-as-tuples collection operations
+  `Pull Request 6312`_
+* Replace unmaintained pycrypto dependency with pycryptodome
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6324`_
+*  Add py34-first_startup to Travis and default tox tests
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6325`_
+* Visualization static staging
+  `Pull Request 6344`_
+* Add period to the list of allowed characters in user names
+  (thanks to `@moskalenko <https://github.com/moskalenko>`__).
+  `Pull Request 6365`_
+* Optimizations for dynamic output file collection.
+  `Pull Request 6367`_
+* More correct, more efficient collection operations.
+  `Pull Request 6370`_
+* Add gafa.sqlite datatype
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6372`_
+* Create client build hash on toplevel concurrent watch in addition to
+  individual builds.
+  `Pull Request 6381`_
+* change a file read to use with statement
+  (thanks to `@qiagu <https://github.com/qiagu>`__).
+  `Pull Request 6388`_
+* Client library upgrades.
+  `Pull Request 6400`_
+* Allow resource selection for data managers
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6402`_
+* Update dev dependencies
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6403`_
+* Add py34-unit (allowed to fail) job to Travis
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6406`_
+* Allow supplying name of pasted data
+  (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
+  `Pull Request 6415`_
+* Fixes for uploading empty files to Galaxy.
+  `Pull Request 6418`_
+* Remove installation of python-lzo system dependencies
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6425`_
+* Citation style work
+  `Pull Request 6427`_
+* Run workflows from published workflows menu
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6428`_
+* fix a few tool_deps test errors
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 6436`_
+* replace the administration header in admin menu with version
+  `Pull Request 6440`_
+* Add zoom support to workflow editor.
+  `Pull Request 6441`_
+* Intermine Enhancements
+  `Pull Request 6444`_
+* Changing menu tabs without hard refresh
+  (thanks to `@almahmoud <https://github.com/almahmoud>`__).
+  `Pull Request 6447`_
+* Let data managers also use conda python.
+  (thanks to `@rhpvorderman <https://github.com/rhpvorderman>`__).
+  `Pull Request 6466`_
+* Make upload tool python3 compatible
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6467`_
+* Allow including paths in inputs json files.
+  `Pull Request 6468`_
+* Update cliff and other related dependencies
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6469`_
+* Fix bug noticed in sentry
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 6474`_
+* Rulebuilder: Special case auto URL schema detection for SRA inputs.
+  `Pull Request 6476`_
+* GRT: fix the upload logging init
+  `Pull Request 6478`_
+* Add more information to the dataset template
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 6480`_
+* Use bootstrap vue classes for workflow import form
+  `Pull Request 6489`_
+* small improvement to the too xsd docs regarding discovered_datasets
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 6490`_
+* Implement ``group:`` tags (toward multi-factor analysis with group tagging)
+  `Pull Request 6491`_
+* Allow setting tags on targets & contents in data fetch API.
+  `Pull Request 6499`_
+* Integrate tagging into the rule builder.
+  `Pull Request 6500`_
+* Cache chrom_info generation when mapping over collections.
+  `Pull Request 6515`_
+* More optimized HID generation - in one commit instead of two.
+  `Pull Request 6516`_
+* Improvements to Cloud Storage Manager
+  (thanks to `@VJalili <https://github.com/VJalili>`__).
+  `Pull Request 6519`_
+* Handle pasted content in fetch API.
+  `Pull Request 6523`_
+* Use cached database identity to avoid many DB requests when creating jobs.
+  `Pull Request 6524`_
+* Removal of unreachable exit()
+  `Pull Request 6529`_
+* Optimizations for history copying.
+  `Pull Request 6531`_
+* Notify if newer tool version is available
+  `Pull Request 6533`_
+* Convert tool parameter XML attribute 'hidden' into the correct boolean
+  Python type
+  (thanks to `@andreyto <https://github.com/andreyto>`__).
+  `Pull Request 6539`_
+* Test case for nested collection input to flatten in a workflow.
+  `Pull Request 6541`_
+* Allow Consuming Tags in the Apply Rules Tool
+  `Pull Request 6545`_
+* Integration test for the interaction of nested object stores and jobs.
+  `Pull Request 6546`_
+* Configure object store for datasets in job handler instead of web thread.
+  `Pull Request 6550`_
+* Allow configuring object stores on a per-job-destination basis.
+  `Pull Request 6552`_
+* Unified dataset permission API.
+  `Pull Request 6568`_
+* Add tagging rule to history level rule builder, copy HDAs when building
+  collection
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6572`_
+* Add API endpoint to fetch a history's workflow invocations.
+  `Pull Request 6580`_
+* Improve robustness of tour Selenium test.
+  `Pull Request 6582`_
+* Smarter Test Histories (Part I)
+  `Pull Request 6586`_
+* Add download option to workflow editor menu
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 6596`_
+* add trr datatype
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 6597`_
+* Refresh an expired OIDC ID token
+  (thanks to `@VJalili <https://github.com/VJalili>`__).
+  `Pull Request 6606`_
+* Handle driver shutdown, show all tests in pytest
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6608`_
+* add dcd datatype for molecular dynamics
+  (thanks to `@chrisbarnettster <https://github.com/chrisbarnettster>`__).
+  `Pull Request 6613`_
+* Py3 testing cleanups
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6616`_
+* Integration test for job recovery.
+  `Pull Request 6620`_
+* Update all dependencies
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6628`_
+* Update some run_tests.sh docs for recent changes.
+  `Pull Request 6629`_
+* Remove check_python_dependencies job from Travis
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6630`_
+* Testing framework improvements
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6632`_
+* Optimize tool execution permission checking
+  `Pull Request 6635`_
+* document config for sniffing compressed files, enable by default
+  `Pull Request 6641`_
+* Small Optimizations to Adding Datasets to History
+  `Pull Request 6644`_
+* Add Seurat datatype: rdata.seurat
+  (thanks to `@mblue9 <https://github.com/mblue9>`__).
+  `Pull Request 6648`_
+* Allow group tag selection also for multiple="true" inputs
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6661`_
+* Various link and documentation fixes
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6662`_
+* Upgraded genomespaceclient to newer version
+  (thanks to `@gvlproject <https://github.com/gvlproject>`__).
+  `Pull Request 6668`_
+* Workflow replacement parameters polish.
+  `Pull Request 6678`_
+* Keep newly broken tool in toolbox
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6681`_
+* Add self help to error reporting interface
+  `Pull Request 6711`_
+
+.. small_enhancement
+
+* Remove duplicate metric sending
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 6011`_
+* This strips the graphite-specific middleware
+  `Pull Request 6018`_
+* Make `interactor._{get,post,put,...}` less repetitive
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6070`_
+* Workflow and remote-user related refactoring and a bug fix
+  `Pull Request 6076`_
+* Drop unused files
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6150`_
+* History import safari fix, overhaul
+  `Pull Request 6153`_
+* Strip legacy history structure view
+  `Pull Request 6241`_
+* Fix typo (UnitializedTree -> UninitializedTree)
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6315`_
+* Rewrite admin data types as vue component
+  (thanks to `@scrathat <https://github.com/scrathat>`__).
+  `Pull Request 6383`_
+* Some style cleanup.
+  `Pull Request 6386`_
+* py3 compat
+  (thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
+  `Pull Request 6434`_
+* Python3: Encode return values of JSON encoder
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6439`_
+* Python3: Drop fix_json, doesn't seem to be necessary and fixes workflow unit
+  t…
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6446`_
+* py3: fixes test_DatasetManager.py:DatasetManagerTestCase
+  (thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
+  `Pull Request 6452`_
+* Fix test_toolbox for python 3
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6463`_
+* Remove redundant/duplicate endpoint to edit user info
+  `Pull Request 6501`_
+* Remove the deprecated AOL openid backend.
+  (thanks to `@VJalili <https://github.com/VJalili>`__).
+  `Pull Request 6505`_
+* Fix all py3 api tests
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6561`_
+* Setup py3 test job
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6565`_
+* Remove backbone version of thumbnail element
+  `Pull Request 6587`_
+* Migrate API tests in test_jobs.py to use test_history context.
+  `Pull Request 6593`_
+* Modernize data manager testing and strip twill
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6595`_
+* Enable and fix framework py3 tests
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6605`_
+* Order data parameters before unlinked multiplication
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6609`_
+* Fix remaining selenium py3 test failures
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6610`_
+* Raise an exception if a history with decoded id does not exist.
+  (thanks to `@VJalili <https://github.com/VJalili>`__).
+  `Pull Request 6611`_
+* Test tools shipped with Galaxy
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6627`_
+* Tweak conda_* setting in test driver
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6633`_
+* Move tests to pytest setup
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6638`_
+* Upgrade CloudBridge to v1.0.1
+  (thanks to `@VJalili <https://github.com/VJalili>`__).
+  `Pull Request 6660`_
+* Increase robustness and accuracy of job search / cache use
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6669`_
+
+
+Fixes
+-------------------------------
+
+.. major_bug
+
+
+.. bug
+
+* fix bowtie2 link
+  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
+  `Pull Request 6009`_
+* Fix some imports
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6014`_
+* Fix JobWrapper.get_destination_configuration() so that it actually checks
+  the JobDestination params
+  `Pull Request 6087`_
+* fixed small typo
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 6094`_
+* History click-to-rename bugfix
+  `Pull Request 6159`_
+* Remove defunct sharing column link
+  `Pull Request 6177`_
+* cutWrapper: fix wrong path in error message
+  (thanks to `@abretaud <https://github.com/abretaud>`__).
+  `Pull Request 6211`_
+* Fix optional="True" inputs
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6222`_
+* Two minor aliases for (exterior) backwards compatibility, minor badge tweaks
+  `Pull Request 6226`_
+* Fix broken collection_type_source tool and test.
+  `Pull Request 6227`_
+* Add io_details and link_details in api tools doc
+  (thanks to `@ValentinChCloud <https://github.com/ValentinChCloud>`__).
+  `Pull Request 6228`_
+* Fix file type error in RuleCollectionBuilder.
+  `Pull Request 6231`_
+* Fix non-strict tabular relabel operation
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6234`_
+* Hack paster args to not duplicate pid file stuff for RUN_ALL.
+  (thanks to `@lparsons <https://github.com/lparsons>`__).
+  `Pull Request 6239`_
+* Backport of Workflow Execution Text Fixup
+  `Pull Request 6243`_
+* Hyperlink DOIs against preferred resolver
+  (thanks to `@katrinleinweber <https://github.com/katrinleinweber>`__).
+  `Pull Request 6244`_
+* Check context for textable mode of select fields
+  `Pull Request 6251`_
+* Mapping over from_param fixes
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6253`_
+* Fix history shared with me 'view' link
+  `Pull Request 6257`_
+* History view 'import' button display based on ownership.
+  `Pull Request 6260`_
+* Various fixes for the run scripts
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6262`_
+* Fix dataset sizes in GRT export script
+  (thanks to `@atyryshkina <https://github.com/atyryshkina>`__).
+  `Pull Request 6263`_
+* Allow invalid optional param values for tools profile versions < 18.09
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6264`_
+* Python3 fixes
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6265`_
+* Fixes for phenotype association tools
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6269`_
+* fix link to workflow list
+  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
+  `Pull Request 6270`_
+*  Fix help text for renaming operation in workflows
+  `Pull Request 6274`_
+* Various fixes for mapping over collections
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6278`_
+* Fix tool search overlay selector
+  (thanks to `@scrathat <https://github.com/scrathat>`__).
+  `Pull Request 6279`_
+* Fix delete "Collection Only" option in history menu.
+  `Pull Request 6281`_
+* telescope export: change to a more defensive approach
+  `Pull Request 6285`_
+* Only update options if provided in parameter definition
+  `Pull Request 6289`_
+* Update tabular.py
+  (thanks to `@hrhotz <https://github.com/hrhotz>`__).
+  `Pull Request 6292`_
+* Strip a spurious Slurm warning from job stderr
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6293`_
+* Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon`
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6295`_
+* add the canonical url to grt config
+  `Pull Request 6301`_
+* Stop listening to history changes after job submission
+  `Pull Request 6303`_
+* Increase sleep if encountering (DB locking) exception
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6304`_
+* Fix undefined success_message
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6316`_
+* Allow #if $datasets #end if pattern for file lists
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6317`_
+* Fix target update for rule collection builder after input selection
+  (thanks to `@scrathat <https://github.com/scrathat>`__).
+  `Pull Request 6326`_
+* Added missing level fatal_oom to xsd
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 6341`_
+* Update description for installing pbs-python
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6345`_
+* Prevent throwing an exception if a dataset doesn't exist (and never w…
+  (thanks to `@dpryan79 <https://github.com/dpryan79>`__).
+  `Pull Request 6349`_
+* Fix the --log-file option in the job handlers
+  (thanks to `@dpryan79 <https://github.com/dpryan79>`__).
+  `Pull Request 6351`_
+* grt - wrap every write in try-except
+  `Pull Request 6354`_
+* Fix 'share with another user'
+  `Pull Request 6358`_
+* Add fasta datatype to msa viewer
+  `Pull Request 6361`_
+* Fix small bug in logging output name in job finish.
+  `Pull Request 6366`_
+* Fix for rendering multiple dependent dynamic select lists
+  (thanks to `@gregvonkuster <https://github.com/gregvonkuster>`__).
+  `Pull Request 6374`_
+* Specify standard HTTPTransport for Sentry
+  `Pull Request 6375`_
+* Comma-separate tool names in missing tools error message
+  `Pull Request 6378`_
+* Revert "Remove bam to bai converter"
+  `Pull Request 6385`_
+* fix data_column cast error when multiple is false
+  (thanks to `@qiagu <https://github.com/qiagu>`__).
+  `Pull Request 6389`_
+* Optimize setting large numbers of HIDs for collection outputs.
+  `Pull Request 6394`_
+* Fixing <conditional> XML example
+  (thanks to `@almahmoud <https://github.com/almahmoud>`__).
+  `Pull Request 6399`_
+* Fix positioning for tool search box.
+  `Pull Request 6416`_
+* removing binary as input for python compatibility
+  (thanks to `@eslerm <https://github.com/eslerm>`__).
+  `Pull Request 6417`_
+* GCC2018 python3 unit-test fixes
+  (thanks to `@ycgong <https://github.com/ycgong>`__).
+  `Pull Request 6419`_
+* python 3 porting
+  (thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
+  `Pull Request 6420`_
+* Fix panel drag resize.
+  `Pull Request 6421`_
+* Fix message fadeout by relying on hiding the message instead
+  `Pull Request 6424`_
+* Python 3 fixes from GCC-BOSC-2018
+  (thanks to `@johnbradley <https://github.com/johnbradley>`__).
+  `Pull Request 6429`_
+* Unit testing with Python 3
+  (thanks to `@NicHerndon <https://github.com/NicHerndon>`__).
+  `Pull Request 6430`_
+* Do not encode a rendered Mako template
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6431`_
+* decode potential encoded id
+  `Pull Request 6433`_
+* fixes test/unit/jobs/test_job_output_checker.py; strange default?
+  (thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
+  `Pull Request 6438`_
+* py3 compat: fixes test_vcf, test_sniff_compressed*
+  (thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
+  `Pull Request 6442`_
+* fix TS: resolve missing closing div and three extra closing divs
+  `Pull Request 6445`_
+* Fix all remaining unit tests under Python 3
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6450`_
+* Fix droptarget:drop trigger (drag/drop in the multiview)
+  `Pull Request 6451`_
+* py3: Fix the dynamic tool destination unit test
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6453`_
+* py3: replace e.message with str(e)
+  (thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
+  `Pull Request 6454`_
+* Various Python 3 fixes
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6455`_
+* GIE static url
+  (thanks to `@thobalose <https://github.com/thobalose>`__).
+  `Pull Request 6460`_
+* Update common_startup_functions.sh
+  (thanks to `@nagoue <https://github.com/nagoue>`__).
+  `Pull Request 6481`_
+* Fix for show params server error
+  `Pull Request 6486`_
+* Fix ftp_upload_purge in galaxy.yml
+  (thanks to `@phac-nml <https://github.com/phac-nml>`__).
+  `Pull Request 6494`_
+* Fix resume from history panel
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6498`_
+* Fix bam to bigwig error detection.
+  (thanks to `@pvanheus <https://github.com/pvanheus>`__).
+  `Pull Request 6502`_
+* Fix and docs for advanced container options in job_conf.xml.
+  `Pull Request 6503`_
+* Return a json blob containing redirect URI in OIDC login controller
+  (thanks to `@VJalili <https://github.com/VJalili>`__).
+  `Pull Request 6517`_
+* Fix warning in CONVERTER_bam_to_bigwig_0 and CONVERTER_sam_to_bigwig_0
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6528`_
+* Fix dataset copy tags
+  `Pull Request 6532`_
+* Fix to_dict with io_details=True for tools with collection outputs.
+  `Pull Request 6538`_
+* Fix "filter empty" rule in Python rule handling framework.
+  `Pull Request 6542`_
+* Fixes for API installation bugs.
+  `Pull Request 6544`_
+* Redirect unidentified routes in admin panel
+  `Pull Request 6551`_
+* Remove the sharing of toolbox in GRT
+  (thanks to `@erasche <https://github.com/erasche>`__).
+  `Pull Request 6553`_
+* Restore log_destination = stdout configuration option.
+  `Pull Request 6555`_
+* Many selenium tests fixes for recent dev changes.
+  `Pull Request 6557`_
+* More Selenium test fixes.
+  `Pull Request 6562`_
+* Misc Admin TS Panel Fixes
+  `Pull Request 6564`_
+* Use subworkflow index when setting auto-label
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6570`_
+* Fix workflow run link for extracted workflows
+  `Pull Request 6571`_
+* Typo and wording fixes for dependency resolvers docs
+  `Pull Request 6575`_
+* Use object store to check for existence of extra_files_path
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6588`_
+* Update UCSC genome-test server URLs
+  `Pull Request 6591`_
+* Resolve overlap of workflow parameter container with gear-icon in editor
+  header
+  `Pull Request 6592`_
+* Respect unavailable display peek
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6594`_
+* Fix Location of Plugin Static Content In Documentation for 18.05
+  (thanks to `@phac-nml <https://github.com/phac-nml>`__).
+  `Pull Request 6602`_
+*  Fix cron/build_chrom_db.py and update UCSC builds
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6623`_
+* Fix for workflow extraction cleanup routine.
+  `Pull Request 6636`_
+* row ids that are all numeric become ints...
+  (thanks to `@bwlang <https://github.com/bwlang>`__).
+  `Pull Request 6639`_
+* Allow running scripts/galaxy-main without Galaxy on sys.path
+  `Pull Request 6642`_
+* Fix color of workflow panel background
+  `Pull Request 6643`_
+* Pages - fixes for encoded ids in the database
+  `Pull Request 6647`_
+* Strip API keys option from admin panel left side
+  `Pull Request 6651`_
+* Fix get_fileobj() call in Eland.set_meta()
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6659`_
+* Update bx-python to 0.8.2
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6670`_
+* Serialize select field options, fixes beta install
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6677`_
+* Fix wf-editor when loading subworkflow with parenthesis in label
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6680`_
+* Add missing route for API endpoint.
+  `Pull Request 6703`_
+* Catch additional permutations of Slurm cgroup creation warnings
+  `Pull Request 6705`_
+* unquote the tool_version in the tools API
+  `Pull Request 6707`_
+* Badge default fix
+  `Pull Request 6726`_
+* remove html tags and newlines from the help text
+  `Pull Request 6728`_
+
+.. github_links
+.. _Pull Request 5457: https://github.com/galaxyproject/galaxy/pull/5457
+.. _Pull Request 5640: https://github.com/galaxyproject/galaxy/pull/5640
+.. _Pull Request 5835: https://github.com/galaxyproject/galaxy/pull/5835
+.. _Pull Request 5982: https://github.com/galaxyproject/galaxy/pull/5982
+.. _Pull Request 5993: https://github.com/galaxyproject/galaxy/pull/5993
+.. _Pull Request 5995: https://github.com/galaxyproject/galaxy/pull/5995
+.. _Pull Request 6004: https://github.com/galaxyproject/galaxy/pull/6004
+.. _Pull Request 6009: https://github.com/galaxyproject/galaxy/pull/6009
+.. _Pull Request 6011: https://github.com/galaxyproject/galaxy/pull/6011
+.. _Pull Request 6013: https://github.com/galaxyproject/galaxy/pull/6013
+.. _Pull Request 6014: https://github.com/galaxyproject/galaxy/pull/6014
+.. _Pull Request 6018: https://github.com/galaxyproject/galaxy/pull/6018
+.. _Pull Request 6021: https://github.com/galaxyproject/galaxy/pull/6021
+.. _Pull Request 6036: https://github.com/galaxyproject/galaxy/pull/6036
+.. _Pull Request 6048: https://github.com/galaxyproject/galaxy/pull/6048
+.. _Pull Request 6066: https://github.com/galaxyproject/galaxy/pull/6066
+.. _Pull Request 6070: https://github.com/galaxyproject/galaxy/pull/6070
+.. _Pull Request 6072: https://github.com/galaxyproject/galaxy/pull/6072
+.. _Pull Request 6076: https://github.com/galaxyproject/galaxy/pull/6076
+.. _Pull Request 6078: https://github.com/galaxyproject/galaxy/pull/6078
+.. _Pull Request 6087: https://github.com/galaxyproject/galaxy/pull/6087
+.. _Pull Request 6092: https://github.com/galaxyproject/galaxy/pull/6092
+.. _Pull Request 6094: https://github.com/galaxyproject/galaxy/pull/6094
+.. _Pull Request 6110: https://github.com/galaxyproject/galaxy/pull/6110
+.. _Pull Request 6122: https://github.com/galaxyproject/galaxy/pull/6122
+.. _Pull Request 6132: https://github.com/galaxyproject/galaxy/pull/6132
+.. _Pull Request 6135: https://github.com/galaxyproject/galaxy/pull/6135
+.. _Pull Request 6142: https://github.com/galaxyproject/galaxy/pull/6142
+.. _Pull Request 6148: https://github.com/galaxyproject/galaxy/pull/6148
+.. _Pull Request 6150: https://github.com/galaxyproject/galaxy/pull/6150
+.. _Pull Request 6153: https://github.com/galaxyproject/galaxy/pull/6153
+.. _Pull Request 6159: https://github.com/galaxyproject/galaxy/pull/6159
+.. _Pull Request 6171: https://github.com/galaxyproject/galaxy/pull/6171
+.. _Pull Request 6176: https://github.com/galaxyproject/galaxy/pull/6176
+.. _Pull Request 6177: https://github.com/galaxyproject/galaxy/pull/6177
+.. _Pull Request 6195: https://github.com/galaxyproject/galaxy/pull/6195
+.. _Pull Request 6200: https://github.com/galaxyproject/galaxy/pull/6200
+.. _Pull Request 6201: https://github.com/galaxyproject/galaxy/pull/6201
+.. _Pull Request 6206: https://github.com/galaxyproject/galaxy/pull/6206
+.. _Pull Request 6211: https://github.com/galaxyproject/galaxy/pull/6211
+.. _Pull Request 6212: https://github.com/galaxyproject/galaxy/pull/6212
+.. _Pull Request 6213: https://github.com/galaxyproject/galaxy/pull/6213
+.. _Pull Request 6215: https://github.com/galaxyproject/galaxy/pull/6215
+.. _Pull Request 6216: https://github.com/galaxyproject/galaxy/pull/6216
+.. _Pull Request 6221: https://github.com/galaxyproject/galaxy/pull/6221
+.. _Pull Request 6222: https://github.com/galaxyproject/galaxy/pull/6222
+.. _Pull Request 6226: https://github.com/galaxyproject/galaxy/pull/6226
+.. _Pull Request 6227: https://github.com/galaxyproject/galaxy/pull/6227
+.. _Pull Request 6228: https://github.com/galaxyproject/galaxy/pull/6228
+.. _Pull Request 6231: https://github.com/galaxyproject/galaxy/pull/6231
+.. _Pull Request 6234: https://github.com/galaxyproject/galaxy/pull/6234
+.. _Pull Request 6237: https://github.com/galaxyproject/galaxy/pull/6237
+.. _Pull Request 6239: https://github.com/galaxyproject/galaxy/pull/6239
+.. _Pull Request 6240: https://github.com/galaxyproject/galaxy/pull/6240
+.. _Pull Request 6241: https://github.com/galaxyproject/galaxy/pull/6241
+.. _Pull Request 6242: https://github.com/galaxyproject/galaxy/pull/6242
+.. _Pull Request 6243: https://github.com/galaxyproject/galaxy/pull/6243
+.. _Pull Request 6244: https://github.com/galaxyproject/galaxy/pull/6244
+.. _Pull Request 6248: https://github.com/galaxyproject/galaxy/pull/6248
+.. _Pull Request 6251: https://github.com/galaxyproject/galaxy/pull/6251
+.. _Pull Request 6252: https://github.com/galaxyproject/galaxy/pull/6252
+.. _Pull Request 6253: https://github.com/galaxyproject/galaxy/pull/6253
+.. _Pull Request 6255: https://github.com/galaxyproject/galaxy/pull/6255
+.. _Pull Request 6257: https://github.com/galaxyproject/galaxy/pull/6257
+.. _Pull Request 6260: https://github.com/galaxyproject/galaxy/pull/6260
+.. _Pull Request 6262: https://github.com/galaxyproject/galaxy/pull/6262
+.. _Pull Request 6263: https://github.com/galaxyproject/galaxy/pull/6263
+.. _Pull Request 6264: https://github.com/galaxyproject/galaxy/pull/6264
+.. _Pull Request 6265: https://github.com/galaxyproject/galaxy/pull/6265
+.. _Pull Request 6269: https://github.com/galaxyproject/galaxy/pull/6269
+.. _Pull Request 6270: https://github.com/galaxyproject/galaxy/pull/6270
+.. _Pull Request 6273: https://github.com/galaxyproject/galaxy/pull/6273
+.. _Pull Request 6274: https://github.com/galaxyproject/galaxy/pull/6274
+.. _Pull Request 6277: https://github.com/galaxyproject/galaxy/pull/6277
+.. _Pull Request 6278: https://github.com/galaxyproject/galaxy/pull/6278
+.. _Pull Request 6279: https://github.com/galaxyproject/galaxy/pull/6279
+.. _Pull Request 6281: https://github.com/galaxyproject/galaxy/pull/6281
+.. _Pull Request 6285: https://github.com/galaxyproject/galaxy/pull/6285
+.. _Pull Request 6286: https://github.com/galaxyproject/galaxy/pull/6286
+.. _Pull Request 6288: https://github.com/galaxyproject/galaxy/pull/6288
+.. _Pull Request 6289: https://github.com/galaxyproject/galaxy/pull/6289
+.. _Pull Request 6290: https://github.com/galaxyproject/galaxy/pull/6290
+.. _Pull Request 6292: https://github.com/galaxyproject/galaxy/pull/6292
+.. _Pull Request 6293: https://github.com/galaxyproject/galaxy/pull/6293
+.. _Pull Request 6294: https://github.com/galaxyproject/galaxy/pull/6294
+.. _Pull Request 6295: https://github.com/galaxyproject/galaxy/pull/6295
+.. _Pull Request 6300: https://github.com/galaxyproject/galaxy/pull/6300
+.. _Pull Request 6301: https://github.com/galaxyproject/galaxy/pull/6301
+.. _Pull Request 6302: https://github.com/galaxyproject/galaxy/pull/6302
+.. _Pull Request 6303: https://github.com/galaxyproject/galaxy/pull/6303
+.. _Pull Request 6304: https://github.com/galaxyproject/galaxy/pull/6304
+.. _Pull Request 6305: https://github.com/galaxyproject/galaxy/pull/6305
+.. _Pull Request 6307: https://github.com/galaxyproject/galaxy/pull/6307
+.. _Pull Request 6312: https://github.com/galaxyproject/galaxy/pull/6312
+.. _Pull Request 6313: https://github.com/galaxyproject/galaxy/pull/6313
+.. _Pull Request 6315: https://github.com/galaxyproject/galaxy/pull/6315
+.. _Pull Request 6316: https://github.com/galaxyproject/galaxy/pull/6316
+.. _Pull Request 6317: https://github.com/galaxyproject/galaxy/pull/6317
+.. _Pull Request 6324: https://github.com/galaxyproject/galaxy/pull/6324
+.. _Pull Request 6325: https://github.com/galaxyproject/galaxy/pull/6325
+.. _Pull Request 6326: https://github.com/galaxyproject/galaxy/pull/6326
+.. _Pull Request 6341: https://github.com/galaxyproject/galaxy/pull/6341
+.. _Pull Request 6344: https://github.com/galaxyproject/galaxy/pull/6344
+.. _Pull Request 6345: https://github.com/galaxyproject/galaxy/pull/6345
+.. _Pull Request 6349: https://github.com/galaxyproject/galaxy/pull/6349
+.. _Pull Request 6351: https://github.com/galaxyproject/galaxy/pull/6351
+.. _Pull Request 6354: https://github.com/galaxyproject/galaxy/pull/6354
+.. _Pull Request 6358: https://github.com/galaxyproject/galaxy/pull/6358
+.. _Pull Request 6361: https://github.com/galaxyproject/galaxy/pull/6361
+.. _Pull Request 6365: https://github.com/galaxyproject/galaxy/pull/6365
+.. _Pull Request 6366: https://github.com/galaxyproject/galaxy/pull/6366
+.. _Pull Request 6367: https://github.com/galaxyproject/galaxy/pull/6367
+.. _Pull Request 6370: https://github.com/galaxyproject/galaxy/pull/6370
+.. _Pull Request 6371: https://github.com/galaxyproject/galaxy/pull/6371
+.. _Pull Request 6372: https://github.com/galaxyproject/galaxy/pull/6372
+.. _Pull Request 6374: https://github.com/galaxyproject/galaxy/pull/6374
+.. _Pull Request 6375: https://github.com/galaxyproject/galaxy/pull/6375
+.. _Pull Request 6377: https://github.com/galaxyproject/galaxy/pull/6377
+.. _Pull Request 6378: https://github.com/galaxyproject/galaxy/pull/6378
+.. _Pull Request 6381: https://github.com/galaxyproject/galaxy/pull/6381
+.. _Pull Request 6383: https://github.com/galaxyproject/galaxy/pull/6383
+.. _Pull Request 6385: https://github.com/galaxyproject/galaxy/pull/6385
+.. _Pull Request 6386: https://github.com/galaxyproject/galaxy/pull/6386
+.. _Pull Request 6388: https://github.com/galaxyproject/galaxy/pull/6388
+.. _Pull Request 6389: https://github.com/galaxyproject/galaxy/pull/6389
+.. _Pull Request 6394: https://github.com/galaxyproject/galaxy/pull/6394
+.. _Pull Request 6399: https://github.com/galaxyproject/galaxy/pull/6399
+.. _Pull Request 6400: https://github.com/galaxyproject/galaxy/pull/6400
+.. _Pull Request 6402: https://github.com/galaxyproject/galaxy/pull/6402
+.. _Pull Request 6403: https://github.com/galaxyproject/galaxy/pull/6403
+.. _Pull Request 6406: https://github.com/galaxyproject/galaxy/pull/6406
+.. _Pull Request 6415: https://github.com/galaxyproject/galaxy/pull/6415
+.. _Pull Request 6416: https://github.com/galaxyproject/galaxy/pull/6416
+.. _Pull Request 6417: https://github.com/galaxyproject/galaxy/pull/6417
+.. _Pull Request 6418: https://github.com/galaxyproject/galaxy/pull/6418
+.. _Pull Request 6419: https://github.com/galaxyproject/galaxy/pull/6419
+.. _Pull Request 6420: https://github.com/galaxyproject/galaxy/pull/6420
+.. _Pull Request 6421: https://github.com/galaxyproject/galaxy/pull/6421
+.. _Pull Request 6424: https://github.com/galaxyproject/galaxy/pull/6424
+.. _Pull Request 6425: https://github.com/galaxyproject/galaxy/pull/6425
+.. _Pull Request 6427: https://github.com/galaxyproject/galaxy/pull/6427
+.. _Pull Request 6428: https://github.com/galaxyproject/galaxy/pull/6428
+.. _Pull Request 6429: https://github.com/galaxyproject/galaxy/pull/6429
+.. _Pull Request 6430: https://github.com/galaxyproject/galaxy/pull/6430
+.. _Pull Request 6431: https://github.com/galaxyproject/galaxy/pull/6431
+.. _Pull Request 6433: https://github.com/galaxyproject/galaxy/pull/6433
+.. _Pull Request 6434: https://github.com/galaxyproject/galaxy/pull/6434
+.. _Pull Request 6436: https://github.com/galaxyproject/galaxy/pull/6436
+.. _Pull Request 6438: https://github.com/galaxyproject/galaxy/pull/6438
+.. _Pull Request 6439: https://github.com/galaxyproject/galaxy/pull/6439
+.. _Pull Request 6440: https://github.com/galaxyproject/galaxy/pull/6440
+.. _Pull Request 6441: https://github.com/galaxyproject/galaxy/pull/6441
+.. _Pull Request 6442: https://github.com/galaxyproject/galaxy/pull/6442
+.. _Pull Request 6443: https://github.com/galaxyproject/galaxy/pull/6443
+.. _Pull Request 6444: https://github.com/galaxyproject/galaxy/pull/6444
+.. _Pull Request 6445: https://github.com/galaxyproject/galaxy/pull/6445
+.. _Pull Request 6446: https://github.com/galaxyproject/galaxy/pull/6446
+.. _Pull Request 6447: https://github.com/galaxyproject/galaxy/pull/6447
+.. _Pull Request 6449: https://github.com/galaxyproject/galaxy/pull/6449
+.. _Pull Request 6450: https://github.com/galaxyproject/galaxy/pull/6450
+.. _Pull Request 6451: https://github.com/galaxyproject/galaxy/pull/6451
+.. _Pull Request 6452: https://github.com/galaxyproject/galaxy/pull/6452
+.. _Pull Request 6453: https://github.com/galaxyproject/galaxy/pull/6453
+.. _Pull Request 6454: https://github.com/galaxyproject/galaxy/pull/6454
+.. _Pull Request 6455: https://github.com/galaxyproject/galaxy/pull/6455
+.. _Pull Request 6460: https://github.com/galaxyproject/galaxy/pull/6460
+.. _Pull Request 6463: https://github.com/galaxyproject/galaxy/pull/6463
+.. _Pull Request 6466: https://github.com/galaxyproject/galaxy/pull/6466
+.. _Pull Request 6467: https://github.com/galaxyproject/galaxy/pull/6467
+.. _Pull Request 6468: https://github.com/galaxyproject/galaxy/pull/6468
+.. _Pull Request 6469: https://github.com/galaxyproject/galaxy/pull/6469
+.. _Pull Request 6474: https://github.com/galaxyproject/galaxy/pull/6474
+.. _Pull Request 6476: https://github.com/galaxyproject/galaxy/pull/6476
+.. _Pull Request 6478: https://github.com/galaxyproject/galaxy/pull/6478
+.. _Pull Request 6480: https://github.com/galaxyproject/galaxy/pull/6480
+.. _Pull Request 6481: https://github.com/galaxyproject/galaxy/pull/6481
+.. _Pull Request 6486: https://github.com/galaxyproject/galaxy/pull/6486
+.. _Pull Request 6489: https://github.com/galaxyproject/galaxy/pull/6489
+.. _Pull Request 6490: https://github.com/galaxyproject/galaxy/pull/6490
+.. _Pull Request 6491: https://github.com/galaxyproject/galaxy/pull/6491
+.. _Pull Request 6494: https://github.com/galaxyproject/galaxy/pull/6494
+.. _Pull Request 6496: https://github.com/galaxyproject/galaxy/pull/6496
+.. _Pull Request 6498: https://github.com/galaxyproject/galaxy/pull/6498
+.. _Pull Request 6499: https://github.com/galaxyproject/galaxy/pull/6499
+.. _Pull Request 6500: https://github.com/galaxyproject/galaxy/pull/6500
+.. _Pull Request 6501: https://github.com/galaxyproject/galaxy/pull/6501
+.. _Pull Request 6502: https://github.com/galaxyproject/galaxy/pull/6502
+.. _Pull Request 6503: https://github.com/galaxyproject/galaxy/pull/6503
+.. _Pull Request 6505: https://github.com/galaxyproject/galaxy/pull/6505
+.. _Pull Request 6515: https://github.com/galaxyproject/galaxy/pull/6515
+.. _Pull Request 6516: https://github.com/galaxyproject/galaxy/pull/6516
+.. _Pull Request 6517: https://github.com/galaxyproject/galaxy/pull/6517
+.. _Pull Request 6519: https://github.com/galaxyproject/galaxy/pull/6519
+.. _Pull Request 6520: https://github.com/galaxyproject/galaxy/pull/6520
+.. _Pull Request 6521: https://github.com/galaxyproject/galaxy/pull/6521
+.. _Pull Request 6523: https://github.com/galaxyproject/galaxy/pull/6523
+.. _Pull Request 6524: https://github.com/galaxyproject/galaxy/pull/6524
+.. _Pull Request 6528: https://github.com/galaxyproject/galaxy/pull/6528
+.. _Pull Request 6529: https://github.com/galaxyproject/galaxy/pull/6529
+.. _Pull Request 6531: https://github.com/galaxyproject/galaxy/pull/6531
+.. _Pull Request 6532: https://github.com/galaxyproject/galaxy/pull/6532
+.. _Pull Request 6533: https://github.com/galaxyproject/galaxy/pull/6533
+.. _Pull Request 6538: https://github.com/galaxyproject/galaxy/pull/6538
+.. _Pull Request 6539: https://github.com/galaxyproject/galaxy/pull/6539
+.. _Pull Request 6541: https://github.com/galaxyproject/galaxy/pull/6541
+.. _Pull Request 6542: https://github.com/galaxyproject/galaxy/pull/6542
+.. _Pull Request 6544: https://github.com/galaxyproject/galaxy/pull/6544
+.. _Pull Request 6545: https://github.com/galaxyproject/galaxy/pull/6545
+.. _Pull Request 6546: https://github.com/galaxyproject/galaxy/pull/6546
+.. _Pull Request 6550: https://github.com/galaxyproject/galaxy/pull/6550
+.. _Pull Request 6551: https://github.com/galaxyproject/galaxy/pull/6551
+.. _Pull Request 6552: https://github.com/galaxyproject/galaxy/pull/6552
+.. _Pull Request 6553: https://github.com/galaxyproject/galaxy/pull/6553
+.. _Pull Request 6554: https://github.com/galaxyproject/galaxy/pull/6554
+.. _Pull Request 6555: https://github.com/galaxyproject/galaxy/pull/6555
+.. _Pull Request 6557: https://github.com/galaxyproject/galaxy/pull/6557
+.. _Pull Request 6561: https://github.com/galaxyproject/galaxy/pull/6561
+.. _Pull Request 6562: https://github.com/galaxyproject/galaxy/pull/6562
+.. _Pull Request 6564: https://github.com/galaxyproject/galaxy/pull/6564
+.. _Pull Request 6565: https://github.com/galaxyproject/galaxy/pull/6565
+.. _Pull Request 6567: https://github.com/galaxyproject/galaxy/pull/6567
+.. _Pull Request 6568: https://github.com/galaxyproject/galaxy/pull/6568
+.. _Pull Request 6570: https://github.com/galaxyproject/galaxy/pull/6570
+.. _Pull Request 6571: https://github.com/galaxyproject/galaxy/pull/6571
+.. _Pull Request 6572: https://github.com/galaxyproject/galaxy/pull/6572
+.. _Pull Request 6575: https://github.com/galaxyproject/galaxy/pull/6575
+.. _Pull Request 6578: https://github.com/galaxyproject/galaxy/pull/6578
+.. _Pull Request 6580: https://github.com/galaxyproject/galaxy/pull/6580
+.. _Pull Request 6582: https://github.com/galaxyproject/galaxy/pull/6582
+.. _Pull Request 6586: https://github.com/galaxyproject/galaxy/pull/6586
+.. _Pull Request 6587: https://github.com/galaxyproject/galaxy/pull/6587
+.. _Pull Request 6588: https://github.com/galaxyproject/galaxy/pull/6588
+.. _Pull Request 6591: https://github.com/galaxyproject/galaxy/pull/6591
+.. _Pull Request 6592: https://github.com/galaxyproject/galaxy/pull/6592
+.. _Pull Request 6593: https://github.com/galaxyproject/galaxy/pull/6593
+.. _Pull Request 6594: https://github.com/galaxyproject/galaxy/pull/6594
+.. _Pull Request 6595: https://github.com/galaxyproject/galaxy/pull/6595
+.. _Pull Request 6596: https://github.com/galaxyproject/galaxy/pull/6596
+.. _Pull Request 6597: https://github.com/galaxyproject/galaxy/pull/6597
+.. _Pull Request 6602: https://github.com/galaxyproject/galaxy/pull/6602
+.. _Pull Request 6605: https://github.com/galaxyproject/galaxy/pull/6605
+.. _Pull Request 6606: https://github.com/galaxyproject/galaxy/pull/6606
+.. _Pull Request 6608: https://github.com/galaxyproject/galaxy/pull/6608
+.. _Pull Request 6609: https://github.com/galaxyproject/galaxy/pull/6609
+.. _Pull Request 6610: https://github.com/galaxyproject/galaxy/pull/6610
+.. _Pull Request 6611: https://github.com/galaxyproject/galaxy/pull/6611
+.. _Pull Request 6613: https://github.com/galaxyproject/galaxy/pull/6613
+.. _Pull Request 6616: https://github.com/galaxyproject/galaxy/pull/6616
+.. _Pull Request 6620: https://github.com/galaxyproject/galaxy/pull/6620
+.. _Pull Request 6622: https://github.com/galaxyproject/galaxy/pull/6622
+.. _Pull Request 6623: https://github.com/galaxyproject/galaxy/pull/6623
+.. _Pull Request 6627: https://github.com/galaxyproject/galaxy/pull/6627
+.. _Pull Request 6628: https://github.com/galaxyproject/galaxy/pull/6628
+.. _Pull Request 6629: https://github.com/galaxyproject/galaxy/pull/6629
+.. _Pull Request 6630: https://github.com/galaxyproject/galaxy/pull/6630
+.. _Pull Request 6631: https://github.com/galaxyproject/galaxy/pull/6631
+.. _Pull Request 6632: https://github.com/galaxyproject/galaxy/pull/6632
+.. _Pull Request 6633: https://github.com/galaxyproject/galaxy/pull/6633
+.. _Pull Request 6635: https://github.com/galaxyproject/galaxy/pull/6635
+.. _Pull Request 6636: https://github.com/galaxyproject/galaxy/pull/6636
+.. _Pull Request 6638: https://github.com/galaxyproject/galaxy/pull/6638
+.. _Pull Request 6639: https://github.com/galaxyproject/galaxy/pull/6639
+.. _Pull Request 6641: https://github.com/galaxyproject/galaxy/pull/6641
+.. _Pull Request 6642: https://github.com/galaxyproject/galaxy/pull/6642
+.. _Pull Request 6643: https://github.com/galaxyproject/galaxy/pull/6643
+.. _Pull Request 6644: https://github.com/galaxyproject/galaxy/pull/6644
+.. _Pull Request 6647: https://github.com/galaxyproject/galaxy/pull/6647
+.. _Pull Request 6648: https://github.com/galaxyproject/galaxy/pull/6648
+.. _Pull Request 6651: https://github.com/galaxyproject/galaxy/pull/6651
+.. _Pull Request 6655: https://github.com/galaxyproject/galaxy/pull/6655
+.. _Pull Request 6656: https://github.com/galaxyproject/galaxy/pull/6656
+.. _Pull Request 6659: https://github.com/galaxyproject/galaxy/pull/6659
+.. _Pull Request 6660: https://github.com/galaxyproject/galaxy/pull/6660
+.. _Pull Request 6661: https://github.com/galaxyproject/galaxy/pull/6661
+.. _Pull Request 6662: https://github.com/galaxyproject/galaxy/pull/6662
+.. _Pull Request 6664: https://github.com/galaxyproject/galaxy/pull/6664
+.. _Pull Request 6668: https://github.com/galaxyproject/galaxy/pull/6668
+.. _Pull Request 6669: https://github.com/galaxyproject/galaxy/pull/6669
+.. _Pull Request 6670: https://github.com/galaxyproject/galaxy/pull/6670
+.. _Pull Request 6672: https://github.com/galaxyproject/galaxy/pull/6672
+.. _Pull Request 6676: https://github.com/galaxyproject/galaxy/pull/6676
+.. _Pull Request 6677: https://github.com/galaxyproject/galaxy/pull/6677
+.. _Pull Request 6678: https://github.com/galaxyproject/galaxy/pull/6678
+.. _Pull Request 6680: https://github.com/galaxyproject/galaxy/pull/6680
+.. _Pull Request 6681: https://github.com/galaxyproject/galaxy/pull/6681
+.. _Pull Request 6683: https://github.com/galaxyproject/galaxy/pull/6683
+.. _Pull Request 6687: https://github.com/galaxyproject/galaxy/pull/6687
+.. _Pull Request 6692: https://github.com/galaxyproject/galaxy/pull/6692
+.. _Pull Request 6695: https://github.com/galaxyproject/galaxy/pull/6695
+.. _Pull Request 6703: https://github.com/galaxyproject/galaxy/pull/6703
+.. _Pull Request 6705: https://github.com/galaxyproject/galaxy/pull/6705
+.. _Pull Request 6707: https://github.com/galaxyproject/galaxy/pull/6707
+.. _Pull Request 6711: https://github.com/galaxyproject/galaxy/pull/6711
+.. _Pull Request 6726: https://github.com/galaxyproject/galaxy/pull/6726
+.. _Pull Request 6728: https://github.com/galaxyproject/galaxy/pull/6728
+.. _Pull Request 6730: https://github.com/galaxyproject/galaxy/pull/6730
+
diff --git a/doc/source/releases/18.09_announce.rst b/doc/source/releases/18.09_announce.rst
new file mode 100644
index 00000000000..df4869240eb
--- /dev/null
+++ b/doc/source/releases/18.09_announce.rst
@@ -0,0 +1,43 @@
+
+===========================================================
+September 2018 Galaxy Release (v 18.09)
+===========================================================
+
+.. include:: _header.rst
+
+Highlights
+===========================================================
+
+**Feature1**
+  Feature description.
+
+**Feature2**
+  Feature description.
+
+**Feature3**
+  Feature description.
+
+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_18.09 https://github.com/galaxyproject/galaxy.git
+
+To update an existing Galaxy repository run:
+  .. code-block:: shell
+
+      $ git fetch origin && git checkout release_18.09 && git pull --ff-only origin release_18.09
+
+See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
+
+Release Notes
+===========================================================
+
+.. include:: 18.09.rst
+   :start-after: announce_start
+
+.. include:: _thanks.rst
diff --git a/doc/source/releases/19.01_announce.rst b/doc/source/releases/19.01_announce.rst
new file mode 100644
index 00000000000..7400038de79
--- /dev/null
+++ b/doc/source/releases/19.01_announce.rst
@@ -0,0 +1,10 @@
+
+===========================================================
+January 2019 Galaxy Release (v 19.01)
+===========================================================
+
+
+Schedule
+===========================================================
+ * Planned Freeze Date: 2019-01-07
+ * Planned Release Date: 2019-01-28

From 25fc1617030d392f85abb65ccd95f913561919e2 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 24 Sep 2018 09:52:01 -0400
Subject: [PATCH 02/24] Update RN with new merges.

---
 doc/source/releases/18.09.rst | 36 +++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index 5ae74596ccc..bd3a1c5811c 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -42,6 +42,8 @@ Enhancements
 * Expose workflow versions
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6683`_
+* Add Loom datatype and remove rdata.seurat
+  `Pull Request 6723`_
 
 .. enhancement
 
@@ -331,6 +333,8 @@ Enhancements
   `Pull Request 6681`_
 * Add self help to error reporting interface
   `Pull Request 6711`_
+* Undo auto-propagation of group tags.
+  `Pull Request 6750`_
 
 .. small_enhancement
 
@@ -724,10 +728,29 @@ Fixes
   `Pull Request 6705`_
 * unquote the tool_version in the tools API
   `Pull Request 6707`_
+* Fix active highlight
+  `Pull Request 6725`_
 * Badge default fix
   `Pull Request 6726`_
 * remove html tags and newlines from the help text
   `Pull Request 6728`_
+* Fix missing tests for data source sniffing.
+  `Pull Request 6733`_
+* Decode tool id and version in the client, not in the API
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6737`_
+* Fix and test anonymous error reports
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6742`_
+* fix favicon.ico for uwsgi deployments
+  `Pull Request 6743`_
+* dispose of dataset tooltip when the delete is being called
+  `Pull Request 6744`_
+* Fix page editor height for flex panels.
+  `Pull Request 6747`_
+* Use mapped-over collectionType when inferring collectionType through …
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6749`_
 
 .. github_links
 .. _Pull Request 5457: https://github.com/galaxyproject/galaxy/pull/5457
@@ -1023,7 +1046,20 @@ Fixes
 .. _Pull Request 6705: https://github.com/galaxyproject/galaxy/pull/6705
 .. _Pull Request 6707: https://github.com/galaxyproject/galaxy/pull/6707
 .. _Pull Request 6711: https://github.com/galaxyproject/galaxy/pull/6711
+.. _Pull Request 6723: https://github.com/galaxyproject/galaxy/pull/6723
+.. _Pull Request 6725: https://github.com/galaxyproject/galaxy/pull/6725
 .. _Pull Request 6726: https://github.com/galaxyproject/galaxy/pull/6726
 .. _Pull Request 6728: https://github.com/galaxyproject/galaxy/pull/6728
 .. _Pull Request 6730: https://github.com/galaxyproject/galaxy/pull/6730
+.. _Pull Request 6733: https://github.com/galaxyproject/galaxy/pull/6733
+.. _Pull Request 6737: https://github.com/galaxyproject/galaxy/pull/6737
+.. _Pull Request 6739: https://github.com/galaxyproject/galaxy/pull/6739
+.. _Pull Request 6741: https://github.com/galaxyproject/galaxy/pull/6741
+.. _Pull Request 6742: https://github.com/galaxyproject/galaxy/pull/6742
+.. _Pull Request 6743: https://github.com/galaxyproject/galaxy/pull/6743
+.. _Pull Request 6744: https://github.com/galaxyproject/galaxy/pull/6744
+.. _Pull Request 6747: https://github.com/galaxyproject/galaxy/pull/6747
+.. _Pull Request 6748: https://github.com/galaxyproject/galaxy/pull/6748
+.. _Pull Request 6749: https://github.com/galaxyproject/galaxy/pull/6749
+.. _Pull Request 6750: https://github.com/galaxyproject/galaxy/pull/6750
 

From 8c05e2f5f1677950a3279ffa30ccbf8949aa35e4 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 24 Sep 2018 10:47:10 -0400
Subject: [PATCH 03/24] Add grapdot datatype.

---
 doc/source/releases/18.09.rst | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index bd3a1c5811c..be6332073df 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -335,6 +335,9 @@ Enhancements
   `Pull Request 6711`_
 * Undo auto-propagation of group tags.
   `Pull Request 6750`_
+* Add graph dot datatype and enable it in visualisations
+  (thanks to `@bgruening <https://github.com/bgruening>`__).
+  `Pull Request 6760`_
 
 .. small_enhancement
 
@@ -1062,4 +1065,5 @@ Fixes
 .. _Pull Request 6748: https://github.com/galaxyproject/galaxy/pull/6748
 .. _Pull Request 6749: https://github.com/galaxyproject/galaxy/pull/6749
 .. _Pull Request 6750: https://github.com/galaxyproject/galaxy/pull/6750
+.. _Pull Request 6760: https://github.com/galaxyproject/galaxy/pull/6760
 

From 6ac5966c5e1a95e93c5923a4eddf5fa971518bd6 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 24 Sep 2018 16:21:19 -0400
Subject: [PATCH 04/24] Add removal of upgrade logic specific to datatypes from
 17.05

---
 doc/source/releases/18.09.rst | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index be6332073df..379e25766dd 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -338,6 +338,8 @@ Enhancements
 * Add graph dot datatype and enable it in visualisations
   (thanks to `@bgruening <https://github.com/bgruening>`__).
   `Pull Request 6760`_
+* Remove upgrade cruft related to datatypes.
+  `Pull Request 6761`_
 
 .. small_enhancement
 
@@ -1066,4 +1068,5 @@ Fixes
 .. _Pull Request 6749: https://github.com/galaxyproject/galaxy/pull/6749
 .. _Pull Request 6750: https://github.com/galaxyproject/galaxy/pull/6750
 .. _Pull Request 6760: https://github.com/galaxyproject/galaxy/pull/6760
+.. _Pull Request 6761: https://github.com/galaxyproject/galaxy/pull/6761
 

From 0698a71861afadb7f16be765223819178d294c30 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 25 Sep 2018 14:06:50 -0400
Subject: [PATCH 05/24] Another few stragglers.

---
 doc/source/releases/18.09.rst | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index 379e25766dd..5824badcf96 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -756,6 +756,12 @@ Fixes
 * Use mapped-over collectionType when inferring collectionType through …
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6749`_
+* Don't attempt len(None), ensure stdout/stderr are strings in
+  Job(Like).set_streams().
+  `Pull Request 6765`_
+* Increase the maximum number of stderr lines that will be scanned for slurm
+  warnings
+  `Pull Request 6766`_
 
 .. github_links
 .. _Pull Request 5457: https://github.com/galaxyproject/galaxy/pull/5457
@@ -1069,4 +1075,6 @@ Fixes
 .. _Pull Request 6750: https://github.com/galaxyproject/galaxy/pull/6750
 .. _Pull Request 6760: https://github.com/galaxyproject/galaxy/pull/6760
 .. _Pull Request 6761: https://github.com/galaxyproject/galaxy/pull/6761
+.. _Pull Request 6765: https://github.com/galaxyproject/galaxy/pull/6765
+.. _Pull Request 6766: https://github.com/galaxyproject/galaxy/pull/6766
 

From d3db21fa82a834d0d9fa90106b3fa2b4911708dc Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 25 Sep 2018 14:31:41 -0400
Subject: [PATCH 06/24] Add 6755

---
 doc/source/releases/18.09.rst | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index 5824badcf96..51aefe6c455 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -756,6 +756,9 @@ Fixes
 * Use mapped-over collectionType when inferring collectionType through …
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6749`_
+* Catch any failures encountered while pausing/stopping jobs whose inputs are
+  terminal and non-ok
+  `Pull Request 6755`_
 * Don't attempt len(None), ensure stdout/stderr are strings in
   Job(Like).set_streams().
   `Pull Request 6765`_
@@ -1073,6 +1076,7 @@ Fixes
 .. _Pull Request 6748: https://github.com/galaxyproject/galaxy/pull/6748
 .. _Pull Request 6749: https://github.com/galaxyproject/galaxy/pull/6749
 .. _Pull Request 6750: https://github.com/galaxyproject/galaxy/pull/6750
+.. _Pull Request 6755: https://github.com/galaxyproject/galaxy/pull/6755
 .. _Pull Request 6760: https://github.com/galaxyproject/galaxy/pull/6760
 .. _Pull Request 6761: https://github.com/galaxyproject/galaxy/pull/6761
 .. _Pull Request 6765: https://github.com/galaxyproject/galaxy/pull/6765

From 6cb4c32eb4e613b4d90680450d11804779e5b4a5 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 26 Sep 2018 07:21:00 -0400
Subject: [PATCH 07/24] Add 6768

---
 doc/source/releases/18.09.rst | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index 51aefe6c455..e17c8f0db60 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -765,6 +765,8 @@ Fixes
 * Increase the maximum number of stderr lines that will be scanned for slurm
   warnings
   `Pull Request 6766`_
+* backport of: Resilience of success message handling
+  `Pull Request 6768`_
 
 .. github_links
 .. _Pull Request 5457: https://github.com/galaxyproject/galaxy/pull/5457
@@ -1081,4 +1083,5 @@ Fixes
 .. _Pull Request 6761: https://github.com/galaxyproject/galaxy/pull/6761
 .. _Pull Request 6765: https://github.com/galaxyproject/galaxy/pull/6765
 .. _Pull Request 6766: https://github.com/galaxyproject/galaxy/pull/6766
+.. _Pull Request 6768: https://github.com/galaxyproject/galaxy/pull/6768
 

From ee47fdb50cef70dd2b940c42594611863e51bde7 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 26 Sep 2018 12:58:41 -0400
Subject: [PATCH 08/24] Add 6753, 6771

---
 doc/source/releases/18.09.rst | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index e17c8f0db60..8a2969a24d4 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -335,6 +335,8 @@ Enhancements
   `Pull Request 6711`_
 * Undo auto-propagation of group tags.
   `Pull Request 6750`_
+* Client build startup changes
+  `Pull Request 6753`_
 * Add graph dot datatype and enable it in visualisations
   (thanks to `@bgruening <https://github.com/bgruening>`__).
   `Pull Request 6760`_
@@ -767,6 +769,9 @@ Fixes
   `Pull Request 6766`_
 * backport of: Resilience of success message handling
   `Pull Request 6768`_
+* Use UserRoleAssociation to get private roles
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6771`_
 
 .. github_links
 .. _Pull Request 5457: https://github.com/galaxyproject/galaxy/pull/5457
@@ -1078,10 +1083,12 @@ Fixes
 .. _Pull Request 6748: https://github.com/galaxyproject/galaxy/pull/6748
 .. _Pull Request 6749: https://github.com/galaxyproject/galaxy/pull/6749
 .. _Pull Request 6750: https://github.com/galaxyproject/galaxy/pull/6750
+.. _Pull Request 6753: https://github.com/galaxyproject/galaxy/pull/6753
 .. _Pull Request 6755: https://github.com/galaxyproject/galaxy/pull/6755
 .. _Pull Request 6760: https://github.com/galaxyproject/galaxy/pull/6760
 .. _Pull Request 6761: https://github.com/galaxyproject/galaxy/pull/6761
 .. _Pull Request 6765: https://github.com/galaxyproject/galaxy/pull/6765
 .. _Pull Request 6766: https://github.com/galaxyproject/galaxy/pull/6766
 .. _Pull Request 6768: https://github.com/galaxyproject/galaxy/pull/6768
+.. _Pull Request 6771: https://github.com/galaxyproject/galaxy/pull/6771
 

From c51178578dcf67c8dbe16d3d8320f660e0c80027 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 28 Sep 2018 09:14:57 -0400
Subject: [PATCH 09/24] Four more PRs

---
 doc/source/releases/18.09.rst | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index 8a2969a24d4..3384abe2989 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -772,6 +772,16 @@ Fixes
 * Use UserRoleAssociation to get private roles
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6771`_
+* All extracted datasets should be visible
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6780`_
+* Fix __encode_invocation signature
+  `Pull Request 6782`_
+* Strip all control characters from rules
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6785`_
+* allow making all datasets within history public, when sharing
+  `Pull Request 6793`_
 
 .. github_links
 .. _Pull Request 5457: https://github.com/galaxyproject/galaxy/pull/5457
@@ -1091,4 +1101,8 @@ Fixes
 .. _Pull Request 6766: https://github.com/galaxyproject/galaxy/pull/6766
 .. _Pull Request 6768: https://github.com/galaxyproject/galaxy/pull/6768
 .. _Pull Request 6771: https://github.com/galaxyproject/galaxy/pull/6771
+.. _Pull Request 6780: https://github.com/galaxyproject/galaxy/pull/6780
+.. _Pull Request 6782: https://github.com/galaxyproject/galaxy/pull/6782
+.. _Pull Request 6785: https://github.com/galaxyproject/galaxy/pull/6785
+.. _Pull Request 6793: https://github.com/galaxyproject/galaxy/pull/6793
 

From ff65263ab2ee1351bbed11709d8536de694a5776 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Fri, 28 Sep 2018 10:50:30 -0400
Subject: [PATCH 10/24] Add 6789

---
 doc/source/releases/18.09.rst | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index 3384abe2989..5b86a7f6917 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -780,6 +780,9 @@ Fixes
 * Strip all control characters from rules
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6785`_
+* Fix bam upload resulting in 'auto' datatype
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6789`_
 * allow making all datasets within history public, when sharing
   `Pull Request 6793`_
 
@@ -1104,5 +1107,6 @@ Fixes
 .. _Pull Request 6780: https://github.com/galaxyproject/galaxy/pull/6780
 .. _Pull Request 6782: https://github.com/galaxyproject/galaxy/pull/6782
 .. _Pull Request 6785: https://github.com/galaxyproject/galaxy/pull/6785
+.. _Pull Request 6789: https://github.com/galaxyproject/galaxy/pull/6789
 .. _Pull Request 6793: https://github.com/galaxyproject/galaxy/pull/6793
 

From 96d77b0791592b35fb6e4201d011f5c223060cfe Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Sun, 30 Sep 2018 21:55:23 -0400
Subject: [PATCH 11/24] More PRs, stub out proposed features.

---
 doc/source/releases/18.09.rst          | 22 +++++++++++++++----
 doc/source/releases/18.09_announce.rst | 30 ++++++++++++++++++++------
 2 files changed, 42 insertions(+), 10 deletions(-)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index 5b86a7f6917..24a4e610874 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -9,9 +9,6 @@
 Enhancements
 -------------------------------
 
-.. major_feature
-
-
 .. feature
 
 * Allow selecting subset of collection by group tag
@@ -431,6 +428,9 @@ Enhancements
 * Increase robustness and accuracy of job search / cache use
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6669`_
+* Fix remaining selenium py3 errors
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6803`_
 
 
 Fixes
@@ -772,6 +772,9 @@ Fixes
 * Use UserRoleAssociation to get private roles
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6771`_
+* Update name of Workflow when updating StoredWorkflow name
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6774`_
 * All extracted datasets should be visible
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6780`_
@@ -785,6 +788,13 @@ Fixes
   `Pull Request 6789`_
 * allow making all datasets within history public, when sharing
   `Pull Request 6793`_
+* Drop unused peek method
+  `Pull Request 6796`_
+* Fix element identifier for non multiple true mapover in conditionals
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6798`_
+* Provide a useful exception message for object store exceptions
+  `Pull Request 6799`_
 
 .. github_links
 .. _Pull Request 5457: https://github.com/galaxyproject/galaxy/pull/5457
@@ -1104,9 +1114,13 @@ Fixes
 .. _Pull Request 6766: https://github.com/galaxyproject/galaxy/pull/6766
 .. _Pull Request 6768: https://github.com/galaxyproject/galaxy/pull/6768
 .. _Pull Request 6771: https://github.com/galaxyproject/galaxy/pull/6771
+.. _Pull Request 6774: https://github.com/galaxyproject/galaxy/pull/6774
 .. _Pull Request 6780: https://github.com/galaxyproject/galaxy/pull/6780
 .. _Pull Request 6782: https://github.com/galaxyproject/galaxy/pull/6782
 .. _Pull Request 6785: https://github.com/galaxyproject/galaxy/pull/6785
 .. _Pull Request 6789: https://github.com/galaxyproject/galaxy/pull/6789
 .. _Pull Request 6793: https://github.com/galaxyproject/galaxy/pull/6793
-
+.. _Pull Request 6796: https://github.com/galaxyproject/galaxy/pull/6796
+.. _Pull Request 6798: https://github.com/galaxyproject/galaxy/pull/6798
+.. _Pull Request 6799: https://github.com/galaxyproject/galaxy/pull/6799
+.. _Pull Request 6803: https://github.com/galaxyproject/galaxy/pull/6803
diff --git a/doc/source/releases/18.09_announce.rst b/doc/source/releases/18.09_announce.rst
index df4869240eb..074420d62f8 100644
--- a/doc/source/releases/18.09_announce.rst
+++ b/doc/source/releases/18.09_announce.rst
@@ -8,14 +8,24 @@ September 2018 Galaxy Release (v 18.09)
 Highlights
 ===========================================================
 
-**Feature1**
-  Feature description.
+**OpenID Connect Support**
+  Galaxy now supports using OpenID Connect for user login, relying on trusted
+  identity providers to manage authentication.  This is intended to replace the
+  old (and mostly deprecated, on the web) OpenID 2.0 logins.  Read more at
+  https://galaxyproject.org/admin/authentication/
 
-**Feature2**
-  Feature description.
+    `https://github.com/galaxyproject/galaxy/pull/4474`
 
-**Feature3**
-  Feature description.
+**Extensive Workflow Enhancements**
+  Workflows got a lot of love this time around, with new runtime parameters for
+  subworkflows, exposed workflow versions, and zoom capability in the editor, to
+  name a few.  There were also a number of usability enhancements including
+  better labeling, links, overhauled workflow import interfaces, and many more.
+
+  (link up PRs)
+
+**Python3 Beta Support**
+  @nsoranzo py3 text
 
 Get Galaxy
 ==========
@@ -34,6 +44,14 @@ To update an existing Galaxy repository run:
 
 See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
 
+Security
+========
+(TODO: Add notes)
+
+Breaking Changes
+================
+(TODO: Deprecation search -- I know of at least one)
+
 Release Notes
 ===========================================================
 

From 3d772dc03bf0ffa1c6d010596488c5cd3a26901d Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 1 Oct 2018 10:34:56 -0400
Subject: [PATCH 12/24] Add 6791

---
 doc/source/releases/18.09.rst | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index 24a4e610874..2ed091c13f7 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -786,6 +786,8 @@ Fixes
 * Fix bam upload resulting in 'auto' datatype
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6789`_
+* Flex-related style fixes
+  `Pull Request 6791`_
 * allow making all datasets within history public, when sharing
   `Pull Request 6793`_
 * Drop unused peek method
@@ -1119,8 +1121,10 @@ Fixes
 .. _Pull Request 6782: https://github.com/galaxyproject/galaxy/pull/6782
 .. _Pull Request 6785: https://github.com/galaxyproject/galaxy/pull/6785
 .. _Pull Request 6789: https://github.com/galaxyproject/galaxy/pull/6789
+.. _Pull Request 6791: https://github.com/galaxyproject/galaxy/pull/6791
 .. _Pull Request 6793: https://github.com/galaxyproject/galaxy/pull/6793
 .. _Pull Request 6796: https://github.com/galaxyproject/galaxy/pull/6796
 .. _Pull Request 6798: https://github.com/galaxyproject/galaxy/pull/6798
 .. _Pull Request 6799: https://github.com/galaxyproject/galaxy/pull/6799
 .. _Pull Request 6803: https://github.com/galaxyproject/galaxy/pull/6803
+

From ce3d43221a8d4e843a25c49c679a4ab75fd3756c Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 1 Oct 2018 16:03:37 -0400
Subject: [PATCH 13/24] More Prs for the release notes.

---
 doc/source/releases/18.09.rst | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index 2ed091c13f7..aae09b94638 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -339,6 +339,9 @@ Enhancements
   `Pull Request 6760`_
 * Remove upgrade cruft related to datatypes.
   `Pull Request 6761`_
+* Allow starting Galaxy under gunicorn when using galaxy.ini
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6805`_
 
 .. small_enhancement
 
@@ -431,6 +434,8 @@ Enhancements
 * Fix remaining selenium py3 errors
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6803`_
+* Drop gulp plugin staging task from default tasks
+  `Pull Request 6808`_
 
 
 Fixes
@@ -753,6 +758,8 @@ Fixes
   `Pull Request 6743`_
 * dispose of dataset tooltip when the delete is being called
   `Pull Request 6744`_
+* Generic tooltip hide for onclick faIconButtons
+  `Pull Request 6745`_
 * Fix page editor height for flex panels.
   `Pull Request 6747`_
 * Use mapped-over collectionType when inferring collectionType through …
@@ -797,6 +804,11 @@ Fixes
   `Pull Request 6798`_
 * Provide a useful exception message for object store exceptions
   `Pull Request 6799`_
+* Cast rule.length to int when parsing rules
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6802`_
+* Don't delete referenced Datasets when purging users
+  `Pull Request 6809`_
 
 .. github_links
 .. _Pull Request 5457: https://github.com/galaxyproject/galaxy/pull/5457
@@ -1104,6 +1116,7 @@ Fixes
 .. _Pull Request 6742: https://github.com/galaxyproject/galaxy/pull/6742
 .. _Pull Request 6743: https://github.com/galaxyproject/galaxy/pull/6743
 .. _Pull Request 6744: https://github.com/galaxyproject/galaxy/pull/6744
+.. _Pull Request 6745: https://github.com/galaxyproject/galaxy/pull/6745
 .. _Pull Request 6747: https://github.com/galaxyproject/galaxy/pull/6747
 .. _Pull Request 6748: https://github.com/galaxyproject/galaxy/pull/6748
 .. _Pull Request 6749: https://github.com/galaxyproject/galaxy/pull/6749
@@ -1126,5 +1139,9 @@ Fixes
 .. _Pull Request 6796: https://github.com/galaxyproject/galaxy/pull/6796
 .. _Pull Request 6798: https://github.com/galaxyproject/galaxy/pull/6798
 .. _Pull Request 6799: https://github.com/galaxyproject/galaxy/pull/6799
+.. _Pull Request 6802: https://github.com/galaxyproject/galaxy/pull/6802
 .. _Pull Request 6803: https://github.com/galaxyproject/galaxy/pull/6803
+.. _Pull Request 6805: https://github.com/galaxyproject/galaxy/pull/6805
+.. _Pull Request 6808: https://github.com/galaxyproject/galaxy/pull/6808
+.. _Pull Request 6809: https://github.com/galaxyproject/galaxy/pull/6809
 

From b5f7955c5addba2664b6375aa87c9873b2949fad Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 4 Oct 2018 15:01:33 +0100
Subject: [PATCH 14/24] Announce Python 3 Beta Support

---
 doc/source/releases/18.09_announce.rst | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/doc/source/releases/18.09_announce.rst b/doc/source/releases/18.09_announce.rst
index 074420d62f8..ec63852de17 100644
--- a/doc/source/releases/18.09_announce.rst
+++ b/doc/source/releases/18.09_announce.rst
@@ -24,8 +24,13 @@ Highlights
 
   (link up PRs)
 
-**Python3 Beta Support**
-  @nsoranzo py3 text
+**Python 3 Beta Support**
+  After almost 3 years of work and more than 100 pull requests, we are proud
+  to announce the Beta-stage support for running Galaxy under Python 3.
+  Lint, unit, API, framework, integration and Selenium tests all pass, time
+  for you to give it a try and report any bug you find!
+
+    `https://github.com/galaxyproject/galaxy/issues/1715`
 
 Get Galaxy
 ==========

From 90718843096f115324be8a086d7a6089e0086703 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 4 Oct 2018 12:31:33 -0400
Subject: [PATCH 15/24] Add deprecation notice for username being null

---
 doc/source/releases/18.09_announce.rst | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/doc/source/releases/18.09_announce.rst b/doc/source/releases/18.09_announce.rst
index ec63852de17..d829867558c 100644
--- a/doc/source/releases/18.09_announce.rst
+++ b/doc/source/releases/18.09_announce.rst
@@ -8,13 +8,8 @@ September 2018 Galaxy Release (v 18.09)
 Highlights
 ===========================================================
 
-**OpenID Connect Support**
-  Galaxy now supports using OpenID Connect for user login, relying on trusted
-  identity providers to manage authentication.  This is intended to replace the
-  old (and mostly deprecated, on the web) OpenID 2.0 logins.  Read more at
-  https://galaxyproject.org/admin/authentication/
-
-    `https://github.com/galaxyproject/galaxy/pull/4474`
+**Group Tag Support**
+  Forthcoming text.
 
 **Extensive Workflow Enhancements**
   Workflows got a lot of love this time around, with new runtime parameters for
@@ -53,9 +48,15 @@ Security
 ========
 (TODO: Add notes)
 
-Breaking Changes
-================
-(TODO: Deprecation search -- I know of at least one)
+Deprecation Notice
+==================
+
+With 19.01, all Galaxy users will be forced to have a username.  This
+requirement has been enforced on user creation for years, though we've never
+taken steps to coerce users created in the past who did not have one.  The
+19.01 release will come with a migration script that will coerce this in the
+database, which will allow us to have consistent handling of this field.
+
 
 Release Notes
 ===========================================================

From afffd9bdaa66b4fcadbd790a25387654c23e4aa6 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 4 Oct 2018 13:11:59 -0400
Subject: [PATCH 16/24] Add final PR.

---
 doc/source/releases/18.09.rst | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index aae09b94638..a7d8aedfc82 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -809,6 +809,8 @@ Fixes
   `Pull Request 6802`_
 * Don't delete referenced Datasets when purging users
   `Pull Request 6809`_
+* do not rule out numbers that are accessed with shift modifier
+  `Pull Request 6810`_
 
 .. github_links
 .. _Pull Request 5457: https://github.com/galaxyproject/galaxy/pull/5457
@@ -1144,4 +1146,5 @@ Fixes
 .. _Pull Request 6805: https://github.com/galaxyproject/galaxy/pull/6805
 .. _Pull Request 6808: https://github.com/galaxyproject/galaxy/pull/6808
 .. _Pull Request 6809: https://github.com/galaxyproject/galaxy/pull/6809
+.. _Pull Request 6810: https://github.com/galaxyproject/galaxy/pull/6810
 

From eacec03d10c00503fdbb4da107254c06082507bb Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 4 Oct 2018 14:11:08 -0400
Subject: [PATCH 17/24] Update....

---
 doc/source/releases/18.09.rst          | 21 +------------------
 doc/source/releases/18.09_announce.rst | 29 ++++++++++++++++++--------
 2 files changed, 21 insertions(+), 29 deletions(-)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index aae09b94638..803b506d638 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -11,9 +11,7 @@ Enhancements
 
 .. feature
 
-* Allow selecting subset of collection by group tag
-  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
-  `Pull Request 5457`_
+
 * Copy data from a cloud-based storage to a Galaxy history
   (thanks to `@VJalili <https://github.com/VJalili>`__).
   `Pull Request 5835`_
@@ -225,12 +223,6 @@ Enhancements
 * small improvement to the too xsd docs regarding discovered_datasets
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 6490`_
-* Implement ``group:`` tags (toward multi-factor analysis with group tagging)
-  `Pull Request 6491`_
-* Allow setting tags on targets & contents in data fetch API.
-  `Pull Request 6499`_
-* Integrate tagging into the rule builder.
-  `Pull Request 6500`_
 * Cache chrom_info generation when mapping over collections.
   `Pull Request 6515`_
 * More optimized HID generation - in one commit instead of two.
@@ -254,8 +246,6 @@ Enhancements
   `Pull Request 6539`_
 * Test case for nested collection input to flatten in a workflow.
   `Pull Request 6541`_
-* Allow Consuming Tags in the Apply Rules Tool
-  `Pull Request 6545`_
 * Integration test for the interaction of nested object stores and jobs.
   `Pull Request 6546`_
 * Configure object store for datasets in job handler instead of web thread.
@@ -264,10 +254,6 @@ Enhancements
   `Pull Request 6552`_
 * Unified dataset permission API.
   `Pull Request 6568`_
-* Add tagging rule to history level rule builder, copy HDAs when building
-  collection
-  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
-  `Pull Request 6572`_
 * Add API endpoint to fetch a history's workflow invocations.
   `Pull Request 6580`_
 * Improve robustness of tour Selenium test.
@@ -314,9 +300,6 @@ Enhancements
 * Add Seurat datatype: rdata.seurat
   (thanks to `@mblue9 <https://github.com/mblue9>`__).
   `Pull Request 6648`_
-* Allow group tag selection also for multiple="true" inputs
-  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
-  `Pull Request 6661`_
 * Various link and documentation fixes
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6662`_
@@ -330,8 +313,6 @@ Enhancements
   `Pull Request 6681`_
 * Add self help to error reporting interface
   `Pull Request 6711`_
-* Undo auto-propagation of group tags.
-  `Pull Request 6750`_
 * Client build startup changes
   `Pull Request 6753`_
 * Add graph dot datatype and enable it in visualisations
diff --git a/doc/source/releases/18.09_announce.rst b/doc/source/releases/18.09_announce.rst
index ec63852de17..2f4832b9f9b 100644
--- a/doc/source/releases/18.09_announce.rst
+++ b/doc/source/releases/18.09_announce.rst
@@ -8,14 +8,6 @@ September 2018 Galaxy Release (v 18.09)
 Highlights
 ===========================================================
 
-**OpenID Connect Support**
-  Galaxy now supports using OpenID Connect for user login, relying on trusted
-  identity providers to manage authentication.  This is intended to replace the
-  old (and mostly deprecated, on the web) OpenID 2.0 logins.  Read more at
-  https://galaxyproject.org/admin/authentication/
-
-    `https://github.com/galaxyproject/galaxy/pull/4474`
-
 **Extensive Workflow Enhancements**
   Workflows got a lot of love this time around, with new runtime parameters for
   subworkflows, exposed workflow versions, and zoom capability in the editor, to
@@ -24,6 +16,19 @@ Highlights
 
   (link up PRs)
 
+**Group Tags**
+  Galaxy now contains powerful new features for multiple factor analysis of collections
+  of datasets. The concept of group tags has been added to Galaxy. These are a special
+  class of tags that describe key-value pairs that can be attached to the contents of a
+  collection during upload or using collection operation tools. These tags can describe
+  multiple sets of variables for the contents of a collection. Once set, these tags can
+  be consumed intelligently by tools that need to divide collections into multiple
+  overlapping factors or sets of datasets. A special thanks to `@mvdbeek <https://github.com/mvdbeek>`__ for devising and implementing this approach.
+
+  `Pull Request 5457`_, `Pull Request 6491`_, `Pull Request 6661`_,
+  `Pull Request 6750`_, `Pull Request 6499`_, `Pull Request 6500`_,
+  `Pull Request 6572`_, `Pull Request 6545`_
+
 **Python 3 Beta Support**
   After almost 3 years of work and more than 100 pull requests, we are proud
   to announce the Beta-stage support for running Galaxy under Python 3.
@@ -51,7 +56,13 @@ See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for a
 
 Security
 ========
-(TODO: Add notes)
+
+Unauthorized File System Operations via New Upload API
+------------------------------------------------------
+
+Tracked as GX-2018-0006. Servers running Galaxy 18.05 should be updated as soon as possible.
+See `the public announcement for full details
+<http://announce.list.galaxyproject.org/GX-2018-0006-Unauthorized-File-System-Operations-via-New-Upload-API-td4639432.html>`__.
 
 Breaking Changes
 ================

From 386229d1ce58522be4bece11b8f9473f5dce56b9 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 4 Oct 2018 15:20:33 -0400
Subject: [PATCH 18/24] Re-add removed PRs (bad merge I think)

---
 doc/source/releases/18.09.rst | 21 ++++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index 5b9fa5d55c2..a7d8aedfc82 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -11,7 +11,9 @@ Enhancements
 
 .. feature
 
-
+* Allow selecting subset of collection by group tag
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 5457`_
 * Copy data from a cloud-based storage to a Galaxy history
   (thanks to `@VJalili <https://github.com/VJalili>`__).
   `Pull Request 5835`_
@@ -223,6 +225,12 @@ Enhancements
 * small improvement to the too xsd docs regarding discovered_datasets
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 6490`_
+* Implement ``group:`` tags (toward multi-factor analysis with group tagging)
+  `Pull Request 6491`_
+* Allow setting tags on targets & contents in data fetch API.
+  `Pull Request 6499`_
+* Integrate tagging into the rule builder.
+  `Pull Request 6500`_
 * Cache chrom_info generation when mapping over collections.
   `Pull Request 6515`_
 * More optimized HID generation - in one commit instead of two.
@@ -246,6 +254,8 @@ Enhancements
   `Pull Request 6539`_
 * Test case for nested collection input to flatten in a workflow.
   `Pull Request 6541`_
+* Allow Consuming Tags in the Apply Rules Tool
+  `Pull Request 6545`_
 * Integration test for the interaction of nested object stores and jobs.
   `Pull Request 6546`_
 * Configure object store for datasets in job handler instead of web thread.
@@ -254,6 +264,10 @@ Enhancements
   `Pull Request 6552`_
 * Unified dataset permission API.
   `Pull Request 6568`_
+* Add tagging rule to history level rule builder, copy HDAs when building
+  collection
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6572`_
 * Add API endpoint to fetch a history's workflow invocations.
   `Pull Request 6580`_
 * Improve robustness of tour Selenium test.
@@ -300,6 +314,9 @@ Enhancements
 * Add Seurat datatype: rdata.seurat
   (thanks to `@mblue9 <https://github.com/mblue9>`__).
   `Pull Request 6648`_
+* Allow group tag selection also for multiple="true" inputs
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6661`_
 * Various link and documentation fixes
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6662`_
@@ -313,6 +330,8 @@ Enhancements
   `Pull Request 6681`_
 * Add self help to error reporting interface
   `Pull Request 6711`_
+* Undo auto-propagation of group tags.
+  `Pull Request 6750`_
 * Client build startup changes
   `Pull Request 6753`_
 * Add graph dot datatype and enable it in visualisations

From fdaf9ac8641cfa5fa0aad706310aec2b31692ac1 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 4 Oct 2018 15:27:56 -0400
Subject: [PATCH 19/24] Link up workflow PRs

---
 doc/source/releases/18.09_announce.rst | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/doc/source/releases/18.09_announce.rst b/doc/source/releases/18.09_announce.rst
index 61e7b1a5f81..62cdab9828d 100644
--- a/doc/source/releases/18.09_announce.rst
+++ b/doc/source/releases/18.09_announce.rst
@@ -14,7 +14,11 @@ Highlights
   name a few.  There were also a number of usability enhancements including
   better labeling, links, overhauled workflow import interfaces, and many more.
 
-  (link up PRs)
+  `Pull Request 6664`_, `Pull Request 6683`_, `Pull Request 6142`_,
+  `Pull Request 6240`_, `Pull Request 6290`_, `Pull Request 6428`_,
+  `Pull Request 6441`_, `Pull Request 6580`_, `Pull Request 6596`_,
+  `Pull Request 6678`_, `Pull Request 6076`_, `Pull Request 6274`_,
+  `Pull Request 6570`_, `Pull Request 6680`_, `Pull Request 6774`_
 
 **Group Tags**
   Galaxy now contains powerful new features for multiple factor analysis of collections

From 381d6ad83183a822baebca44622e506d088f10b1 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 8 Oct 2018 15:25:57 -0400
Subject: [PATCH 20/24] Add two recently merged PRs.

---
 doc/source/releases/18.09.rst | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index a7d8aedfc82..6e962d5b26b 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -342,6 +342,8 @@ Enhancements
 * Allow starting Galaxy under gunicorn when using galaxy.ini
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6805`_
+* Allow testing tags in input collections.
+  `Pull Request 6823`_
 
 .. small_enhancement
 
@@ -811,6 +813,8 @@ Fixes
   `Pull Request 6809`_
 * do not rule out numbers that are accessed with shift modifier
   `Pull Request 6810`_
+* Upgrade concurrently for 'null' return fix
+  `Pull Request 6828`_
 
 .. github_links
 .. _Pull Request 5457: https://github.com/galaxyproject/galaxy/pull/5457
@@ -1147,4 +1151,6 @@ Fixes
 .. _Pull Request 6808: https://github.com/galaxyproject/galaxy/pull/6808
 .. _Pull Request 6809: https://github.com/galaxyproject/galaxy/pull/6809
 .. _Pull Request 6810: https://github.com/galaxyproject/galaxy/pull/6810
+.. _Pull Request 6823: https://github.com/galaxyproject/galaxy/pull/6823
+.. _Pull Request 6828: https://github.com/galaxyproject/galaxy/pull/6828
 

From c1383bc2d55cb6565fbd63eb4088c734a805700e Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@gmail.com>
Date: Thu, 11 Oct 2018 15:22:23 +0100
Subject: [PATCH 21/24] Small fixes

---
 doc/source/releases/18.09_announce.rst | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/source/releases/18.09_announce.rst b/doc/source/releases/18.09_announce.rst
index 62cdab9828d..91ce330f29d 100644
--- a/doc/source/releases/18.09_announce.rst
+++ b/doc/source/releases/18.09_announce.rst
@@ -39,12 +39,12 @@ Highlights
   Lint, unit, API, framework, integration and Selenium tests all pass, time
   for you to give it a try and report any bug you find!
 
-    `https://github.com/galaxyproject/galaxy/issues/1715`
+  `Tracking issue <https://github.com/galaxyproject/galaxy/issues/1715>`__
 
 Get Galaxy
 ==========
 
-The code lives at `Github <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
+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
@@ -72,7 +72,7 @@ Deprecation Notice
 ==================
 
 With 19.01, all Galaxy users will be forced to have a username.  This
-requirement has been enforced on user creation for years, though we've never
+requirement has been enforced on user creation for years, though we have never
 taken steps to coerce users created in the past who did not have one.  The
 19.01 release will come with a migration script that will coerce this in the
 database, which will allow us to have consistent handling of this field.

From c6193ca4406450cdaa01b9c27bcfb871c916544c Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 11 Oct 2018 10:37:54 -0400
Subject: [PATCH 22/24] Update DEVTEAM, rebuild, include a few new PRs.

---
 doc/source/releases/18.09.rst | 19 +++++++++++--------
 scripts/bootstrap_history.py  |  3 ++-
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index 6e962d5b26b..6c36e60612a 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -15,10 +15,8 @@ Enhancements
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 5457`_
 * Copy data from a cloud-based storage to a Galaxy history
-  (thanks to `@VJalili <https://github.com/VJalili>`__).
   `Pull Request 5835`_
 * Upload data to a cloud-based storage
-  (thanks to `@VJalili <https://github.com/VJalili>`__).
   `Pull Request 6078`_
 * New datatype: SBML
   (thanks to `@cmonjeau <https://github.com/cmonjeau>`__).
@@ -236,7 +234,6 @@ Enhancements
 * More optimized HID generation - in one commit instead of two.
   `Pull Request 6516`_
 * Improvements to Cloud Storage Manager
-  (thanks to `@VJalili <https://github.com/VJalili>`__).
   `Pull Request 6519`_
 * Handle pasted content in fetch API.
   `Pull Request 6523`_
@@ -281,7 +278,6 @@ Enhancements
   (thanks to `@bgruening <https://github.com/bgruening>`__).
   `Pull Request 6597`_
 * Refresh an expired OIDC ID token
-  (thanks to `@VJalili <https://github.com/VJalili>`__).
   `Pull Request 6606`_
 * Handle driver shutdown, show all tests in pytest
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -391,7 +387,6 @@ Enhancements
 * Remove redundant/duplicate endpoint to edit user info
   `Pull Request 6501`_
 * Remove the deprecated AOL openid backend.
-  (thanks to `@VJalili <https://github.com/VJalili>`__).
   `Pull Request 6505`_
 * Fix all py3 api tests
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -416,7 +411,6 @@ Enhancements
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6610`_
 * Raise an exception if a history with decoded id does not exist.
-  (thanks to `@VJalili <https://github.com/VJalili>`__).
   `Pull Request 6611`_
 * Test tools shipped with Galaxy
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -428,7 +422,6 @@ Enhancements
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6638`_
 * Upgrade CloudBridge to v1.0.1
-  (thanks to `@VJalili <https://github.com/VJalili>`__).
   `Pull Request 6660`_
 * Increase robustness and accuracy of job search / cache use
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -661,7 +654,6 @@ Fixes
 * Fix and docs for advanced container options in job_conf.xml.
   `Pull Request 6503`_
 * Return a json blob containing redirect URI in OIDC login controller
-  (thanks to `@VJalili <https://github.com/VJalili>`__).
   `Pull Request 6517`_
 * Fix warning in CONVERTER_bam_to_bigwig_0 and CONVERTER_sam_to_bigwig_0
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -815,6 +807,14 @@ Fixes
   `Pull Request 6810`_
 * Upgrade concurrently for 'null' return fix
   `Pull Request 6828`_
+* Update conda channel priority: conda-forge > bioconda
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 6830`_
+* Unified panel style bottom padding fix
+  `Pull Request 6839`_
+* Fix slurm cli on secure shell
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6845`_
 
 .. github_links
 .. _Pull Request 5457: https://github.com/galaxyproject/galaxy/pull/5457
@@ -1153,4 +1153,7 @@ Fixes
 .. _Pull Request 6810: https://github.com/galaxyproject/galaxy/pull/6810
 .. _Pull Request 6823: https://github.com/galaxyproject/galaxy/pull/6823
 .. _Pull Request 6828: https://github.com/galaxyproject/galaxy/pull/6828
+.. _Pull Request 6830: https://github.com/galaxyproject/galaxy/pull/6830
+.. _Pull Request 6839: https://github.com/galaxyproject/galaxy/pull/6839
+.. _Pull Request 6845: https://github.com/galaxyproject/galaxy/pull/6845
 
diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py
index d64439144db..74daafa025c 100644
--- a/scripts/bootstrap_history.py
+++ b/scripts/bootstrap_history.py
@@ -40,7 +40,8 @@ DEVTEAM = [
     "afgane", "dannon", "blankenberg",
     "davebx", "martenson", "jmchilton",
     "tnabtaf", "natefoo", "jgoecks",
-    "guerler", "jennaj", "nekrut", "jxtx"
+    "guerler", "jennaj", "nekrut", "jxtx",
+    "VJalili"
 ]
 
 TEMPLATE = """

From d33006cf33f71f4992eebefb7c3065606088aea1 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 11 Oct 2018 12:28:32 -0400
Subject: [PATCH 23/24] Final docs update

---
 doc/source/releases/18.09.rst | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index 6c36e60612a..de86ecd6bf6 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -112,7 +112,7 @@ Enhancements
 * Fix collection mapping to allow subcollection mapping over multi-data
   inputs.
   `Pull Request 6255`_
-*  Use Mercurial CLI instead of API for archive_repository_revision()
+* Use Mercurial CLI instead of API for archive_repository_revision()
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6273`_
 * Consolidate use of get_repo_for_repository() and clone_repository()
@@ -374,8 +374,8 @@ Enhancements
 * Python3: Encode return values of JSON encoder
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6439`_
-* Python3: Drop fix_json, doesn't seem to be necessary and fixes workflow unit
-  t…
+* Python3: Drop ``json_fix``, doesn't seem to be necessary and fixes workflow
+  unit tests
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6446`_
 * py3: fixes test_DatasetManager.py:DatasetManagerTestCase
@@ -530,10 +530,10 @@ Fixes
 * Strip a spurious Slurm warning from job stderr
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6293`_
-* Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon`
+* Fix ``GALAXY_RUN_ALL=1 ./run.sh --daemon``
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6295`_
-* add the canonical url to grt config
+* Add the canonical URL to grt config
   `Pull Request 6301`_
 * Stop listening to history changes after job submission
   `Pull Request 6303`_
@@ -810,6 +810,9 @@ Fixes
 * Update conda channel priority: conda-forge > bioconda
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6830`_
+* Register job monitor thread as postfork function
+  (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
+  `Pull Request 6836`_
 * Unified panel style bottom padding fix
   `Pull Request 6839`_
 * Fix slurm cli on secure shell
@@ -1154,6 +1157,7 @@ Fixes
 .. _Pull Request 6823: https://github.com/galaxyproject/galaxy/pull/6823
 .. _Pull Request 6828: https://github.com/galaxyproject/galaxy/pull/6828
 .. _Pull Request 6830: https://github.com/galaxyproject/galaxy/pull/6830
+.. _Pull Request 6836: https://github.com/galaxyproject/galaxy/pull/6836
 .. _Pull Request 6839: https://github.com/galaxyproject/galaxy/pull/6839
 .. _Pull Request 6845: https://github.com/galaxyproject/galaxy/pull/6845
 

From d42b899b7805f722a77153c4e33fffcfad846ce0 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 11 Oct 2018 17:49:37 +0100
Subject: [PATCH 24/24] Embellish 18.09 release notes

---
 doc/source/releases/18.09.rst | 130 +++++++++++++++++-----------------
 scripts/bootstrap_history.py  |   4 +-
 2 files changed, 68 insertions(+), 66 deletions(-)

diff --git a/doc/source/releases/18.09.rst b/doc/source/releases/18.09.rst
index de86ecd6bf6..0648f3c8ab2 100644
--- a/doc/source/releases/18.09.rst
+++ b/doc/source/releases/18.09.rst
@@ -23,7 +23,7 @@ Enhancements
   `Pull Request 6201`_
 * Enable automatic reload of dynamic job rules on change
   `Pull Request 6215`_
-* added daa (diamond alignment) datatype
+* Added daa (diamond alignment) datatype
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 6313`_
 * Allows DatasetMatcher to use multiple filters
@@ -42,13 +42,13 @@ Enhancements
 
 .. enhancement
 
-* Add a FilterEmptyDatasetsTool and allow filtering tools to apply to
+* Add a ``FilterEmptyDatasetsTool`` and allow filtering tools to apply to
   arbitrary collection structures
   (thanks to `@Mataivic <https://github.com/Mataivic>`__).
   `Pull Request 5640`_
 * Minor enhancements for cgroup metrics
   `Pull Request 5993`_
-* Optimize safe_walk to call realpath a lot less for typical calls...
+* Optimize ``safe_walk`` to call ``realpath`` a lot less for typical calls
   `Pull Request 5995`_
 * Documentation and typo fixes
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -75,10 +75,10 @@ Enhancements
   `Pull Request 6122`_
 * Sharing.vue bootstrapping and a bugfix
   `Pull Request 6132`_
-* Use from_work_dir in CONVERTER_fasta_to_fai
+* Use ``from_work_dir`` in ``CONVERTER_fasta_to_fai``
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6135`_
-* Make workflow editor toolTitle link include the tools description
+* Make workflow editor ``toolTitle`` link include the tools description
   (thanks to `@scrathat <https://github.com/scrathat>`__).
   `Pull Request 6142`_
 * Small fixes and small refactorings toward reuse in CWL branch (retry)
@@ -95,7 +95,7 @@ Enhancements
   `Pull Request 6206`_
 * Some more upload/sniff tests.
   `Pull Request 6212`_
-* Test element_identifier usage with single data parameters, in repeat/cond.
+* Test ``element_identifier`` usage with single data parameters, in repeat/cond.
   `Pull Request 6213`_
 * Charts filename download fix
   `Pull Request 6216`_
@@ -112,10 +112,10 @@ Enhancements
 * Fix collection mapping to allow subcollection mapping over multi-data
   inputs.
   `Pull Request 6255`_
-* Use Mercurial CLI instead of API for archive_repository_revision()
+* Use Mercurial CLI instead of API for ``archive_repository_revision()``
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6273`_
-* Consolidate use of get_repo_for_repository() and clone_repository()
+* Consolidate use of ``get_repo_for_repository()`` and ``clone_repository()``
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6277`_
 * Index select2 field values
@@ -140,7 +140,7 @@ Enhancements
 * Replace unmaintained pycrypto dependency with pycryptodome
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6324`_
-*  Add py34-first_startup to Travis and default tox tests
+* Add py34-first_startup to Travis and default tox tests
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6325`_
 * Visualization static staging
@@ -158,7 +158,7 @@ Enhancements
 * Create client build hash on toplevel concurrent watch in addition to
   individual builds.
   `Pull Request 6381`_
-* change a file read to use with statement
+* Change a file read to use ``with`` statement
   (thanks to `@qiagu <https://github.com/qiagu>`__).
   `Pull Request 6388`_
 * Client library upgrades.
@@ -185,10 +185,10 @@ Enhancements
 * Run workflows from published workflows menu
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6428`_
-* fix a few tool_deps test errors
+* Fix a few tool_deps test errors
   (thanks to `@bgruening <https://github.com/bgruening>`__).
   `Pull Request 6436`_
-* replace the administration header in admin menu with version
+* Replace the administration header in admin menu with version
   `Pull Request 6440`_
 * Add zoom support to workflow editor.
   `Pull Request 6441`_
@@ -220,7 +220,7 @@ Enhancements
   `Pull Request 6480`_
 * Use bootstrap vue classes for workflow import form
   `Pull Request 6489`_
-* small improvement to the too xsd docs regarding discovered_datasets
+* Small improvement to the tool xsd docs regarding ``discovered_datasets``
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 6490`_
 * Implement ``group:`` tags (toward multi-factor analysis with group tagging)
@@ -229,7 +229,7 @@ Enhancements
   `Pull Request 6499`_
 * Integrate tagging into the rule builder.
   `Pull Request 6500`_
-* Cache chrom_info generation when mapping over collections.
+* Cache ``chrom_info`` generation when mapping over collections.
   `Pull Request 6515`_
 * More optimized HID generation - in one commit instead of two.
   `Pull Request 6516`_
@@ -239,7 +239,7 @@ Enhancements
   `Pull Request 6523`_
 * Use cached database identity to avoid many DB requests when creating jobs.
   `Pull Request 6524`_
-* Removal of unreachable exit()
+* Removal of unreachable ``exit()``
   `Pull Request 6529`_
 * Optimizations for history copying.
   `Pull Request 6531`_
@@ -274,7 +274,7 @@ Enhancements
 * Add download option to workflow editor menu
   (thanks to `@bgruening <https://github.com/bgruening>`__).
   `Pull Request 6596`_
-* add trr datatype
+* Add trr datatype
   (thanks to `@bgruening <https://github.com/bgruening>`__).
   `Pull Request 6597`_
 * Refresh an expired OIDC ID token
@@ -282,7 +282,7 @@ Enhancements
 * Handle driver shutdown, show all tests in pytest
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6608`_
-* add dcd datatype for molecular dynamics
+* Add dcd datatype for molecular dynamics
   (thanks to `@chrisbarnettster <https://github.com/chrisbarnettster>`__).
   `Pull Request 6613`_
 * Py3 testing cleanups
@@ -295,7 +295,7 @@ Enhancements
   `Pull Request 6628`_
 * Update some run_tests.sh docs for recent changes.
   `Pull Request 6629`_
-* Remove check_python_dependencies job from Travis
+* Remove ``check_python_dependencies`` job from Travis
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6630`_
 * Testing framework improvements
@@ -303,7 +303,7 @@ Enhancements
   `Pull Request 6632`_
 * Optimize tool execution permission checking
   `Pull Request 6635`_
-* document config for sniffing compressed files, enable by default
+* Document config for sniffing compressed files, enable by default
   `Pull Request 6641`_
 * Small Optimizations to Adding Datasets to History
   `Pull Request 6644`_
@@ -348,7 +348,7 @@ Enhancements
   `Pull Request 6011`_
 * This strips the graphite-specific middleware
   `Pull Request 6018`_
-* Make `interactor._{get,post,put,...}` less repetitive
+* Make ``interactor._{get,post,put,...}`` less repetitive
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6070`_
 * Workflow and remote-user related refactoring and a bug fix
@@ -378,7 +378,7 @@ Enhancements
   unit tests
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6446`_
-* py3: fixes test_DatasetManager.py:DatasetManagerTestCase
+* py3: fixes ``test_DatasetManager.py:DatasetManagerTestCase``
   (thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
   `Pull Request 6452`_
 * Fix test_toolbox for python 3
@@ -441,16 +441,16 @@ Fixes
 
 .. bug
 
-* fix bowtie2 link
+* Fix bowtie2 link
   (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
   `Pull Request 6009`_
 * Fix some imports
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6014`_
-* Fix JobWrapper.get_destination_configuration() so that it actually checks
-  the JobDestination params
+* Fix ``JobWrapper.get_destination_configuration()`` so that it actually checks
+  the ``JobDestination`` params
   `Pull Request 6087`_
-* fixed small typo
+* Fixed small typo
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 6094`_
 * History click-to-rename bugfix
@@ -460,14 +460,14 @@ Fixes
 * cutWrapper: fix wrong path in error message
   (thanks to `@abretaud <https://github.com/abretaud>`__).
   `Pull Request 6211`_
-* Fix optional="True" inputs
+* Fix ``optional="True"`` inputs
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6222`_
 * Two minor aliases for (exterior) backwards compatibility, minor badge tweaks
   `Pull Request 6226`_
 * Fix broken collection_type_source tool and test.
   `Pull Request 6227`_
-* Add io_details and link_details in api tools doc
+* Add ``io_details`` and ``link_details`` in api tools doc
   (thanks to `@ValentinChCloud <https://github.com/ValentinChCloud>`__).
   `Pull Request 6228`_
 * Fix file type error in RuleCollectionBuilder.
@@ -485,7 +485,7 @@ Fixes
   `Pull Request 6244`_
 * Check context for textable mode of select fields
   `Pull Request 6251`_
-* Mapping over from_param fixes
+* Mapping over ``from_param`` fixes
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6253`_
 * Fix history shared with me 'view' link
@@ -507,10 +507,10 @@ Fixes
 * Fixes for phenotype association tools
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6269`_
-* fix link to workflow list
+* Fix link to workflow list
   (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
   `Pull Request 6270`_
-*  Fix help text for renaming operation in workflows
+* Fix help text for renaming operation in workflows
   `Pull Request 6274`_
 * Various fixes for mapping over collections
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -540,25 +540,26 @@ Fixes
 * Increase sleep if encountering (DB locking) exception
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6304`_
-* Fix undefined success_message
+* Fix undefined ``success_message``
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6316`_
-* Allow #if $datasets #end if pattern for file lists
+* Allow ``#if $datasets #end if`` pattern for file lists
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6317`_
 * Fix target update for rule collection builder after input selection
   (thanks to `@scrathat <https://github.com/scrathat>`__).
   `Pull Request 6326`_
-* Added missing level fatal_oom to xsd
+* Added missing level ``fatal_oom`` to galaxy.xsd
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 6341`_
 * Update description for installing pbs-python
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6345`_
-* Prevent throwing an exception if a dataset doesn't exist (and never w…
+* Prevent throwing an exception if a dataset doesn't exist (and never will) due
+  to a job error
   (thanks to `@dpryan79 <https://github.com/dpryan79>`__).
   `Pull Request 6349`_
-* Fix the --log-file option in the job handlers
+* Fix the ``--log-file`` option in the job handlers
   (thanks to `@dpryan79 <https://github.com/dpryan79>`__).
   `Pull Request 6351`_
 * grt - wrap every write in try-except
@@ -578,23 +579,23 @@ Fixes
   `Pull Request 6378`_
 * Revert "Remove bam to bai converter"
   `Pull Request 6385`_
-* fix data_column cast error when multiple is false
+* Fix ``data_column`` cast error when multiple is false
   (thanks to `@qiagu <https://github.com/qiagu>`__).
   `Pull Request 6389`_
 * Optimize setting large numbers of HIDs for collection outputs.
   `Pull Request 6394`_
-* Fixing <conditional> XML example
+* Fixing ``<conditional>`` XML example
   (thanks to `@almahmoud <https://github.com/almahmoud>`__).
   `Pull Request 6399`_
 * Fix positioning for tool search box.
   `Pull Request 6416`_
-* removing binary as input for python compatibility
+* Removing binary as input for python compatibility
   (thanks to `@eslerm <https://github.com/eslerm>`__).
   `Pull Request 6417`_
 * GCC2018 python3 unit-test fixes
   (thanks to `@ycgong <https://github.com/ycgong>`__).
   `Pull Request 6419`_
-* python 3 porting
+* Python 3 porting
   (thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
   `Pull Request 6420`_
 * Fix panel drag resize.
@@ -610,15 +611,15 @@ Fixes
 * Do not encode a rendered Mako template
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6431`_
-* decode potential encoded id
+* Decode potential encoded id
   `Pull Request 6433`_
-* fixes test/unit/jobs/test_job_output_checker.py; strange default?
+* Fixes test/unit/jobs/test_job_output_checker.py; strange default?
   (thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
   `Pull Request 6438`_
 * py3 compat: fixes test_vcf, test_sniff_compressed*
   (thanks to `@caleb-easterly <https://github.com/caleb-easterly>`__).
   `Pull Request 6442`_
-* fix TS: resolve missing closing div and three extra closing divs
+* Fix TS: resolve missing closing div and three extra closing divs
   `Pull Request 6445`_
 * Fix all remaining unit tests under Python 3
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -642,7 +643,7 @@ Fixes
   `Pull Request 6481`_
 * Fix for show params server error
   `Pull Request 6486`_
-* Fix ftp_upload_purge in galaxy.yml
+* Fix ``ftp_upload_purge`` in galaxy.yml
   (thanks to `@phac-nml <https://github.com/phac-nml>`__).
   `Pull Request 6494`_
 * Fix resume from history panel
@@ -655,12 +656,12 @@ Fixes
   `Pull Request 6503`_
 * Return a json blob containing redirect URI in OIDC login controller
   `Pull Request 6517`_
-* Fix warning in CONVERTER_bam_to_bigwig_0 and CONVERTER_sam_to_bigwig_0
+* Fix warning in ``CONVERTER_bam_to_bigwig_0`` and ``CONVERTER_sam_to_bigwig_0``
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6528`_
 * Fix dataset copy tags
   `Pull Request 6532`_
-* Fix to_dict with io_details=True for tools with collection outputs.
+* Fix ``to_dict`` with ``io_details=True`` for tools with collection outputs.
   `Pull Request 6538`_
 * Fix "filter empty" rule in Python rule handling framework.
   `Pull Request 6542`_
@@ -671,9 +672,9 @@ Fixes
 * Remove the sharing of toolbox in GRT
   (thanks to `@erasche <https://github.com/erasche>`__).
   `Pull Request 6553`_
-* Restore log_destination = stdout configuration option.
+* Restore ``log_destination = stdout`` configuration option.
   `Pull Request 6555`_
-* Many selenium tests fixes for recent dev changes.
+* Many Selenium tests fixes for recent dev changes.
   `Pull Request 6557`_
 * More Selenium test fixes.
   `Pull Request 6562`_
@@ -700,15 +701,15 @@ Fixes
 * Fix Location of Plugin Static Content In Documentation for 18.05
   (thanks to `@phac-nml <https://github.com/phac-nml>`__).
   `Pull Request 6602`_
-*  Fix cron/build_chrom_db.py and update UCSC builds
+* Fix cron/build_chrom_db.py and update UCSC builds
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6623`_
 * Fix for workflow extraction cleanup routine.
   `Pull Request 6636`_
-* row ids that are all numeric become ints...
+* Row ids that are all numeric become ints...
   (thanks to `@bwlang <https://github.com/bwlang>`__).
   `Pull Request 6639`_
-* Allow running scripts/galaxy-main without Galaxy on sys.path
+* Allow running ``scripts/galaxy-main`` without Galaxy on ``sys.path``
   `Pull Request 6642`_
 * Fix color of workflow panel background
   `Pull Request 6643`_
@@ -716,7 +717,7 @@ Fixes
   `Pull Request 6647`_
 * Strip API keys option from admin panel left side
   `Pull Request 6651`_
-* Fix get_fileobj() call in Eland.set_meta()
+* Fix ``get_fileobj()`` call in ``Eland.set_meta()``
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 6659`_
 * Update bx-python to 0.8.2
@@ -732,13 +733,13 @@ Fixes
   `Pull Request 6703`_
 * Catch additional permutations of Slurm cgroup creation warnings
   `Pull Request 6705`_
-* unquote the tool_version in the tools API
+* Unquote the ``tool_version`` in the tools API
   `Pull Request 6707`_
 * Fix active highlight
   `Pull Request 6725`_
 * Badge default fix
   `Pull Request 6726`_
-* remove html tags and newlines from the help text
+* Remove html tags and newlines from the help text
   `Pull Request 6728`_
 * Fix missing tests for data source sniffing.
   `Pull Request 6733`_
@@ -748,38 +749,39 @@ Fixes
 * Fix and test anonymous error reports
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6742`_
-* fix favicon.ico for uwsgi deployments
+* Fix favicon.ico for uWSGI deployments
   `Pull Request 6743`_
-* dispose of dataset tooltip when the delete is being called
+* Dispose of dataset tooltip when the delete is being called
   `Pull Request 6744`_
 * Generic tooltip hide for onclick faIconButtons
   `Pull Request 6745`_
 * Fix page editor height for flex panels.
   `Pull Request 6747`_
-* Use mapped-over collectionType when inferring collectionType through …
+* Use mapped-over ``collectionType`` when inferring ``collectionType`` through
+  ``format_source``
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6749`_
 * Catch any failures encountered while pausing/stopping jobs whose inputs are
   terminal and non-ok
   `Pull Request 6755`_
-* Don't attempt len(None), ensure stdout/stderr are strings in
-  Job(Like).set_streams().
+* Don't attempt ``len(None)``, ensure stdout/stderr are strings in
+  ``Job(Like).set_streams()``.
   `Pull Request 6765`_
 * Increase the maximum number of stderr lines that will be scanned for slurm
   warnings
   `Pull Request 6766`_
-* backport of: Resilience of success message handling
+* Backport of: Resilience of success message handling
   `Pull Request 6768`_
-* Use UserRoleAssociation to get private roles
+* Use ``UserRoleAssociation`` to get private roles
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6771`_
-* Update name of Workflow when updating StoredWorkflow name
+* Update name of ``Workflow`` when updating ``StoredWorkflow`` name
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6774`_
 * All extracted datasets should be visible
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
   `Pull Request 6780`_
-* Fix __encode_invocation signature
+* Fix ``__encode_invocation`` signature
   `Pull Request 6782`_
 * Strip all control characters from rules
   (thanks to `@mvdbeek <https://github.com/mvdbeek>`__).
@@ -789,7 +791,7 @@ Fixes
   `Pull Request 6789`_
 * Flex-related style fixes
   `Pull Request 6791`_
-* allow making all datasets within history public, when sharing
+* Allow making all datasets within history public, when sharing
   `Pull Request 6793`_
 * Drop unused peek method
   `Pull Request 6796`_
@@ -803,7 +805,7 @@ Fixes
   `Pull Request 6802`_
 * Don't delete referenced Datasets when purging users
   `Pull Request 6809`_
-* do not rule out numbers that are accessed with shift modifier
+* Do not rule out numbers that are accessed with shift modifier
   `Pull Request 6810`_
 * Upgrade concurrently for 'null' return fix
   `Pull Request 6828`_
diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py
index 74daafa025c..4c29cacba66 100644
--- a/scripts/bootstrap_history.py
+++ b/scripts/bootstrap_history.py
@@ -103,7 +103,7 @@ Highlights
 Get Galaxy
 ==========
 
-The code lives at `Github <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
+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
@@ -199,7 +199,7 @@ RELEASE_ISSUE_TEMPLATE = string.Template("""
     - [ ] Ensure all [blocking milestone PRs](https://github.com/galaxyproject/galaxy/pulls?q=is%3Aopen+is%3Apr+milestone%3A${version}) have been merged or closed.
 
           make release-check-blocking-prs RELEASE_CURR=${version}
-    - [ ] Ensure previous release is merged into current. [Github branch comparison](https://github.com/galaxyproject/galaxy/compare/release_${version}...release_${previous_version})
+    - [ ] Ensure previous release is merged into current. [GitHub branch comparison](https://github.com/galaxyproject/galaxy/compare/release_${version}...release_${previous_version})
     - [ ] Create and push release tag:
 
           make release-create RELEASE_CURR=${version}