From 2dc072609f2a9ca83348fa822dffa89886ef6dba Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 28 Jan 2020 16:28:38 +0100
Subject: [PATCH 01/26] Update scripts/bootstrap_history.py for python 3 /
 pygithub

---
 scripts/bootstrap_history.py | 55 ++++++++++++++++++++----------------
 1 file changed, 30 insertions(+), 25 deletions(-)

diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py
index 216595bc6ff..4440138f7b8 100644
--- a/scripts/bootstrap_history.py
+++ b/scripts/bootstrap_history.py
@@ -6,6 +6,7 @@ from __future__ import print_function
 import calendar
 import datetime
 import json
+import logging
 import os
 import re
 import string
@@ -18,12 +19,14 @@ try:
 except ImportError:
     requests = None
 try:
-    from pygithub3 import Github
+    from github import Github
 except ImportError:
     Github = None
 from six import string_types
 from six.moves.urllib.parse import urljoin
 
+log = logging.getLogger(__name__)
+
 PROJECT_DIRECTORY = os.path.join(os.path.dirname(__file__), os.pardir)
 GALAXY_VERSION_FILE = os.path.join(PROJECT_DIRECTORY, "lib", "galaxy", "version.py")
 PROJECT_OWNER = "galaxyproject"
@@ -40,7 +43,7 @@ DEVTEAM = [
     "tnabtaf", "natefoo", "jgoecks",
     "guerler", "jennaj", "nekrut", "jxtx",
     "VJalili", "WilliamHolden", "Nerdinacan",
-    "ic4f",
+    "ic4f", "mvdbeek"
 ]
 
 TEMPLATE = """
@@ -350,7 +353,7 @@ def do_release(argv):
     template = template.replace(".. enhancement", "%s\n\n.. enhancement" % enhancement_targets)
     template = template.replace(".. bug", "%s\n\n.. bug" % bug_targets)
     release_info = string.Template(template).safe_substitute(release=release_name)
-    open(release_file, "w").write(release_info.encode("utf-8"))
+    open(release_file, "w").write(release_info)
     month = int(release_name.split(".")[1])
     month_name = calendar.month_name[month]
     year = release_name.split(".")[0]
@@ -379,7 +382,7 @@ def do_release(argv):
     next_release_file = _release_file(next_version + "_announce.rst")
 
     next_announce = NEXT_TEMPLATE.substitute(**next_version_params)
-    open(next_release_file, "w").write(next_announce.encode("utf-8"))
+    open(next_release_file, "w").write(next_announce)
     releases_index = _release_file("index.rst")
     releases_index_contents = _read_file(releases_index)
     releases_index_contents = releases_index_contents.replace(".. announcements\n", ".. announcements\n   " + next_version + "_announce\n")
@@ -471,29 +474,30 @@ def _release_dates(version):
     return freeze_date, release_date
 
 
-def _get_prs(release_name, state="closed"):
+def _get_prs(release_name, state="closed", pr_cache=[]):
     github = _github_client()
-    pull_requests = github.pull_requests.list(
+    repo = github.get_repo("%s/%s" % (PROJECT_OWNER, PROJECT_NAME))
+    add_to_cache = not pr_cache
+    pull_requests = pr_cache or repo.get_pulls(
         state=state,
-        user=PROJECT_OWNER,
-        repo=PROJECT_NAME,
     )
     reached_old_prs = False
 
-    for page in pull_requests:
+    for pr in pull_requests:
         if reached_old_prs:
             break
 
-        for pr in page:
-            if pr.created_at < datetime.datetime(2016, 11, 1, 0, 0):
-                reached_old_prs = True
-                pass
-            merged_at = pr.merged_at
-            milestone = pr.milestone
-            proper_state = state != "closed" or merged_at
-            if not proper_state or not milestone or milestone['title'] != release_name:
-                continue
-            yield pr
+        if pr.created_at < datetime.datetime(2018, 11, 1, 0, 0):
+            reached_old_prs = True
+            pass
+        merged_at = pr.merged_at
+        milestone = pr.milestone
+        proper_state = state != "closed" or merged_at
+        if not proper_state or not milestone or milestone.title != release_name:
+            continue
+        if add_to_cache:
+            pr_cache.append(pr)
+        yield pr
 
 
 def main(argv):
@@ -585,8 +589,8 @@ def main(argv):
     owner = None
     if ident.startswith("pr"):
         pull_request = ident[len("pr"):]
-        user = req["head"]["user"]
-        owner = user["login"]
+        user = req["head"].user
+        owner = user.login
         if owner in DEVTEAM:
             owner = None
         text = ".. _Pull Request {0}: {1}/pull/{0}".format(pull_request, PROJECT_URL)
@@ -615,7 +619,7 @@ def main(argv):
     to_doc = wrap(to_doc)
     if text_target is not None:
         history = extend_target(text_target, to_doc, history)
-    if req and 'labels' in req:
+    if req and req['labels']:
         labels = req['labels']
         if 'area/datatypes' in labels:
             user_announce = extend_target("datatypes", to_doc, user_announce)
@@ -630,12 +634,12 @@ def main(argv):
 
 def _read_file(path):
     with open(path, "r") as f:
-        return f.read().decode("utf-8")
+        return f.read()
 
 
 def _write_file(path, contents):
     with open(path, "w") as f:
-        f.write(contents.encode("utf-8"))
+        f.write(contents)
 
 
 def _text_target(github, pull_request, labels=None):
@@ -713,7 +717,7 @@ def _text_target(github, pull_request, labels=None):
 
 
 def _pr_to_labels(pr):
-    labels = [l["name"].lower() for l in pr.labels]
+    labels = [l.name.lower() for l in pr.labels]
     return labels
 
 
@@ -740,6 +744,7 @@ def _github_client():
         github_json = os.path.expanduser("~/.github.json")
         github = Github(**json.load(open(github_json, "r")))
     except Exception:
+        log.exception()
         github = None
     return github
 

From 08e97198c935dbef8965e383f62bd073c38c6190 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 28 Jan 2020 19:41:06 +0100
Subject: [PATCH 02/26] Release notes for 20.01

---
 doc/source/releases/20.01.rst               | 655 ++++++++++++++++++++
 doc/source/releases/20.01_announce.rst      |  62 +-
 doc/source/releases/20.01_announce_user.rst |  93 +++
 doc/source/releases/20.01_prs.rst           | 277 +++++++++
 4 files changed, 1084 insertions(+), 3 deletions(-)
 create mode 100644 doc/source/releases/20.01.rst
 create mode 100644 doc/source/releases/20.01_announce_user.rst
 create mode 100644 doc/source/releases/20.01_prs.rst

diff --git a/doc/source/releases/20.01.rst b/doc/source/releases/20.01.rst
new file mode 100644
index 00000000000..db6791476c2
--- /dev/null
+++ b/doc/source/releases/20.01.rst
@@ -0,0 +1,655 @@
+
+.. to_doc
+
+20.01
+===============================
+
+.. announce_start
+
+Enhancements
+-------------------------------
+
+.. major_feature
+
+
+.. feature
+* CLI tools for installing/testing Docker and Singularity containers
+  (thanks to `@simonbray <https://github.com/simonbray>`__).
+  `Pull Request 7936`_
+* Markdown-based Galaxy Pages.
+  `Pull Request 8512`_
+* Make Masthead and workflow page screenreader friendly
+  `Pull Request 8700`_
+* Add data dialog input element to client form parameter list
+  `Pull Request 8774`_
+* Add has_size option
+  (thanks to `@simonbray <https://github.com/simonbray>`__).
+  `Pull Request 8852`_
+* Email notifications on job completion
+  `Pull Request 8948`_
+* Make tours reloadable
+  `Pull Request 9032`_
+* Add a config option to allow customizing the brand title
+  `Pull Request 9062`_
+* IT fixes and 3 new ITs
+  `Pull Request 9141`_
+
+.. enhancement_tag_viz
+
+.. enhancement_tag_datatypes
+* Datatypes for MassSpec DIA dlib,elib
+  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
+  `Pull Request 8657`_
+* Add bus as binary, remove extra datatype
+  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
+  `Pull Request 8705`_
+* remove dada2_derep data type
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 8902`_
+* Add new GROMACS datatypes: ndx, xvg, edr
+  (thanks to `@simonbray <https://github.com/simonbray>`__).
+  `Pull Request 8964`_
+* add gff3.gz and gff3.bz2 datatypes
+  (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
+  `Pull Request 8967`_
+* Make mol2 visible
+  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
+  `Pull Request 8995`_
+* Add a datatype subclass for CAT (Contig Annotation Tool)
+  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
+  `Pull Request 9087`_
+
+.. enhancement_tag_tools
+* Upgrade askomics interactive tool
+  (thanks to `@xgaia <https://github.com/xgaia>`__).
+  `Pull Request 8517`_
+* Remove collection ID character restriction from 'Relabel collection from
+  file' tool
+  (thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
+  `Pull Request 8571`_
+* Allow space, dot and comma in relabel identifier tool
+  `Pull Request 8757`_
+* Fix script shebangs
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8888`_
+* Allow admins to import tools/workflows from paths.
+  `Pull Request 9003`_
+
+.. enhancement_tag_workflows
+* Interactive modification of invocation report.
+  `Pull Request 8691`_
+* User-facing Workflow Invocation Grid
+  `Pull Request 8699`_
+* PDF Export of Galaxy Markdown
+  `Pull Request 8893`_
+* Refactor some workflow editor plumbing to VueJS
+  `Pull Request 8931`_
+* Track non-history content outputs.
+  `Pull Request 9009`_
+* Default format 2 workflows to be downloaded as YAML.
+  `Pull Request 9023`_
+* Even Richer Workflow Inputs
+  `Pull Request 9086`_
+* Separate Markdown Validation into its own module.
+  `Pull Request 9099`_
+* add option select_type_workflow_threshold (rebase)
+  `Pull Request 9105`_
+
+.. enhancement_tag_ui
+* Upgrade eslint (major version), fix compliance with new standard rules.
+  `Pull Request 8708`_
+* JobMetrics.vue unit test.
+  `Pull Request 8732`_
+* Fix the flexible Data Dialog to work independent of the page layout
+  initialization hooks.
+  `Pull Request 8744`_
+* axios-mock-adapter for cleaner, more expansive testing
+  `Pull Request 8749`_
+* Added client-side application configs for each target environment
+  `Pull Request 8827`_
+
+.. enhancement_tag_jobs
+* Small cleanup for job runners kill
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8523`_
+* Improvements to Galaxy and Pulsar job execution
+  `Pull Request 8625`_
+* Allow assigning UUID job ids with Pulsar in MQ mode.
+  `Pull Request 8718`_
+* Do not re-compute job input_ext/dbkey in job finish.
+  `Pull Request 8910`_
+* Implement extended job metadata collection
+  `Pull Request 8930`_
+* Move Jobs updated time display logic to client.
+  `Pull Request 8943`_
+* Implement extended job metadata collection + fixes
+  `Pull Request 8984`_
+* Place version output file in a writable directory for containerized jobs.
+  `Pull Request 8997`_
+* Fix deletion of outputs and working before job
+  `Pull Request 9245`_
+
+.. enhancement_tag_admin
+* Add Tool Manager Component for Admin Panel
+  `Pull Request 8601`_
+* Add process ID to worker_process table
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 8972`_
+
+.. enhancement
+* Use official "login with" buttons for OIDC
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
+  `Pull Request 8107`_
+* Add data types to docs.galaxyproject.org
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 8531`_
+* python-ldap python3 update and documentation change
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 8618`_
+* GitLab error reporting
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 8620`_
+* Extend the list of attributes to be reported.
+  `Pull Request 8661`_
+* Have CI ensure client PRs are formatted.
+  `Pull Request 8662`_
+* Add area/configuration label
+  `Pull Request 8665`_
+* Update BootstrapVue to 2.0.1
+  `Pull Request 8666`_
+* add .gitattributes file and normalize line endings to use LF in…
+  `Pull Request 8677`_
+* Improve CI reliability by annotating external resources.
+  `Pull Request 8678`_
+* Restrict `/api/histories/shared_with_me` to logged-in users
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8685`_
+* Automate path resolution for config options
+  `Pull Request 8689`_
+* Remove unused Docker Swarm options
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8690`_
+* LDAP search member of filter
+  (thanks to `@BioinformaticsPlatformWIV-ISP
+  <https://github.com/BioinformaticsPlatformWIV-ISP>`__).
+  `Pull Request 8697`_
+* Rebuild and prettify config sample and doc
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8713`_
+* Update zh/locale.js
+  (thanks to `@shenweiyan <https://github.com/shenweiyan>`__).
+  `Pull Request 8725`_
+* Start using path_resolves_to; add integration tests
+  `Pull Request 8737`_
+* Significant overhaul to container+dependency management
+  `Pull Request 8741`_
+* Multi subdomains cookie support
+  (thanks to `@julozi <https://github.com/julozi>`__).
+  `Pull Request 8746`_
+* One test case to rule them all
+  `Pull Request 8793`_
+* Allow recording more performance statistics to statsd.
+  `Pull Request 8800`_
+* Add installation monitor popup to toolshed client
+  `Pull Request 8810`_
+* General server dependency updates (was/including catalina fix)
+  `Pull Request 8843`_
+* Add badge to indicate availability of a newer toolshed repository version
+  `Pull Request 8860`_
+* Add config options to integration test for abs path
+  `Pull Request 8862`_
+* Make message_box style and visible options reloadable
+  `Pull Request 8863`_
+* Remove 'area/cleanup', edit 'kind/refactoring'
+  `Pull Request 8874`_
+* Unpin bdbag.
+  `Pull Request 8883`_
+* Add separate knob for masthead colors
+  `Pull Request 8904`_
+* Refactor galaxy_install and required dependencies into Galaxy's namespace.
+  `Pull Request 8905`_
+* Enable interactivetools with other beta tools...
+  `Pull Request 8913`_
+* Simplify logo replacement, fix height and alignment
+  `Pull Request 8914`_
+* Simplify Python deps installation in `testing-base` Dockerfile
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8921`_
+* Config: drop redundant `template_cache` attribute
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8924`_
+* Enable secondary authorization
+  `Pull Request 8926`_
+* Set up a cache dir for pip when running tests with Docker
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8929`_
+* Add link for interactive tools
+  (thanks to `@anuprulez <https://github.com/anuprulez>`__).
+  `Pull Request 8936`_
+* Remove deprecated tool dependency scripts.
+  `Pull Request 8955`_
+* Remove tool shed API examples.
+  `Pull Request 8956`_
+* Remove script for migrating tools to the tool shed...
+  `Pull Request 8957`_
+* Move galaxy testing utilities into cleaner package structure.
+  `Pull Request 8960`_
+* Create packages for Galaxy tests and infrastructure.
+  `Pull Request 8962`_
+* Remove workflow support from tool shed.
+  `Pull Request 8978`_
+* Remove capsule feature from tool shed.
+  `Pull Request 8979`_
+* trim long ldda messages; improve fluid media css
+  `Pull Request 9000`_
+* Expose python version in api/config
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
+  `Pull Request 9010`_
+* Hot module reloading using webpack-dev-server for client dev
+  `Pull Request 9029`_
+* when building ts index log parse errors at debug level
+  `Pull Request 9033`_
+* Update quickstart.rst
+  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
+  `Pull Request 9044`_
+* Add Sergey Golitsynskiy to committers group
+  `Pull Request 9056`_
+* Update Mercurial to Py3-compatible v5.2, and all other deps
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9065`_
+* Automatically redirect to OIDC provider when only auth option
+  (thanks to `@machristie <https://github.com/machristie>`__).
+  `Pull Request 9115`_
+* Automatically use extended-base-image if necessary
+  `Pull Request 9116`_
+* Add HMR to client readme.
+  `Pull Request 9121`_
+* Add admin functionality to histories API
+  (thanks to `@thomcuddihy <https://github.com/thomcuddihy>`__).
+  `Pull Request 9124`_
+* Don't break generated reStructuredText and YAML on hyphens
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9128`_
+* mulled: use threading.Event in PrintProgress to avoid unnecessary wai…
+  `Pull Request 9163`_
+* Update my username
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
+  `Pull Request 9195`_
+* Add base_image column to mulled-build-files
+  `Pull Request 9199`_
+* Allow passing conda_context to any_target_requires_extended_base
+  `Pull Request 9202`_
+* Backport 9175: Update galaxy.tool_util.cwl for latest changes in CWL branch.
+  `Pull Request 9210`_
+* Extended base annotation fixes
+  `Pull Request 9224`_
+
+.. small_enhancement
+* Factor out yaml read/write from config_manage.py
+  `Pull Request 8509`_
+* Implementation of the workflow list as vue component
+  `Pull Request 8551`_
+* Refactor config loading
+  `Pull Request 8573`_
+* Change reloadable config + misc cleanup
+  `Pull Request 8600`_
+* Case-insensitive match user-supplied email when logging in
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8631`_
+* Modify schema defaults and their loading
+  `Pull Request 8639`_
+* Replace resolve_path() with os.path.join()
+  `Pull Request 8646`_
+* Simplify config code (minor edits)
+  `Pull Request 8648`_
+* Refactor/cleanup config loading (misc edits)
+  `Pull Request 8651`_
+* Remove unused Tags file since it was converted to a Vue component
+  `Pull Request 8722`_
+* Update slot syntax to v-slot across the board.
+  `Pull Request 8730`_
+* Remove deprecated Toolshed API endpoints
+  `Pull Request 8734`_
+* Client build process refinement
+  `Pull Request 8742`_
+* Add vue component and endpoint to reset repository metadata
+  `Pull Request 8754`_
+* Cleanup SQL query in ``_calculate_or_set_disk_usage()``
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8776`_
+* Drop DetachedInstanceError workaround
+  `Pull Request 8785`_
+* Simplify code for expand_meta_parameters
+  (thanks to `@qiagu <https://github.com/qiagu>`__).
+  `Pull Request 8794`_
+* Convert User Preferences page to Vue Component
+  `Pull Request 8803`_
+* client-side current user store module
+  `Pull Request 8813`_
+* Refactor database_connection config loading
+  `Pull Request 8855`_
+* Refactor default_locale config option; test
+  `Pull Request 8856`_
+* Refactor infrastructure_url/port values; fix tests
+  `Pull Request 8857`_
+* Refactor pretty-datatime_format config loading
+  `Pull Request 8858`_
+* Fix misc. integration tests for config values
+  `Pull Request 8859`_
+* Do not specify None as default in dict.get()
+  `Pull Request 8865`_
+* Delete 'resolve path' integration tests
+  `Pull Request 8870`_
+* Do not raise Exception to manage control flow
+  `Pull Request 8876`_
+* Eliminate interactive debugging middleware
+  `Pull Request 8877`_
+* Normalize myexperiment_target_url / myexperiment_url
+  `Pull Request 8882`_
+* Do not override schema defaults if they exist
+  `Pull Request 8884`_
+* Use schema defaults in galaxy masthead
+  `Pull Request 8885`_
+* Cleanup config loading (minor fixes)
+  `Pull Request 8890`_
+* Refactor _set_config_base; fix config_dir value
+  `Pull Request 8915`_
+* Library tags tweaks and tests
+  `Pull Request 8947`_
+* Refactor Toolshed webapp into tool_shed package.
+  `Pull Request 8949`_
+* Separate Shed and Galaxy makos, package shed makos.
+  `Pull Request 8958`_
+* Remove admin tool shed controller code (Part 1)
+  `Pull Request 8988`_
+* Remove unused helper code from twilltestcase.
+  `Pull Request 8989`_
+* Fix tool image loading (was broken due to failing repo dir resolution)
+  `Pull Request 9006`_
+* Convert Custom builds vue
+  `Pull Request 9016`_
+* Implement datasets grid as vue component
+  `Pull Request 9018`_
+* remove unused toolshed template code
+  `Pull Request 9084`_
+* Default the authnz_manager to None
+  `Pull Request 9117`_
+* Update github username @erasche to @hexylena and correct inconsistencies
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
+  `Pull Request 9194`_
+
+
+
+Fixes
+-------------------------------
+
+.. major_bug
+
+
+.. bug_tag_viz
+* Wrap SQL statement in a text() function as required by sqlalchemy
+  (thanks to `@kaukrise <https://github.com/kaukrise>`__).
+  `Pull Request 9216`_
+* Ensure visible overflow on navbar container
+  (thanks to `@kaukrise <https://github.com/kaukrise>`__).
+  `Pull Request 9217`_
+
+.. bug_tag_datatypes
+* Fix cool sniffing on python3
+  `Pull Request 9153`_
+
+.. bug_tag_tools
+* grouping: strip newlines
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 8953`_
+* Add requirements to interval_to_bed_converter.xml
+  `Pull Request 9041`_
+
+.. bug_tag_workflows
+* Exports reports with workflows (if configured).
+  `Pull Request 9055`_
+* Rev gxformat2 dependency to fix various export issues.
+  `Pull Request 9075`_
+
+.. bug_tag_ui
+* Run prettier after `#8107
+  <https://github.com/galaxyproject/galaxy/issues/8107>`__
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9102`_
+
+.. bug_tag_jobs
+* Small fixes for k8s.
+  `Pull Request 8759`_
+* Fix output.file_path writing to read-only path on Docker
+  `Pull Request 9048`_
+* Add job home to writable paths
+  `Pull Request 9051`_
+* Fix LocalShell returncode
+  `Pull Request 9171`_
+* Fix: Added support for specifying k8s job pod priority class
+  (thanks to `@nuwang <https://github.com/nuwang>`__).
+  `Pull Request 9219`_
+* Fix: Added support for specifying k8s job affinity and tolerations
+  (thanks to `@nuwang <https://github.com/nuwang>`__).
+  `Pull Request 9225`_
+* Mount job_working_directory/configs rw
+  `Pull Request 9234`_
+* Limit async hack to async tools
+  `Pull Request 9242`_
+* Fix moving of data manager output for entries
+  `Pull Request 9243`_
+* python3 fixes for setups using drmaa and realuser setups
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 9246`_
+* fix bug introduced in https://github.com/galaxyproject/galaxy/pull/9246
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 9253`_
+
+.. bug_tag_admin
+* Encode lines in filter_file_fields
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 8652`_
+* Git error reporting - bug fixes and better error handling
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 8900`_
+* Assorted admin panel fixes
+  `Pull Request 9097`_
+* Run integration tests on github, fix various bugs (interactive tools,
+  kubernetes, test framework)
+  `Pull Request 9193`_
+
+.. bug
+* Documentation update
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 8508`_
+* Asynchronous data source: unable to create the file
+  (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
+  `Pull Request 8515`_
+* OIDC config patch
+  (thanks to `@almahmoud <https://github.com/almahmoud>`__).
+  `Pull Request 8572`_
+* set uwsgi umask default
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 8581`_
+* Fix `test_validate_simple_config` unit test
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8632`_
+* Fix a bug that occurs while installing a data manager.
+  (thanks to `@selten <https://github.com/selten>`__).
+  `Pull Request 8634`_
+* Fix bug in build_dependency_manager()
+  `Pull Request 8660`_
+* Get rid of fix timeout in admin app Selenium test.
+  `Pull Request 8667`_
+* More robust login/logout with Selenium.
+  `Pull Request 8676`_
+* Fixes for BootstrapVue Tables
+  `Pull Request 8684`_
+* More bootstrap vue upgrade fixes.
+  `Pull Request 8692`_
+* GRT: Ensure correct encoding, no partial lines
+  (thanks to `@hexylena <https://github.com/hexylena>`__).
+  `Pull Request 8712`_
+* Revise toolshed config dependency check error message in repository install
+  manager
+  `Pull Request 8720`_
+* Fix data dialog height, modal test case and table slots
+  `Pull Request 8724`_
+* Do not overwrite existing attributes
+  `Pull Request 8728`_
+* Replace hardcoded configuration
+  `Pull Request 8731`_
+* Fix `new_secure_hash()` when passed an empty string
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8739`_
+* data_manager_conf.xml.sample is missing
+  (thanks to `@lecorguille <https://github.com/lecorguille>`__).
+  `Pull Request 8784`_
+* Revert "[19.09] Fix detached parent instance error in 8769"
+  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
+  `Pull Request 8791`_
+* Handles k8s job recently created with no status set yet
+  (thanks to `@pcm32 <https://github.com/pcm32>`__).
+  `Pull Request 8799`_
+* Add postcss-loader and autoprefixer dependencies
+  `Pull Request 8821`_
+* LDAP fixes
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8823`_
+* Ensure app.config.config_file is an absolute path
+  `Pull Request 8836`_
+* Fix rare bug in config loading + add unit test
+  `Pull Request 8837`_
+* fix plugin name
+  (thanks to `@gmauro <https://github.com/gmauro>`__).
+  `Pull Request 8840`_
+* Restore portlet section style for repeat blocks
+  `Pull Request 8864`_
+* Prevent potential bug in config loading; test
+  `Pull Request 8866`_
+* Fix authnz manager's oidc config parsing for python3
+  `Pull Request 8871`_
+* Update check_py3_compatibility script for new ack versions.
+  `Pull Request 8872`_
+* If config_file is None, use cwd, not its parent
+  `Pull Request 8894`_
+* Log LDAP authenticate exceptions at the right level
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8907`_
+* make pgcleanup also delete HDAs
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 8908`_
+* Fix unbounded variable error in `GET /api/datasets/{encoded_dataset_id}`
+  exception handling
+  `Pull Request 8935`_
+* Set `deleted` attribute of history datasets when purging histories from grid
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8940`_
+* Fix default logo path in configuration manager
+  `Pull Request 8941`_
+* Fix API decorator order
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9015`_
+* do not use var from inner scope
+  `Pull Request 9026`_
+* escape double hyphen in IT sample config, making it valid XML
+  `Pull Request 9034`_
+* Fix input parameter comparisons
+  `Pull Request 9047`_
+* Restore casting a boolean param to str when comparing with one
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9052`_
+* Fix comparison if parameter is optional and value is not provided
+  `Pull Request 9054`_
+* Small refactor of ``InputValueWrapper`` comparison methods
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9059`_
+* Add create_time to the signature of Repository constructor.
+  `Pull Request 9063`_
+* Listify value for multiple SelectToolParameterWrapper
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9067`_
+* Use newer psycopg2 conditional requirement for wheels on 3.7
+  `Pull Request 9068`_
+* Fix mulled version comparison
+  `Pull Request 9078`_
+* linter: accept outputs with auto_format only
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 9081`_
+* Create temporary files for cgi.FieldsStorage with delete=False
+  `Pull Request 9082`_
+* Fix importing a directory from user_library_import_dir
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9090`_
+* Make callbacks for tour and config watchers a control task
+  `Pull Request 9092`_
+* Don't watch tool files through watchdog
+  `Pull Request 9094`_
+* Allow html in registration warning message.
+  `Pull Request 9098`_
+* Admin job info display fix
+  `Pull Request 9120`_
+* Client build readme followup
+  `Pull Request 9122`_
+* Fix mulled cache/data locations, rebuild schema
+  `Pull Request 9125`_
+* More fixes for publishing decomposed packages.
+  `Pull Request 9126`_
+* fix url for workflow sharing
+  `Pull Request 9132`_
+* Add click prevent to workflow list dropdowns
+  `Pull Request 9133`_
+* Remove legacy admin panel entry for installation monitor, fix typo
+  `Pull Request 9134`_
+* Parse brand label option in legacy mako
+  `Pull Request 9136`_
+* Restore returning "None" when casting unselected multiselect param to str
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9144`_
+* Misc fixes
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9145`_
+* Add implementation of `parse_interactivetool` to `CwlToolSource` class
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9146`_
+* Fix optional unset integer and float params
+  `Pull Request 9149`_
+* Assorted OIDC fixes
+  `Pull Request 9150`_
+* Cast to None for optional params if not comparing strings
+  `Pull Request 9156`_
+* Ensure that users have a private role before login
+  `Pull Request 9168`_
+* Add static-safe mapping to config management
+  `Pull Request 9179`_
+* Fix tool shed tests for `#9168
+  <https://github.com/galaxyproject/galaxy/issues/9168>`__.
+  `Pull Request 9182`_
+* Add require_login bypass for entire authnz controller.
+  `Pull Request 9192`_
+* Fix runtime error in ToolConfWatcher
+  `Pull Request 9212`_
+* Fix extended base for singularity and add base_image_for_targets
+  `Pull Request 9215`_
+* More mulled-build-files fixes
+  `Pull Request 9228`_
+* Fix mailto hrefs in menus
+  `Pull Request 9232`_
+* Move meme_fimo out of unversioned lib tools
+  `Pull Request 9237`_
+* Fallback to binary download if header lies about content encoding
+  `Pull Request 9239`_
+* Fix lint warning string formatting
+  `Pull Request 9240`_
+* Fix unselected select parameter comparison to empty string
+  `Pull Request 9260`_
+* Fix iteritems use in build_from_current_history.mako
+  `Pull Request 9266`_
+* Fix suffix for single target mulled builds
+  `Pull Request 9267`_
+* backport 9268: Fix target_str_to_targets
+  `Pull Request 9269`_
+
+
+.. include:: 20.01_prs.rst
+
diff --git a/doc/source/releases/20.01_announce.rst b/doc/source/releases/20.01_announce.rst
index 2c7a6a98ff5..406a076c09a 100644
--- a/doc/source/releases/20.01_announce.rst
+++ b/doc/source/releases/20.01_announce.rst
@@ -3,8 +3,64 @@
 January 2020 Galaxy Release (v 20.01)
 ===========================================================
 
+.. include:: _header.rst
 
-Schedule
+Highlights
 ===========================================================
- * Planned Freeze Date: 2020-01-06
- * Planned Release Date: 2020-01-27
+
+**Enhanced workflow functionality** 
+  Workflows can now now make use of optional datasets and optional parameters,
+  optional parameter default values and dataset inputs can now be restricted to
+  user-defined datatypes. The workflow editor and execution engine have been
+  enhanced to allow defining options to choose from, and these options can be
+  connected to compatible text, integer, float, color and select tool parameters
+  for more flexible and universally re-usable workflows (`Pull Request 9086`_, `Pull Request 9073`_, `Pull Request 8264`_). 
+
+**Major update to container and dependency management interface**
+  The manage dependencies interface has been ported to vue.js and displays
+  additional information about installed, missing and available dependencies
+  and conveniently summarizes dependency status for all installed tools.
+  Additionally the user interface now displays whether a `Biocontainers <https://biocontainers.pro/#/registry>`__ image
+  is available at `quay.io <https://quay.io>`__ (`Pull Request 8741`_).
+
+**Extended job metadata collection**
+  Creating Job metadata has been reworked so that the dataset transfer that
+  occurs after a Galaxy job can be initiated by the compute node that runs a
+  Galaxy job. Previously the transfer was done by Galaxy under many production
+  scenarios.  This reduces IO load on Galaxy instances and should allow running
+  many more jobs in parallel. This work will also make jobs running on remote
+  compute resources much more efficient if the remote resources can write to
+  Galaxy'so object store. To benefit from this new metadata setting Galaxy needs
+  to use object stores that use uuids for storing datasets and set the
+  ``metadata_strategy`` configuration value to ``extended``. This feature is in beta
+  testing, but work is ongoing to mix existing object store configuration and
+  choose the most efficient way of transfering datasets automatically (`Pull
+  Request 8930`_ ).
+
+
+Also check out the `20.01 user release notes <https://docs.galaxyproject.org/en/release_20.01/releases/20.01_announce_user.html>`__
+
+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_20.01 https://github.com/galaxyproject/galaxy.git
+
+To update an existing Galaxy repository run:
+  .. code-block:: shell
+
+      $ git fetch origin && git checkout release_20.01 && git pull --ff-only origin release_20.01
+
+See the `community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
+
+Release Notes
+===========================================================
+
+.. include:: 20.01.rst
+   :start-after: announce_start
+
+.. include:: _thanks.rst
diff --git a/doc/source/releases/20.01_announce_user.rst b/doc/source/releases/20.01_announce_user.rst
new file mode 100644
index 00000000000..c4d19b4cedd
--- /dev/null
+++ b/doc/source/releases/20.01_announce_user.rst
@@ -0,0 +1,93 @@
+
+===========================================================
+January 2020 Galaxy Release (v 20.01)
+===========================================================
+
+.. include:: _header.rst
+
+Highlights
+===========================================================
+
+**Feature1**
+  Feature description.
+
+**Feature2**
+  Feature description.
+
+**Feature3**
+  Feature description.
+
+
+New Visualizations
+===========================================================
+
+.. visualizations
+* Add data dialog input element to client form parameter list
+  `Pull Request 8774`_
+* Wrap SQL statement in a text() function as required by sqlalchemy
+  (thanks to `@kaukrise <https://github.com/kaukrise>`__).
+  `Pull Request 9216`_
+* Ensure visible overflow on navbar container
+  (thanks to `@kaukrise <https://github.com/kaukrise>`__).
+  `Pull Request 9217`_
+
+New Datatypes
+===========================================================
+
+.. datatypes
+* Datatypes for MassSpec DIA dlib,elib
+  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
+  `Pull Request 8657`_
+* Add bus as binary, remove extra datatype
+  (thanks to `@astrovsky01 <https://github.com/astrovsky01>`__).
+  `Pull Request 8705`_
+* remove dada2_derep data type
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 8902`_
+* Add new GROMACS datatypes: ndx, xvg, edr
+  (thanks to `@simonbray <https://github.com/simonbray>`__).
+  `Pull Request 8964`_
+* add gff3.gz and gff3.bz2 datatypes
+  (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
+  `Pull Request 8967`_
+* Make mol2 visible
+  (thanks to `@galaxyproject <https://github.com/galaxyproject>`__).
+  `Pull Request 8995`_
+* Add a datatype subclass for CAT (Contig Annotation Tool)
+  (thanks to `@jj-umn <https://github.com/jj-umn>`__).
+  `Pull Request 9087`_
+* Fix cool sniffing on python3
+  `Pull Request 9153`_
+
+Builtin Tool Updates
+===========================================================
+
+.. tools
+* Upgrade askomics interactive tool
+  (thanks to `@xgaia <https://github.com/xgaia>`__).
+  `Pull Request 8517`_
+* Remove collection ID character restriction from 'Relabel collection from
+  file' tool
+  (thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
+  `Pull Request 8571`_
+* Allow space, dot and comma in relabel identifier tool
+  `Pull Request 8757`_
+* Fix script shebangs
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 8888`_
+* grouping: strip newlines
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 8953`_
+* Allow admins to import tools/workflows from paths.
+  `Pull Request 9003`_
+* Add requirements to interval_to_bed_converter.xml
+  `Pull Request 9041`_
+
+Release Notes
+===========================================================
+
+Please see the `full release notes <20.01_announce.html>`_ for more details.
+
+.. include:: 20.01_prs.rst
+
+.. include:: _thanks.rst
diff --git a/doc/source/releases/20.01_prs.rst b/doc/source/releases/20.01_prs.rst
new file mode 100644
index 00000000000..8911eb66e40
--- /dev/null
+++ b/doc/source/releases/20.01_prs.rst
@@ -0,0 +1,277 @@
+
+.. github_links
+.. _Pull Request 7936: https://github.com/galaxyproject/galaxy/pull/7936
+.. _Pull Request 8107: https://github.com/galaxyproject/galaxy/pull/8107
+.. _Pull Request 8508: https://github.com/galaxyproject/galaxy/pull/8508
+.. _Pull Request 8509: https://github.com/galaxyproject/galaxy/pull/8509
+.. _Pull Request 8512: https://github.com/galaxyproject/galaxy/pull/8512
+.. _Pull Request 8515: https://github.com/galaxyproject/galaxy/pull/8515
+.. _Pull Request 8517: https://github.com/galaxyproject/galaxy/pull/8517
+.. _Pull Request 8523: https://github.com/galaxyproject/galaxy/pull/8523
+.. _Pull Request 8531: https://github.com/galaxyproject/galaxy/pull/8531
+.. _Pull Request 8551: https://github.com/galaxyproject/galaxy/pull/8551
+.. _Pull Request 8571: https://github.com/galaxyproject/galaxy/pull/8571
+.. _Pull Request 8572: https://github.com/galaxyproject/galaxy/pull/8572
+.. _Pull Request 8573: https://github.com/galaxyproject/galaxy/pull/8573
+.. _Pull Request 8581: https://github.com/galaxyproject/galaxy/pull/8581
+.. _Pull Request 8600: https://github.com/galaxyproject/galaxy/pull/8600
+.. _Pull Request 8601: https://github.com/galaxyproject/galaxy/pull/8601
+.. _Pull Request 8618: https://github.com/galaxyproject/galaxy/pull/8618
+.. _Pull Request 8620: https://github.com/galaxyproject/galaxy/pull/8620
+.. _Pull Request 8625: https://github.com/galaxyproject/galaxy/pull/8625
+.. _Pull Request 8631: https://github.com/galaxyproject/galaxy/pull/8631
+.. _Pull Request 8632: https://github.com/galaxyproject/galaxy/pull/8632
+.. _Pull Request 8634: https://github.com/galaxyproject/galaxy/pull/8634
+.. _Pull Request 8639: https://github.com/galaxyproject/galaxy/pull/8639
+.. _Pull Request 8646: https://github.com/galaxyproject/galaxy/pull/8646
+.. _Pull Request 8648: https://github.com/galaxyproject/galaxy/pull/8648
+.. _Pull Request 8651: https://github.com/galaxyproject/galaxy/pull/8651
+.. _Pull Request 8652: https://github.com/galaxyproject/galaxy/pull/8652
+.. _Pull Request 8657: https://github.com/galaxyproject/galaxy/pull/8657
+.. _Pull Request 8660: https://github.com/galaxyproject/galaxy/pull/8660
+.. _Pull Request 8661: https://github.com/galaxyproject/galaxy/pull/8661
+.. _Pull Request 8662: https://github.com/galaxyproject/galaxy/pull/8662
+.. _Pull Request 8665: https://github.com/galaxyproject/galaxy/pull/8665
+.. _Pull Request 8666: https://github.com/galaxyproject/galaxy/pull/8666
+.. _Pull Request 8667: https://github.com/galaxyproject/galaxy/pull/8667
+.. _Pull Request 8676: https://github.com/galaxyproject/galaxy/pull/8676
+.. _Pull Request 8677: https://github.com/galaxyproject/galaxy/pull/8677
+.. _Pull Request 8678: https://github.com/galaxyproject/galaxy/pull/8678
+.. _Pull Request 8684: https://github.com/galaxyproject/galaxy/pull/8684
+.. _Pull Request 8685: https://github.com/galaxyproject/galaxy/pull/8685
+.. _Pull Request 8689: https://github.com/galaxyproject/galaxy/pull/8689
+.. _Pull Request 8690: https://github.com/galaxyproject/galaxy/pull/8690
+.. _Pull Request 8691: https://github.com/galaxyproject/galaxy/pull/8691
+.. _Pull Request 8692: https://github.com/galaxyproject/galaxy/pull/8692
+.. _Pull Request 8694: https://github.com/galaxyproject/galaxy/pull/8694
+.. _Pull Request 8697: https://github.com/galaxyproject/galaxy/pull/8697
+.. _Pull Request 8699: https://github.com/galaxyproject/galaxy/pull/8699
+.. _Pull Request 8700: https://github.com/galaxyproject/galaxy/pull/8700
+.. _Pull Request 8705: https://github.com/galaxyproject/galaxy/pull/8705
+.. _Pull Request 8708: https://github.com/galaxyproject/galaxy/pull/8708
+.. _Pull Request 8709: https://github.com/galaxyproject/galaxy/pull/8709
+.. _Pull Request 8712: https://github.com/galaxyproject/galaxy/pull/8712
+.. _Pull Request 8713: https://github.com/galaxyproject/galaxy/pull/8713
+.. _Pull Request 8718: https://github.com/galaxyproject/galaxy/pull/8718
+.. _Pull Request 8720: https://github.com/galaxyproject/galaxy/pull/8720
+.. _Pull Request 8722: https://github.com/galaxyproject/galaxy/pull/8722
+.. _Pull Request 8724: https://github.com/galaxyproject/galaxy/pull/8724
+.. _Pull Request 8725: https://github.com/galaxyproject/galaxy/pull/8725
+.. _Pull Request 8726: https://github.com/galaxyproject/galaxy/pull/8726
+.. _Pull Request 8728: https://github.com/galaxyproject/galaxy/pull/8728
+.. _Pull Request 8730: https://github.com/galaxyproject/galaxy/pull/8730
+.. _Pull Request 8731: https://github.com/galaxyproject/galaxy/pull/8731
+.. _Pull Request 8732: https://github.com/galaxyproject/galaxy/pull/8732
+.. _Pull Request 8734: https://github.com/galaxyproject/galaxy/pull/8734
+.. _Pull Request 8735: https://github.com/galaxyproject/galaxy/pull/8735
+.. _Pull Request 8737: https://github.com/galaxyproject/galaxy/pull/8737
+.. _Pull Request 8739: https://github.com/galaxyproject/galaxy/pull/8739
+.. _Pull Request 8741: https://github.com/galaxyproject/galaxy/pull/8741
+.. _Pull Request 8742: https://github.com/galaxyproject/galaxy/pull/8742
+.. _Pull Request 8744: https://github.com/galaxyproject/galaxy/pull/8744
+.. _Pull Request 8746: https://github.com/galaxyproject/galaxy/pull/8746
+.. _Pull Request 8749: https://github.com/galaxyproject/galaxy/pull/8749
+.. _Pull Request 8754: https://github.com/galaxyproject/galaxy/pull/8754
+.. _Pull Request 8757: https://github.com/galaxyproject/galaxy/pull/8757
+.. _Pull Request 8759: https://github.com/galaxyproject/galaxy/pull/8759
+.. _Pull Request 8762: https://github.com/galaxyproject/galaxy/pull/8762
+.. _Pull Request 8774: https://github.com/galaxyproject/galaxy/pull/8774
+.. _Pull Request 8776: https://github.com/galaxyproject/galaxy/pull/8776
+.. _Pull Request 8784: https://github.com/galaxyproject/galaxy/pull/8784
+.. _Pull Request 8785: https://github.com/galaxyproject/galaxy/pull/8785
+.. _Pull Request 8791: https://github.com/galaxyproject/galaxy/pull/8791
+.. _Pull Request 8793: https://github.com/galaxyproject/galaxy/pull/8793
+.. _Pull Request 8794: https://github.com/galaxyproject/galaxy/pull/8794
+.. _Pull Request 8799: https://github.com/galaxyproject/galaxy/pull/8799
+.. _Pull Request 8800: https://github.com/galaxyproject/galaxy/pull/8800
+.. _Pull Request 8803: https://github.com/galaxyproject/galaxy/pull/8803
+.. _Pull Request 8810: https://github.com/galaxyproject/galaxy/pull/8810
+.. _Pull Request 8813: https://github.com/galaxyproject/galaxy/pull/8813
+.. _Pull Request 8821: https://github.com/galaxyproject/galaxy/pull/8821
+.. _Pull Request 8823: https://github.com/galaxyproject/galaxy/pull/8823
+.. _Pull Request 8827: https://github.com/galaxyproject/galaxy/pull/8827
+.. _Pull Request 8836: https://github.com/galaxyproject/galaxy/pull/8836
+.. _Pull Request 8837: https://github.com/galaxyproject/galaxy/pull/8837
+.. _Pull Request 8839: https://github.com/galaxyproject/galaxy/pull/8839
+.. _Pull Request 8840: https://github.com/galaxyproject/galaxy/pull/8840
+.. _Pull Request 8843: https://github.com/galaxyproject/galaxy/pull/8843
+.. _Pull Request 8852: https://github.com/galaxyproject/galaxy/pull/8852
+.. _Pull Request 8855: https://github.com/galaxyproject/galaxy/pull/8855
+.. _Pull Request 8856: https://github.com/galaxyproject/galaxy/pull/8856
+.. _Pull Request 8857: https://github.com/galaxyproject/galaxy/pull/8857
+.. _Pull Request 8858: https://github.com/galaxyproject/galaxy/pull/8858
+.. _Pull Request 8859: https://github.com/galaxyproject/galaxy/pull/8859
+.. _Pull Request 8860: https://github.com/galaxyproject/galaxy/pull/8860
+.. _Pull Request 8862: https://github.com/galaxyproject/galaxy/pull/8862
+.. _Pull Request 8863: https://github.com/galaxyproject/galaxy/pull/8863
+.. _Pull Request 8864: https://github.com/galaxyproject/galaxy/pull/8864
+.. _Pull Request 8865: https://github.com/galaxyproject/galaxy/pull/8865
+.. _Pull Request 8866: https://github.com/galaxyproject/galaxy/pull/8866
+.. _Pull Request 8870: https://github.com/galaxyproject/galaxy/pull/8870
+.. _Pull Request 8871: https://github.com/galaxyproject/galaxy/pull/8871
+.. _Pull Request 8872: https://github.com/galaxyproject/galaxy/pull/8872
+.. _Pull Request 8873: https://github.com/galaxyproject/galaxy/pull/8873
+.. _Pull Request 8874: https://github.com/galaxyproject/galaxy/pull/8874
+.. _Pull Request 8876: https://github.com/galaxyproject/galaxy/pull/8876
+.. _Pull Request 8877: https://github.com/galaxyproject/galaxy/pull/8877
+.. _Pull Request 8882: https://github.com/galaxyproject/galaxy/pull/8882
+.. _Pull Request 8883: https://github.com/galaxyproject/galaxy/pull/8883
+.. _Pull Request 8884: https://github.com/galaxyproject/galaxy/pull/8884
+.. _Pull Request 8885: https://github.com/galaxyproject/galaxy/pull/8885
+.. _Pull Request 8888: https://github.com/galaxyproject/galaxy/pull/8888
+.. _Pull Request 8890: https://github.com/galaxyproject/galaxy/pull/8890
+.. _Pull Request 8893: https://github.com/galaxyproject/galaxy/pull/8893
+.. _Pull Request 8894: https://github.com/galaxyproject/galaxy/pull/8894
+.. _Pull Request 8900: https://github.com/galaxyproject/galaxy/pull/8900
+.. _Pull Request 8902: https://github.com/galaxyproject/galaxy/pull/8902
+.. _Pull Request 8904: https://github.com/galaxyproject/galaxy/pull/8904
+.. _Pull Request 8905: https://github.com/galaxyproject/galaxy/pull/8905
+.. _Pull Request 8907: https://github.com/galaxyproject/galaxy/pull/8907
+.. _Pull Request 8908: https://github.com/galaxyproject/galaxy/pull/8908
+.. _Pull Request 8910: https://github.com/galaxyproject/galaxy/pull/8910
+.. _Pull Request 8913: https://github.com/galaxyproject/galaxy/pull/8913
+.. _Pull Request 8914: https://github.com/galaxyproject/galaxy/pull/8914
+.. _Pull Request 8915: https://github.com/galaxyproject/galaxy/pull/8915
+.. _Pull Request 8921: https://github.com/galaxyproject/galaxy/pull/8921
+.. _Pull Request 8922: https://github.com/galaxyproject/galaxy/pull/8922
+.. _Pull Request 8924: https://github.com/galaxyproject/galaxy/pull/8924
+.. _Pull Request 8926: https://github.com/galaxyproject/galaxy/pull/8926
+.. _Pull Request 8929: https://github.com/galaxyproject/galaxy/pull/8929
+.. _Pull Request 8930: https://github.com/galaxyproject/galaxy/pull/8930
+.. _Pull Request 8931: https://github.com/galaxyproject/galaxy/pull/8931
+.. _Pull Request 8935: https://github.com/galaxyproject/galaxy/pull/8935
+.. _Pull Request 8936: https://github.com/galaxyproject/galaxy/pull/8936
+.. _Pull Request 8940: https://github.com/galaxyproject/galaxy/pull/8940
+.. _Pull Request 8941: https://github.com/galaxyproject/galaxy/pull/8941
+.. _Pull Request 8943: https://github.com/galaxyproject/galaxy/pull/8943
+.. _Pull Request 8947: https://github.com/galaxyproject/galaxy/pull/8947
+.. _Pull Request 8948: https://github.com/galaxyproject/galaxy/pull/8948
+.. _Pull Request 8949: https://github.com/galaxyproject/galaxy/pull/8949
+.. _Pull Request 8953: https://github.com/galaxyproject/galaxy/pull/8953
+.. _Pull Request 8955: https://github.com/galaxyproject/galaxy/pull/8955
+.. _Pull Request 8956: https://github.com/galaxyproject/galaxy/pull/8956
+.. _Pull Request 8957: https://github.com/galaxyproject/galaxy/pull/8957
+.. _Pull Request 8958: https://github.com/galaxyproject/galaxy/pull/8958
+.. _Pull Request 8960: https://github.com/galaxyproject/galaxy/pull/8960
+.. _Pull Request 8962: https://github.com/galaxyproject/galaxy/pull/8962
+.. _Pull Request 8964: https://github.com/galaxyproject/galaxy/pull/8964
+.. _Pull Request 8967: https://github.com/galaxyproject/galaxy/pull/8967
+.. _Pull Request 8972: https://github.com/galaxyproject/galaxy/pull/8972
+.. _Pull Request 8978: https://github.com/galaxyproject/galaxy/pull/8978
+.. _Pull Request 8979: https://github.com/galaxyproject/galaxy/pull/8979
+.. _Pull Request 8984: https://github.com/galaxyproject/galaxy/pull/8984
+.. _Pull Request 8988: https://github.com/galaxyproject/galaxy/pull/8988
+.. _Pull Request 8989: https://github.com/galaxyproject/galaxy/pull/8989
+.. _Pull Request 8990: https://github.com/galaxyproject/galaxy/pull/8990
+.. _Pull Request 8991: https://github.com/galaxyproject/galaxy/pull/8991
+.. _Pull Request 8994: https://github.com/galaxyproject/galaxy/pull/8994
+.. _Pull Request 8995: https://github.com/galaxyproject/galaxy/pull/8995
+.. _Pull Request 8997: https://github.com/galaxyproject/galaxy/pull/8997
+.. _Pull Request 9000: https://github.com/galaxyproject/galaxy/pull/9000
+.. _Pull Request 9003: https://github.com/galaxyproject/galaxy/pull/9003
+.. _Pull Request 9006: https://github.com/galaxyproject/galaxy/pull/9006
+.. _Pull Request 9009: https://github.com/galaxyproject/galaxy/pull/9009
+.. _Pull Request 9010: https://github.com/galaxyproject/galaxy/pull/9010
+.. _Pull Request 9013: https://github.com/galaxyproject/galaxy/pull/9013
+.. _Pull Request 9015: https://github.com/galaxyproject/galaxy/pull/9015
+.. _Pull Request 9016: https://github.com/galaxyproject/galaxy/pull/9016
+.. _Pull Request 9018: https://github.com/galaxyproject/galaxy/pull/9018
+.. _Pull Request 9019: https://github.com/galaxyproject/galaxy/pull/9019
+.. _Pull Request 9023: https://github.com/galaxyproject/galaxy/pull/9023
+.. _Pull Request 9026: https://github.com/galaxyproject/galaxy/pull/9026
+.. _Pull Request 9029: https://github.com/galaxyproject/galaxy/pull/9029
+.. _Pull Request 9032: https://github.com/galaxyproject/galaxy/pull/9032
+.. _Pull Request 9033: https://github.com/galaxyproject/galaxy/pull/9033
+.. _Pull Request 9034: https://github.com/galaxyproject/galaxy/pull/9034
+.. _Pull Request 9041: https://github.com/galaxyproject/galaxy/pull/9041
+.. _Pull Request 9044: https://github.com/galaxyproject/galaxy/pull/9044
+.. _Pull Request 9047: https://github.com/galaxyproject/galaxy/pull/9047
+.. _Pull Request 9048: https://github.com/galaxyproject/galaxy/pull/9048
+.. _Pull Request 9051: https://github.com/galaxyproject/galaxy/pull/9051
+.. _Pull Request 9052: https://github.com/galaxyproject/galaxy/pull/9052
+.. _Pull Request 9054: https://github.com/galaxyproject/galaxy/pull/9054
+.. _Pull Request 9055: https://github.com/galaxyproject/galaxy/pull/9055
+.. _Pull Request 9056: https://github.com/galaxyproject/galaxy/pull/9056
+.. _Pull Request 9059: https://github.com/galaxyproject/galaxy/pull/9059
+.. _Pull Request 9062: https://github.com/galaxyproject/galaxy/pull/9062
+.. _Pull Request 9063: https://github.com/galaxyproject/galaxy/pull/9063
+.. _Pull Request 9064: https://github.com/galaxyproject/galaxy/pull/9064
+.. _Pull Request 9065: https://github.com/galaxyproject/galaxy/pull/9065
+.. _Pull Request 9067: https://github.com/galaxyproject/galaxy/pull/9067
+.. _Pull Request 9068: https://github.com/galaxyproject/galaxy/pull/9068
+.. _Pull Request 9075: https://github.com/galaxyproject/galaxy/pull/9075
+.. _Pull Request 9078: https://github.com/galaxyproject/galaxy/pull/9078
+.. _Pull Request 9081: https://github.com/galaxyproject/galaxy/pull/9081
+.. _Pull Request 9082: https://github.com/galaxyproject/galaxy/pull/9082
+.. _Pull Request 9084: https://github.com/galaxyproject/galaxy/pull/9084
+.. _Pull Request 9086: https://github.com/galaxyproject/galaxy/pull/9086
+.. _Pull Request 9087: https://github.com/galaxyproject/galaxy/pull/9087
+.. _Pull Request 9089: https://github.com/galaxyproject/galaxy/pull/9089
+.. _Pull Request 9090: https://github.com/galaxyproject/galaxy/pull/9090
+.. _Pull Request 9092: https://github.com/galaxyproject/galaxy/pull/9092
+.. _Pull Request 9094: https://github.com/galaxyproject/galaxy/pull/9094
+.. _Pull Request 9097: https://github.com/galaxyproject/galaxy/pull/9097
+.. _Pull Request 9098: https://github.com/galaxyproject/galaxy/pull/9098
+.. _Pull Request 9099: https://github.com/galaxyproject/galaxy/pull/9099
+.. _Pull Request 9102: https://github.com/galaxyproject/galaxy/pull/9102
+.. _Pull Request 9104: https://github.com/galaxyproject/galaxy/pull/9104
+.. _Pull Request 9105: https://github.com/galaxyproject/galaxy/pull/9105
+.. _Pull Request 9115: https://github.com/galaxyproject/galaxy/pull/9115
+.. _Pull Request 9116: https://github.com/galaxyproject/galaxy/pull/9116
+.. _Pull Request 9117: https://github.com/galaxyproject/galaxy/pull/9117
+.. _Pull Request 9120: https://github.com/galaxyproject/galaxy/pull/9120
+.. _Pull Request 9121: https://github.com/galaxyproject/galaxy/pull/9121
+.. _Pull Request 9122: https://github.com/galaxyproject/galaxy/pull/9122
+.. _Pull Request 9124: https://github.com/galaxyproject/galaxy/pull/9124
+.. _Pull Request 9125: https://github.com/galaxyproject/galaxy/pull/9125
+.. _Pull Request 9126: https://github.com/galaxyproject/galaxy/pull/9126
+.. _Pull Request 9128: https://github.com/galaxyproject/galaxy/pull/9128
+.. _Pull Request 9132: https://github.com/galaxyproject/galaxy/pull/9132
+.. _Pull Request 9133: https://github.com/galaxyproject/galaxy/pull/9133
+.. _Pull Request 9134: https://github.com/galaxyproject/galaxy/pull/9134
+.. _Pull Request 9136: https://github.com/galaxyproject/galaxy/pull/9136
+.. _Pull Request 9137: https://github.com/galaxyproject/galaxy/pull/9137
+.. _Pull Request 9141: https://github.com/galaxyproject/galaxy/pull/9141
+.. _Pull Request 9144: https://github.com/galaxyproject/galaxy/pull/9144
+.. _Pull Request 9145: https://github.com/galaxyproject/galaxy/pull/9145
+.. _Pull Request 9146: https://github.com/galaxyproject/galaxy/pull/9146
+.. _Pull Request 9149: https://github.com/galaxyproject/galaxy/pull/9149
+.. _Pull Request 9150: https://github.com/galaxyproject/galaxy/pull/9150
+.. _Pull Request 9153: https://github.com/galaxyproject/galaxy/pull/9153
+.. _Pull Request 9155: https://github.com/galaxyproject/galaxy/pull/9155
+.. _Pull Request 9156: https://github.com/galaxyproject/galaxy/pull/9156
+.. _Pull Request 9163: https://github.com/galaxyproject/galaxy/pull/9163
+.. _Pull Request 9168: https://github.com/galaxyproject/galaxy/pull/9168
+.. _Pull Request 9171: https://github.com/galaxyproject/galaxy/pull/9171
+.. _Pull Request 9179: https://github.com/galaxyproject/galaxy/pull/9179
+.. _Pull Request 9182: https://github.com/galaxyproject/galaxy/pull/9182
+.. _Pull Request 9192: https://github.com/galaxyproject/galaxy/pull/9192
+.. _Pull Request 9193: https://github.com/galaxyproject/galaxy/pull/9193
+.. _Pull Request 9194: https://github.com/galaxyproject/galaxy/pull/9194
+.. _Pull Request 9195: https://github.com/galaxyproject/galaxy/pull/9195
+.. _Pull Request 9199: https://github.com/galaxyproject/galaxy/pull/9199
+.. _Pull Request 9202: https://github.com/galaxyproject/galaxy/pull/9202
+.. _Pull Request 9210: https://github.com/galaxyproject/galaxy/pull/9210
+.. _Pull Request 9212: https://github.com/galaxyproject/galaxy/pull/9212
+.. _Pull Request 9215: https://github.com/galaxyproject/galaxy/pull/9215
+.. _Pull Request 9216: https://github.com/galaxyproject/galaxy/pull/9216
+.. _Pull Request 9217: https://github.com/galaxyproject/galaxy/pull/9217
+.. _Pull Request 9219: https://github.com/galaxyproject/galaxy/pull/9219
+.. _Pull Request 9224: https://github.com/galaxyproject/galaxy/pull/9224
+.. _Pull Request 9225: https://github.com/galaxyproject/galaxy/pull/9225
+.. _Pull Request 9228: https://github.com/galaxyproject/galaxy/pull/9228
+.. _Pull Request 9232: https://github.com/galaxyproject/galaxy/pull/9232
+.. _Pull Request 9234: https://github.com/galaxyproject/galaxy/pull/9234
+.. _Pull Request 9237: https://github.com/galaxyproject/galaxy/pull/9237
+.. _Pull Request 9239: https://github.com/galaxyproject/galaxy/pull/9239
+.. _Pull Request 9240: https://github.com/galaxyproject/galaxy/pull/9240
+.. _Pull Request 9242: https://github.com/galaxyproject/galaxy/pull/9242
+.. _Pull Request 9243: https://github.com/galaxyproject/galaxy/pull/9243
+.. _Pull Request 9245: https://github.com/galaxyproject/galaxy/pull/9245
+.. _Pull Request 9246: https://github.com/galaxyproject/galaxy/pull/9246
+.. _Pull Request 9253: https://github.com/galaxyproject/galaxy/pull/9253
+.. _Pull Request 9260: https://github.com/galaxyproject/galaxy/pull/9260
+.. _Pull Request 9263: https://github.com/galaxyproject/galaxy/pull/9263
+.. _Pull Request 9266: https://github.com/galaxyproject/galaxy/pull/9266
+.. _Pull Request 9267: https://github.com/galaxyproject/galaxy/pull/9267
+.. _Pull Request 9269: https://github.com/galaxyproject/galaxy/pull/9269

From 8619c2d01f842c048ecee69fa295f0ec938e7f6f Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Wed, 29 Jan 2020 10:24:14 +0100
Subject: [PATCH 03/26] Update doc/source/releases/20.01_announce.rst

Co-Authored-By: Helena Rasche <hxr@hx42.org>
---
 doc/source/releases/20.01_announce.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/releases/20.01_announce.rst b/doc/source/releases/20.01_announce.rst
index 406a076c09a..fe32dee8759 100644
--- a/doc/source/releases/20.01_announce.rst
+++ b/doc/source/releases/20.01_announce.rst
@@ -30,7 +30,7 @@ Highlights
   scenarios.  This reduces IO load on Galaxy instances and should allow running
   many more jobs in parallel. This work will also make jobs running on remote
   compute resources much more efficient if the remote resources can write to
-  Galaxy'so object store. To benefit from this new metadata setting Galaxy needs
+  Galaxy's object store. To benefit from this new metadata setting Galaxy needs
   to use object stores that use uuids for storing datasets and set the
   ``metadata_strategy`` configuration value to ``extended``. This feature is in beta
   testing, but work is ongoing to mix existing object store configuration and

From d217b6d117dd268093a3ddd73ad956bc25b6cc95 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 29 Jan 2020 10:33:45 +0100
Subject: [PATCH 04/26] Edit to 20.01_announce.rst

---
 doc/source/releases/20.01_announce.rst | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/doc/source/releases/20.01_announce.rst b/doc/source/releases/20.01_announce.rst
index fe32dee8759..b54341b3115 100644
--- a/doc/source/releases/20.01_announce.rst
+++ b/doc/source/releases/20.01_announce.rst
@@ -8,13 +8,13 @@ January 2020 Galaxy Release (v 20.01)
 Highlights
 ===========================================================
 
-**Enhanced workflow functionality** 
-  Workflows can now now make use of optional datasets and optional parameters,
+**Enhanced workflow functionality**
+  Workflows can now make use of optional datasets and optional parameters,
   optional parameter default values and dataset inputs can now be restricted to
   user-defined datatypes. The workflow editor and execution engine have been
   enhanced to allow defining options to choose from, and these options can be
   connected to compatible text, integer, float, color and select tool parameters
-  for more flexible and universally re-usable workflows (`Pull Request 9086`_, `Pull Request 9073`_, `Pull Request 8264`_). 
+  for more flexible and universally re-usable workflows (`Pull Request 9086`_).
 
 **Major update to container and dependency management interface**
   The manage dependencies interface has been ported to vue.js and displays
@@ -26,16 +26,15 @@ Highlights
 **Extended job metadata collection**
   Creating Job metadata has been reworked so that the dataset transfer that
   occurs after a Galaxy job can be initiated by the compute node that runs a
-  Galaxy job. Previously the transfer was done by Galaxy under many production
-  scenarios.  This reduces IO load on Galaxy instances and should allow running
-  many more jobs in parallel. This work will also make jobs running on remote
-  compute resources much more efficient if the remote resources can write to
-  Galaxy's object store. To benefit from this new metadata setting Galaxy needs
-  to use object stores that use uuids for storing datasets and set the
-  ``metadata_strategy`` configuration value to ``extended``. This feature is in beta
-  testing, but work is ongoing to mix existing object store configuration and
-  choose the most efficient way of transfering datasets automatically (`Pull
-  Request 8930`_ ).
+  Galaxy job. Previously the transfer was often done by Galaxy. Offloading this
+  task to the compute node should allow handling many more jobs in parallel. This
+  work will also make jobs running on remote compute resources much more
+  efficient if the remote resources can write to Galaxy's object store. To
+  benefit from this new metadata setting Galaxy needs to use object stores that
+  use uuids for storing datasets and set the ``metadata_strategy`` configuration
+  value to ``extended``. This feature is in beta testing, but work is ongoing to
+  mix existing object store configuration and choose the most efficient way of
+  transfering datasets automatically (`Pull Request 8930`_ ).
 
 
 Also check out the `20.01 user release notes <https://docs.galaxyproject.org/en/release_20.01/releases/20.01_announce_user.html>`__

From 722c2f251a88978828eba25a5658ae526db68110 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 4 Feb 2020 11:47:25 +0100
Subject: [PATCH 05/26] First pass at user announements

---
 doc/source/releases/20.01_announce_user.rst | 31 +++++++++++++++++----
 1 file changed, 25 insertions(+), 6 deletions(-)

diff --git a/doc/source/releases/20.01_announce_user.rst b/doc/source/releases/20.01_announce_user.rst
index c4d19b4cedd..367b2c552d9 100644
--- a/doc/source/releases/20.01_announce_user.rst
+++ b/doc/source/releases/20.01_announce_user.rst
@@ -8,20 +8,37 @@ January 2020 Galaxy Release (v 20.01)
 Highlights
 ===========================================================
 
-**Feature1**
-  Feature description.
+**Workflow Executions Menu**
+  This menu can be reached from the User menu -> Workflow Invocations
+  and lists your recent Workflow executions, their status and links
+  to the Workflow Editor and the History with the results of the
+  Workflow run.
 
-**Feature2**
-  Feature description.
+.. figure:: https://user-images.githubusercontent.com/216771/65520097-0a041f80-deb5-11e9-80ac-2557b36c252f.png
+   :alt: Workflow invocation menu
 
-**Feature3**
-  Feature description.
+.. figure:: https://user-images.githubusercontent.com/6804901/73737075-345ac900-4742-11ea-9f50-0f0e4c3d9271.png
+   :alt: Workflow invocatios
+
+**Galay Markdown Pages and Workflow Reports as PDF**
+  An additional link has been added to Galaxy Markdown Pahes and Workflow reports
+  that exports your document as a standalone PDF.
+
+**Screenreader-friendly Navigation**
+  The top menu and the Workflow Editor have been improved for easier navigation
+  using Screenreaders and the Keyboard.
+  Thanks goes to `@WilliamHolden  <https://github.com/WilliamHolden>`__
+
+**Email-notification for completed jobs**
+  You can now select to be notified by email when a tool run has finished.
+  Thanks goes to `@astrovsky01 <https://github.com/astrovsky01>`__
 
 
 New Visualizations
 ===========================================================
 
 .. visualizations
+
 * Add data dialog input element to client form parameter list
   `Pull Request 8774`_
 * Wrap SQL statement in a text() function as required by sqlalchemy
@@ -35,6 +52,7 @@ New Datatypes
 ===========================================================
 
 .. datatypes
+
 * Datatypes for MassSpec DIA dlib,elib
   (thanks to `@jj-umn <https://github.com/jj-umn>`__).
   `Pull Request 8657`_
@@ -63,6 +81,7 @@ Builtin Tool Updates
 ===========================================================
 
 .. tools
+
 * Upgrade askomics interactive tool
   (thanks to `@xgaia <https://github.com/xgaia>`__).
   `Pull Request 8517`_

From b76e29a267d9dec714316053b8fef54562c70dc1 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 4 Feb 2020 20:29:00 +0100
Subject: [PATCH 06/26] Add workflow report and email button screenshots

---
 doc/source/releases/20.01_announce_user.rst | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/doc/source/releases/20.01_announce_user.rst b/doc/source/releases/20.01_announce_user.rst
index 367b2c552d9..7bbad894bdc 100644
--- a/doc/source/releases/20.01_announce_user.rst
+++ b/doc/source/releases/20.01_announce_user.rst
@@ -24,6 +24,9 @@ Highlights
   An additional link has been added to Galaxy Markdown Pahes and Workflow reports
   that exports your document as a standalone PDF.
 
+.. figure:: https://user-images.githubusercontent.com/6804901/73776256-b7524280-4787-11ea-821f-d9a8c6339ee9.png
+   :alt: Example PDF export
+
 **Screenreader-friendly Navigation**
   The top menu and the Workflow Editor have been improved for easier navigation
   using Screenreaders and the Keyboard.
@@ -33,6 +36,8 @@ Highlights
   You can now select to be notified by email when a tool run has finished.
   Thanks goes to `@astrovsky01 <https://github.com/astrovsky01>`__
 
+.. figure:: https://user-images.githubusercontent.com/6804901/73779180-a2c47900-478c-11ea-98ab-7355276b6f6d.png
+   :alt: Example of email button
 
 New Visualizations
 ===========================================================

From 090bef14fb595fffdb69ca55621fcac487e543b6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 4 Feb 2020 21:32:35 +0100
Subject: [PATCH 07/26] Tweak image size and add 20.01_annouce to index

---
 doc/source/releases/20.01_announce_user.rst | 2 ++
 doc/source/releases/index.rst               | 1 +
 2 files changed, 3 insertions(+)

diff --git a/doc/source/releases/20.01_announce_user.rst b/doc/source/releases/20.01_announce_user.rst
index 7bbad894bdc..c33c887f338 100644
--- a/doc/source/releases/20.01_announce_user.rst
+++ b/doc/source/releases/20.01_announce_user.rst
@@ -16,6 +16,7 @@ Highlights
 
 .. figure:: https://user-images.githubusercontent.com/216771/65520097-0a041f80-deb5-11e9-80ac-2557b36c252f.png
    :alt: Workflow invocation menu
+   :width: 400px
 
 .. figure:: https://user-images.githubusercontent.com/6804901/73737075-345ac900-4742-11ea-9f50-0f0e4c3d9271.png
    :alt: Workflow invocatios
@@ -38,6 +39,7 @@ Highlights
 
 .. figure:: https://user-images.githubusercontent.com/6804901/73779180-a2c47900-478c-11ea-98ab-7355276b6f6d.png
    :alt: Example of email button
+   :width: 300px
 
 New Visualizations
 ===========================================================
diff --git a/doc/source/releases/index.rst b/doc/source/releases/index.rst
index 98c88cbf52a..044163d7f08 100644
--- a/doc/source/releases/index.rst
+++ b/doc/source/releases/index.rst
@@ -4,6 +4,7 @@ Releases
 .. toctree::
    :maxdepth: 1
 
+   20.01_announce
    19.09_announce
    19.05_announce
    19.01_announce

From 3d22c726fc3c4a78ce3598da7af80b33c5b4b50d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 4 Feb 2020 21:34:11 +0100
Subject: [PATCH 08/26] Fix RST formatting

---
 doc/source/releases/20.01.rst | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/doc/source/releases/20.01.rst b/doc/source/releases/20.01.rst
index db6791476c2..651138e8ac4 100644
--- a/doc/source/releases/20.01.rst
+++ b/doc/source/releases/20.01.rst
@@ -13,6 +13,7 @@ Enhancements
 
 
 .. feature
+
 * CLI tools for installing/testing Docker and Singularity containers
   (thanks to `@simonbray <https://github.com/simonbray>`__).
   `Pull Request 7936`_
@@ -37,6 +38,7 @@ Enhancements
 .. enhancement_tag_viz
 
 .. enhancement_tag_datatypes
+
 * Datatypes for MassSpec DIA dlib,elib
   (thanks to `@jj-umn <https://github.com/jj-umn>`__).
   `Pull Request 8657`_
@@ -60,6 +62,7 @@ Enhancements
   `Pull Request 9087`_
 
 .. enhancement_tag_tools
+
 * Upgrade askomics interactive tool
   (thanks to `@xgaia <https://github.com/xgaia>`__).
   `Pull Request 8517`_
@@ -76,6 +79,7 @@ Enhancements
   `Pull Request 9003`_
 
 .. enhancement_tag_workflows
+
 * Interactive modification of invocation report.
   `Pull Request 8691`_
 * User-facing Workflow Invocation Grid
@@ -96,6 +100,7 @@ Enhancements
   `Pull Request 9105`_
 
 .. enhancement_tag_ui
+
 * Upgrade eslint (major version), fix compliance with new standard rules.
   `Pull Request 8708`_
 * JobMetrics.vue unit test.
@@ -109,6 +114,7 @@ Enhancements
   `Pull Request 8827`_
 
 .. enhancement_tag_jobs
+
 * Small cleanup for job runners kill
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 8523`_
@@ -130,6 +136,7 @@ Enhancements
   `Pull Request 9245`_
 
 .. enhancement_tag_admin
+
 * Add Tool Manager Component for Admin Panel
   `Pull Request 8601`_
 * Add process ID to worker_process table
@@ -137,6 +144,7 @@ Enhancements
   `Pull Request 8972`_
 
 .. enhancement
+
 * Use official "login with" buttons for OIDC
   (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 8107`_
@@ -285,6 +293,7 @@ Enhancements
   `Pull Request 9224`_
 
 .. small_enhancement
+
 * Factor out yaml read/write from config_manage.py
   `Pull Request 8509`_
 * Implementation of the workflow list as vue component
@@ -387,6 +396,7 @@ Fixes
 
 
 .. bug_tag_viz
+
 * Wrap SQL statement in a text() function as required by sqlalchemy
   (thanks to `@kaukrise <https://github.com/kaukrise>`__).
   `Pull Request 9216`_
@@ -394,30 +404,38 @@ Fixes
   (thanks to `@kaukrise <https://github.com/kaukrise>`__).
   `Pull Request 9217`_
 
+
 .. bug_tag_datatypes
+
 * Fix cool sniffing on python3
   `Pull Request 9153`_
 
+
 .. bug_tag_tools
+
 * grouping: strip newlines
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 8953`_
 * Add requirements to interval_to_bed_converter.xml
   `Pull Request 9041`_
 
+
 .. bug_tag_workflows
+
 * Exports reports with workflows (if configured).
   `Pull Request 9055`_
 * Rev gxformat2 dependency to fix various export issues.
   `Pull Request 9075`_
 
 .. bug_tag_ui
+
 * Run prettier after `#8107
   <https://github.com/galaxyproject/galaxy/issues/8107>`__
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 9102`_
 
 .. bug_tag_jobs
+
 * Small fixes for k8s.
   `Pull Request 8759`_
 * Fix output.file_path writing to read-only path on Docker
@@ -446,6 +464,7 @@ Fixes
   `Pull Request 9253`_
 
 .. bug_tag_admin
+
 * Encode lines in filter_file_fields
   (thanks to `@selten <https://github.com/selten>`__).
   `Pull Request 8652`_
@@ -459,6 +478,7 @@ Fixes
   `Pull Request 9193`_
 
 .. bug
+
 * Documentation update
   (thanks to `@selten <https://github.com/selten>`__).
   `Pull Request 8508`_

From 6b304586c46e7382903e04d7b3e1bbacc83392af Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 4 Feb 2020 22:04:31 +0100
Subject: [PATCH 09/26] Fix missing newline after section

---
 scripts/bootstrap_history.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py
index 4440138f7b8..dde83dd5c60 100644
--- a/scripts/bootstrap_history.py
+++ b/scripts/bootstrap_history.py
@@ -713,6 +713,8 @@ def _text_target(github, pull_request, labels=None):
     else:
         print("Logic problem, cannot determine section for %s" % _pr_to_str(pull_request))
         text_target = None
+    if text_target:
+        text_target += "\n"
     return text_target
 
 
@@ -775,7 +777,7 @@ def wrap(message):
     message = process_sentence(message)
     wrapper = textwrap.TextWrapper(initial_indent="* ")
     wrapper.subsequent_indent = '  '
-    wrapper.width = 78
+    wrapper.width = 160
     message_lines = message.splitlines()
     first_lines = "\n".join(wrapper.wrap(message_lines[0]))
     wrapper.initial_indent = "  "

From fe68dede4dc5c0dfa83722236d6df995713df432 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Tue, 11 Feb 2020 19:39:46 +0100
Subject: [PATCH 10/26] Pahes typo

---
 doc/source/releases/20.01_announce_user.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/releases/20.01_announce_user.rst b/doc/source/releases/20.01_announce_user.rst
index c33c887f338..5d5dbda7235 100644
--- a/doc/source/releases/20.01_announce_user.rst
+++ b/doc/source/releases/20.01_announce_user.rst
@@ -22,7 +22,7 @@ Highlights
    :alt: Workflow invocatios
 
 **Galay Markdown Pages and Workflow Reports as PDF**
-  An additional link has been added to Galaxy Markdown Pahes and Workflow reports
+  An additional link has been added to Galaxy Markdown Pages and Workflow reports
   that exports your document as a standalone PDF.
 
 .. figure:: https://user-images.githubusercontent.com/6804901/73776256-b7524280-4787-11ea-821f-d9a8c6339ee9.png

From 07a69221059064b964e48c040ac265b0bcd1223d Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Fri, 21 Feb 2020 17:57:08 +0100
Subject: [PATCH 11/26] Update with new 20.01 PRs

---
 doc/source/releases/20.01.rst               | 139 ++++++++++++++++----
 doc/source/releases/20.01_announce_user.rst |  23 +++-
 doc/source/releases/20.01_prs.rst           |  51 +++++++
 3 files changed, 183 insertions(+), 30 deletions(-)

diff --git a/doc/source/releases/20.01.rst b/doc/source/releases/20.01.rst
index 651138e8ac4..3aed23a4270 100644
--- a/doc/source/releases/20.01.rst
+++ b/doc/source/releases/20.01.rst
@@ -34,9 +34,15 @@ Enhancements
   `Pull Request 9062`_
 * IT fixes and 3 new ITs
   `Pull Request 9141`_
+* Remove GenomeSpace tools, OpenID, UI and requirements
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9363`_
 
 .. enhancement_tag_viz
 
+* Hyphy-vision fixes and updates.
+  `Pull Request 9384`_
+
 .. enhancement_tag_datatypes
 
 * Datatypes for MassSpec DIA dlib,elib
@@ -51,7 +57,7 @@ Enhancements
 * Add new GROMACS datatypes: ndx, xvg, edr
   (thanks to `@simonbray <https://github.com/simonbray>`__).
   `Pull Request 8964`_
-* add gff3.gz and gff3.bz2 datatypes
+* Add gff3.gz and gff3.bz2 datatypes
   (thanks to `@FredericBGA <https://github.com/FredericBGA>`__).
   `Pull Request 8967`_
 * Make mol2 visible
@@ -60,14 +66,15 @@ Enhancements
 * Add a datatype subclass for CAT (Contig Annotation Tool)
   (thanks to `@jj-umn <https://github.com/jj-umn>`__).
   `Pull Request 9087`_
+* Add tabular.gz datatype and add embl to uploadable formats
+  `Pull Request 9293`_
 
 .. enhancement_tag_tools
 
 * Upgrade askomics interactive tool
   (thanks to `@xgaia <https://github.com/xgaia>`__).
   `Pull Request 8517`_
-* Remove collection ID character restriction from 'Relabel collection from
-  file' tool
+* Remove collection ID character restriction from 'Relabel collection from file' tool
   (thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
   `Pull Request 8571`_
 * Allow space, dot and comma in relabel identifier tool
@@ -77,6 +84,8 @@ Enhancements
   `Pull Request 8888`_
 * Allow admins to import tools/workflows from paths.
   `Pull Request 9003`_
+* Move sam_pileup to GALAXY_LIB_TOOLS_VERSIONED
+  `Pull Request 9320`_
 
 .. enhancement_tag_workflows
 
@@ -105,8 +114,7 @@ Enhancements
   `Pull Request 8708`_
 * JobMetrics.vue unit test.
   `Pull Request 8732`_
-* Fix the flexible Data Dialog to work independent of the page layout
-  initialization hooks.
+* Fix the flexible Data Dialog to work independent of the page layout initialization hooks.
   `Pull Request 8744`_
 * axios-mock-adapter for cleaner, more expansive testing
   `Pull Request 8749`_
@@ -134,6 +142,10 @@ Enhancements
   `Pull Request 8997`_
 * Fix deletion of outputs and working before job
   `Pull Request 9245`_
+* Mount tool_data_path (ro) when running containerized tools
+  `Pull Request 9314`_
+* Allow remote jobs to configure Interactive Tool entry points.
+  `Pull Request 9349`_
 
 .. enhancement_tag_admin
 
@@ -147,7 +159,7 @@ Enhancements
 
 * Use official "login with" buttons for OIDC
   (thanks to `@hexylena <https://github.com/hexylena>`__).
-  `Pull Request 8107`_
+  `Pull Request 8107`_, `Pull Request 9102`_
 * Add data types to docs.galaxyproject.org
   (thanks to `@selten <https://github.com/selten>`__).
   `Pull Request 8531`_
@@ -178,8 +190,7 @@ Enhancements
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 8690`_
 * LDAP search member of filter
-  (thanks to `@BioinformaticsPlatformWIV-ISP
-  <https://github.com/BioinformaticsPlatformWIV-ISP>`__).
+  (thanks to `@BioinformaticsPlatformWIV-ISP <https://github.com/BioinformaticsPlatformWIV-ISP>`__).
   `Pull Request 8697`_
 * Rebuild and prettify config sample and doc
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -280,6 +291,8 @@ Enhancements
   `Pull Request 9128`_
 * mulled: use threading.Event in PrintProgress to avoid unnecessary wai…
   `Pull Request 9163`_
+* Set Conda environment variables  when running biocontainers
+  `Pull Request 9170`_
 * Update my username
   (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 9195`_
@@ -291,6 +304,10 @@ Enhancements
   `Pull Request 9210`_
 * Extended base annotation fixes
   `Pull Request 9224`_
+* External auth login refinement
+  `Pull Request 9233`_
+* Fixes for IGV GEDA handling of genomes
+  `Pull Request 9413`_
 
 .. small_enhancement
 
@@ -386,7 +403,10 @@ Enhancements
 * Update github username @erasche to @hexylena and correct inconsistencies
   (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 9194`_
-
+* Add requirements, fix legacy tools and move them out of GALAXY_LIB_TOOLS_UNVERSIONED
+  `Pull Request 9336`_
+* Add requirements to (almost) all converters, profile and minor fixes
+  `Pull Request 9345`_
 
 
 Fixes
@@ -403,14 +423,14 @@ Fixes
 * Ensure visible overflow on navbar container
   (thanks to `@kaukrise <https://github.com/kaukrise>`__).
   `Pull Request 9217`_
-
+* Various python 3 fixes from sentry
+  `Pull Request 9337`_
 
 .. bug_tag_datatypes
 
 * Fix cool sniffing on python3
   `Pull Request 9153`_
 
-
 .. bug_tag_tools
 
 * grouping: strip newlines
@@ -418,7 +438,13 @@ Fixes
   `Pull Request 8953`_
 * Add requirements to interval_to_bed_converter.xml
   `Pull Request 9041`_
-
+* Fix version in which ``sam_pileup`` was fixed
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9350`_
+* Expunge tool shed repository objects, prevents ParentInstanceDetachedError
+  `Pull Request 9354`_
+* Fix maf tools
+  `Pull Request 9393`_
 
 .. bug_tag_workflows
 
@@ -426,13 +452,10 @@ Fixes
   `Pull Request 9055`_
 * Rev gxformat2 dependency to fix various export issues.
   `Pull Request 9075`_
-
-.. bug_tag_ui
-
-* Run prettier after `#8107
-  <https://github.com/galaxyproject/galaxy/issues/8107>`__
-  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
-  `Pull Request 9102`_
+* Fix workflow editor save as functionality
+  `Pull Request 9315`_
+* Various fixes and enhancements to reports
+  `Pull Request 9316`_
 
 .. bug_tag_jobs
 
@@ -462,6 +485,13 @@ Fixes
 * fix bug introduced in https://github.com/galaxyproject/galaxy/pull/9246
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 9253`_
+* Email notifications aren't used from just workflow steps anymore.
+  `Pull Request 9276`_
+* Use requests for slots instead of limit
+  (thanks to `@nuwang <https://github.com/nuwang>`__).
+  `Pull Request 9322`_
+* Make set metadata exec after process more robust
+  `Pull Request 9395`_
 
 .. bug_tag_admin
 
@@ -473,9 +503,10 @@ Fixes
   `Pull Request 8900`_
 * Assorted admin panel fixes
   `Pull Request 9097`_
-* Run integration tests on github, fix various bugs (interactive tools,
-  kubernetes, test framework)
+* Run integration tests on github, fix various bugs (interactive tools, kubernetes, test framework)
   `Pull Request 9193`_
+* Always add shed_tool_config file to tool_configs
+  `Pull Request 9364`_
 
 .. bug
 
@@ -510,8 +541,7 @@ Fixes
 * GRT: Ensure correct encoding, no partial lines
   (thanks to `@hexylena <https://github.com/hexylena>`__).
   `Pull Request 8712`_
-* Revise toolshed config dependency check error message in repository install
-  manager
+* Revise toolshed config dependency check error message in repository install manager
   `Pull Request 8720`_
 * Fix data dialog height, modal test case and table slots
   `Pull Request 8724`_
@@ -559,8 +589,7 @@ Fixes
 * make pgcleanup also delete HDAs
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
   `Pull Request 8908`_
-* Fix unbounded variable error in `GET /api/datasets/{encoded_dataset_id}`
-  exception handling
+* Fix unbounded variable error in `GET /api/datasets/{encoded_dataset_id}` exception handling
   `Pull Request 8935`_
 * Set `deleted` attribute of history datasets when purging histories from grid
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
@@ -642,8 +671,7 @@ Fixes
   `Pull Request 9168`_
 * Add static-safe mapping to config management
   `Pull Request 9179`_
-* Fix tool shed tests for `#9168
-  <https://github.com/galaxyproject/galaxy/issues/9168>`__.
+* Fix tool shed tests for `#9168 <https://github.com/galaxyproject/galaxy/issues/9168>`__.
   `Pull Request 9182`_
 * Add require_login bypass for entire authnz controller.
   `Pull Request 9192`_
@@ -669,7 +697,62 @@ Fixes
   `Pull Request 9267`_
 * backport 9268: Fix target_str_to_targets
   `Pull Request 9269`_
-
+* Backwards compatible build number parsing
+  `Pull Request 9278`_
+* Tag display fixes for ui-select.
+  `Pull Request 9281`_
+* Python3: don't check for has_key attribute
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9290`_
+* Prevent caching of bootstrapped client data
+  `Pull Request 9294`_
+* Add build_sites_config_file option to config_schema
+  `Pull Request 9297`_
+* Backport reports config/py3 fix
+  `Pull Request 9309`_
+* Python3: unicodify the output of ``subprocess.check_output()``
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9319`_
+* Fix reports disk usage query for python 3
+  `Pull Request 9321`_
+* Fix string module use
+  `Pull Request 9327`_
+* Fix Python 3 error in containers lib
+  `Pull Request 9329`_
+* Fix use of next() as a meethod instead of a function
+  `Pull Request 9330`_
+* Automatically resolve and add static-safe mappings for client-based images
+  `Pull Request 9331`_
+* Various doc fixes
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9334`_
+* Fix app reference in guess_shed_config
+  `Pull Request 9339`_
+* Make linters more robust on python 3
+  `Pull Request 9348`_
+* Use RenamedTemporaryFile for safer integrated_tool_panel_file writing
+  `Pull Request 9359`_
+* Only get non-deleted datasets when listing custom dbkeys
+  `Pull Request 9360`_
+* Prevent duplicate listing of doi link and link (text, with href doi link)
+  `Pull Request 9366`_
+* Styleguide fixes
+  `Pull Request 9367`_
+* Prevent tool execution getting stuck in history when a chromInfo data…
+  `Pull Request 9385`_
+* Move migrated_tools_conf > mutable_config_dir (`#9376 <https://github.com/galaxyproject/galaxy/issues/9376>`__)
+  `Pull Request 9388`_
+* Fix dependency for CONVERTER_tar_to_directory
+  `Pull Request 9389`_
+* Fix for qp method used in GEDAs.
+  `Pull Request 9391`_
+* Fix hid comparison failing with hdas without hid
+  `Pull Request 9398`_
+* Don't raise exception if anon goes to <galaxy_url>/user/resend_verification
+  `Pull Request 9404`_
+* Update bleach to 3.1.1
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9408`_
 
 .. include:: 20.01_prs.rst
 
diff --git a/doc/source/releases/20.01_announce_user.rst b/doc/source/releases/20.01_announce_user.rst
index 5d5dbda7235..62da797d5e9 100644
--- a/doc/source/releases/20.01_announce_user.rst
+++ b/doc/source/releases/20.01_announce_user.rst
@@ -83,6 +83,8 @@ New Datatypes
   `Pull Request 9087`_
 * Fix cool sniffing on python3
   `Pull Request 9153`_
+* Allow tabular.gz / add embl to uploadable formats
+  `Pull Request 9293`_
 
 Builtin Tool Updates
 ===========================================================
@@ -92,8 +94,7 @@ Builtin Tool Updates
 * Upgrade askomics interactive tool
   (thanks to `@xgaia <https://github.com/xgaia>`__).
   `Pull Request 8517`_
-* Remove collection ID character restriction from 'Relabel collection from
-  file' tool
+* Remove collection ID character restriction from 'Relabel collection from file' tool
   (thanks to `@brinkmanlab <https://github.com/brinkmanlab>`__).
   `Pull Request 8571`_
 * Allow space, dot and comma in relabel identifier tool
@@ -108,6 +109,24 @@ Builtin Tool Updates
   `Pull Request 9003`_
 * Add requirements to interval_to_bed_converter.xml
   `Pull Request 9041`_
+* Move sam_pileup to GALAXY_LIB_TOOLS_VERSIONED
+  `Pull Request 9320`_
+* Add requirements, fix legacy tools and move them out of GALAXY_LIB_TOOLS_UNVERSIONED
+  `Pull Request 9336`_
+* Add requirements to (almost) all converters, profile and minor fixes
+  `Pull Request 9345`_
+* Fix version in which ``sam_pileup`` was fixed
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9350`_
+* Expunge tool shed repository objects, prevents ParentInstanceDetachedError
+  `Pull Request 9354`_
+* Remove GenomeSpace tools, OpenID, UI and requirements
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9363`_
+* Fix maf tools
+  `Pull Request 9393`_
+* XML fix for joiner.xml.
+  `Pull Request 9399`_
 
 Release Notes
 ===========================================================
diff --git a/doc/source/releases/20.01_prs.rst b/doc/source/releases/20.01_prs.rst
index 8911eb66e40..93605645687 100644
--- a/doc/source/releases/20.01_prs.rst
+++ b/doc/source/releases/20.01_prs.rst
@@ -242,6 +242,7 @@
 .. _Pull Request 9156: https://github.com/galaxyproject/galaxy/pull/9156
 .. _Pull Request 9163: https://github.com/galaxyproject/galaxy/pull/9163
 .. _Pull Request 9168: https://github.com/galaxyproject/galaxy/pull/9168
+.. _Pull Request 9170: https://github.com/galaxyproject/galaxy/pull/9170
 .. _Pull Request 9171: https://github.com/galaxyproject/galaxy/pull/9171
 .. _Pull Request 9179: https://github.com/galaxyproject/galaxy/pull/9179
 .. _Pull Request 9182: https://github.com/galaxyproject/galaxy/pull/9182
@@ -261,6 +262,7 @@
 .. _Pull Request 9225: https://github.com/galaxyproject/galaxy/pull/9225
 .. _Pull Request 9228: https://github.com/galaxyproject/galaxy/pull/9228
 .. _Pull Request 9232: https://github.com/galaxyproject/galaxy/pull/9232
+.. _Pull Request 9233: https://github.com/galaxyproject/galaxy/pull/9233
 .. _Pull Request 9234: https://github.com/galaxyproject/galaxy/pull/9234
 .. _Pull Request 9237: https://github.com/galaxyproject/galaxy/pull/9237
 .. _Pull Request 9239: https://github.com/galaxyproject/galaxy/pull/9239
@@ -275,3 +277,52 @@
 .. _Pull Request 9266: https://github.com/galaxyproject/galaxy/pull/9266
 .. _Pull Request 9267: https://github.com/galaxyproject/galaxy/pull/9267
 .. _Pull Request 9269: https://github.com/galaxyproject/galaxy/pull/9269
+.. _Pull Request 9276: https://github.com/galaxyproject/galaxy/pull/9276
+.. _Pull Request 9278: https://github.com/galaxyproject/galaxy/pull/9278
+.. _Pull Request 9281: https://github.com/galaxyproject/galaxy/pull/9281
+.. _Pull Request 9290: https://github.com/galaxyproject/galaxy/pull/9290
+.. _Pull Request 9293: https://github.com/galaxyproject/galaxy/pull/9293
+.. _Pull Request 9294: https://github.com/galaxyproject/galaxy/pull/9294
+.. _Pull Request 9297: https://github.com/galaxyproject/galaxy/pull/9297
+.. _Pull Request 9309: https://github.com/galaxyproject/galaxy/pull/9309
+.. _Pull Request 9314: https://github.com/galaxyproject/galaxy/pull/9314
+.. _Pull Request 9315: https://github.com/galaxyproject/galaxy/pull/9315
+.. _Pull Request 9316: https://github.com/galaxyproject/galaxy/pull/9316
+.. _Pull Request 9319: https://github.com/galaxyproject/galaxy/pull/9319
+.. _Pull Request 9320: https://github.com/galaxyproject/galaxy/pull/9320
+.. _Pull Request 9321: https://github.com/galaxyproject/galaxy/pull/9321
+.. _Pull Request 9322: https://github.com/galaxyproject/galaxy/pull/9322
+.. _Pull Request 9327: https://github.com/galaxyproject/galaxy/pull/9327
+.. _Pull Request 9329: https://github.com/galaxyproject/galaxy/pull/9329
+.. _Pull Request 9330: https://github.com/galaxyproject/galaxy/pull/9330
+.. _Pull Request 9331: https://github.com/galaxyproject/galaxy/pull/9331
+.. _Pull Request 9334: https://github.com/galaxyproject/galaxy/pull/9334
+.. _Pull Request 9336: https://github.com/galaxyproject/galaxy/pull/9336
+.. _Pull Request 9337: https://github.com/galaxyproject/galaxy/pull/9337
+.. _Pull Request 9339: https://github.com/galaxyproject/galaxy/pull/9339
+.. _Pull Request 9345: https://github.com/galaxyproject/galaxy/pull/9345
+.. _Pull Request 9348: https://github.com/galaxyproject/galaxy/pull/9348
+.. _Pull Request 9349: https://github.com/galaxyproject/galaxy/pull/9349
+.. _Pull Request 9350: https://github.com/galaxyproject/galaxy/pull/9350
+.. _Pull Request 9354: https://github.com/galaxyproject/galaxy/pull/9354
+.. _Pull Request 9359: https://github.com/galaxyproject/galaxy/pull/9359
+.. _Pull Request 9360: https://github.com/galaxyproject/galaxy/pull/9360
+.. _Pull Request 9363: https://github.com/galaxyproject/galaxy/pull/9363
+.. _Pull Request 9364: https://github.com/galaxyproject/galaxy/pull/9364
+.. _Pull Request 9366: https://github.com/galaxyproject/galaxy/pull/9366
+.. _Pull Request 9367: https://github.com/galaxyproject/galaxy/pull/9367
+.. _Pull Request 9375: https://github.com/galaxyproject/galaxy/pull/9375
+.. _Pull Request 9384: https://github.com/galaxyproject/galaxy/pull/9384
+.. _Pull Request 9385: https://github.com/galaxyproject/galaxy/pull/9385
+.. _Pull Request 9388: https://github.com/galaxyproject/galaxy/pull/9388
+.. _Pull Request 9389: https://github.com/galaxyproject/galaxy/pull/9389
+.. _Pull Request 9391: https://github.com/galaxyproject/galaxy/pull/9391
+.. _Pull Request 9393: https://github.com/galaxyproject/galaxy/pull/9393
+.. _Pull Request 9395: https://github.com/galaxyproject/galaxy/pull/9395
+.. _Pull Request 9397: https://github.com/galaxyproject/galaxy/pull/9397
+.. _Pull Request 9398: https://github.com/galaxyproject/galaxy/pull/9398
+.. _Pull Request 9399: https://github.com/galaxyproject/galaxy/pull/9399
+.. _Pull Request 9400: https://github.com/galaxyproject/galaxy/pull/9400
+.. _Pull Request 9404: https://github.com/galaxyproject/galaxy/pull/9404
+.. _Pull Request 9408: https://github.com/galaxyproject/galaxy/pull/9408
+.. _Pull Request 9413: https://github.com/galaxyproject/galaxy/pull/9413

From 05d5fd1da84de9d357e38b797d44d3a57c75b836 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 10:21:46 +0100
Subject: [PATCH 12/26] Update with latest PRs

---
 doc/source/releases/20.01.rst     | 28 ++++++++++++++++++++++++++++
 doc/source/releases/20.01_prs.rst | 13 +++++++++++++
 2 files changed, 41 insertions(+)

diff --git a/doc/source/releases/20.01.rst b/doc/source/releases/20.01.rst
index 3aed23a4270..6f4f1538989 100644
--- a/doc/source/releases/20.01.rst
+++ b/doc/source/releases/20.01.rst
@@ -492,6 +492,10 @@ Fixes
   `Pull Request 9322`_
 * Make set metadata exec after process more robust
   `Pull Request 9395`_
+* Make dataset discovery respect final_job_state
+  `Pull Request 9406`_
+* Strip unicode null characters from traceback and job_messages
+  `Pull Request 9430`_
 
 .. bug_tag_admin
 
@@ -753,6 +757,30 @@ Fixes
 * Update bleach to 3.1.1
   (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
   `Pull Request 9408`_
+* Fix shed image resolution
+  `Pull Request 9411`_
+* Fixes for get_estimated_display_viewport
+  `Pull Request 9415`_
+* Fix wrong map use in many places
+  `Pull Request 9416`_
+* Conda startup fixes
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9421`_
+* fix two cases of opening a file binary
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 9424`_
+* Remove '.sample' from default value; rebuild schema
+  `Pull Request 9427`_
+* Fix login to accounts using different email capitalization
+  `Pull Request 9432`_
+* Fix TwoBitFile handle not opened in binary mode
+  `Pull Request 9433`_
+* Fix uploading workflow archives
+  `Pull Request 9434`_
+* Fix to_dict for upload1 tool
+  `Pull Request 9441`_
+* Fix data tables vue display
+  `Pull Request 9442`_
 
 .. include:: 20.01_prs.rst
 
diff --git a/doc/source/releases/20.01_prs.rst b/doc/source/releases/20.01_prs.rst
index 93605645687..b59e8a524b5 100644
--- a/doc/source/releases/20.01_prs.rst
+++ b/doc/source/releases/20.01_prs.rst
@@ -324,5 +324,18 @@
 .. _Pull Request 9399: https://github.com/galaxyproject/galaxy/pull/9399
 .. _Pull Request 9400: https://github.com/galaxyproject/galaxy/pull/9400
 .. _Pull Request 9404: https://github.com/galaxyproject/galaxy/pull/9404
+.. _Pull Request 9406: https://github.com/galaxyproject/galaxy/pull/9406
 .. _Pull Request 9408: https://github.com/galaxyproject/galaxy/pull/9408
+.. _Pull Request 9411: https://github.com/galaxyproject/galaxy/pull/9411
 .. _Pull Request 9413: https://github.com/galaxyproject/galaxy/pull/9413
+.. _Pull Request 9415: https://github.com/galaxyproject/galaxy/pull/9415
+.. _Pull Request 9416: https://github.com/galaxyproject/galaxy/pull/9416
+.. _Pull Request 9421: https://github.com/galaxyproject/galaxy/pull/9421
+.. _Pull Request 9424: https://github.com/galaxyproject/galaxy/pull/9424
+.. _Pull Request 9427: https://github.com/galaxyproject/galaxy/pull/9427
+.. _Pull Request 9430: https://github.com/galaxyproject/galaxy/pull/9430
+.. _Pull Request 9432: https://github.com/galaxyproject/galaxy/pull/9432
+.. _Pull Request 9433: https://github.com/galaxyproject/galaxy/pull/9433
+.. _Pull Request 9434: https://github.com/galaxyproject/galaxy/pull/9434
+.. _Pull Request 9441: https://github.com/galaxyproject/galaxy/pull/9441
+.. _Pull Request 9442: https://github.com/galaxyproject/galaxy/pull/9442

From 9748452b1b5321c533db81832fa8dde4dc569306 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 10:24:49 +0100
Subject: [PATCH 13/26] Merge followup PR into original announcement

---
 doc/source/releases/20.01.rst | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/doc/source/releases/20.01.rst b/doc/source/releases/20.01.rst
index 6f4f1538989..c20608d61f1 100644
--- a/doc/source/releases/20.01.rst
+++ b/doc/source/releases/20.01.rst
@@ -481,10 +481,7 @@ Fixes
   `Pull Request 9243`_
 * python3 fixes for setups using drmaa and realuser setups
   (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
-  `Pull Request 9246`_
-* fix bug introduced in https://github.com/galaxyproject/galaxy/pull/9246
-  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
-  `Pull Request 9253`_
+  `Pull Request 9246`_, `Pull Request 9253`_
 * Email notifications aren't used from just workflow steps anymore.
   `Pull Request 9276`_
 * Use requests for slots instead of limit

From 765f59175c3b3bdb1d83a1d1cdf824f3d522b96d Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Fri, 7 Feb 2020 20:01:42 +0000
Subject: [PATCH 14/26] Create Python3 virtualenv by default

- Allow specifying Python to use to create virtualenv using GALAXY_PYTHON
  environment variable.
- Integrate Python support docs from https://galaxyproject.org/admin/python/
- Update virtualenv installation to use v16.7.9
---
 .circleci/config.yml                        | 12 +++----
 doc/source/admin/framework_dependencies.rst |  2 +-
 doc/source/admin/index.rst                  |  9 ++---
 doc/source/admin/python.md                  | 37 +++++++++++++++++++++
 run_tests.sh                                |  3 +-
 scripts/check_python.py                     | 26 ++++++++++-----
 scripts/common_startup.sh                   | 23 ++++++++-----
 tox.ini                                     | 12 +++----
 8 files changed, 85 insertions(+), 39 deletions(-)
 create mode 100644 doc/source/admin/python.md

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 833e897606c..7904c41fac3 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -97,24 +97,20 @@ jobs:
       - *restore_repo_cache
       - *install_tox
       - run: tox -e py27-unit
-  py27_docstring:
+  py35_docstring:
     docker:
-      - image: circleci/python:2.7
+      - image: circleci/python:3.5
     <<: *set_workdir
     steps:
       - *restore_repo_cache
       - *install_tox
-      - run: tox -e py27-lint_docstring_include_list
+      - run: tox -e py35-lint_docstring_include_list
   py27_first_startup:
     docker:
       - image: circleci/python:2.7
     <<: *set_workdir
     steps:
       - *restore_repo_cache
-      - run: sh scripts/common_startup.sh
-      - run: wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite
-      - run: mv db_gx_rev_0127.sqlite database/universe.sqlite
-      - run: sh manage_db.sh -c ./config/galaxy.yml.sample upgrade
       - *install_tox
       - run: tox -e py27-first_startup
   py35_lint:
@@ -200,7 +196,7 @@ workflows:
           <<: *requires_get_code
       - py27_first_startup:
           <<: *requires_get_code
-      - py27_docstring:
+      - py35_docstring:
           <<: *requires_get_code
       - py35_lint:
           <<: *requires_get_code
diff --git a/doc/source/admin/framework_dependencies.rst b/doc/source/admin/framework_dependencies.rst
index fa1c0e9f8f6..8d7bb7aafcb 100644
--- a/doc/source/admin/framework_dependencies.rst
+++ b/doc/source/admin/framework_dependencies.rst
@@ -181,7 +181,7 @@ Galaxy can create a virtualenv using the adapted virtualenv package. Once a vali
         3. Start galaxy using ``sh run.sh`` or execute ``sh scripts/common_startup.sh``.
 
 
-    A Conda environment named ``_galaxy_`` will be created using python 2 and the appropriate virtualenv package will be installed into this environment.
+    A Conda environment named ``_galaxy_`` will be created and the appropriate virtualenv package will be installed into this environment.
     Using this environment a ``.venv`` is initialized. This is a one-time setup, and all other activation and dependency
     management happens exactly as if a system Python was used for creating ``.venv``.
 
diff --git a/doc/source/admin/index.rst b/doc/source/admin/index.rst
index e667df8cabe..690774a1e66 100644
--- a/doc/source/admin/index.rst
+++ b/doc/source/admin/index.rst
@@ -6,19 +6,20 @@ This documentation is in the midst of being ported and unified based on resource
 .. toctree::
    :maxdepth: 2
 
+   python
+   framework_dependencies
    config
    config_logging
    production
-   scaling
    nginx
    apache
+   scaling
    cluster
    jobs
-   tool_panel
    authentication
+   tool_panel
    dependency_resolvers
    conda_faq
-   framework_dependencies
-   options
    reports
    useful_scripts
+   options
diff --git a/doc/source/admin/python.md b/doc/source/admin/python.md
new file mode 100644
index 00000000000..018bff5319a
--- /dev/null
+++ b/doc/source/admin/python.md
@@ -0,0 +1,37 @@
+# Supported Python versions
+
+Galaxy's core functionality is currently supported on Python **2.7** (although
+deprecated) and **>=3.5** .
+
+If Galaxy complains about the version of Python you are using, check that
+`python --version` reports a supported version. If this is not the case:
+
+1. Completely remove the virtualenv used by Galaxy, e.g. with:
+   `rm -rf /path/to/galaxy/.venv`
+
+2. Let Galaxy know the path of the correct version of Python.
+
+    - If you are using Galaxy >= 20.05, just execute:
+      `export GALAXY_PYTHON=/path/to/python`
+    - If instead you are using an older version of Galaxy, you can manipulate
+      your shell's `$PATH` variable to place the correct version first. This can
+      be done for just Python by creating a new directory, adding a symbolic
+      link to python in there, and putting that directory at the front of
+      `$PATH`:
+
+        ```sh
+        % mkdir ~/galaxy-python
+        % ln -s /path/to/python ~/galaxy-python/python
+        % export PATH=~/galaxy-python:$PATH
+        ```
+
+3. Start Galaxy again.
+
+N.B. If you have compiled your own Python interpreter from source, please ensure
+that the `ssl`, `sqlite3`, `curses` and `bz2` modules were built and can be
+imported after installation. These "extra" modules are built at the end of the
+compilation process and are required by the Galaxy framework. If building on
+Linux, you may need to install the appropriate `-dev` packages for OpenSSL and
+Bzip2. You may also need to build Python with shared libraries
+(`--enable-shared`).
+
diff --git a/run_tests.sh b/run_tests.sh
index 77c7871043c..7e6bdb798f2 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -1,4 +1,3 @@
-
 #!/bin/sh
 
 cd "$(dirname "$0")"
@@ -313,7 +312,7 @@ then
     echo "Docker version:"
     docker --version
     echo "Launching docker container for testing with extra args ${DOCKER_RUN_EXTRA_ARGS}..."
-    name=$(python -c 'import re; import uuid; print re.sub("-","",str(uuid.uuid4()))')
+    name=$(python -c 'import re; import uuid; print re.sub("-", "", str(uuid.uuid4()))')
     # Create a cache dir for pip, so it has the right owner
     DOCKER_PIP_CACHE_DIR="$HOME"/.cache/docker_galaxy_pip
     mkdir -p "$DOCKER_PIP_CACHE_DIR"
diff --git a/scripts/check_python.py b/scripts/check_python.py
index 2a5175e29e6..adccedf27b0 100644
--- a/scripts/check_python.py
+++ b/scripts/check_python.py
@@ -6,20 +6,28 @@ from __future__ import print_function
 
 import sys
 
-version_string = '.'.join(str(_) for _ in sys.version_info[:3])
-
-msg = """ERROR: Your Python version is: %s
-Galaxy is currently supported on Python 2.7 and >=3.5 . To run Galaxy, please
-install a supported Python version. If a supported version is already
-installed but is not your default, https://galaxyproject.org/admin/python/
-contains instructions on how to force Galaxy to use a different version.""" % version_string
-
 
 def check_python():
-    if sys.version_info[:2] == (2, 7) or sys.version_info[:2] >= (3, 5):
+    if sys.version_info[:2] >= (3, 5):
         # supported
         return
+    elif sys.version_info[:2] == (2, 7):
+        msg = """\
+Galaxy support for Python 2.7 is deprecated, please consider moving to
+Python >= 3.5 .
+https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions
+on how to force Galaxy to use a different version."""
+        print(msg, file=sys.stderr)
+        return
     else:
+        version_string = '.'.join(str(_) for _ in sys.version_info[:3])
+        msg = """\
+ERROR: Your Python version is: %s
+Galaxy is currently supported on Python 2.7 (although deprecated) and >=3.5 .
+To run Galaxy, please install a supported Python version.
+If a supported version is already installed but is not your default,
+https://docs.galaxyproject.org/en/latest/admin/python.html contains instructions
+on how to force Galaxy to use a different version.""" % version_string
         print(msg, file=sys.stderr)
         raise Exception(msg)
 
diff --git a/scripts/common_startup.sh b/scripts/common_startup.sh
index df3656e9cf4..51a574de2c1 100755
--- a/scripts/common_startup.sh
+++ b/scripts/common_startup.sh
@@ -121,7 +121,7 @@ if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
                     echo "Creating Conda environment for Galaxy: $GALAXY_CONDA_ENV"
                     echo "To avoid this, use the --no-create-venv flag or set \$GALAXY_CONDA_ENV to an"
                     echo "existing environment before starting Galaxy."
-                    $CONDA_EXE create --yes --override-channels --channel conda-forge --channel defaults --name "$GALAXY_CONDA_ENV" 'python=2.7' 'pip>=9' 'virtualenv>=16'
+                    $CONDA_EXE create --yes --override-channels --channel conda-forge --channel defaults --name "$GALAXY_CONDA_ENV" 'python=3.6' 'pip>=9' 'virtualenv>=16'
                     unset __CONDA_INFO
                 fi
                 conda_activate
@@ -133,13 +133,20 @@ if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
             echo "Creating Python virtual environment for Galaxy: $GALAXY_VIRTUAL_ENV"
             echo "To avoid this, use the --no-create-venv flag or set \$GALAXY_VIRTUAL_ENV to an"
             echo "existing environment before starting Galaxy."
-            python ./scripts/check_python.py || exit 1
+            if [ -z "$GALAXY_PYTHON" ]; then
+                if command -v python3 >/dev/null; then
+                    GALAXY_PYTHON=python3
+                else
+                    GALAXY_PYTHON=python
+                fi
+            fi
+            "$GALAXY_PYTHON" ./scripts/check_python.py || exit 1
             if command -v virtualenv >/dev/null; then
-                virtualenv -p "$(command -v python)" "$GALAXY_VIRTUAL_ENV"
+                virtualenv -p "$GALAXY_PYTHON" "$GALAXY_VIRTUAL_ENV"
             else
-                vvers=16.1.0
+                vvers=16.7.9
                 vurl="https://files.pythonhosted.org/packages/source/v/virtualenv/virtualenv-${vvers}.tar.gz"
-                vsha=f899fafcd92e1150f40c8215328be38ff24b519cd95357fa6e78e006c7638208
+                vsha=0d62c70883c0342d59c11d0ddac0d954d0431321a41ab20851facf2b222598f3
                 vtmp=$(mktemp -d -t galaxy-virtualenv-XXXXXX)
                 vsrc="$vtmp/$(basename $vurl)"
                 # SSL certificates are not checked to prevent problems with messed
@@ -151,16 +158,16 @@ if [ $SET_VENV -eq 1 ] && [ $CREATE_VENV -eq 1 ]; then
                 elif command -v wget >/dev/null; then
                     wget --no-check-certificate -O "$vsrc" "$vurl"
                 else
-                    python -c "try:
+                    "$GALAXY_PYTHON" -c "try:
     from urllib import urlretrieve
 except:
     from urllib.request import urlretrieve
 urlretrieve('$vurl', '$vsrc')"
                 fi
                 echo "Verifying $vsrc checksum is $vsha"
-                python -c "import hashlib; assert hashlib.sha256(open('$vsrc', 'rb').read()).hexdigest() == '$vsha', '$vsrc: invalid checksum'"
+                "$GALAXY_PYTHON" -c "import hashlib; assert hashlib.sha256(open('$vsrc', 'rb').read()).hexdigest() == '$vsha', '$vsrc: invalid checksum'"
                 tar zxf "$vsrc" -C "$vtmp"
-                python "$vtmp/virtualenv-$vvers/src/virtualenv.py" "$GALAXY_VIRTUAL_ENV"
+                "$GALAXY_PYTHON" "$vtmp/virtualenv-$vvers/virtualenv.py" "$GALAXY_VIRTUAL_ENV"
                 rm -rf "$vtmp"
             fi
         fi
diff --git a/tox.ini b/tox.ini
index 3fe6643ade9..fd02ce81dda 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,17 +1,21 @@
 [tox]
 # envlist is the list of environments that are tested when `tox` is run without any option
 # hyphens in an environment name are used to delimit factors
-envlist = check_py3_compatibility, py{27,35}-first_startup, py{27,35}-lint, py27-lint_docstring_include_list, py{27,35}-unit, test_galaxy_packages, validate_test_tools
+envlist = check_py3_compatibility, py{27,35}-first_startup, py{27,35}-lint, py35-lint_docstring_include_list, py{27,35}-unit, test_galaxy_packages, validate_test_tools
 skipsdist = True
 
 [testenv]
 commands =
     first_startup: bash .ci/first_startup.sh
     lint: bash .ci/flake8_wrapper.sh
+    lint_docstring: bash .ci/flake8_wrapper_docstrings.sh --exclude
+    lint_docstring_include_list: bash .ci/flake8_wrapper_docstrings.sh --include
+
     unit: bash run_tests.sh -u
 whitelist_externals = bash
 passenv = CI CONDA_EXE
 setenv =
+    first_startup: GALAXY_PYTHON=python
     py{35,36,37}-first_startup: GALAXY_VIRTUAL_ENV=.venv3
     unit: GALAXY_VIRTUAL_ENV={envdir}
     unit: GALAXY_ENABLE_BETA_COMPRESSED_GENBANK_SNIFFING=1
@@ -34,12 +38,6 @@ whitelist_externals = make
 [testenv:mako_count]
 commands = bash .ci/check_mako.sh
 
-[testenv:py27-lint_docstring]
-commands = bash .ci/flake8_wrapper_docstrings.sh --exclude
-
-[testenv:py27-lint_docstring_include_list]
-commands = bash .ci/flake8_wrapper_docstrings.sh --include
-
 [testenv:test_galaxy_packages]
 commands = bash packages/test.sh
 

From 58ae3e43e3bc053c93406fd19a7b1fb523b10831 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Sun, 9 Feb 2020 16:03:28 +0000
Subject: [PATCH 15/26] Python3: decode the output of
 ``subprocess.check_output()``

---
 doc/source/conf.versioning.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/doc/source/conf.versioning.py b/doc/source/conf.versioning.py
index 65a85d7fd2d..8b112f7afca 100644
--- a/doc/source/conf.versioning.py
+++ b/doc/source/conf.versioning.py
@@ -43,7 +43,8 @@ if TARGET_GIT_BRANCH.startswith('release_'):
     _target_ver = TARGET_GIT_BRANCH[len('release_'):]
 
 # Use tags to determine versions - a stable version will have a branch before it's released, but not a tag.
-for _tag in reversed(check_output(('git', 'tag')).splitlines()):
+tags = check_output(('git', 'tag')).decode().splitlines()
+for _tag in reversed(tags):
     if _tag.startswith('v') and _tag.count('.') == 1:
         # this version is released
         _ver = _tag[1:]

From 4c712f0f2d6386873e322de5efb64a236631fe7b Mon Sep 17 00:00:00 2001
From: Alex Ostrovsky <40246333+astrovsky01@users.noreply.github.com>
Date: Tue, 18 Feb 2020 15:31:29 -0500
Subject: [PATCH 16/26] Added conda python update

---
 doc/source/admin/python.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/source/admin/python.md b/doc/source/admin/python.md
index 018bff5319a..228af9e9fd1 100644
--- a/doc/source/admin/python.md
+++ b/doc/source/admin/python.md
@@ -24,6 +24,8 @@ If Galaxy complains about the version of Python you are using, check that
         % ln -s /path/to/python ~/galaxy-python/python
         % export PATH=~/galaxy-python:$PATH
         ```
+        
+    - If using Galaxy with a conda environment, remove conda environment (e.g. ```rm -rf /path/to/conda/__galaxy__```)
 
 3. Start Galaxy again.
 

From 99bc25f4ccabf29b4fdaf2e8fd35e9d4abe617a5 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 19 Feb 2020 16:09:12 +0000
Subject: [PATCH 17/26] Add more details

---
 doc/source/admin/python.md | 49 ++++++++++++++++++++++----------------
 1 file changed, 29 insertions(+), 20 deletions(-)

diff --git a/doc/source/admin/python.md b/doc/source/admin/python.md
index 228af9e9fd1..6209bebba8e 100644
--- a/doc/source/admin/python.md
+++ b/doc/source/admin/python.md
@@ -3,31 +3,40 @@
 Galaxy's core functionality is currently supported on Python **2.7** (although
 deprecated) and **>=3.5** .
 
-If Galaxy complains about the version of Python you are using, check that
-`python --version` reports a supported version. If this is not the case:
+If Galaxy complains about the version of Python you are using:
 
-1. Completely remove the virtualenv used by Galaxy, e.g. with:
-   `rm -rf /path/to/galaxy/.venv`
+1. Completely remove the Python virtualenv used by Galaxy (which can be
+   configured with the `GALAXY_VIRTUAL_ENV` environment variable and defaults to
+   `.venv`), e.g. with: `rm -rf /path/to/galaxy/.venv`
 
-2. Let Galaxy know the path of the correct version of Python.
+2. If you were using a Python from a conda environment (which can be configured
+   with the `GALAXY_CONDA_ENV` environment variable and defaults to `_galaxy_`),
+   remove it, e.g. with: `conda env remove -n _galaxy_`
 
-    - If you are using Galaxy >= 20.05, just execute:
-      `export GALAXY_PYTHON=/path/to/python`
-    - If instead you are using an older version of Galaxy, you can manipulate
-      your shell's `$PATH` variable to place the correct version first. This can
-      be done for just Python by creating a new directory, adding a symbolic
-      link to python in there, and putting that directory at the front of
-      `$PATH`:
+3. Let Galaxy know which Python to use in one of the following methods:
 
-        ```sh
-        % mkdir ~/galaxy-python
-        % ln -s /path/to/python ~/galaxy-python/python
-        % export PATH=~/galaxy-python:$PATH
-        ```
-        
-    - If using Galaxy with a conda environment, remove conda environment (e.g. ```rm -rf /path/to/conda/__galaxy__```)
+    - If you want to use Python from conda, just activate the `base` environment
+      and Galaxy will create a new conda environment for itself.
+    - Otherwise:
+        1. Make sure a supported version of Python is installed.
+        2. Verify that the Python interpreter you want to use is first in the
+           output of `which -a python3 python` (or `which -a python` if you are
+           using Galaxy <=20.01). If this is not the case:
+           - If you are using Galaxy >= 20.05, just execute:
+             `export GALAXY_PYTHON=/path/to/python`
+           - If instead you are using an older version of Galaxy, you can
+            manipulate your shell's `PATH` variable to place the correct version
+            first. This can be done for just Python by creating a new directory,
+            adding a symbolic link to `python` in there, and putting that
+            directory at the front of `PATH`:
 
-3. Start Galaxy again.
+              ```sh
+              % mkdir ~/galaxy-python
+              % ln -s /path/to/python ~/galaxy-python/python
+              % export PATH=~/galaxy-python:$PATH
+              ```
+
+4. Start Galaxy again.
 
 N.B. If you have compiled your own Python interpreter from source, please ensure
 that the `ssl`, `sqlite3`, `curses` and `bz2` modules were built and can be

From 1169db7c9ee25c5bfcf7f2e8312e0ba0624760b0 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 11:02:24 +0100
Subject: [PATCH 18/26] Mention that database/compiled_templates needs to be
 removed when upgrading python

---
 doc/source/admin/python.md | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/doc/source/admin/python.md b/doc/source/admin/python.md
index 6209bebba8e..ba75e2f1e4f 100644
--- a/doc/source/admin/python.md
+++ b/doc/source/admin/python.md
@@ -36,7 +36,13 @@ If Galaxy complains about the version of Python you are using:
               % export PATH=~/galaxy-python:$PATH
               ```
 
-4. Start Galaxy again.
+4. Remove compiled mako templates when upgrading from Python 2:
+     ```sh
+     % rm -rf /path/to/galaxy/database/compiled_templates/
+     ```
+   These templated will be regenerated automatically when starting Galaxy.
+
+5. Start Galaxy again.
 
 N.B. If you have compiled your own Python interpreter from source, please ensure
 that the `ssl`, `sqlite3`, `curses` and `bz2` modules were built and can be

From 48e015d362bcb131d644409952e9fff0c12dffae Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 11:02:39 +0100
Subject: [PATCH 19/26] Link to Python upgrade instructions

---
 doc/source/releases/20.01_announce.rst | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/doc/source/releases/20.01_announce.rst b/doc/source/releases/20.01_announce.rst
index b54341b3115..065f1b66cea 100644
--- a/doc/source/releases/20.01_announce.rst
+++ b/doc/source/releases/20.01_announce.rst
@@ -56,6 +56,13 @@ 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.
 
+Deprecation Notice
+==================
+
+With the release of Galaxy 20.01 we strongly encourage all deployers to run Galaxy under Python 3.
+For instructions on how to transition to Python 3 please see `here <https://docs.galaxyproject.org/en/release_20.01/admin/python.html>`__.
+
+
 Release Notes
 ===========================================================
 

From 9fdbad72471631284b2418c5b844d1bcc45bc4d6 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 11:13:45 +0100
Subject: [PATCH 20/26] Mention that more distribution tools/converters need
 dependencies now

---
 doc/source/releases/20.01_announce.rst | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/doc/source/releases/20.01_announce.rst b/doc/source/releases/20.01_announce.rst
index 065f1b66cea..cc8ff3f0c7a 100644
--- a/doc/source/releases/20.01_announce.rst
+++ b/doc/source/releases/20.01_announce.rst
@@ -56,6 +56,13 @@ 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.
 
+Updates to Tools and Converters in the Galaxy distribution
+==========================================================
+
+Many tools and Converters have been updated in the 20.01 release.
+As a consequence deployers need to install dependencies for these in the
+Admin Menu -> Manage Dependencies.
+
 Deprecation Notice
 ==================
 

From 4066d1bd757732fa7893f62e08e565a0a76d7331 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 14:01:33 +0100
Subject: [PATCH 21/26] Restore database migration test

---
 .circleci/config.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 7904c41fac3..a87c6269b74 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -135,6 +135,10 @@ jobs:
     <<: *set_workdir
     steps:
       - *restore_repo_cache
+      - run: sh scripts/common_startup.sh
+      - run: wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite
+      - run: mv db_gx_rev_0127.sqlite database/universe.sqlite
+      - run: sh manage_db.sh -c ./config/galaxy.yml.sample upgrade
       - *install_tox
       - run: tox -e py35-first_startup
   validate_test_tools:

From 4f0cce0c270e2c0feaa1b8302e91d497b9653fe4 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 14:06:55 +0100
Subject: [PATCH 22/26] Adjust docs for when we started preferring python3

---
 doc/source/admin/python.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/source/admin/python.md b/doc/source/admin/python.md
index ba75e2f1e4f..691cf8bd847 100644
--- a/doc/source/admin/python.md
+++ b/doc/source/admin/python.md
@@ -21,7 +21,7 @@ If Galaxy complains about the version of Python you are using:
         1. Make sure a supported version of Python is installed.
         2. Verify that the Python interpreter you want to use is first in the
            output of `which -a python3 python` (or `which -a python` if you are
-           using Galaxy <=20.01). If this is not the case:
+           using Galaxy <=19.09). If this is not the case:
            - If you are using Galaxy >= 20.05, just execute:
              `export GALAXY_PYTHON=/path/to/python`
            - If instead you are using an older version of Galaxy, you can

From 0aa5c4b21c5e76dfc08f918b667a82508f8f50d1 Mon Sep 17 00:00:00 2001
From: Marius van den Beek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 14:25:10 +0100
Subject: [PATCH 23/26] One more version change

Co-Authored-By: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 doc/source/admin/python.md | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/doc/source/admin/python.md b/doc/source/admin/python.md
index 691cf8bd847..a8ef04c7669 100644
--- a/doc/source/admin/python.md
+++ b/doc/source/admin/python.md
@@ -22,7 +22,7 @@ If Galaxy complains about the version of Python you are using:
         2. Verify that the Python interpreter you want to use is first in the
            output of `which -a python3 python` (or `which -a python` if you are
            using Galaxy <=19.09). If this is not the case:
-           - If you are using Galaxy >= 20.05, just execute:
+           - If you are using Galaxy >= 20.01, just execute:
              `export GALAXY_PYTHON=/path/to/python`
            - If instead you are using an older version of Galaxy, you can
             manipulate your shell's `PATH` variable to place the correct version
@@ -51,4 +51,3 @@ compilation process and are required by the Galaxy framework. If building on
 Linux, you may need to install the appropriate `-dev` packages for OpenSSL and
 Bzip2. You may also need to build Python with shared libraries
 (`--enable-shared`).
-

From b6d05e3d0959a6590910e637372598a3b12b729e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 26 Feb 2020 16:17:08 +0100
Subject: [PATCH 24/26] Update for new 20.01 PRs

---
 doc/source/releases/20.01.rst     | 6 ++++++
 doc/source/releases/20.01_prs.rst | 2 ++
 2 files changed, 8 insertions(+)

diff --git a/doc/source/releases/20.01.rst b/doc/source/releases/20.01.rst
index c20608d61f1..fffe8a32f5e 100644
--- a/doc/source/releases/20.01.rst
+++ b/doc/source/releases/20.01.rst
@@ -430,6 +430,9 @@ Fixes
 
 * Fix cool sniffing on python3
   `Pull Request 9153`_
+* Fix `SearchGuiArchive.set_meta()`
+  (thanks to `@bernt-matthias <https://github.com/bernt-matthias>`__).
+  `Pull Request 9437`_
 
 .. bug_tag_tools
 
@@ -778,6 +781,9 @@ Fixes
   `Pull Request 9441`_
 * Fix data tables vue display
   `Pull Request 9442`_
+* Fix `UserManager.get_reset_token()` after `#9432 <https://github.com/galaxyproject/galaxy/issues/9432>`__
+  (thanks to `@nsoranzo <https://github.com/nsoranzo>`__).
+  `Pull Request 9446`_
 
 .. include:: 20.01_prs.rst
 
diff --git a/doc/source/releases/20.01_prs.rst b/doc/source/releases/20.01_prs.rst
index b59e8a524b5..0a6d9e4ee35 100644
--- a/doc/source/releases/20.01_prs.rst
+++ b/doc/source/releases/20.01_prs.rst
@@ -337,5 +337,7 @@
 .. _Pull Request 9432: https://github.com/galaxyproject/galaxy/pull/9432
 .. _Pull Request 9433: https://github.com/galaxyproject/galaxy/pull/9433
 .. _Pull Request 9434: https://github.com/galaxyproject/galaxy/pull/9434
+.. _Pull Request 9437: https://github.com/galaxyproject/galaxy/pull/9437
 .. _Pull Request 9441: https://github.com/galaxyproject/galaxy/pull/9441
 .. _Pull Request 9442: https://github.com/galaxyproject/galaxy/pull/9442
+.. _Pull Request 9446: https://github.com/galaxyproject/galaxy/pull/9446

From 4e96e3edce5147aba68afde48bbbca61a4560417 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 27 Feb 2020 11:49:49 +0000
Subject: [PATCH 25/26] Use `with` statement to open file

---
 scripts/bootstrap_history.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/scripts/bootstrap_history.py b/scripts/bootstrap_history.py
index dde83dd5c60..87c471a4289 100644
--- a/scripts/bootstrap_history.py
+++ b/scripts/bootstrap_history.py
@@ -743,8 +743,10 @@ def _releases():
 
 def _github_client():
     try:
-        github_json = os.path.expanduser("~/.github.json")
-        github = Github(**json.load(open(github_json, "r")))
+        github_json_path = os.path.expanduser("~/.github.json")
+        with open(github_json_path, "r") as fh:
+            github_json_dict = json.load(fh)
+        github = Github(**github_json_dict)
     except Exception:
         log.exception()
         github = None

From 2bfeeec299990e154b56438a80869b09325e271e Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 27 Feb 2020 16:04:40 +0000
Subject: [PATCH 26/26] Drop pygithub3 dev requirement

---
 lib/galaxy/dependencies/pipfiles/default/Pipfile                 | 1 -
 .../dependencies/pipfiles/default/pinned-dev-requirements.txt    | 1 -
 2 files changed, 2 deletions(-)

diff --git a/lib/galaxy/dependencies/pipfiles/default/Pipfile b/lib/galaxy/dependencies/pipfiles/default/Pipfile
index 3c3ce61385a..67964f85612 100644
--- a/lib/galaxy/dependencies/pipfiles/default/Pipfile
+++ b/lib/galaxy/dependencies/pipfiles/default/Pipfile
@@ -13,7 +13,6 @@ gunicorn = "*"
 lxml = "!=4.2.2"
 mock = "*"
 NoseHTML = "*"
-pygithub3 = {version = "*", markers = "python_version < '3'"}
 pytest = "*"
 pytest-cov = "*"
 pytest-html = "*"
diff --git a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
index 7388ad1a691..cbf02baf09f 100644
--- a/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
+++ b/lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt
@@ -34,7 +34,6 @@ pluggy==0.13.1
 port-for==0.4
 psutil==5.6.7
 py==1.8.0
-pygithub3==0.5.1 ; python_version < '3'
 pygments==2.5.2
 pyparsing==2.4.5
 pytest-cov==2.8.1