From 0af72e56b20ea20da139c3b101dedf9e30a7d66a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 31 Jan 2022 15:55:10 +0100
Subject: [PATCH 01/21] Update version to 22.05.dev0

---
 Makefile                                                      | 2 +-
 lib/galaxy/version.py                                         | 2 +-
 packages/app/galaxy/project_galaxy_app.py                     | 2 +-
 packages/auth/galaxy/project_galaxy_auth.py                   | 2 +-
 packages/containers/galaxy/project_galaxy_containers.py       | 2 +-
 packages/data/galaxy/project_galaxy_data.py                   | 2 +-
 packages/files/galaxy/project_galaxy_files.py                 | 2 +-
 packages/job_execution/galaxy/project_galaxy_job_execution.py | 2 +-
 packages/job_metrics/galaxy/project_galaxy_job_metrics.py     | 2 +-
 packages/meta/galaxy/project_galaxy_meta.py                   | 2 +-
 packages/objectstore/galaxy/project_galaxy_objectstore.py     | 2 +-
 packages/selenium/galaxy/project_galaxy_selenium.py           | 2 +-
 packages/test_api/galaxy/project_galaxy_test_api.py           | 2 +-
 packages/test_base/galaxy/project_galaxy_test_base.py         | 2 +-
 packages/test_driver/galaxy/project_galaxy_test_driver.py     | 2 +-
 packages/test_selenium/galaxy/project_galaxy_test_selenium.py | 2 +-
 packages/tool_util/galaxy/project_galaxy_tool_util.py         | 2 +-
 packages/util/galaxy/project_galaxy_util.py                   | 2 +-
 packages/web_framework/galaxy/project_galaxy_web_framework.py | 2 +-
 packages/web_stack/galaxy/project_galaxy_web_stack.py         | 2 +-
 packages/webapps/galaxy/project_galaxy_webapps.py             | 2 +-
 21 files changed, 21 insertions(+), 21 deletions(-)

diff --git a/Makefile b/Makefile
index 93e632030d2..679a56cb5a1 100644
--- a/Makefile
+++ b/Makefile
@@ -2,7 +2,7 @@
 VENV?=.venv
 # Source virtualenv to execute command (flake8, sphinx, twine, etc...)
 IN_VENV=if [ -f "$(VENV)/bin/activate" ]; then . "$(VENV)/bin/activate"; fi;
-RELEASE_CURR:=22.01
+RELEASE_CURR:=22.05
 RELEASE_UPSTREAM:=upstream
 TARGET_BRANCH=$(RELEASE_UPSTREAM)/dev
 CONFIG_MANAGE=$(IN_VENV) python lib/galaxy/config/config_manage.py
diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py
index b8aeb0faa15..79769b43d65 100644
--- a/lib/galaxy/version.py
+++ b/lib/galaxy/version.py
@@ -1,3 +1,3 @@
-VERSION_MAJOR = "22.01"
+VERSION_MAJOR = "22.05"
 VERSION_MINOR = "dev0"
 VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else '')
diff --git a/packages/app/galaxy/project_galaxy_app.py b/packages/app/galaxy/project_galaxy_app.py
index 0f4e92e4a70..ba96ebd1069 100644
--- a/packages/app/galaxy/project_galaxy_app.py
+++ b/packages/app/galaxy/project_galaxy_app.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-app"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/auth/galaxy/project_galaxy_auth.py b/packages/auth/galaxy/project_galaxy_auth.py
index 721cc233e76..63acedc18a2 100644
--- a/packages/auth/galaxy/project_galaxy_auth.py
+++ b/packages/auth/galaxy/project_galaxy_auth.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-auth"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/containers/galaxy/project_galaxy_containers.py b/packages/containers/galaxy/project_galaxy_containers.py
index 9ef9dbc3e52..ef17dab59c4 100644
--- a/packages/containers/galaxy/project_galaxy_containers.py
+++ b/packages/containers/galaxy/project_galaxy_containers.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-containers"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/data/galaxy/project_galaxy_data.py b/packages/data/galaxy/project_galaxy_data.py
index 97f5003b044..04511fff74a 100644
--- a/packages/data/galaxy/project_galaxy_data.py
+++ b/packages/data/galaxy/project_galaxy_data.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-data"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/files/galaxy/project_galaxy_files.py b/packages/files/galaxy/project_galaxy_files.py
index b60e0f13295..6f23ffc97a4 100644
--- a/packages/files/galaxy/project_galaxy_files.py
+++ b/packages/files/galaxy/project_galaxy_files.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-files"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/job_execution/galaxy/project_galaxy_job_execution.py b/packages/job_execution/galaxy/project_galaxy_job_execution.py
index cd5a0d743fe..876af88bb96 100644
--- a/packages/job_execution/galaxy/project_galaxy_job_execution.py
+++ b/packages/job_execution/galaxy/project_galaxy_job_execution.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-job-execution"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
index a0019c4c0d8..fac857f4b31 100644
--- a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
+++ b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-job-metrics"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/meta/galaxy/project_galaxy_meta.py b/packages/meta/galaxy/project_galaxy_meta.py
index acf06f4cca8..ad5b8c70161 100644
--- a/packages/meta/galaxy/project_galaxy_meta.py
+++ b/packages/meta/galaxy/project_galaxy_meta.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/objectstore/galaxy/project_galaxy_objectstore.py b/packages/objectstore/galaxy/project_galaxy_objectstore.py
index 28c1ad69b2c..01c59388dbd 100644
--- a/packages/objectstore/galaxy/project_galaxy_objectstore.py
+++ b/packages/objectstore/galaxy/project_galaxy_objectstore.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-objectstore"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/selenium/galaxy/project_galaxy_selenium.py b/packages/selenium/galaxy/project_galaxy_selenium.py
index c848ea40bfb..8b850e4b346 100644
--- a/packages/selenium/galaxy/project_galaxy_selenium.py
+++ b/packages/selenium/galaxy/project_galaxy_selenium.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-selenium"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/test_api/galaxy/project_galaxy_test_api.py b/packages/test_api/galaxy/project_galaxy_test_api.py
index e4ce8d65553..49ec4de5872 100644
--- a/packages/test_api/galaxy/project_galaxy_test_api.py
+++ b/packages/test_api/galaxy/project_galaxy_test_api.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-test-api"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/test_base/galaxy/project_galaxy_test_base.py b/packages/test_base/galaxy/project_galaxy_test_base.py
index ce8393d482a..6ae155ad9e2 100644
--- a/packages/test_base/galaxy/project_galaxy_test_base.py
+++ b/packages/test_base/galaxy/project_galaxy_test_base.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-test-base"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/test_driver/galaxy/project_galaxy_test_driver.py b/packages/test_driver/galaxy/project_galaxy_test_driver.py
index af8547be390..749feb08998 100644
--- a/packages/test_driver/galaxy/project_galaxy_test_driver.py
+++ b/packages/test_driver/galaxy/project_galaxy_test_driver.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-test-driver"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/test_selenium/galaxy/project_galaxy_test_selenium.py b/packages/test_selenium/galaxy/project_galaxy_test_selenium.py
index 31711bcd5b0..f9cd081e9a9 100644
--- a/packages/test_selenium/galaxy/project_galaxy_test_selenium.py
+++ b/packages/test_selenium/galaxy/project_galaxy_test_selenium.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-test-selenium"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/tool_util/galaxy/project_galaxy_tool_util.py b/packages/tool_util/galaxy/project_galaxy_tool_util.py
index eef5254d469..bb6ef15384e 100644
--- a/packages/tool_util/galaxy/project_galaxy_tool_util.py
+++ b/packages/tool_util/galaxy/project_galaxy_tool_util.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-tool-util"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/util/galaxy/project_galaxy_util.py b/packages/util/galaxy/project_galaxy_util.py
index 9689175c5e1..1da41efe45e 100644
--- a/packages/util/galaxy/project_galaxy_util.py
+++ b/packages/util/galaxy/project_galaxy_util.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-util"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/web_framework/galaxy/project_galaxy_web_framework.py b/packages/web_framework/galaxy/project_galaxy_web_framework.py
index b43ad31c51a..579f8a96ee3 100644
--- a/packages/web_framework/galaxy/project_galaxy_web_framework.py
+++ b/packages/web_framework/galaxy/project_galaxy_web_framework.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-web-framework"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/web_stack/galaxy/project_galaxy_web_stack.py b/packages/web_stack/galaxy/project_galaxy_web_stack.py
index 052f88ad9f3..97af8d53985 100644
--- a/packages/web_stack/galaxy/project_galaxy_web_stack.py
+++ b/packages/web_stack/galaxy/project_galaxy_web_stack.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-web-stack"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
diff --git a/packages/webapps/galaxy/project_galaxy_webapps.py b/packages/webapps/galaxy/project_galaxy_webapps.py
index 21dd8a43eae..7c669f1eac9 100644
--- a/packages/webapps/galaxy/project_galaxy_webapps.py
+++ b/packages/webapps/galaxy/project_galaxy_webapps.py
@@ -1,4 +1,4 @@
-__version__ = "22.1.0.dev0"
+__version__ = "22.5.0.dev0"
 
 PROJECT_NAME = "galaxy-webapps"
 PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"

From 275ad1217f9e023f3a563544309a68717da1b959 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Tue, 19 Jan 2021 10:27:58 -0500
Subject: [PATCH 02/21] Introduce pyproject.toml for black settings

---
 pyproject.toml | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index f0cc84f1e01..be52ef801f5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -120,3 +120,14 @@ testfixtures = "*"
 tuspy = "*"
 twill = "*"
 watchdog = "*"
+
+[tool.black]
+line-length = 120
+target-version = ['py37']
+include = '\.pyi?$'
+extend-exclude = '''
+/(
+  | packages
+  | tools
+)/
+'''

From d21474fc8410840ef16b0f3a02db476083179c15 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 2 Feb 2022 09:32:20 -0500
Subject: [PATCH 03/21] Add black to dev-dependencies

---
 lib/galaxy/dependencies/dev-requirements.txt | 20 ++++++++++----------
 pyproject.toml                               |  1 +
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 1513ba45325..9e02e9b9843 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -20,7 +20,7 @@ bdbag==1.6.3; (python_version >= "2.7" and python_full_version < "3.0.0") or (py
 beaker==1.11.0
 billiard==3.6.4.0; python_version >= "3.7"
 bioblend==0.16.0; python_version >= "3.6"
-black==22.1.0; python_full_version >= "3.6.2" and python_version >= "3.6"
+black==22.1.0; python_full_version >= "3.6.2"
 bleach==4.1.0; python_version >= "3.6"
 boltons==21.0.0
 boto==2.49.0
@@ -36,13 +36,13 @@ circus==0.17.1
 click-didyoumean==0.3.0; python_full_version >= "3.6.2" and python_full_version < "4.0.0" and python_version >= "3.7"
 click-plugins==1.1.1; python_version >= "3.7"
 click-repl==0.2.0; python_version >= "3.7"
-click==8.0.3; python_full_version >= "3.6.2" and python_full_version < "4.0.0" and python_version >= "3.7"
+click==8.0.3; python_version >= "3.7" and python_full_version >= "3.6.2" and python_full_version < "4.0.0"
 cloudauthz==0.6.0
 cloudbridge==3.0.0
 colorama==0.4.4; sys_platform == "win32" and python_version >= "3.7" and python_full_version >= "3.6.2" and platform_system == "Windows" and python_full_version < "4.0.0" and (python_version >= "2.7" and python_full_version < "3.0.0" and platform_system == "Windows" or python_full_version >= "3.5.0" and platform_system == "Windows") and (python_version >= "3.7" and python_full_version < "3.0.0" and sys_platform == "win32" or sys_platform == "win32" and python_version >= "3.7" and python_full_version >= "3.5.0") and (python_version >= "3.6" and python_full_version < "3.0.0" and sys_platform == "win32" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") or sys_platform == "win32" and python_version >= "3.6" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6") and python_full_version >= "3.5.0")
 coloredlogs==15.0.1; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0"
 commonmark==0.9.1; python_full_version >= "3.6.2" and python_full_version < "4.0.0"
-coverage==6.3; python_version >= "3.7"
+coverage==6.3.1; python_version >= "3.7"
 cryptography==36.0.1; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.7"
 cwltest==2.2.20210901154959; python_version >= "3.6" and python_version < "4"
 cwltool==3.1.20211107152837; python_version >= "3.6" and python_version < "4"
@@ -70,12 +70,12 @@ gunicorn==20.1.0; python_version >= "3.5"
 gxformat2==0.15.0
 h11==0.12.0; python_version >= "3.7" and python_version < "4.0" and python_full_version >= "3.6.1"
 h5py==3.6.0; python_version >= "3.7"
-httpcore==0.14.5; python_version >= "3.6"
+httpcore==0.14.6; python_version >= "3.6"
 httpx==0.22.0; python_version >= "3.6"
 humanfriendly==10.0; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.5.0"
 idna==3.3
 imagesize==1.3.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
-importlib-metadata==4.10.1; python_version == "3.7" and (python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.6.0" and python_version < "3.8" and python_version >= "3.7") and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6")
+importlib-metadata==4.10.1; python_version == "3.7" and (python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.6.0" and python_version < "3.8" and python_version >= "3.7") and python_full_version >= "3.6.2" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6")
 importlib-resources==5.4.0; python_version >= "3.6"
 iniconfig==1.1.1; python_version >= "3.7"
 isa-rwval==0.10.10
@@ -112,7 +112,7 @@ paste==3.5.0
 pastedeploy==2.1.1
 pathspec==0.9.0; python_full_version >= "3.6.2" and python_version >= "3.6"
 pbr==5.8.0; python_version >= "2.6"
-platformdirs==2.4.1; python_full_version >= "3.6.2" and python_version >= "3.7"
+platformdirs==2.4.1; python_version >= "3.7" and python_full_version >= "3.6.2"
 pluggy==1.0.0; python_version >= "3.7"
 port-for==0.6.1; python_version >= "3.7"
 prettytable==3.0.0; python_version >= "3.7"
@@ -127,7 +127,7 @@ pycryptodome==3.14.0; (python_version >= "2.7" and python_full_version < "3.0.0"
 pydantic==1.9.0; python_full_version >= "3.6.1"
 pydot==1.4.2; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.4.0"
 pyeventsystem==0.1.0
-pyfaidx==0.6.3.1
+pyfaidx==0.6.4
 pygithub==1.55; python_version >= "3.6"
 pygments==2.11.2; python_full_version >= "3.6.2" and python_full_version < "4.0.0" and python_version >= "3.6" and (python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6")
 pyjwt==2.3.0; python_version >= "3.6"
@@ -151,7 +151,7 @@ pytest-pythonpath==0.7.3
 pytest-shard==0.1.2; python_version >= "3.6"
 pytest==6.2.5; python_version >= "3.6"
 python-dateutil==2.8.2; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.3.0"
-python-irodsclient==1.1.0
+python-irodsclient==1.1.1
 python-jose==3.3.0
 python-multipart==0.0.5
 python3-openid==3.2.0; python_version >= "3.0"
@@ -206,7 +206,7 @@ testfixtures==6.18.3
 tifffile==2021.11.2; python_version >= "3.7"
 tinydb==4.6.1; python_version >= "3.6" and python_version < "4.0"
 toml==0.10.2; python_version >= "3.7" and python_full_version < "3.0.0" or python_full_version >= "3.3.0" and python_version >= "3.7"
-tomli==2.0.0; python_full_version >= "3.6.2" and python_version >= "3.7"
+tomli==2.0.0; python_version >= "3.7" and python_full_version >= "3.6.2"
 tornado==6.1; python_version >= "3.5"
 tqdm==4.62.3; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
 trio-websocket==0.9.2; python_version >= "3.7" and python_version < "4.0"
@@ -230,5 +230,5 @@ whoosh==2.7.4
 wrapt==1.13.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version >= "3.6"
 wsproto==1.0.0; python_version >= "3.7" and python_version < "4.0" and python_full_version >= "3.6.1"
 yacman==0.8.4
-zipp==3.7.0; python_version == "3.7" and (python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.6.0" and python_version < "3.8" and python_version >= "3.7")
+zipp==3.7.0; python_version == "3.7" and (python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "3.8" or python_full_version >= "3.6.0" and python_version < "3.8" and python_version >= "3.7") and python_full_version >= "3.6.2"
 zipstream-new==1.1.8
diff --git a/pyproject.toml b/pyproject.toml
index be52ef801f5..25767756218 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -91,6 +91,7 @@ zipstream-new = "*"
 
 [tool.poetry.dev-dependencies]
 cwltest = "2.2.20210901154959"
+black = "^22.1.0"
 darker = "*"
 fluent-logger = "*"
 httpx = "*"

From 3987b11805689e29cc1a87484f3301246530fe4b Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 2 Feb 2022 09:41:58 -0500
Subject: [PATCH 04/21] Add black check action to python linting

---
 .github/workflows/lint.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index 9dfd554cf3c..2e8b61d85b1 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -43,3 +43,4 @@ jobs:
         run: tox -e lint_docstring_include_list
       - name: Run mypy checks
         run: tox -e mypy
+      - uses: psf/black@stable

From 412b6dc78df5f24c68e831a56ff586e3454d2166 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 2 Feb 2022 11:40:36 -0500
Subject: [PATCH 05/21] Update shared pyfaidx to match (regenerated from
 poetry, this is the only change that should be required)

---
 lib/galaxy/dependencies/pinned-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 1aaed9f9450..c5fd30801a5 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -103,7 +103,7 @@ pycryptodome==3.14.0; (python_version >= "2.7" and python_full_version < "3.0.0"
 pydantic==1.9.0; python_full_version >= "3.6.1"
 pydot==1.4.2; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_version >= "3.6" and python_version < "4" and python_full_version >= "3.4.0"
 pyeventsystem==0.1.0
-pyfaidx==0.6.3.1
+pyfaidx==0.6.4
 pygments==2.11.2; python_full_version >= "3.6.2" and python_full_version < "4.0.0" and python_version >= "3.5"
 pyjwt==2.3.0; python_version >= "3.6"
 pykwalify==1.8.0

From 78e262922978f57e974d6b6833d7fc0057b7a4da Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 2 Feb 2022 11:47:31 -0500
Subject: [PATCH 06/21] E203 handling -- see discussion in See
 https://black.readthedocs.io/en/stable/faq.html#why-are-flake8-s-e203-and-w503-violated

---
 setup.cfg | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 41a9a481e9e..e4a4adbd984 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -7,9 +7,10 @@ universal = 1
 # E128 continuation line under-indented for visual indent
 # E402 module level import not at top of file # TODO, we would like to improve this.
 # E501 is line length
+# E203 is whitespace before ':'; we follow black's formatting here.  See https://github.com/psf/black/issues/315
 # W503 is line breaks before binary operators, which has been reversed in PEP 8.
 # D** are docstring linting - which we mostly ignore except D302. (Hopefully we will solve more over time).
-ignore = B008,E128,E501,E402,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
+ignore = B008,E128,E203,E501,E402,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
 exclude = lib/galaxy/util/jstree.py
 # For flake8-import-order
 # https://github.com/PyCQA/flake8-import-order/blob/master/tests/test_cases/complete_smarkets.py

From 0b63c1f50491fd60cfa97fa5495ba019ce281400 Mon Sep 17 00:00:00 2001
From: Dannon <dannon.baker@gmail.com>
Date: Wed, 2 Feb 2022 15:23:45 -0500
Subject: [PATCH 07/21] Apply suggestions from code review

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 pyproject.toml | 5 +++--
 setup.cfg      | 4 ++--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 25767756218..b7437904ee5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -90,8 +90,8 @@ Whoosh = "*"
 zipstream-new = "*"
 
 [tool.poetry.dev-dependencies]
-cwltest = "2.2.20210901154959"
 black = "^22.1.0"
+cwltest = "2.2.20210901154959"
 darker = "*"
 fluent-logger = "*"
 httpx = "*"
@@ -127,8 +127,9 @@ line-length = 120
 target-version = ['py37']
 include = '\.pyi?$'
 extend-exclude = '''
-/(
+^/(
   | packages
   | tools
 )/
 '''
+force-exclude = 'lib/galaxy/util/jstree.py'
diff --git a/setup.cfg b/setup.cfg
index e4a4adbd984..017ae8f9915 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -5,12 +5,12 @@ universal = 1
 # These are exceptions allowed by Galaxy style guidelines:
 # B008 Do not perform function calls in argument defaults (for FastAPI Depends and Body)
 # E128 continuation line under-indented for visual indent
+# E203 is whitespace before ':'; we follow black's formatting here. See https://black.readthedocs.io/en/stable/faq.html#why-are-flake8-s-e203-and-w503-violated
 # E402 module level import not at top of file # TODO, we would like to improve this.
 # E501 is line length
-# E203 is whitespace before ':'; we follow black's formatting here.  See https://github.com/psf/black/issues/315
 # W503 is line breaks before binary operators, which has been reversed in PEP 8.
 # D** are docstring linting - which we mostly ignore except D302. (Hopefully we will solve more over time).
-ignore = B008,E128,E203,E501,E402,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
+ignore = B008,E128,E203,E402,E501,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
 exclude = lib/galaxy/util/jstree.py
 # For flake8-import-order
 # https://github.com/PyCQA/flake8-import-order/blob/master/tests/test_cases/complete_smarkets.py

From ae59ab561b5ccbbe8cadfd9a133bf4bc814c1029 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 2 Feb 2022 15:25:22 -0500
Subject: [PATCH 08/21] Reorder pyproject.toml

---
 pyproject.toml | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index b7437904ee5..0a19ddcc294 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,15 @@
+[tool.black]
+line-length = 120
+target-version = ['py37']
+include = '\.pyi?$'
+extend-exclude = '''
+^/(
+  | packages
+  | tools
+)/
+'''
+force-exclude = 'lib/galaxy/util/jstree.py'
+
 [tool.poetry]
 name = "galaxy"
 version = "22.01.dev0"
@@ -121,15 +133,3 @@ testfixtures = "*"
 tuspy = "*"
 twill = "*"
 watchdog = "*"
-
-[tool.black]
-line-length = 120
-target-version = ['py37']
-include = '\.pyi?$'
-extend-exclude = '''
-^/(
-  | packages
-  | tools
-)/
-'''
-force-exclude = 'lib/galaxy/util/jstree.py'

From 94a512b5586ddd296c5d0a2e2f589f4fca517a49 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 30 Jan 2022 13:24:12 +0100
Subject: [PATCH 09/21] Drop python3.6 compat import

---
 test/unit/webapps/test_request_scoped_sqlalchemy_sessions.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/test/unit/webapps/test_request_scoped_sqlalchemy_sessions.py b/test/unit/webapps/test_request_scoped_sqlalchemy_sessions.py
index 6c619059a74..c4ea6e26fea 100644
--- a/test/unit/webapps/test_request_scoped_sqlalchemy_sessions.py
+++ b/test/unit/webapps/test_request_scoped_sqlalchemy_sessions.py
@@ -9,7 +9,6 @@ import pytest
 from fastapi import FastAPI
 from fastapi.param_functions import Depends
 from httpx import AsyncClient
-pytest.importorskip("starlette_context")
 from starlette_context import context as request_context
 
 from galaxy.app_unittest_utils.galaxy_mock import MockApp

From f6f9d119a30f08aabdd552506cf387364682947a Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 30 Jan 2022 13:13:27 +0100
Subject: [PATCH 10/21] Move conditional import to end of section

This is necessary so that isort doesn't add extra lines between
statements and import order linting doesn't fail.
---
 lib/galaxy/util/__init__.py      | 22 ++++++++++------------
 lib/galaxy/util/path/__init__.py | 10 +++++-----
 lib/galaxy/util/yaml_util.py     |  2 +-
 3 files changed, 16 insertions(+), 18 deletions(-)

diff --git a/lib/galaxy/util/__init__.py b/lib/galaxy/util/__init__.py
index c45285715b1..a259fbb4f52 100644
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -38,24 +38,27 @@ from urllib.parse import (
 )
 
 import requests
+from boltons.iterutils import (
+    default_enter,
+    remap,
+)
+from requests.adapters import HTTPAdapter
+from requests.packages.urllib3.util.retry import Retry
 try:
     import grp
 except ImportError:
     # For Pulsar on Windows (which does not use the function that uses grp)
     grp = None  # type: ignore[assignment]
-from boltons.iterutils import (
-    default_enter,
-    remap,
-)
+try:
+    import uwsgi
+except ImportError:
+    uwsgi = None
 LXML_AVAILABLE = True
 try:
     from lxml import etree
 except ImportError:
     LXML_AVAILABLE = False
     import xml.etree.ElementTree as etree  # type: ignore[assignment,no-redef]
-from requests.adapters import HTTPAdapter
-from requests.packages.urllib3.util.retry import Retry
-
 try:
     import docutils.core as docutils_core
     import docutils.writers.html4css1 as docutils_html4css1
@@ -63,11 +66,6 @@ except ImportError:
     docutils_core = None  # type: ignore[assignment]
     docutils_html4css1 = None  # type: ignore[assignment]
 
-try:
-    import uwsgi
-except ImportError:
-    uwsgi = None
-
 from .custom_logging import get_logger
 from .inflection import Inflector
 from .path import safe_contains, safe_makedirs, safe_relpath  # noqa: F401
diff --git a/lib/galaxy/util/path/__init__.py b/lib/galaxy/util/path/__init__.py
index 5d8b4bffbaa..d77854448df 100644
--- a/lib/galaxy/util/path/__init__.py
+++ b/lib/galaxy/util/path/__init__.py
@@ -6,10 +6,6 @@ import imp
 import logging
 import shlex
 from functools import partial
-try:
-    from grp import getgrgid
-except ImportError:
-    getgrgid = None  # type: ignore[assignment]
 from itertools import starmap
 from operator import getitem
 from os import (
@@ -33,12 +29,16 @@ from os.path import (
     sep as separator,
 )
 from pathlib import Path
+try:
+    from grp import getgrgid
+except ImportError:
+    getgrgid = None  # type: ignore[assignment]
+
 try:
     from pwd import getpwuid
 except ImportError:
     getpwuid = None  # type: ignore[assignment]
 
-
 import galaxy.util
 
 WALK_MAX_DIRS = 10000
diff --git a/lib/galaxy/util/yaml_util.py b/lib/galaxy/util/yaml_util.py
index 3427a70fd16..60b02f736b4 100644
--- a/lib/galaxy/util/yaml_util.py
+++ b/lib/galaxy/util/yaml_util.py
@@ -3,11 +3,11 @@ import os
 from collections import OrderedDict
 
 import yaml
+from yaml.constructor import ConstructorError
 try:
     from yaml import CSafeLoader as SafeLoader
 except ImportError:
     from yaml import SafeLoader  # type: ignore[misc]
-from yaml.constructor import ConstructorError
 
 
 log = logging.getLogger(__name__)

From 73bd2597bdd62ad3fea182216f0b5d23f5426163 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 30 Jan 2022 11:46:51 +0100
Subject: [PATCH 11/21] Configure isort to produce the right import order style

---
 pyproject.toml | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 0a19ddcc294..6788afd0fee 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -133,3 +133,14 @@ testfixtures = "*"
 tuspy = "*"
 twill = "*"
 watchdog = "*"
+
+[tool.isort]
+force_alphabetical_sort_within_sections = true
+multi_line_output = 3
+force_grid_wrap = 2
+include_trailing_comma = true
+src_paths = ['lib']
+known_first_party = ['galaxy_test']
+no_lines_before = ['LOCALFOLDER']
+reverse_relative = true
+skip_gitignore = true

From 0484e3061cc63b292b7c269275d0cf9f55bb5933 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 30 Jan 2022 13:45:34 +0100
Subject: [PATCH 12/21] Increase line length so long import statements aren't
 split

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 6788afd0fee..f172449c4a4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -144,3 +144,4 @@ known_first_party = ['galaxy_test']
 no_lines_before = ['LOCALFOLDER']
 reverse_relative = true
 skip_gitignore = true
+line_length = 200

From 54bde2cc2a846bf83be7193d5e65221e63bafa7e Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 30 Jan 2022 17:18:52 +0100
Subject: [PATCH 13/21] Move config to .isort.cfg

---
 .isort.cfg     | 11 +++++++++++
 pyproject.toml | 12 ------------
 2 files changed, 11 insertions(+), 12 deletions(-)
 create mode 100644 .isort.cfg

diff --git a/.isort.cfg b/.isort.cfg
new file mode 100644
index 00000000000..2197e0fc2f6
--- /dev/null
+++ b/.isort.cfg
@@ -0,0 +1,11 @@
+[settings]
+force_alphabetical_sort_within_sections=true
+multi_line_output=3
+force_grid_wrap=2
+include_trailing_comma=true
+src_paths=lib
+known_first_party=galaxy_test
+no_lines_before=LOCALFOLDER
+reverse_relative=true
+skip_gitignore=true
+line_length=200
diff --git a/pyproject.toml b/pyproject.toml
index f172449c4a4..0a19ddcc294 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -133,15 +133,3 @@ testfixtures = "*"
 tuspy = "*"
 twill = "*"
 watchdog = "*"
-
-[tool.isort]
-force_alphabetical_sort_within_sections = true
-multi_line_output = 3
-force_grid_wrap = 2
-include_trailing_comma = true
-src_paths = ['lib']
-known_first_party = ['galaxy_test']
-no_lines_before = ['LOCALFOLDER']
-reverse_relative = true
-skip_gitignore = true
-line_length = 200

From 480b62f372117eece3c4c87bf555bd02be095a23 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 2 Feb 2022 22:00:15 -0500
Subject: [PATCH 14/21] Add isort devdependency

---
 lib/galaxy/dependencies/dev-requirements.txt    | 9 +++++----
 lib/galaxy/dependencies/pinned-requirements.txt | 3 ++-
 pyproject.toml                                  | 1 +
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt
index 9e02e9b9843..80742143f6f 100644
--- a/lib/galaxy/dependencies/dev-requirements.txt
+++ b/lib/galaxy/dependencies/dev-requirements.txt
@@ -30,7 +30,7 @@ cached-property==1.5.2; python_version < "3.8" and python_version >= "3.7"
 celery==5.2.3; python_version >= "3.7"
 certifi==2021.10.8; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.7"
 cffi==1.15.0
-charset-normalizer==2.0.11; python_full_version >= "3.6.0" and python_version >= "3.6" and python_version < "4"
+charset-normalizer==2.0.11; python_full_version >= "3.6.0" and python_version >= "3.7" and python_version < "4"
 cheetah3==3.2.6.post1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
 circus==0.17.1
 click-didyoumean==0.3.0; python_full_version >= "3.6.2" and python_full_version < "4.0.0" and python_version >= "3.7"
@@ -80,6 +80,7 @@ importlib-resources==5.4.0; python_version >= "3.6"
 iniconfig==1.1.1; python_version >= "3.7"
 isa-rwval==0.10.10
 isodate==0.6.1; python_version >= "3.7" and python_version < "4"
+isort==5.10.1; python_full_version >= "3.6.1" and python_version < "4.0"
 jinja2==3.0.3; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
 jsonschema==4.4.0; python_version >= "3.7"
 junit-xml==1.9; python_version >= "3.6" and python_version < "4"
@@ -91,7 +92,7 @@ mako==1.1.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (pyt
 markdown-it-reporter==0.0.2
 markdown==3.3.6; python_version >= "3.6"
 markupsafe==2.0.1; python_version >= "3.6"
-mercurial==6.0.1
+mercurial==6.0.2
 mirakuru==2.4.1; python_version >= "3.7"
 mistune==0.8.4; python_version >= "3.7" and python_version < "4"
 mrcfile==1.3.0
@@ -166,7 +167,7 @@ repoze.lru==0.7
 requests-oauthlib==1.3.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0"
 requests-toolbelt==0.9.1; python_version >= "3.6"
 requests==2.27.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.6.0")
-responses==0.17.0; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.5.0")
+responses==0.18.0; python_version >= "3.7"
 rfc3986==1.5.0; python_version >= "3.6"
 rich==11.1.0; python_full_version >= "3.6.2" and python_full_version < "4.0.0"
 routes==2.5.1
@@ -177,7 +178,7 @@ schema-salad==8.2.20220103095339; python_version >= "3.7" and python_version < "
 selenium==4.1.0; python_version >= "3.7" and python_version < "4.0"
 setuptools-scm==5.0.2; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
 shellescape==3.8.1; python_version >= "3.6" and python_version < "4"
-six==1.16.0; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.5.0" and python_version >= "3.7" and python_version < "4"
+six==1.16.0; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.3.0" and python_version >= "3.7" and python_version < "4"
 sniffio==1.2.0; python_version >= "3.7" and python_full_version >= "3.6.2" and python_version < "4.0"
 snowballstemmer==2.2.0; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.4.0" and python_version >= "3.6"
 social-auth-core==4.0.3
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index c5fd30801a5..4a98d727db5 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -67,6 +67,7 @@ importlib-metadata==4.10.1; python_version == "3.7" and (python_version >= "3.7"
 importlib-resources==5.4.0; python_version >= "3.6"
 isa-rwval==0.10.10
 isodate==0.6.1; python_version >= "3.7" and python_version < "4"
+isort==5.10.1; python_full_version >= "3.6.1" and python_version < "4.0"
 jsonschema==4.4.0; python_version >= "3.7"
 kombu==5.2.3; python_version >= "3.7"
 lagom==1.7.0; python_version >= "3.6" and python_version < "4.0"
@@ -75,7 +76,7 @@ lxml==4.7.1; (python_version >= "2.7" and python_full_version < "3.0.0") or (pyt
 mako==1.1.6; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
 markdown==3.3.6; python_version >= "3.6"
 markupsafe==2.0.1; python_version >= "3.6"
-mercurial==6.0.1
+mercurial==6.0.2
 mistune==0.8.4; python_version >= "3.7" and python_version < "4"
 mrcfile==1.3.0
 msgpack==1.0.3; python_version >= "3.7" and python_version < "4"
diff --git a/pyproject.toml b/pyproject.toml
index 0a19ddcc294..f15c7bf6c54 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -100,6 +100,7 @@ uvloop = "*"
 WebOb = "*"
 Whoosh = "*"
 zipstream-new = "*"
+isort = "^5.10.1"
 
 [tool.poetry.dev-dependencies]
 black = "^22.1.0"

From 3dc305433cb2cb40251bbf21a14c08ada983594c Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 2 Feb 2022 22:03:21 -0500
Subject: [PATCH 15/21] Isort config update from Nicola at
 https://github.com/galaxyproject/galaxy/pull/13270\#discussion_r798123586

---
 .isort.cfg | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.isort.cfg b/.isort.cfg
index 2197e0fc2f6..99c5810d05d 100644
--- a/.isort.cfg
+++ b/.isort.cfg
@@ -1,11 +1,11 @@
 [settings]
+extend_skip=doc/source/conf.py,lib/galaxy/util/jstree.py
 force_alphabetical_sort_within_sections=true
-multi_line_output=3
-force_grid_wrap=2
-include_trailing_comma=true
-src_paths=lib
-known_first_party=galaxy_test
+force_grid_wrap=2  # Override value from profile=black, but black is still happy
+line_length=120  # Same as for black
 no_lines_before=LOCALFOLDER
+profile=black
 reverse_relative=true
 skip_gitignore=true
-line_length=200
+skip_glob=database/*  # Make isort run faster
+src_paths=lib

From 2ee2adae5d6e7c67a8ec5c1851dfc16adf0c49da Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 2 Feb 2022 22:14:20 -0500
Subject: [PATCH 16/21] Fix comments in .isort.cfg -- looks like you can't have
 inline comments here?

---
 .isort.cfg | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.isort.cfg b/.isort.cfg
index 99c5810d05d..b3778fdf7c4 100644
--- a/.isort.cfg
+++ b/.isort.cfg
@@ -1,11 +1,14 @@
 [settings]
 extend_skip=doc/source/conf.py,lib/galaxy/util/jstree.py
 force_alphabetical_sort_within_sections=true
-force_grid_wrap=2  # Override value from profile=black, but black is still happy
-line_length=120  # Same as for black
+# Override force_grid_wrap value from profile=black, but black is still happy
+force_grid_wrap=2
+# Same line length as for black
+line_length=120
 no_lines_before=LOCALFOLDER
 profile=black
 reverse_relative=true
 skip_gitignore=true
-skip_glob=database/*  # Make isort run faster
+# Make isort run faster by skipping database
+skip_glob=database/*  
 src_paths=lib

From bf0ad06e22ff514646beed8fd53a77108d154ec2 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 3 Feb 2022 07:00:28 -0500
Subject: [PATCH 17/21] Move isort back into devDependencies.

---
 lib/galaxy/dependencies/pinned-requirements.txt | 1 -
 pyproject.toml                                  | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index 4a98d727db5..808cc037714 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -67,7 +67,6 @@ importlib-metadata==4.10.1; python_version == "3.7" and (python_version >= "3.7"
 importlib-resources==5.4.0; python_version >= "3.6"
 isa-rwval==0.10.10
 isodate==0.6.1; python_version >= "3.7" and python_version < "4"
-isort==5.10.1; python_full_version >= "3.6.1" and python_version < "4.0"
 jsonschema==4.4.0; python_version >= "3.7"
 kombu==5.2.3; python_version >= "3.7"
 lagom==1.7.0; python_version >= "3.6" and python_version < "4.0"
diff --git a/pyproject.toml b/pyproject.toml
index f15c7bf6c54..fe6c0bd55d1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -100,7 +100,6 @@ uvloop = "*"
 WebOb = "*"
 Whoosh = "*"
 zipstream-new = "*"
-isort = "^5.10.1"
 
 [tool.poetry.dev-dependencies]
 black = "^22.1.0"
@@ -108,6 +107,7 @@ cwltest = "2.2.20210901154959"
 darker = "*"
 fluent-logger = "*"
 httpx = "*"
+isort = "^5.10.1"
 lxml = "!=4.2.2"
 markdown-it-reporter = "*"
 NoseHTML = "*"

From ff08c9c75e9e5cbbf6bd2df2ea23471487139a5e Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 2 Feb 2022 22:22:35 -0500
Subject: [PATCH 18/21] Drop flake8-import-order (this will all be
 automagically reordered by isort, so there's no need to lint the order)

---
 lib/galaxy/dependencies/lint-requirements.txt        | 1 -
 lib/galaxy/dependencies/pinned-lint-requirements.txt | 1 -
 setup.cfg                                            | 4 ----
 3 files changed, 6 deletions(-)

diff --git a/lib/galaxy/dependencies/lint-requirements.txt b/lib/galaxy/dependencies/lint-requirements.txt
index 4360f8e7166..b629fbe1728 100644
--- a/lib/galaxy/dependencies/lint-requirements.txt
+++ b/lib/galaxy/dependencies/lint-requirements.txt
@@ -1,6 +1,5 @@
 flake8
 flake8-bugbear
-flake8-import-order
 mypy==0.910
 types-bleach
 types-boto
diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index f6212039a2f..f0ee2ef900f 100644
--- a/lib/galaxy/dependencies/pinned-lint-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -1,7 +1,6 @@
 attrs==21.4.0
 flake8==4.0.1
 flake8-bugbear==22.1.11
-flake8-import-order==0.18.1
 importlib-metadata==4.2.0
 mccabe==0.6.1
 mypy==0.910
diff --git a/setup.cfg b/setup.cfg
index 017ae8f9915..1ae7ccabadc 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -12,10 +12,6 @@ universal = 1
 # D** are docstring linting - which we mostly ignore except D302. (Hopefully we will solve more over time).
 ignore = B008,E128,E203,E402,E501,W503,D100,D101,D102,D103,D104,D105,D106,D107,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
 exclude = lib/galaxy/util/jstree.py
-# For flake8-import-order
-# https://github.com/PyCQA/flake8-import-order/blob/master/tests/test_cases/complete_smarkets.py
-import-order-style = smarkets
-application-import-names = galaxy,galaxy_test,tool_shed
 
 [mypy]
 show_error_codes = True

From fb454041b1d13e08589e14c6b5ba28a9e78075a8 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 2 Feb 2022 22:35:36 -0500
Subject: [PATCH 19/21] Ignore E203 even for stricter linting subset

---
 .ci/flake8_wrapper.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.ci/flake8_wrapper.sh b/.ci/flake8_wrapper.sh
index b6fb1a2e0f6..522a7b2abb2 100755
--- a/.ci/flake8_wrapper.sh
+++ b/.ci/flake8_wrapper.sh
@@ -5,4 +5,4 @@ set -e
 flake8 --exclude $(paste -sd, .ci/flake8_ignorelist.txt) .
 
 # Apply stricter rules for the directories shared with Pulsar
-flake8 --ignore=D --max-line-length=150 lib/galaxy/jobs/runners/util/
+flake8 --ignore=E203,D --max-line-length=150 lib/galaxy/jobs/runners/util/

From c6d250516e269127a7e5e34aefe94734ded31f2a Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Wed, 2 Feb 2022 22:38:49 -0500
Subject: [PATCH 20/21] Add simple make target for formatting everything
 (non-diff)

---
 Makefile | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/Makefile b/Makefile
index 679a56cb5a1..22ac7eba74a 100644
--- a/Makefile
+++ b/Makefile
@@ -41,6 +41,10 @@ setup-venv:
 diff-format:
 	$(IN_VENV) darker -r $(TARGET_BRANCH)
 
+format:
+	$(IN_VENV) black .
+	$(IN_VENV) isort .
+
 list-dependency-updates: setup-venv
 	$(IN_VENV) pip list --outdated --format=columns
 

From ff2f3600f4315eb0165103e7c37285a46f5e5ccf Mon Sep 17 00:00:00 2001
From: Dannon <dannon.baker@gmail.com>
Date: Thu, 3 Feb 2022 06:56:42 -0500
Subject: [PATCH 21/21] Update Makefile

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 22ac7eba74a..1c8d1e0a6d1 100644
--- a/Makefile
+++ b/Makefile
@@ -42,8 +42,8 @@ diff-format:
 	$(IN_VENV) darker -r $(TARGET_BRANCH)
 
 format:
-	$(IN_VENV) black .
 	$(IN_VENV) isort .
+	$(IN_VENV) black .
 
 list-dependency-updates: setup-venv
 	$(IN_VENV) pip list --outdated --format=columns