From ec0cdc718aef1f46e457f1c9194dd9079f8b4ff1 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 16 Nov 2022 19:54:38 -0500
Subject: [PATCH 01/27] Fix implicit reexport error for selenium

lib/galaxy/selenium/smart_components.py:1: error: Module "selenium.webdriver.support.ui" does not explicitly export attribute "Select"; implicit reexport disabled  [attr-defined]
    from selenium.webdriver.support.ui import Select
    ^
lib/galaxy/selenium/sizzle.py:6: error: Module "selenium.webdriver.support.ui" does not explicitly export attribute "WebDriverWait"; implicit reexport disabled  [attr-defined]
    from selenium.webdriver.support.ui import WebDriverWait
---
 mypy.ini | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/mypy.ini b/mypy.ini
index bbefdbab609..4df64f6629d 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -7,6 +7,10 @@ pretty = True
 no_implicit_reexport = True
 no_implicit_optional = True
 
+# overrides for external code
+[mypy-selenium.webdriver.support.ui]
+no_implicit_reexport = False
+
 # green list - work on growing these please!
 [mypy-galaxy.util.compression_utils]
 disallow_any_generics = True

From 4c96135b6c11bd4c19a1f1124e91c52feb31bb6d Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 28 Nov 2022 10:35:15 -0500
Subject: [PATCH 02/27] Fix reexport error (selenium) by direct import

---
 lib/galaxy/selenium/smart_components.py | 2 +-
 mypy.ini                                | 4 ----
 2 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/lib/galaxy/selenium/smart_components.py b/lib/galaxy/selenium/smart_components.py
index 3f1d3d17fca..3f25f7d4a11 100644
--- a/lib/galaxy/selenium/smart_components.py
+++ b/lib/galaxy/selenium/smart_components.py
@@ -1,4 +1,4 @@
-from selenium.webdriver.support.ui import Select
+from selenium.webdriver.support.select import Select
 
 from galaxy.navigation.components import (
     Component,
diff --git a/mypy.ini b/mypy.ini
index 4df64f6629d..bbefdbab609 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -7,10 +7,6 @@ pretty = True
 no_implicit_reexport = True
 no_implicit_optional = True
 
-# overrides for external code
-[mypy-selenium.webdriver.support.ui]
-no_implicit_reexport = False
-
 # green list - work on growing these please!
 [mypy-galaxy.util.compression_utils]
 disallow_any_generics = True

From 9c4bf23a61b3a8bdeb2d7ef3eb1a826764a6b0ef Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 16 Nov 2022 23:44:15 -0500
Subject: [PATCH 03/27] Fix mypy error (incompatible type)

lib/galaxy/managers/model_stores.py:59: error: Argument "app" to "DirectoryModelExportStore" has incompatible type "MinimalManagerApp"; expected "Optional[StoreAppProtocol]"  [arg-type]
            with DirectoryModelExportStore(store_directory, app=self._app, export_files="symlink") as export_store:
                                                                ^~~~~~~~~
lib/galaxy/managers/model_stores.py:59: note: Following member(s) of "MinimalManagerApp" have conflicts:
lib/galaxy/managers/model_stores.py:59: note:     object_store: expected "ObjectStore", got "BaseObjectStore"
lib/galaxy/managers/model_stores.py:186: error: Argument 2 to "source_to_import_store" has incompatible type "MinimalManagerApp"; expected "StoreAppProtocol"  [arg-type]
                self._app,
                ^~~~~~~~~
lib/galaxy/managers/model_stores.py:186: note: Following member(s) of "MinimalManagerApp" have conflicts:
lib/galaxy/managers/model_stores.py:186: note:     object_store: expected "ObjectStore", got "BaseObjectStore"
lib/galaxy/managers/model_stores.py:218: error: Argument "app" to "source_to_import_store" has incompatible type "MinimalManagerApp"; expected "StoreAppProtocol"  [arg-type]
            app=app,
                ^~~
lib/galaxy/managers/model_stores.py:218: note: Following member(s) of "MinimalManagerApp" have conflicts:
lib/galaxy/managers/model_stores.py:218: note:     object_store: expected "ObjectStore", got "BaseObjectStore"
---
 lib/galaxy/model/store/__init__.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index b6f1bcef74e..00faf353109 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -63,7 +63,6 @@ from galaxy.model.tags import GalaxyTagHandler
 from galaxy.objectstore import (
     BaseObjectStore,
     ObjectStore,
-)
 from galaxy.schema.bco import (
     BioComputeObjectCore,
     DescriptionDomain,

From aba2b4c52a4297cc92ae1339ba5de51a85065205 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Thu, 17 Nov 2022 00:07:33 -0500
Subject: [PATCH 04/27] Fix mypy error (has-type)

Fixes this error: (the value is of type sqlalchemy.orm.Session; I don't
know what it's not inferred)

test/unit/app/authnz/test_custos_authnz.py:225: error: Cannot determine type of "sa_session"  [has-type]
                    self.session = self.sa_session
---
 test/unit/app/authnz/test_custos_authnz.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/unit/app/authnz/test_custos_authnz.py b/test/unit/app/authnz/test_custos_authnz.py
index 9b8d5402f3a..3ae2dc1f9e3 100644
--- a/test/unit/app/authnz/test_custos_authnz.py
+++ b/test/unit/app/authnz/test_custos_authnz.py
@@ -222,7 +222,7 @@ class TestCustosAuthnz(TestCase):
                 self.cookies = {}
                 self.cookies_args = {}
                 self.request = Request()
-                self.session = self.sa_session
+                self.session = self.sa_session  # type: ignore[has-type]
                 self.sa_session = Session()
                 self.user = None
 

From 3b351e0e437401ffd8ddc36503606e70a63e84f7 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Thu, 17 Nov 2022 22:58:34 -0500
Subject: [PATCH 05/27] Fix mypy errors for workflow refactor actions

---
 lib/galaxy/workflow/refactor/schema.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/lib/galaxy/workflow/refactor/schema.py b/lib/galaxy/workflow/refactor/schema.py
index f6c3e7434f6..c30671b65cc 100644
--- a/lib/galaxy/workflow/refactor/schema.py
+++ b/lib/galaxy/workflow/refactor/schema.py
@@ -76,6 +76,15 @@ class BaseAction(BaseModel):
 
 class Action(BaseAction):
     action_type: str
+    default: Any
+    input: Any
+    label: str
+    name: str
+    output: Any
+    optional: bool
+    step: Any
+    type: str
+    tool_state: Any
 
     @classmethod
     def __get_validators__(cls):

From ac25a305a3110cd9e3484879433c3e6f7d74b61e Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 28 Nov 2022 10:55:46 -0500
Subject: [PATCH 06/27] Revert "Fix mypy errors for workflow refactor actions"

This reverts commit 0c1ff39f72fb56afd04121c49e98cf58cfa597b7.
---
 lib/galaxy/workflow/refactor/schema.py | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/lib/galaxy/workflow/refactor/schema.py b/lib/galaxy/workflow/refactor/schema.py
index c30671b65cc..f6c3e7434f6 100644
--- a/lib/galaxy/workflow/refactor/schema.py
+++ b/lib/galaxy/workflow/refactor/schema.py
@@ -76,15 +76,6 @@ class BaseAction(BaseModel):
 
 class Action(BaseAction):
     action_type: str
-    default: Any
-    input: Any
-    label: str
-    name: str
-    output: Any
-    optional: bool
-    step: Any
-    type: str
-    tool_state: Any
 
     @classmethod
     def __get_validators__(cls):

From 99cc5adee5ed05a408dd6db79bdb087b30df7b27 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 28 Nov 2022 11:11:16 -0500
Subject: [PATCH 07/27] Do not type-check workflow unit test test_refactor_
 models

---
 mypy.ini | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/mypy.ini b/mypy.ini
index bbefdbab609..aeac561f64a 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -685,6 +685,8 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-*.workflows.test_modules]
 check_untyped_defs = False
+[mypy-*.workflows.test_refactor_models]
+check_untyped_defs = False
 [mypy-*.managers.test_HDAManager]
 check_untyped_defs = False
 [mypy-*.managers.test_DatasetManager]

From ad59ae54bf7bf02543cb2b073c9f74e77cb74817 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Mon, 28 Nov 2022 11:14:02 -0500
Subject: [PATCH 08/27] Fix another selenium reexport error

---
 lib/galaxy/model/store/__init__.py | 1 +
 lib/galaxy/selenium/sizzle.py      | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py
index 00faf353109..b6f1bcef74e 100644
--- a/lib/galaxy/model/store/__init__.py
+++ b/lib/galaxy/model/store/__init__.py
@@ -63,6 +63,7 @@ from galaxy.model.tags import GalaxyTagHandler
 from galaxy.objectstore import (
     BaseObjectStore,
     ObjectStore,
+)
 from galaxy.schema.bco import (
     BioComputeObjectCore,
     DescriptionDomain,
diff --git a/lib/galaxy/selenium/sizzle.py b/lib/galaxy/selenium/sizzle.py
index 1282f016ee7..8716a2c55b9 100644
--- a/lib/galaxy/selenium/sizzle.py
+++ b/lib/galaxy/selenium/sizzle.py
@@ -3,7 +3,7 @@
 import json
 
 from selenium.common.exceptions import NoSuchElementException
-from selenium.webdriver.support.ui import WebDriverWait
+from selenium.webdriver.support.wait import WebDriverWait
 
 from .has_driver import exception_indicates_stale_element
 

From cbabba8f4968430815fbe9ab30590dfa45ecaea2 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 29 Nov 2022 13:32:50 -0500
Subject: [PATCH 09/27] Fix typing error in unit test

---
 test/unit/webapps/test_webapp_base.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/test/unit/webapps/test_webapp_base.py b/test/unit/webapps/test_webapp_base.py
index 9f329b9ea98..7fffb3a98cc 100644
--- a/test/unit/webapps/test_webapp_base.py
+++ b/test/unit/webapps/test_webapp_base.py
@@ -10,6 +10,7 @@ from typing import (
 
 import galaxy.config
 from galaxy.app_unittest_utils import galaxy_mock
+from galaxy.structured_app import BasicSharedApp
 from galaxy.webapps.base.webapp import (
     GalaxyWebTransaction,
     WebApplication,
@@ -36,7 +37,7 @@ class CORSParsingMockConfig(galaxy_mock.MockAppConfig):
 
 class TestGalaxyWebTransactionHeaders:
     def _new_trans(self, allowed_origin_hostnames: Optional[str] = None) -> StubGalaxyWebTransaction:
-        app = galaxy_mock.MockApp()
+        app = galaxy_mock.MockApp()[BasicSharedApp]
         app.config = CORSParsingMockConfig(allowed_origin_hostnames=allowed_origin_hostnames)
         webapp = cast(WebApplication, galaxy_mock.MockWebapp(app.security))
         environ = galaxy_mock.buildMockEnviron()

From 71769182b6167b33e0feaedd66c25e303cbbcbc6 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 29 Nov 2022 14:11:13 -0500
Subject: [PATCH 10/27] Ignore 2 type errors in tests

---
 test/integration/test_celery_tasks.py  | 2 +-
 test/unit/app/tools/test_evaluation.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/integration/test_celery_tasks.py b/test/integration/test_celery_tasks.py
index 7bf22660ae8..41e93814239 100644
--- a/test/integration/test_celery_tasks.py
+++ b/test/integration/test_celery_tasks.py
@@ -72,7 +72,7 @@ class TestCeleryTasksIntegration(IntegrationTestCase):
         assert hda_purged()
 
     def test_pdf_download(self):
-        short_term_storage_allocator = self._app[ShortTermStorageAllocator]
+        short_term_storage_allocator = self._app[ShortTermStorageAllocator]  # type: ignore[type-abstract]
         short_term_storage_target = short_term_storage_allocator.new_target("moo.pdf", "application/pdf")
         request_id = short_term_storage_target.request_id
         pdf_download_request = GeneratePdfDownload(
diff --git a/test/unit/app/tools/test_evaluation.py b/test/unit/app/tools/test_evaluation.py
index 24473b5d7fc..69f50e641d5 100644
--- a/test/unit/app/tools/test_evaluation.py
+++ b/test/unit/app/tools/test_evaluation.py
@@ -45,7 +45,7 @@ class TestToolEvaluator(TestCase, UsesApp):
         self.job.history = History()
         self.job.history.id = 42
         self.job.parameters = [JobParameter(name="thresh", value="4")]
-        self.evaluator = ToolEvaluator(self.app, self.tool, self.job, self.test_directory)
+        self.evaluator = ToolEvaluator(self.app, self.tool, self.job, self.test_directory)  # type: ignore[arg-type]
 
     def tearDown(self):
         self.tear_down_app()

From a673687ff84995568972d0c28f70699987508e0e Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 29 Nov 2022 18:13:44 -0500
Subject: [PATCH 11/27] Split lint requirements into lint and typecheck

---
 lib/galaxy/dependencies/lint-requirements.txt      | 13 -------------
 lib/galaxy/dependencies/typecheck-requirements.txt | 13 +++++++++++++
 2 files changed, 13 insertions(+), 13 deletions(-)
 create mode 100644 lib/galaxy/dependencies/typecheck-requirements.txt

diff --git a/lib/galaxy/dependencies/lint-requirements.txt b/lib/galaxy/dependencies/lint-requirements.txt
index a1909d9164d..675b2c5d0d8 100644
--- a/lib/galaxy/dependencies/lint-requirements.txt
+++ b/lib/galaxy/dependencies/lint-requirements.txt
@@ -1,15 +1,2 @@
 flake8
 flake8-bugbear
-mypy
-types-bleach
-types-boto
-types-contextvars
-types-dataclasses
-types-docutils
-types-Markdown
-types-paramiko
-types-pkg-resources
-types-python-dateutil
-types-PyYAML
-types-requests
-types-six
diff --git a/lib/galaxy/dependencies/typecheck-requirements.txt b/lib/galaxy/dependencies/typecheck-requirements.txt
new file mode 100644
index 00000000000..007c33348ec
--- /dev/null
+++ b/lib/galaxy/dependencies/typecheck-requirements.txt
@@ -0,0 +1,13 @@
+mypy
+types-bleach
+types-boto
+types-contextvars
+types-dataclasses
+types-docutils
+types-Markdown
+types-paramiko
+types-pkg-resources
+types-python-dateutil
+types-PyYAML
+types-requests
+types-six

From 15916a007481f606688b10d48aca4ab903edec7a Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 29 Nov 2022 18:14:21 -0500
Subject: [PATCH 12/27] Add script to update pinned typecheck requirments

---
 .../dependencies/update_typecheck_requirements.sh   | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100755 lib/galaxy/dependencies/update_typecheck_requirements.sh

diff --git a/lib/galaxy/dependencies/update_typecheck_requirements.sh b/lib/galaxy/dependencies/update_typecheck_requirements.sh
new file mode 100755
index 00000000000..2ca07e332aa
--- /dev/null
+++ b/lib/galaxy/dependencies/update_typecheck_requirements.sh
@@ -0,0 +1,13 @@
+#!/bin/sh
+set -e
+
+THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)"
+
+TYPECHECK_VENV=$(mktemp -d "${TMPDIR:-/tmp}/typecheck_venv.XXXXXXXXXX")
+python3.7 -m venv "${TYPECHECK_VENV}"
+. "${TYPECHECK_VENV}/bin/activate"
+pip install --upgrade pip setuptools
+pip install -r "${THIS_DIRECTORY}/typecheck-requirements.txt"
+# The grep below is needed to workaround https://github.com/pypa/pip/issues/8331
+pip freeze -l | grep -v 'pkg_resources==0.0.0' > "${THIS_DIRECTORY}/pinned-typecheck-requirements.txt"
+rm -rf "${TYPECHECK_VENV}"

From ca0fb5c2d42ad17c5c85c880621882229587c0a2 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 29 Nov 2022 18:15:02 -0500
Subject: [PATCH 13/27] Update pinned lint and typecheck requirements

---
 .../dependencies/pinned-lint-requirements.txt | 18 ------------------
 .../pinned-typecheck-requirements.txt         | 19 +++++++++++++++++++
 2 files changed, 19 insertions(+), 18 deletions(-)
 create mode 100644 lib/galaxy/dependencies/pinned-typecheck-requirements.txt

diff --git a/lib/galaxy/dependencies/pinned-lint-requirements.txt b/lib/galaxy/dependencies/pinned-lint-requirements.txt
index bc57d184442..0d242b5c6c6 100644
--- a/lib/galaxy/dependencies/pinned-lint-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-lint-requirements.txt
@@ -3,25 +3,7 @@ flake8==5.0.4
 flake8-bugbear==22.10.27
 importlib-metadata==4.2.0
 mccabe==0.7.0
-mypy==0.991
-mypy-extensions==0.4.3
 pycodestyle==2.9.1
 pyflakes==2.5.0
-tomli==2.0.1
-typed-ast==1.5.4
-types-bleach==5.0.3.1
-types-boto==2.49.18.3
-types-contextvars==2.4.7
-types-cryptography==3.3.23.2
-types-dataclasses==0.6.6
-types-docutils==0.19.1.1
-types-Markdown==3.4.2.1
-types-paramiko==2.12.0.1
-types-pkg-resources==0.1.3
-types-python-dateutil==2.8.19.4
-types-PyYAML==6.0.12.2
-types-requests==2.28.11.5
-types-six==1.16.21.4
-types-urllib3==1.26.25.4
 typing_extensions==4.4.0
 zipp==3.11.0
diff --git a/lib/galaxy/dependencies/pinned-typecheck-requirements.txt b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
new file mode 100644
index 00000000000..0f43f72f17a
--- /dev/null
+++ b/lib/galaxy/dependencies/pinned-typecheck-requirements.txt
@@ -0,0 +1,19 @@
+mypy==0.991
+mypy-extensions==0.4.3
+tomli==2.0.1
+typed-ast==1.5.4
+types-bleach==5.0.3.1
+types-boto==2.49.18.3
+types-contextvars==2.4.7
+types-cryptography==3.3.23.2
+types-dataclasses==0.6.6
+types-docutils==0.19.1.1
+types-Markdown==3.4.2.1
+types-paramiko==2.12.0.1
+types-pkg-resources==0.1.3
+types-python-dateutil==2.8.19.4
+types-PyYAML==6.0.12.2
+types-requests==2.28.11.5
+types-six==1.16.21.4
+types-urllib3==1.26.25.4
+typing_extensions==4.4.0

From 9f42c7b71a95d0fd9e18ba036f8a14511e501b47 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 29 Nov 2022 18:16:25 -0500
Subject: [PATCH 14/27] Add new target to Makefile

---
 Makefile | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/Makefile b/Makefile
index ca88e90de8a..72ef8212692 100644
--- a/Makefile
+++ b/Makefile
@@ -134,6 +134,9 @@ release-check-blocking-prs: ## Check github for release blocking PRs
 release-bootstrap-history: ## bootstrap history for a new release
 	$(IN_VENV) python scripts/bootstrap_history.py --release $(RELEASE_CURR)
 
+update-typecheck-requirements:
+	./lib/galaxy/dependencies/update_typecheck_requirements.sh
+
 update-lint-requirements:
 	./lib/galaxy/dependencies/update_lint_requirements.sh
 

From 10f838f94548ba77d9c52e42d50ff9a2176d748d Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 29 Nov 2022 18:25:34 -0500
Subject: [PATCH 15/27] Update tox.ini

---
 tox.ini | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tox.ini b/tox.ini
index 14030c6a210..bb0c5b5d95e 100644
--- a/tox.ini
+++ b/tox.ini
@@ -36,7 +36,9 @@ setenv =
     check_indexes: GALAXY_SKIP_CLIENT_BUILD=1
 deps =
     coverage: coverage
-    lint,lint_docstring,lint_docstring_include_list,mypy: -rlib/galaxy/dependencies/pinned-lint-requirements.txt
+    lint,lint_docstring,lint_docstring_include_list: -rlib/galaxy/dependencies/pinned-lint-requirements.txt
+    mypy: -rlib/galaxy/dependencies/pinned-typecheck-requirements.txt
+    mypy: -rlib/galaxy/dependencies/pinned-requirements.txt
     test_galaxy_packages: pyyaml
     unit: mock-ssh-server
 

From 724ff9e17b6c368ac6c06b588da81cdf0b7eb76b Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 29 Nov 2022 18:40:18 -0500
Subject: [PATCH 16/27] Install mypy for package tests

---
 packages/test.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/packages/test.sh b/packages/test.sh
index d2334003e41..08aca436312 100755
--- a/packages/test.sh
+++ b/packages/test.sh
@@ -16,6 +16,7 @@ virtualenv -p "$TEST_PYTHON" "$TEST_ENV_DIR"
 . "${TEST_ENV_DIR}/bin/activate"
 pip install --upgrade pip setuptools wheel
 pip install -r../lib/galaxy/dependencies/pinned-lint-requirements.txt
+pip install -r../lib/galaxy/dependencies/pinned-typecheck-requirements.txt
 
 # ensure ordered by dependency DAG
 # TODO: add selenium in once type issues are cleared up

From d797c10ae8230b2de28ea476a00397695a5f4f9e Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Tue, 29 Nov 2022 22:02:32 -0500
Subject: [PATCH 17/27] Update github lint workflow

---
 .github/workflows/lint.yaml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index 11cbabf98d8..5949d69df58 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -37,10 +37,14 @@ jobs:
           path: ~/.cache/pip
           key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('lib/galaxy/dependencies/pinned-lint-requirements.txt') }}
       - name: Cache tox env
+        env:
+          LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt'
+          TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'
+          CORE_PATH: 'lib/galaxy/dependencies/pinned-requirements.txt'
         uses: actions/cache@v3
         with:
           path: .tox
-          key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('lib/galaxy/dependencies/pinned-lint-requirements.txt') }}-lint
+          key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles(env.LINT_PATH, env.TYPE_PATH, env.CORE_PATH) }}-lint-and-typecheck
       - name: Install tox
         run: pip install tox
       - name: Run linting

From 1d75a584d658e42087b0534a8bd3850f5f8e255e Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 30 Nov 2022 11:27:41 -0500
Subject: [PATCH 18/27] Keep cache key suffix same as workflow filename

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

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index 5949d69df58..7bff665a705 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -44,7 +44,7 @@ jobs:
         uses: actions/cache@v3
         with:
           path: .tox
-          key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles(env.LINT_PATH, env.TYPE_PATH, env.CORE_PATH) }}-lint-and-typecheck
+          key: tox-cache-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles(env.LINT_PATH, env.TYPE_PATH, env.CORE_PATH) }}-lint
       - name: Install tox
         run: pip install tox
       - name: Run linting

From 786a3e43757895e51d52b3c96f935ddf27c6f18a Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 30 Nov 2022 11:31:22 -0500
Subject: [PATCH 19/27] Don't pip-install lint requirements for package tests

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 packages/test.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/packages/test.sh b/packages/test.sh
index 08aca436312..ee0cef696b5 100755
--- a/packages/test.sh
+++ b/packages/test.sh
@@ -15,7 +15,6 @@ TEST_ENV_DIR=${TEST_ENV_DIR:-$(mktemp -d -t gxpkgtestenvXXXXXX)}
 virtualenv -p "$TEST_PYTHON" "$TEST_ENV_DIR"
 . "${TEST_ENV_DIR}/bin/activate"
 pip install --upgrade pip setuptools wheel
-pip install -r../lib/galaxy/dependencies/pinned-lint-requirements.txt
 pip install -r../lib/galaxy/dependencies/pinned-typecheck-requirements.txt
 
 # ensure ordered by dependency DAG

From 139d14e95280cfd5c0f391ef36b5e875908aa585 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 30 Nov 2022 17:55:04 +0000
Subject: [PATCH 20/27] Fix ``object_store`` type in ``MinimalToolApp``
 protocol

---
 lib/galaxy/structured_app.py           | 7 ++-----
 lib/galaxy/tools/remote_tool_eval.py   | 4 ++--
 test/unit/app/tools/test_evaluation.py | 2 +-
 3 files changed, 5 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/structured_app.py b/lib/galaxy/structured_app.py
index fc55a642de0..217e67bde9f 100644
--- a/lib/galaxy/structured_app.py
+++ b/lib/galaxy/structured_app.py
@@ -24,10 +24,7 @@ from galaxy.model.security import (
     HostAgent,
 )
 from galaxy.model.tags import GalaxyTagHandler
-from galaxy.objectstore import (
-    BaseObjectStore,
-    ObjectStore,
-)
+from galaxy.objectstore import BaseObjectStore
 from galaxy.quota import QuotaAgent
 from galaxy.security.idencoding import IdEncodingHelper
 from galaxy.security.vault import Vault
@@ -78,7 +75,7 @@ class MinimalToolApp(Protocol):
     name: str
     config: Any  # 'galaxy.config.BaseAppConfiguration'
     datatypes_registry: Registry
-    object_store: ObjectStore
+    object_store: BaseObjectStore
     tool_data_tables: "ToolDataTableManager"
     file_sources: ConfiguredFileSources
     security: IdEncodingHelper
diff --git a/lib/galaxy/tools/remote_tool_eval.py b/lib/galaxy/tools/remote_tool_eval.py
index d7c5a62b4f2..8dd158f822d 100644
--- a/lib/galaxy/tools/remote_tool_eval.py
+++ b/lib/galaxy/tools/remote_tool_eval.py
@@ -19,7 +19,7 @@ from galaxy.metadata.set_metadata import (
 )
 from galaxy.model import store
 from galaxy.model.store import SessionlessContext
-from galaxy.objectstore import ObjectStore
+from galaxy.objectstore import BaseObjectStore
 from galaxy.structured_app import MinimalToolApp
 from galaxy.tools import (
     create_tool_from_representation,
@@ -55,7 +55,7 @@ class ToolApp(MinimalToolApp):
         sa_session: SessionlessContext,
         tool_app_config: ToolAppConfig,
         datatypes_registry: Registry,
-        object_store: ObjectStore,
+        object_store: BaseObjectStore,
         tool_data_table_manager: ToolDataTableManager,
         file_sources: ConfiguredFileSources,
     ):
diff --git a/test/unit/app/tools/test_evaluation.py b/test/unit/app/tools/test_evaluation.py
index 69f50e641d5..24473b5d7fc 100644
--- a/test/unit/app/tools/test_evaluation.py
+++ b/test/unit/app/tools/test_evaluation.py
@@ -45,7 +45,7 @@ class TestToolEvaluator(TestCase, UsesApp):
         self.job.history = History()
         self.job.history.id = 42
         self.job.parameters = [JobParameter(name="thresh", value="4")]
-        self.evaluator = ToolEvaluator(self.app, self.tool, self.job, self.test_directory)  # type: ignore[arg-type]
+        self.evaluator = ToolEvaluator(self.app, self.tool, self.job, self.test_directory)
 
     def tearDown(self):
         self.tear_down_app()

From b1c35bfc6a49deb6dfe41fb9093909e65d4ce920 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Wed, 30 Nov 2022 17:57:29 +0000
Subject: [PATCH 21/27] Add type annotation to ``config`` attribute of
 ``MinimalToolApp`` protocol

---
 lib/galaxy/structured_app.py         | 3 ++-
 lib/galaxy/tools/remote_tool_eval.py | 4 +++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/structured_app.py b/lib/galaxy/structured_app.py
index 217e67bde9f..7d1ca6830ee 100644
--- a/lib/galaxy/structured_app.py
+++ b/lib/galaxy/structured_app.py
@@ -38,6 +38,7 @@ from galaxy.webhooks import WebhooksRegistry
 from galaxy.workflow.trs_proxy import TrsProxy
 
 if TYPE_CHECKING:
+    from galaxy.config import GalaxyAppConfiguration
     from galaxy.config_watchers import ConfigWatchers
     from galaxy.jobs import JobConfiguration
     from galaxy.managers.collections import DatasetCollectionManager
@@ -73,7 +74,7 @@ class BasicSharedApp(Container):
 
 class MinimalToolApp(Protocol):
     name: str
-    config: Any  # 'galaxy.config.BaseAppConfiguration'
+    config: "GalaxyAppConfiguration"
     datatypes_registry: Registry
     object_store: BaseObjectStore
     tool_data_tables: "ToolDataTableManager"
diff --git a/lib/galaxy/tools/remote_tool_eval.py b/lib/galaxy/tools/remote_tool_eval.py
index 8dd158f822d..dc979c03ae4 100644
--- a/lib/galaxy/tools/remote_tool_eval.py
+++ b/lib/galaxy/tools/remote_tool_eval.py
@@ -5,9 +5,11 @@ import tempfile
 import traceback
 from typing import (
     Callable,
+    cast,
     NamedTuple,
 )
 
+from galaxy.config import GalaxyAppConfiguration
 from galaxy.datatypes.registry import Registry
 from galaxy.files import ConfiguredFileSources
 from galaxy.job_execution.compute_environment import SharedComputeEnvironment
@@ -60,7 +62,7 @@ class ToolApp(MinimalToolApp):
         file_sources: ConfiguredFileSources,
     ):
         self.model = Bunch(context=sa_session)
-        self.config = tool_app_config
+        self.config = cast(GalaxyAppConfiguration, tool_app_config)
         self.datatypes_registry = datatypes_registry
         self.object_store = object_store
         self.genome_builds = GenomeBuilds(self)

From 67c7e7d1acb210d6c1af7c57fd8ad3a4f1f341f6 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 30 Nov 2022 13:33:42 -0500
Subject: [PATCH 22/27] Use a simple cast instead of relying on dependency
 injection

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 test/unit/webapps/test_webapp_base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/unit/webapps/test_webapp_base.py b/test/unit/webapps/test_webapp_base.py
index 7fffb3a98cc..d0aa4a42f22 100644
--- a/test/unit/webapps/test_webapp_base.py
+++ b/test/unit/webapps/test_webapp_base.py
@@ -37,7 +37,7 @@ class CORSParsingMockConfig(galaxy_mock.MockAppConfig):
 
 class TestGalaxyWebTransactionHeaders:
     def _new_trans(self, allowed_origin_hostnames: Optional[str] = None) -> StubGalaxyWebTransaction:
-        app = galaxy_mock.MockApp()[BasicSharedApp]
+        app = cast(BasicSharedApp, galaxy_mock.MockApp())
         app.config = CORSParsingMockConfig(allowed_origin_hostnames=allowed_origin_hostnames)
         webapp = cast(WebApplication, galaxy_mock.MockWebapp(app.security))
         environ = galaxy_mock.buildMockEnviron()

From 02ea4f531edddd0f518551eb85d9974c6e60e69a Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 30 Nov 2022 13:39:16 -0500
Subject: [PATCH 23/27] Drop unused attr

Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
---
 test/unit/app/authnz/test_custos_authnz.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/test/unit/app/authnz/test_custos_authnz.py b/test/unit/app/authnz/test_custos_authnz.py
index 3ae2dc1f9e3..e308bb8f9c1 100644
--- a/test/unit/app/authnz/test_custos_authnz.py
+++ b/test/unit/app/authnz/test_custos_authnz.py
@@ -222,7 +222,6 @@ class TestCustosAuthnz(TestCase):
                 self.cookies = {}
                 self.cookies_args = {}
                 self.request = Request()
-                self.session = self.sa_session  # type: ignore[has-type]
                 self.sa_session = Session()
                 self.user = None
 

From 578fe8ae98a48e0d49393c72394e5afa602d9e2a Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 30 Nov 2022 13:41:16 -0500
Subject: [PATCH 24/27] Revert "Add new target to Makefile"

This reverts commit 9f42c7b71a95d0fd9e18ba036f8a14511e501b47.
---
 Makefile | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/Makefile b/Makefile
index 72ef8212692..ca88e90de8a 100644
--- a/Makefile
+++ b/Makefile
@@ -134,9 +134,6 @@ release-check-blocking-prs: ## Check github for release blocking PRs
 release-bootstrap-history: ## bootstrap history for a new release
 	$(IN_VENV) python scripts/bootstrap_history.py --release $(RELEASE_CURR)
 
-update-typecheck-requirements:
-	./lib/galaxy/dependencies/update_typecheck_requirements.sh
-
 update-lint-requirements:
 	./lib/galaxy/dependencies/update_lint_requirements.sh
 

From b8f2aec15515baf8563320f276014c2a3301969d Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 30 Nov 2022 14:44:30 -0500
Subject: [PATCH 25/27] Combine update lint/typecheck reqs scripts

---
 .../dependencies/update_lint_requirements.sh  | 29 ++++++++++++++-----
 .../update_typecheck_requirements.sh          | 13 ---------
 2 files changed, 21 insertions(+), 21 deletions(-)
 delete mode 100755 lib/galaxy/dependencies/update_typecheck_requirements.sh

diff --git a/lib/galaxy/dependencies/update_lint_requirements.sh b/lib/galaxy/dependencies/update_lint_requirements.sh
index d477d941ab9..58c503e2e3f 100755
--- a/lib/galaxy/dependencies/update_lint_requirements.sh
+++ b/lib/galaxy/dependencies/update_lint_requirements.sh
@@ -1,13 +1,26 @@
 #!/bin/sh
+
 set -e
 
+# This script updates the pinned requirements for both linting and typechecking.
+# The requirements are split into two parts due to incompatible dependencies:
+# flake8 requires importlib-metadata 4.2; typecheck requirements do not
+# depende on importlib-metadata; however, they must be installed into the same
+# virtual environment as Galaxy's core dependencies, which depend on
+# importlib-metadata 4.13.
+
 THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)"
 
-LINT_VENV=$(mktemp -d "${TMPDIR:-/tmp}/lint_venv.XXXXXXXXXX")
-python3.7 -m venv "${LINT_VENV}"
-. "${LINT_VENV}/bin/activate"
-pip install --upgrade pip setuptools
-pip install -r "${THIS_DIRECTORY}/lint-requirements.txt"
-# The grep below is needed to workaround https://github.com/pypa/pip/issues/8331
-pip freeze -l | grep -v 'pkg_resources==0.0.0' > "${THIS_DIRECTORY}/pinned-lint-requirements.txt"
-rm -rf "${LINT_VENV}"
+update_pinned_reqs() {
+    VENV=$(mktemp -d "${TMPDIR:-/tmp}/$1_venv.XXXXXXXXXX")
+    python3.7 -m venv "${VENV}"
+    . "${VENV}/bin/activate"
+    pip install --upgrade pip setuptools
+    pip install -r "${THIS_DIRECTORY}/$1-requirements.txt"
+    # The grep below is needed to workaround https://github.com/pypa/pip/issues/8331
+    pip freeze -l | grep -v 'pkg_resources==0.0.0' > "${THIS_DIRECTORY}/pinned-$1-requirements.txt"
+    rm -rf "${VENV}"
+}
+
+update_pinned_reqs lint
+update_pinned_reqs typecheck
diff --git a/lib/galaxy/dependencies/update_typecheck_requirements.sh b/lib/galaxy/dependencies/update_typecheck_requirements.sh
deleted file mode 100755
index 2ca07e332aa..00000000000
--- a/lib/galaxy/dependencies/update_typecheck_requirements.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/bin/sh
-set -e
-
-THIS_DIRECTORY="$(cd "$(dirname "$0")" > /dev/null && pwd)"
-
-TYPECHECK_VENV=$(mktemp -d "${TMPDIR:-/tmp}/typecheck_venv.XXXXXXXXXX")
-python3.7 -m venv "${TYPECHECK_VENV}"
-. "${TYPECHECK_VENV}/bin/activate"
-pip install --upgrade pip setuptools
-pip install -r "${THIS_DIRECTORY}/typecheck-requirements.txt"
-# The grep below is needed to workaround https://github.com/pypa/pip/issues/8331
-pip freeze -l | grep -v 'pkg_resources==0.0.0' > "${THIS_DIRECTORY}/pinned-typecheck-requirements.txt"
-rm -rf "${TYPECHECK_VENV}"

From 303f1a04af34af4295f94d46c26f1b8d4bf1b223 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 1 Dec 2022 01:45:33 +0000
Subject: [PATCH 26/27] Revert "Add type annotation to ``config`` attribute of
 ``MinimalToolApp`` protocol"

This reverts commit b1c35bfc6a49deb6dfe41fb9093909e65d4ce920.

Also, add comment about why `MinimalToolApp.config` should be type annotated as `Any`.
---
 lib/galaxy/structured_app.py         | 5 +++--
 lib/galaxy/tools/remote_tool_eval.py | 4 +---
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/structured_app.py b/lib/galaxy/structured_app.py
index 7d1ca6830ee..eaea543fd12 100644
--- a/lib/galaxy/structured_app.py
+++ b/lib/galaxy/structured_app.py
@@ -38,7 +38,6 @@ from galaxy.webhooks import WebhooksRegistry
 from galaxy.workflow.trs_proxy import TrsProxy
 
 if TYPE_CHECKING:
-    from galaxy.config import GalaxyAppConfiguration
     from galaxy.config_watchers import ConfigWatchers
     from galaxy.jobs import JobConfiguration
     from galaxy.managers.collections import DatasetCollectionManager
@@ -74,7 +73,9 @@ class BasicSharedApp(Container):
 
 class MinimalToolApp(Protocol):
     name: str
-    config: "GalaxyAppConfiguration"
+    # Leave config as Any: in a full Galaxy app this is a GalaxyAppConfiguration object, but this is mostly dynamically
+    # generated, and here we want to also allow other kinds of configuration objects (e.g. a Bunch).
+    config: Any
     datatypes_registry: Registry
     object_store: BaseObjectStore
     tool_data_tables: "ToolDataTableManager"
diff --git a/lib/galaxy/tools/remote_tool_eval.py b/lib/galaxy/tools/remote_tool_eval.py
index dc979c03ae4..8dd158f822d 100644
--- a/lib/galaxy/tools/remote_tool_eval.py
+++ b/lib/galaxy/tools/remote_tool_eval.py
@@ -5,11 +5,9 @@ import tempfile
 import traceback
 from typing import (
     Callable,
-    cast,
     NamedTuple,
 )
 
-from galaxy.config import GalaxyAppConfiguration
 from galaxy.datatypes.registry import Registry
 from galaxy.files import ConfiguredFileSources
 from galaxy.job_execution.compute_environment import SharedComputeEnvironment
@@ -62,7 +60,7 @@ class ToolApp(MinimalToolApp):
         file_sources: ConfiguredFileSources,
     ):
         self.model = Bunch(context=sa_session)
-        self.config = cast(GalaxyAppConfiguration, tool_app_config)
+        self.config = tool_app_config
         self.datatypes_registry = datatypes_registry
         self.object_store = object_store
         self.genome_builds = GenomeBuilds(self)

From f07207ad6d2abfa46102f63ec29dca77d1802a94 Mon Sep 17 00:00:00 2001
From: John Davis <jdavcs@gmail.com>
Date: Wed, 30 Nov 2022 21:10:04 -0500
Subject: [PATCH 27/27] Use 3 requirements files in the key for pip cache

---
 .github/workflows/lint.yaml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml
index 7bff665a705..0125f24c4d4 100644
--- a/.github/workflows/lint.yaml
+++ b/.github/workflows/lint.yaml
@@ -22,6 +22,10 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.7', '3.10']
+    env:
+      LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt'
+      TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'
+      CORE_PATH: 'lib/galaxy/dependencies/pinned-requirements.txt'
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
@@ -35,12 +39,8 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ~/.cache/pip
-          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('lib/galaxy/dependencies/pinned-lint-requirements.txt') }}
+          key: pip-cache-${{ matrix.python-version }}-${{ hashFiles(env.LINT_PATH, env.TYPE_PATH, env.CORE_PATH) }}
       - name: Cache tox env
-        env:
-          LINT_PATH: 'lib/galaxy/dependencies/pinned-lint-requirements.txt'
-          TYPE_PATH: 'lib/galaxy/dependencies/pinned-typecheck-requirements.txt'
-          CORE_PATH: 'lib/galaxy/dependencies/pinned-requirements.txt'
         uses: actions/cache@v3
         with:
           path: .tox