From 59ae70052956139768a1c0dc4b9d33417814b24a Mon Sep 17 00:00:00 2001
From: Adrienne Stilp <amstilp@uw.edu>
Date: Fri, 8 Nov 2024 14:56:38 -0800
Subject: [PATCH 01/23] Update ACM version in requirements

---
 requirements/requirements.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/requirements.in b/requirements/requirements.in
index 9e075aeb..50a1f247 100644
--- a/requirements/requirements.in
+++ b/requirements/requirements.in
@@ -38,7 +38,7 @@ django-dbbackup # https://github.com/jazzband/django-dbbackup
 django-extensions  # https://github.com/django-extensions/django-extensions
 
 # anvil_consortium_manager
-django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.25
+django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.26
 
 # Simple history - model history tracking
 django-simple-history

From 7646c2a7d1e0d08348d16adbd27fc44e7ad1f6d3 Mon Sep 17 00:00:00 2001
From: amstilp <3944584+amstilp@users.noreply.github.com>
Date: Fri, 8 Nov 2024 22:57:43 +0000
Subject: [PATCH 02/23] Compile requirements files

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

diff --git a/requirements/requirements.txt b/requirements/requirements.txt
index 666c79a8..def3bf24 100644
--- a/requirements/requirements.txt
+++ b/requirements/requirements.txt
@@ -57,7 +57,7 @@ django==4.2.16
     #   django-tables2
 django-allauth==65.1.0
     # via -r requirements/requirements.in
-django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.25
+django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.26
     # via -r requirements/requirements.in
 django-autocomplete-light==3.11.0
     # via django-anvil-consortium-manager

From b27ff1c309fb0ca59b6e8f4f79e82376898b9745 Mon Sep 17 00:00:00 2001
From: Adrienne Stilp <amstilp@uw.edu>
Date: Fri, 8 Nov 2024 15:58:31 -0800
Subject: [PATCH 03/23] Move account settings from config to AccountAdapter

These are new changes in ACM v0.26 - move the relevant settings from
the config file to the AccountAdapter.
---
 config/settings/base.py         | 6 ------
 primed/primed_anvil/adapters.py | 3 +++
 2 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/config/settings/base.py b/config/settings/base.py
index 2f98275c..3f2c24d9 100644
--- a/config/settings/base.py
+++ b/config/settings/base.py
@@ -394,12 +394,6 @@
 ANVIL_ACCOUNT_ADAPTER = "primed.primed_anvil.adapters.AccountAdapter"
 ANVIL_MANAGED_GROUP_ADAPTER = "primed.primed_anvil.adapters.ManagedGroupAdapter"
 
-# Specify the URL name that AccountLink and AccountLinkVerify redirect to.
-ANVIL_ACCOUNT_LINK_REDIRECT = "users:redirect"
-# Specify the subject for AnVIL account verification emails.
-ANVIL_ACCOUNT_LINK_EMAIL_SUBJECT = "Verify your AnVIL account email"
-ANVIL_ACCOUNT_VERIFY_NOTIFICATION_EMAIL = "primedconsortium@uw.edu"
-
 DRUPAL_API_CLIENT_ID = env("DRUPAL_API_CLIENT_ID", default="")
 DRUPAL_API_CLIENT_SECRET = env("DRUPAL_API_CLIENT_SECRET", default="")
 DRUPAL_API_REL_PATH = env("DRUPAL_API_REL_PATH", default="mockapi")
diff --git a/primed/primed_anvil/adapters.py b/primed/primed_anvil/adapters.py
index 2eba20a4..c821b5f9 100644
--- a/primed/primed_anvil/adapters.py
+++ b/primed/primed_anvil/adapters.py
@@ -18,6 +18,9 @@ class AccountAdapter(BaseAccountAdapter):
 
     list_table_class = AccountTable
     list_filterset_class = AccountListFilter
+    account_link_verify_redirect = "users:redirect"
+    account_link_email_subject = "Verify your AnVIL account email"
+    account_verify_notification_email = "foo@uw.edu"
 
     def get_autocomplete_queryset(self, queryset, q):
         """Filter to Accounts where the email or the associated user name matches the query `q`."""

From 39bb260ecfc87f7fd084aa4b6003aff7777d16e2 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Nov 2024 03:16:50 +0000
Subject: [PATCH 04/23] Bump werkzeug from 3.1.2 to 3.1.3

Bumps [werkzeug](https://github.com/pallets/werkzeug) from 3.1.2 to 3.1.3.
- [Release notes](https://github.com/pallets/werkzeug/releases)
- [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst)
- [Commits](https://github.com/pallets/werkzeug/compare/3.1.2...3.1.3)

---
updated-dependencies:
- dependency-name: werkzeug
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements/dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/dev-requirements.txt b/requirements/dev-requirements.txt
index b215dbc3..c5100ca9 100644
--- a/requirements/dev-requirements.txt
+++ b/requirements/dev-requirements.txt
@@ -218,7 +218,7 @@ wcwidth==0.2.13
     # via prompt-toolkit
 websockets==12.0
     # via sphinx-autobuild
-werkzeug==3.1.2
+werkzeug==3.1.3
     # via -r requirements/dev-requirements.in
 
 # The following packages are considered to be unsafe in a requirements file:

From 6d97f481b558750998ba122d493f34df5e7b0db1 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 12 Nov 2024 19:01:12 +0000
Subject: [PATCH 05/23] Bump django-allauth from 65.1.0 to 65.2.0

Bumps [django-allauth](https://github.com/sponsors/pennersr) from 65.1.0 to 65.2.0.
- [Commits](https://github.com/sponsors/pennersr/commits)

---
updated-dependencies:
- dependency-name: django-allauth
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/requirements.txt b/requirements/requirements.txt
index def3bf24..48470afb 100644
--- a/requirements/requirements.txt
+++ b/requirements/requirements.txt
@@ -55,7 +55,7 @@ django==4.2.16
     #   django-picklefield
     #   django-simple-history
     #   django-tables2
-django-allauth==65.1.0
+django-allauth==65.2.0
     # via -r requirements/requirements.in
 django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.26
     # via -r requirements/requirements.in

From b6f30969fb9dd7cca623de368a347f9e942fc98c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 14 Nov 2024 03:14:34 +0000
Subject: [PATCH 06/23] Bump mysqlclient from 2.2.5 to 2.2.6

Bumps [mysqlclient](https://github.com/PyMySQL/mysqlclient) from 2.2.5 to 2.2.6.
- [Release notes](https://github.com/PyMySQL/mysqlclient/releases)
- [Changelog](https://github.com/PyMySQL/mysqlclient/blob/main/HISTORY.rst)
- [Commits](https://github.com/PyMySQL/mysqlclient/commits)

---
updated-dependencies:
- dependency-name: mysqlclient
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/requirements.txt b/requirements/requirements.txt
index def3bf24..5704fb9f 100644
--- a/requirements/requirements.txt
+++ b/requirements/requirements.txt
@@ -110,7 +110,7 @@ jsonschema==4.23.0
     # via -r requirements/requirements.in
 jsonschema-specifications==2023.12.1
     # via jsonschema
-mysqlclient==2.2.5
+mysqlclient==2.2.6
     # via -r requirements/requirements.in
 networkx==3.1
     # via

From 1d78f767b152e24ecdb28f1acf4814aaafbe5ef7 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Nov 2024 03:17:56 +0000
Subject: [PATCH 07/23] Bump pyjwt from 2.9.0 to 2.10.0

Bumps [pyjwt](https://github.com/jpadilla/pyjwt) from 2.9.0 to 2.10.0.
- [Release notes](https://github.com/jpadilla/pyjwt/releases)
- [Changelog](https://github.com/jpadilla/pyjwt/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/jpadilla/pyjwt/compare/2.9.0...2.10.0)

---
updated-dependencies:
- dependency-name: pyjwt
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/requirements.txt b/requirements/requirements.txt
index def3bf24..3a2a9538 100644
--- a/requirements/requirements.txt
+++ b/requirements/requirements.txt
@@ -144,7 +144,7 @@ pyasn1-modules==0.3.0
     # via google-auth
 pycparser==2.21
     # via cffi
-pyjwt==2.9.0
+pyjwt==2.10.0
     # via -r requirements/requirements.in
 pyparsing==3.1.1
     # via packaging

From b06c3b934ccf420d91f292c53e4ac1f4b9f3c1e3 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 18 Nov 2024 03:18:28 +0000
Subject: [PATCH 08/23] Bump ruff from 0.7.2 to 0.7.4

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.7.2 to 0.7.4.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](https://github.com/astral-sh/ruff/compare/0.7.2...0.7.4)

---
updated-dependencies:
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements/dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/dev-requirements.txt b/requirements/dev-requirements.txt
index b215dbc3..6fb1641a 100644
--- a/requirements/dev-requirements.txt
+++ b/requirements/dev-requirements.txt
@@ -137,7 +137,7 @@ requests==2.32.3
     #   -c requirements/requirements.txt
     #   -c requirements/test-requirements.txt
     #   sphinx
-ruff==0.7.2
+ruff==0.7.4
     # via -r requirements/dev-requirements.in
 six==1.16.0
     # via

From 3dcbd4e96f5d7895f9c9c79b5f8213e46dfa7ca6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 21 Nov 2024 03:47:44 +0000
Subject: [PATCH 09/23] Bump codecov/codecov-action from 4.6.0 to 5.0.7

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4.6.0 to 5.0.7.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v4.6.0...v5.0.7)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 70a3b060..5e2bf190 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -140,6 +140,6 @@ jobs:
           python -m coverage report
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4.6.0
+        uses: codecov/codecov-action@v5.0.7
         with:
           token: ${{ secrets.CODECOV_TOKEN }}

From fb246434b46fbf67c95070304a54a191be30dee2 Mon Sep 17 00:00:00 2001
From: Jonas Carson <jcarson@uw.edu>
Date: Thu, 21 Nov 2024 09:12:24 -0800
Subject: [PATCH 10/23] Update favicon for admin site. Also, because browsers
 will still sometimes request the favicon.ico even when it is not in use - add
 a redirect

---
 config/urls.py                        | 2 ++
 primed/templates/admin/base_site.html | 7 +++++++
 2 files changed, 9 insertions(+)
 create mode 100644 primed/templates/admin/base_site.html

diff --git a/config/urls.py b/config/urls.py
index 9b091d3f..b8d07b29 100644
--- a/config/urls.py
+++ b/config/urls.py
@@ -1,6 +1,7 @@
 from django.conf import settings
 from django.conf.urls.static import static
 from django.contrib import admin
+from django.shortcuts import redirect
 from django.urls import include, path
 from django.views import defaults as default_views
 from django.views.generic import TemplateView
@@ -26,6 +27,7 @@
         "collaborative_analysis/",
         include("primed.collaborative_analysis.urls", namespace="collaborative_analysis"),
     ),
+    path("favicon.ico", lambda _: redirect("static/images/favicons/primed-favicon.png", permanent=True)),
 ] + static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)
 
 
diff --git a/primed/templates/admin/base_site.html b/primed/templates/admin/base_site.html
new file mode 100644
index 00000000..21c0e91c
--- /dev/null
+++ b/primed/templates/admin/base_site.html
@@ -0,0 +1,7 @@
+{% extends "admin/base_site.html" %}
+{% load static %}
+{% block extrahead %}
+
+<link rel="shortcut icon" href="{% static 'images/favicons/primed-favicon.png' %}">
+
+{% endblock %}

From 7270b00428bbdf7e642cf59c957158db760291ef Mon Sep 17 00:00:00 2001
From: Jonas Carson <jcarson@uw.edu>
Date: Thu, 21 Nov 2024 09:30:27 -0800
Subject: [PATCH 11/23] Update to use a RedirectView

---
 config/urls.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/config/urls.py b/config/urls.py
index b8d07b29..ce11199f 100644
--- a/config/urls.py
+++ b/config/urls.py
@@ -1,10 +1,10 @@
 from django.conf import settings
 from django.conf.urls.static import static
 from django.contrib import admin
-from django.shortcuts import redirect
 from django.urls import include, path
 from django.views import defaults as default_views
 from django.views.generic import TemplateView
+from django.views.generic.base import RedirectView
 
 urlpatterns = [
     path("", TemplateView.as_view(template_name="pages/home.html"), name="home"),
@@ -27,7 +27,7 @@
         "collaborative_analysis/",
         include("primed.collaborative_analysis.urls", namespace="collaborative_analysis"),
     ),
-    path("favicon.ico", lambda _: redirect("static/images/favicons/primed-favicon.png", permanent=True)),
+    path("favicon.ico", RedirectView.as_view(url="/static/images/favicons/primed-favicon.png", permanent=True)),
 ] + static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)
 
 

From c406594db5ad4370678670a2500d590dfb9d2a20 Mon Sep 17 00:00:00 2001
From: Jonas Carson <jcarson@uw.edu>
Date: Thu, 21 Nov 2024 12:48:04 -0800
Subject: [PATCH 12/23] Use a better method for determining static file url.
 Make favicon redirect a public view

---
 config/settings/base.py | 1 +
 config/urls.py          | 7 ++++++-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/config/settings/base.py b/config/settings/base.py
index 3f2c24d9..7c7410a4 100644
--- a/config/settings/base.py
+++ b/config/settings/base.py
@@ -310,6 +310,7 @@
     "cdsa:records:user_access",
     "dbgap:records:index",
     "dbgap:records:applications",
+    "favicon",
 ]
 
 # django-dbbackup
diff --git a/config/urls.py b/config/urls.py
index ce11199f..9d82035d 100644
--- a/config/urls.py
+++ b/config/urls.py
@@ -1,6 +1,7 @@
 from django.conf import settings
 from django.conf.urls.static import static
 from django.contrib import admin
+from django.templatetags.static import static as static_url_tag
 from django.urls import include, path
 from django.views import defaults as default_views
 from django.views.generic import TemplateView
@@ -27,7 +28,11 @@
         "collaborative_analysis/",
         include("primed.collaborative_analysis.urls", namespace="collaborative_analysis"),
     ),
-    path("favicon.ico", RedirectView.as_view(url="/static/images/favicons/primed-favicon.png", permanent=True)),
+    path(
+        "favicon.ico",
+        RedirectView.as_view(url=static_url_tag("images/favicons/primed-favicon.png"), permanent=True),
+        name="favicon",
+    ),
 ] + static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)
 
 

From a7dc5c3d673f04a20fac8f6d799b87bb1db62902 Mon Sep 17 00:00:00 2001
From: Jonas Carson <jcarson@uw.edu>
Date: Fri, 22 Nov 2024 08:23:28 -0800
Subject: [PATCH 13/23] Fix breaking change in 2.10 - sub must be a string - to
 align with JWT spec

---
 primed/drupal_oauth_provider/tests.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/primed/drupal_oauth_provider/tests.py b/primed/drupal_oauth_provider/tests.py
index e59eb6f2..c827b551 100644
--- a/primed/drupal_oauth_provider/tests.py
+++ b/primed/drupal_oauth_provider/tests.py
@@ -130,7 +130,7 @@ def get_mocked_response(self):
             "name": "testmaster",
             "email": "test@testmaster.net",
             "email_verified": "True",
-            "sub": 20122
+            "sub": "20122"
         }""",
             ),
         ]
@@ -198,7 +198,7 @@ def get_id_token(self):
                 "iat": self.setup_time,
                 "aud": allowed_audience,
                 "scope": ["authenticated", "oauth_client_user"],
-                "sub": 20122,
+                "sub": "20122",
             }
         )
 

From 1b228618fd3d0cec36578c08349cfb4fc580ac1c Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 28 Nov 2024 03:09:06 +0000
Subject: [PATCH 14/23] Bump cryptography from 43.0.3 to 44.0.0

Bumps [cryptography](https://github.com/pyca/cryptography) from 43.0.3 to 44.0.0.
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pyca/cryptography/compare/43.0.3...44.0.0)

---
updated-dependencies:
- dependency-name: cryptography
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/requirements.txt b/requirements/requirements.txt
index a32dc890..98b390a2 100644
--- a/requirements/requirements.txt
+++ b/requirements/requirements.txt
@@ -37,7 +37,7 @@ crispy-bootstrap5==2024.10
     # via
     #   -r requirements/requirements.in
     #   django-anvil-consortium-manager
-cryptography==43.0.3
+cryptography==44.0.0
     # via -r requirements/requirements.in
 django==4.2.16
     # via

From bd6122c64ac3bef69a5e3870c789a22c0ec2f93a Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 29 Nov 2024 03:57:39 +0000
Subject: [PATCH 15/23] Bump ruff from 0.7.4 to 0.8.1

Bumps [ruff](https://github.com/astral-sh/ruff) from 0.7.4 to 0.8.1.
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](https://github.com/astral-sh/ruff/compare/0.7.4...0.8.1)

---
updated-dependencies:
- dependency-name: ruff
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements/dev-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/dev-requirements.txt b/requirements/dev-requirements.txt
index 3cde109c..c159deb3 100644
--- a/requirements/dev-requirements.txt
+++ b/requirements/dev-requirements.txt
@@ -137,7 +137,7 @@ requests==2.32.3
     #   -c requirements/requirements.txt
     #   -c requirements/test-requirements.txt
     #   sphinx
-ruff==0.7.4
+ruff==0.8.1
     # via -r requirements/dev-requirements.in
 six==1.16.0
     # via

From a6a1035fba37d428ffe9c7301035d3fbcc8a2172 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 29 Nov 2024 03:58:38 +0000
Subject: [PATCH 16/23] Bump pyjwt from 2.10.0 to 2.10.1

Bumps [pyjwt](https://github.com/jpadilla/pyjwt) from 2.10.0 to 2.10.1.
- [Release notes](https://github.com/jpadilla/pyjwt/releases)
- [Changelog](https://github.com/jpadilla/pyjwt/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/jpadilla/pyjwt/compare/2.10.0...2.10.1)

---
updated-dependencies:
- dependency-name: pyjwt
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/requirements.txt b/requirements/requirements.txt
index a32dc890..3c7983a4 100644
--- a/requirements/requirements.txt
+++ b/requirements/requirements.txt
@@ -144,7 +144,7 @@ pyasn1-modules==0.3.0
     # via google-auth
 pycparser==2.21
     # via cffi
-pyjwt==2.10.0
+pyjwt==2.10.1
     # via -r requirements/requirements.in
 pyparsing==3.1.1
     # via packaging

From 72ddfd7ef1f8360db17bf7fdae11cc18122d786f Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 2 Dec 2024 03:42:59 +0000
Subject: [PATCH 17/23] Bump pytest from 8.3.3 to 8.3.4

Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.3.3 to 8.3.4.
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.3.3...8.3.4)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements/test-requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/test-requirements.txt b/requirements/test-requirements.txt
index 2cc02a15..f7c025fa 100644
--- a/requirements/test-requirements.txt
+++ b/requirements/test-requirements.txt
@@ -53,7 +53,7 @@ pyparsing==3.1.1
     # via
     #   -c requirements/requirements.txt
     #   packaging
-pytest==8.3.3
+pytest==8.3.4
     # via
     #   -r requirements/test-requirements.in
     #   pytest-cov

From fb263def65b2af5450cec6aac11344b578791dac Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 2 Dec 2024 03:46:21 +0000
Subject: [PATCH 18/23] Bump django-allauth from 65.2.0 to 65.3.0

Bumps [django-allauth](https://github.com/sponsors/pennersr) from 65.2.0 to 65.3.0.
- [Commits](https://github.com/sponsors/pennersr/commits)

---
updated-dependencies:
- dependency-name: django-allauth
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements/requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/requirements.txt b/requirements/requirements.txt
index a32dc890..980c8d31 100644
--- a/requirements/requirements.txt
+++ b/requirements/requirements.txt
@@ -55,7 +55,7 @@ django==4.2.16
     #   django-picklefield
     #   django-simple-history
     #   django-tables2
-django-allauth==65.2.0
+django-allauth==65.3.0
     # via -r requirements/requirements.in
 django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.26
     # via -r requirements/requirements.in

From 4e68fb2064d02ffa435522f7ca2cdb67c469d698 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 2 Dec 2024 16:25:44 +0000
Subject: [PATCH 19/23] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.7.0 → v0.8.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.7.0...v0.8.1)
- [github.com/gitleaks/gitleaks: v8.21.1 → v8.21.2](https://github.com/gitleaks/gitleaks/compare/v8.21.1...v8.21.2)
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 2c63c131..ba561d95 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -12,7 +12,7 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.7.0
+    rev: v0.8.1
     hooks:
       # Run the linter.
       - id: ruff
@@ -21,7 +21,7 @@ repos:
       - id: ruff-format
 
   - repo: https://github.com/gitleaks/gitleaks
-    rev: v8.21.1
+    rev: v8.21.2
     hooks:
       - id: gitleaks
 

From aa716b622d69698f02e8c11bd25e5e7ff888165e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 2 Dec 2024 18:39:49 +0000
Subject: [PATCH 20/23] Bump pyjwt from 2.10.0 to 2.10.1 in /requirements

Bumps [pyjwt](https://github.com/jpadilla/pyjwt) from 2.10.0 to 2.10.1.
- [Release notes](https://github.com/jpadilla/pyjwt/releases)
- [Changelog](https://github.com/jpadilla/pyjwt/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/jpadilla/pyjwt/compare/2.10.0...2.10.1)

---
updated-dependencies:
- dependency-name: pyjwt
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements/requirements.txt | 62 +++++++++++++++++------------------
 1 file changed, 31 insertions(+), 31 deletions(-)

diff --git a/requirements/requirements.txt b/requirements/requirements.txt
index a32dc890..8d5077b0 100644
--- a/requirements/requirements.txt
+++ b/requirements/requirements.txt
@@ -5,7 +5,7 @@
 #    pip-compile requirements/requirements.in
 #
 argon2-cffi==23.1.0
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 argon2-cffi-bindings==21.2.0
     # via argon2-cffi
 asgiref==3.8.1
@@ -35,13 +35,13 @@ click==8.1.3
     # via pip-tools
 crispy-bootstrap5==2024.10
     # via
-    #   -r requirements/requirements.in
+    #   -r requirements.in
     #   django-anvil-consortium-manager
 cryptography==43.0.3
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 django==4.2.16
     # via
-    #   -r requirements/requirements.in
+    #   -r requirements.in
     #   crispy-bootstrap5
     #   django-allauth
     #   django-anvil-consortium-manager
@@ -56,46 +56,46 @@ django==4.2.16
     #   django-simple-history
     #   django-tables2
 django-allauth==65.2.0
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.26
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 django-autocomplete-light==3.11.0
     # via django-anvil-consortium-manager
 django-constance==4.1.3
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 django-crispy-forms==2.3
     # via
-    #   -r requirements/requirements.in
+    #   -r requirements.in
     #   crispy-bootstrap5
     #   django-anvil-consortium-manager
 django-dbbackup==4.2.1
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 django-environ==0.10.0
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 django-extensions==3.2.3
     # via
-    #   -r requirements/requirements.in
+    #   -r requirements.in
     #   django-anvil-consortium-manager
 django-filter==23.5
     # via django-anvil-consortium-manager
 django-htmx==1.21.0
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 django-login-required-middleware==0.9.0
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 django-maintenance-mode==0.21.1
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 django-model-utils==5.0.0
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 django-picklefield==3.2
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 django-simple-history==3.7.0
     # via
-    #   -r requirements/requirements.in
+    #   -r requirements.in
     #   django-anvil-consortium-manager
 django-tables2==2.7.0
     # via django-anvil-consortium-manager
 django-tree-queries==0.19.0
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 fastobo==0.12.3
     # via pronto
 fontawesomefree==6.5.1
@@ -105,13 +105,13 @@ google-auth==2.28.1
 idna==3.7
     # via requests
 jsonapi-requests==0.8.0
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 jsonschema==4.23.0
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 jsonschema-specifications==2023.12.1
     # via jsonschema
 mysqlclient==2.2.6
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 networkx==3.1
     # via
     #   django-anvil-consortium-manager
@@ -122,20 +122,20 @@ numpy==1.24.4
     #   pandas
 oauthlib==3.2.2
     # via
-    #   -r requirements/requirements.in
+    #   -r requirements.in
     #   requests-oauthlib
 packaging==21.3
     # via
     #   build
     #   plotly
 pandas==2.2.3
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 pip-tools==7.4.1
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 plotly==5.19.0
     # via django-anvil-consortium-manager
 pronto==2.5.8
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 pyasn1==0.5.1
     # via
     #   pyasn1-modules
@@ -144,8 +144,8 @@ pyasn1-modules==0.3.0
     # via google-auth
 pycparser==2.21
     # via cffi
-pyjwt==2.10.0
-    # via -r requirements/requirements.in
+pyjwt==2.10.1
+    # via -r requirements.in
 pyparsing==3.1.1
     # via packaging
 pyproject-hooks==1.0.0
@@ -169,12 +169,12 @@ referencing==0.33.0
     #   jsonschema-specifications
 requests==2.32.3
     # via
-    #   -r requirements/requirements.in
+    #   -r requirements.in
     #   django-anvil-consortium-manager
     #   jsonapi-requests
     #   requests-oauthlib
 requests-oauthlib==2.0.0
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 rpds-py==0.17.1
     # via
     #   jsonschema
@@ -186,7 +186,7 @@ six==1.16.0
 sqlparse==0.5.1
     # via django
 tablib==3.7.0
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 tenacity==8.2.3
     # via
     #   jsonapi-requests
@@ -205,7 +205,7 @@ urllib3==2.2.2
 wheel==0.42.0
     # via pip-tools
 whitenoise==6.8.2
-    # via -r requirements/requirements.in
+    # via -r requirements.in
 
 # The following packages are considered to be unsafe in a requirements file:
 # pip

From 5995f5861507ca8935c511570889da97b8e45ed8 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 2 Dec 2024 18:40:34 +0000
Subject: [PATCH 21/23] Compile requirements files

---
 requirements/requirements.txt | 60 +++++++++++++++++------------------
 1 file changed, 30 insertions(+), 30 deletions(-)

diff --git a/requirements/requirements.txt b/requirements/requirements.txt
index 8d5077b0..3c7983a4 100644
--- a/requirements/requirements.txt
+++ b/requirements/requirements.txt
@@ -5,7 +5,7 @@
 #    pip-compile requirements/requirements.in
 #
 argon2-cffi==23.1.0
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 argon2-cffi-bindings==21.2.0
     # via argon2-cffi
 asgiref==3.8.1
@@ -35,13 +35,13 @@ click==8.1.3
     # via pip-tools
 crispy-bootstrap5==2024.10
     # via
-    #   -r requirements.in
+    #   -r requirements/requirements.in
     #   django-anvil-consortium-manager
 cryptography==43.0.3
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 django==4.2.16
     # via
-    #   -r requirements.in
+    #   -r requirements/requirements.in
     #   crispy-bootstrap5
     #   django-allauth
     #   django-anvil-consortium-manager
@@ -56,46 +56,46 @@ django==4.2.16
     #   django-simple-history
     #   django-tables2
 django-allauth==65.2.0
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.26
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 django-autocomplete-light==3.11.0
     # via django-anvil-consortium-manager
 django-constance==4.1.3
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 django-crispy-forms==2.3
     # via
-    #   -r requirements.in
+    #   -r requirements/requirements.in
     #   crispy-bootstrap5
     #   django-anvil-consortium-manager
 django-dbbackup==4.2.1
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 django-environ==0.10.0
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 django-extensions==3.2.3
     # via
-    #   -r requirements.in
+    #   -r requirements/requirements.in
     #   django-anvil-consortium-manager
 django-filter==23.5
     # via django-anvil-consortium-manager
 django-htmx==1.21.0
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 django-login-required-middleware==0.9.0
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 django-maintenance-mode==0.21.1
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 django-model-utils==5.0.0
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 django-picklefield==3.2
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 django-simple-history==3.7.0
     # via
-    #   -r requirements.in
+    #   -r requirements/requirements.in
     #   django-anvil-consortium-manager
 django-tables2==2.7.0
     # via django-anvil-consortium-manager
 django-tree-queries==0.19.0
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 fastobo==0.12.3
     # via pronto
 fontawesomefree==6.5.1
@@ -105,13 +105,13 @@ google-auth==2.28.1
 idna==3.7
     # via requests
 jsonapi-requests==0.8.0
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 jsonschema==4.23.0
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 jsonschema-specifications==2023.12.1
     # via jsonschema
 mysqlclient==2.2.6
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 networkx==3.1
     # via
     #   django-anvil-consortium-manager
@@ -122,20 +122,20 @@ numpy==1.24.4
     #   pandas
 oauthlib==3.2.2
     # via
-    #   -r requirements.in
+    #   -r requirements/requirements.in
     #   requests-oauthlib
 packaging==21.3
     # via
     #   build
     #   plotly
 pandas==2.2.3
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 pip-tools==7.4.1
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 plotly==5.19.0
     # via django-anvil-consortium-manager
 pronto==2.5.8
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 pyasn1==0.5.1
     # via
     #   pyasn1-modules
@@ -145,7 +145,7 @@ pyasn1-modules==0.3.0
 pycparser==2.21
     # via cffi
 pyjwt==2.10.1
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 pyparsing==3.1.1
     # via packaging
 pyproject-hooks==1.0.0
@@ -169,12 +169,12 @@ referencing==0.33.0
     #   jsonschema-specifications
 requests==2.32.3
     # via
-    #   -r requirements.in
+    #   -r requirements/requirements.in
     #   django-anvil-consortium-manager
     #   jsonapi-requests
     #   requests-oauthlib
 requests-oauthlib==2.0.0
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 rpds-py==0.17.1
     # via
     #   jsonschema
@@ -186,7 +186,7 @@ six==1.16.0
 sqlparse==0.5.1
     # via django
 tablib==3.7.0
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 tenacity==8.2.3
     # via
     #   jsonapi-requests
@@ -205,7 +205,7 @@ urllib3==2.2.2
 wheel==0.42.0
     # via pip-tools
 whitenoise==6.8.2
-    # via -r requirements.in
+    # via -r requirements/requirements.in
 
 # The following packages are considered to be unsafe in a requirements file:
 # pip

From 213dd6b31cc35e01374f8c5260c7763b701f5791 Mon Sep 17 00:00:00 2001
From: Adrienne Stilp <amstilp@uw.edu>
Date: Mon, 2 Dec 2024 14:24:40 -0800
Subject: [PATCH 22/23] Update ACM to v0.26.1 in requirements.in file

---
 requirements/requirements.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements/requirements.in b/requirements/requirements.in
index 50a1f247..6bd99a34 100644
--- a/requirements/requirements.in
+++ b/requirements/requirements.in
@@ -38,7 +38,7 @@ django-dbbackup # https://github.com/jazzband/django-dbbackup
 django-extensions  # https://github.com/django-extensions/django-extensions
 
 # anvil_consortium_manager
-django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.26
+django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.26.1
 
 # Simple history - model history tracking
 django-simple-history

From edc6e36332dba9e905e8df6d58735f6930de85a4 Mon Sep 17 00:00:00 2001
From: amstilp <3944584+amstilp@users.noreply.github.com>
Date: Mon, 2 Dec 2024 22:26:27 +0000
Subject: [PATCH 23/23] Compile requirements files

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

diff --git a/requirements/requirements.txt b/requirements/requirements.txt
index 0bc038c7..038caac3 100644
--- a/requirements/requirements.txt
+++ b/requirements/requirements.txt
@@ -57,7 +57,7 @@ django==4.2.16
     #   django-tables2
 django-allauth==65.3.0
     # via -r requirements/requirements.in
-django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.26
+django-anvil-consortium-manager @ git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.26.1
     # via -r requirements/requirements.in
 django-autocomplete-light==3.11.0
     # via django-anvil-consortium-manager