UW-GAC · amstilp · Dec 3, 2024 · Nov 8, 2024 · Nov 8, 2024 · Nov 8, 2024
diff --git 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 }}
diff --git 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
 

diff --git 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
@@ -394,12 +395,6 @@
 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 = "[email protected]"
-
 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/config/urls.py b/config/urls.py
@@ -1,9 +1,11 @@
 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
+from django.views.generic.base import RedirectView
 
 urlpatterns = [
     path("", TemplateView.as_view(template_name="pages/home.html"), name="home"),
@@ -26,6 +28,11 @@
         "collaborative_analysis/",
         include("primed.collaborative_analysis.urls", namespace="collaborative_analysis"),
     ),
+    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)
 
 

diff --git 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": "[email protected]",
             "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",
             }
         )
 

diff --git 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 = "[email protected]"
 
     def get_autocomplete_queryset(self, queryset, q):
         """Filter to Accounts where the email or the associated user name matches the query `q`."""

diff --git a/primed/templates/admin/base_site.html 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 %}
diff --git 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==0.8.1
     # via -r requirements/dev-requirements.in
 six==1.16.0
     # via
@@ -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:

diff --git 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@v0.26.1
 
 # Simple history - model history tracking
 django-simple-history

diff --git 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
@@ -55,9 +55,9 @@ django==4.2.16
     #   django-picklefield
     #   django-simple-history
     #   django-tables2
-django-allauth==65.1.0
+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@v0.25
+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
@@ -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
@@ -144,7 +144,7 @@ pyasn1-modules==0.3.0
     # via google-auth
 pycparser==2.21
     # via cffi
-pyjwt==2.9.0
+pyjwt==2.10.1
     # via -r requirements/requirements.in
 pyparsing==3.1.1
     # via packaging

diff --git 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