Pre-release cleanup pass (#301)

* Adds missing kwarg check to clean command

* Spelling fixes in autocomplete command

* Updates packaging

* Drops unused celery check

* Remove redundant code

* Auto resolve base names

keystone_api/apps/admin_utils/management/commands/clean.py

@@ -6,7 +6,7 @@
 |------------|------------------------------------------------------------------|
 | --static   | Delete the static root directory                                 |
 | --uploads  | Delete all user uploaded file data                              |
-| --db       | Delete all sqlite database files                                 |
+| --sqlite   | Delete all sqlite database files                                 |
 | --all      | Shorthand for deleting everything                                |
 """
 
@@ -33,18 +33,18 @@ def add_arguments(self, parser: ArgumentParser) -> None:
         group = parser.add_argument_group('clean options')
         group.add_argument('--static', action='store_true', help='Delete the static root directory')
         group.add_argument('--uploads', action='store_true', help='Delete all user uploaded file data')
-        group.add_argument('--db', action='store_true', help='Delete all sqlite database files')
+        group.add_argument('--sqlite', action='store_true', help='Delete all sqlite database files')
         group.add_argument('--all', action='store_true', help='Shorthand for deleting all targets')
 
     def handle(self, *args, **options) -> None:
-        """Handle the command execution.
+        """Handle the command execution
 
         Args:
           *args: Additional positional arguments.
           **options: Additional keyword arguments.
         """
 
-        if not any([options['static'], options['db'], options['all']]):
+        if not any([options['static'], options['uploads'], options['sqlite'], options['all']]):
             self.stderr.write('At least one deletion target is required. `See clean --help` for details.')
 
         if options['static'] or options['all']:
@@ -55,7 +55,7 @@ def handle(self, *args, **options) -> None:
             self.stdout.write(self.style.SUCCESS('Removing user uploads...'))
             shutil.rmtree(settings.MEDIA_ROOT, ignore_errors=True)
 
-        if options['db'] or options['all']:
+        if options['sqlite'] or options['all']:
             self.stdout.write(self.style.SUCCESS('Removing sqlite files...'))
             for db_settings in settings.DATABASES.values():
                 if 'sqlite' in db_settings['ENGINE']:

keystone_api/apps/admin_utils/management/commands/enable_autocomplete.py

@@ -35,7 +35,7 @@ def _handle(self) -> None:
         # Find the user's .bash_prf le or .bashrc file
         profile_path = self.get_profile_path()
         if profile_path is None:
-            self.stderr.write(f'No .bash_profile or .bashrc fie found.')
+            self.stderr.write(f'No .bash_profile or .bashrc file found.')
             exit(1)
 
         # Copy the completion script into the user's home directory
@@ -58,15 +58,15 @@ def prompt_for_confirmation() -> bool:
         print(
             'This command will make the following changes:\n',
             '  - A file `.keystone_autocomplete` will be add to your home directory\n'
-            '  - A line of setup code will be added to your `.bash_profile`\n'
+            '  - A line of setup code will be added to your .bash_profile or .bashrc file`\n'
         )
 
         while True:
-            answer = input('Do you want to continue? [Y/n]: ').lower()
-            if answer in ('y', ''):
+            answer = input('Do you want to continue? [y/N]: ').lower()
+            if answer == 'y':
                 return True
 
-            elif answer == 'n':
+            elif answer in ('n', ''):
                 return False
 
             print('Unrecognized input.')

keystone_api/apps/allocations/models.py

@@ -15,7 +15,6 @@
 from django.template.defaultfilters import truncatechars
 
 from apps.users.models import ResearchGroup, User
-from .managers import *
 
 __all__ = [
     'Allocation',
@@ -45,8 +44,6 @@ class Allocation(RGModelInterface, models.Model):
     cluster: Cluster = models.ForeignKey('Cluster', on_delete=models.CASCADE)
     request: AllocationRequest = models.ForeignKey('AllocationRequest', on_delete=models.CASCADE)
 
-    objects = AllocationManager()
-
     def get_research_group(self) -> ResearchGroup:
         """Return the research group tied to the current record"""
 
@@ -78,8 +75,6 @@ class StatusChoices(models.TextChoices):
 
     group: ResearchGroup = models.ForeignKey(ResearchGroup, on_delete=models.CASCADE)
 
-    objects = AllocationRequestManager()
-
     def clean(self) -> None:
         """Validate the model instance
 
@@ -119,8 +114,6 @@ class StatusChoices(models.TextChoices):
     request: AllocationRequest = models.ForeignKey(AllocationRequest, on_delete=models.CASCADE)
     reviewer: User = models.ForeignKey(User, on_delete=models.CASCADE)
 
-    objects = AllocationRequestReviewManager()
-
     def get_research_group(self) -> ResearchGroup:
         """Return the research group tied to the current record"""
 

keystone_api/apps/allocations/urls.py

@@ -7,9 +7,9 @@
 app_name = 'allocations'
 
 router = DefaultRouter()
-router.register(r'clusters', ClusterViewSet, basename='Cluster')
-router.register(r'allocations', AllocationViewSet, basename='Allocation')
-router.register(r'requests', AllocationRequestViewSet, basename='AllocationRequest')
-router.register(r'reviews', AllocationRequestReviewViewSet, basename='AllocationRequestReview')
+router.register(r'clusters', ClusterViewSet)
+router.register(r'allocations', AllocationViewSet)
+router.register(r'requests', AllocationRequestViewSet)
+router.register(r'reviews', AllocationRequestReviewViewSet)
 
 urlpatterns = router.urls

keystone_api/apps/allocations/views.py

@@ -18,50 +18,58 @@
     'ClusterViewSet'
 ]
 
+from ..users.models import ResearchGroup
+
 
 class AllocationViewSet(viewsets.ModelViewSet):
     """Manage allocations for user research groups."""
 
-    permission_classes = [permissions.IsAuthenticated, StaffWriteGroupRead]
+    queryset = Allocation.objects.all()
     serializer_class = AllocationSerializer
+    permission_classes = [permissions.IsAuthenticated, StaffWriteGroupRead]
 
     def get_queryset(self) -> list[Allocation]:
         """Return a list of allocations for the currently authenticated user"""
 
         if self.request.user.is_staff or self.request.user.is_superuser:
-            return Allocation.objects.all()
+            return self.queryset
 
-        return Allocation.objects.affiliated_with_user(self.request.user).all()
+        research_groups = ResearchGroup.objects.groups_for_user(self.request.user)
+        return Allocation.objects.filter(request__group__in=research_groups)
 
 
 class AllocationRequestViewSet(viewsets.ModelViewSet):
     """Manage allocation requests submitted by user research groups."""
 
-    permission_classes = [permissions.IsAuthenticated, GroupAdminCreateGroupRead]
+    queryset = AllocationRequest.objects.all()
     serializer_class = AllocationRequestSerializer
+    permission_classes = [permissions.IsAuthenticated, GroupAdminCreateGroupRead]
 
     def get_queryset(self) -> list[AllocationRequest]:
         """Return a list of allocation requests for the currently authenticated user"""
 
         if self.request.user.is_staff or self.request.user.is_superuser:
-            return AllocationRequest.objects.all()
+            return self.queryset
 
-        return AllocationRequest.objects.affiliated_with_user(self.request.user).all()
+        research_groups = ResearchGroup.objects.groups_for_user(self.request.user)
+        return AllocationRequest.objects.filter(group__in=research_groups)
 
 
 class AllocationRequestReviewViewSet(viewsets.ModelViewSet):
     """Manage reviews of allocation request submitted by administrators."""
 
-    permission_classes = [permissions.IsAuthenticated, StaffWriteGroupRead]
+    queryset = AllocationRequestReview.objects.all()
     serializer_class = AllocationRequestReviewSerializer
+    permission_classes = [permissions.IsAuthenticated, StaffWriteGroupRead]
 
     def get_queryset(self) -> list[Allocation]:
         """Return a list of allocation reviews for the currently authenticated user"""
 
         if self.request.user.is_staff or self.request.user.is_superuser:
-            return AllocationRequestReview.objects.all()
+            return self.queryset
 
-        return AllocationRequestReview.objects.affiliated_with_user(self.request.user).all()
+        research_groups = ResearchGroup.objects.groups_for_user(self.request.user)
+        return AllocationRequestReview.objects.filter(request__group__in=research_groups)
 
     def create(self, request, *args, **kwargs) -> Response:
         """Create a new `AllocationRequestReview` object"""
@@ -81,5 +89,5 @@ class ClusterViewSet(viewsets.ModelViewSet):
     """Configuration settings for managed Slurm clusters."""
 
     queryset = Cluster.objects.all()
-    permission_classes = [permissions.IsAuthenticated, StaffWriteAuthenticatedRead]
     serializer_class = ClusterSerializer
+    permission_classes = [permissions.IsAuthenticated, StaffWriteAuthenticatedRead]

keystone_api/apps/research_products/urls.py

@@ -7,7 +7,7 @@
 app_name = 'research_products'
 
 router = DefaultRouter()
-router.register(r'publications', PublicationViewSet, basename='publication')
-router.register(r'grants', GrantViewSet, basename='grant')
+router.register(r'publications', PublicationViewSet)
+router.register(r'grants', GrantViewSet)
 
 urlpatterns = router.urls

keystone_api/apps/research_products/views.py

@@ -16,28 +16,36 @@
 class PublicationViewSet(viewsets.ModelViewSet):
     """Manage metadata for research publications."""
 
-    permission_classes = [permissions.IsAuthenticated, permissions.IsAdminUser | GroupMemberAll]
+    queryset = Publication.objects.all()
     serializer_class = PublicationSerializer
+    permission_classes = [
+        permissions.IsAuthenticated,
+        permissions.IsAdminUser | GroupMemberAll
+    ]
 
     def get_queryset(self) -> list[Publication]:
         """Return a list of allocation requests for the currently authenticated user"""
 
         if self.request.user.is_staff:
-            return Publication.objects.all()
+            return self.queryset
 
         return Publication.objects.affiliated_with_user(self.request.user).all()
 
 
 class GrantViewSet(viewsets.ModelViewSet):
     """Track funding awards and grant information."""
 
-    permission_classes = [permissions.IsAuthenticated, permissions.IsAdminUser | GroupMemberReadGroupAdminWrite]
+    queryset = Grant.objects.all()
     serializer_class = GrantSerializer
+    permission_classes = [
+        permissions.IsAuthenticated,
+        permissions.IsAdminUser | GroupMemberReadGroupAdminWrite
+    ]
 
     def get_queryset(self) -> list[Grant]:
         """Return a list of allocation requests for the currently authenticated user"""
 
         if self.request.user.is_staff:
-            return Grant.objects.all()
+            return self.queryset
 
         return Grant.objects.affiliated_with_user(self.request.user).all()

keystone_api/apps/users/models.py

@@ -19,6 +19,10 @@
 class User(auth_models.AbstractBaseUser, auth_models.PermissionsMixin):
     """Proxy model for the built-in django `User` model"""
 
+    USERNAME_FIELD = 'username'
+    EMAIL_FIELD = "email"
+    REQUIRED_FIELDS = ['email', 'first_name', 'last_name']
+
     username = models.CharField('username', max_length=150, unique=True, validators=[UnicodeUsernameValidator()])
     first_name = models.CharField('first name', max_length=150)
     last_name = models.CharField('last name', max_length=150)
@@ -32,10 +36,6 @@ class User(auth_models.AbstractBaseUser, auth_models.PermissionsMixin):
 
     objects = UserManager()
 
-    USERNAME_FIELD = 'username'
-    EMAIL_FIELD = "email"
-    REQUIRED_FIELDS = ['email', 'first_name', 'last_name']
-
 
 class ResearchGroup(models.Model):
     """A user research group tied to a slurm account"""

keystone_api/apps/users/permissions.py

@@ -23,4 +23,4 @@ def has_permission(self, request, view) -> bool:
         if request.method in permissions.SAFE_METHODS:
             return request.user.is_authenticated
 
-        return request.user.is_staff or request.user.is_superuser
+        return request.user.is_staff