Merge pull request #536 from UW-GAC/maint/use-ruff

Switch to ruff
UW-GAC · Apr 26, 2024 · f207995 · f207995
2 parents 4000048 + 950674a
commit f207995
Show file tree

Hide file tree

Showing 33 changed files with 288 additions and 794 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -10,22 +10,15 @@ repos:
       - id: end-of-file-fixer
       - id: check-yaml
 
-  - repo: https://github.com/psf/black
-    rev: 22.3.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.4.2
     hooks:
-      - id: black
-
-  - repo: https://github.com/timothycrosley/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-
-  - repo: https://github.com/PyCQA/flake8
-    rev: 7.0.0
-    hooks:
-      - id: flake8
-        args: ['--config=setup.cfg']
-        additional_dependencies: [flake8-isort]
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
 
   - repo: https://github.com/gitleaks/gitleaks
     rev: v8.16.1

diff --git a/.ruff.toml b/.ruff.toml
@@ -0,0 +1,20 @@
+line-length = 120
+exclude = [
+    "**/migrations/**",
+    "*/static/CACHE/*",
+    "venv",
+    "docs",
+]
+
+[lint]
+extend-select = [
+    "E",
+    "F",
+    "W", # pycodestyle warnings
+    "I", # isort
+    "DJ", # flake8-django
+    "E501", # line-too-long
+]
+
+[lint.isort]
+known-first-party = ["gregor_django", "config", ]
diff --git a/config/settings/base.py b/config/settings/base.py
@@ -1,6 +1,7 @@
 """
 Base settings to build other settings files upon.
 """
+
 from pathlib import Path
 
 import environ
@@ -129,9 +130,7 @@
 ]
 # https://docs.djangoproject.com/en/dev/ref/settings/#auth-password-validators
 AUTH_PASSWORD_VALIDATORS = [
-    {
-        "NAME": "django.contrib.auth.password_validation.UserAttributeSimilarityValidator"
-    },
+    {"NAME": "django.contrib.auth.password_validation.UserAttributeSimilarityValidator"},
     {"NAME": "django.contrib.auth.password_validation.MinimumLengthValidator"},
     {"NAME": "django.contrib.auth.password_validation.CommonPasswordValidator"},
     {"NAME": "django.contrib.auth.password_validation.NumericPasswordValidator"},
@@ -257,12 +256,7 @@
 LOGGING = {
     "version": 1,
     "disable_existing_loggers": False,
-    "formatters": {
-        "verbose": {
-            "format": "%(levelname)s %(asctime)s %(module)s "
-            "%(process)d %(thread)d %(message)s"
-        }
-    },
+    "formatters": {"verbose": {"format": "%(levelname)s %(asctime)s %(module)s " "%(process)d %(thread)d %(message)s"}},
     "handlers": {
         "console": {
             "level": "DEBUG",

diff --git a/config/settings/local.py b/config/settings/local.py
@@ -26,9 +26,7 @@
 # EMAIL
 # ------------------------------------------------------------------------------
 # https://docs.djangoproject.com/en/dev/ref/settings/#email-backend
-EMAIL_BACKEND = env(
-    "DJANGO_EMAIL_BACKEND", default="django.core.mail.backends.console.EmailBackend"
-)
+EMAIL_BACKEND = env("DJANGO_EMAIL_BACKEND", default="django.core.mail.backends.console.EmailBackend")
 
 # WhiteNoise
 # ------------------------------------------------------------------------------

diff --git a/config/settings/production.py b/config/settings/production.py
@@ -57,15 +57,11 @@
 # in our apache configuration. Having in both places causes duplicate header
 SECURE_HSTS_SECONDS = 0
 # https://docs.djangoproject.com/en/dev/ref/settings/#secure-hsts-include-subdomains
-SECURE_HSTS_INCLUDE_SUBDOMAINS = env.bool(
-    "DJANGO_SECURE_HSTS_INCLUDE_SUBDOMAINS", default=True
-)
+SECURE_HSTS_INCLUDE_SUBDOMAINS = env.bool("DJANGO_SECURE_HSTS_INCLUDE_SUBDOMAINS", default=True)
 # https://docs.djangoproject.com/en/dev/ref/settings/#secure-hsts-preload
 SECURE_HSTS_PRELOAD = env.bool("DJANGO_SECURE_HSTS_PRELOAD", default=True)
 # https://docs.djangoproject.com/en/dev/ref/middleware/#x-content-type-options-nosniff
-SECURE_CONTENT_TYPE_NOSNIFF = env.bool(
-    "DJANGO_SECURE_CONTENT_TYPE_NOSNIFF", default=True
-)
+SECURE_CONTENT_TYPE_NOSNIFF = env.bool("DJANGO_SECURE_CONTENT_TYPE_NOSNIFF", default=True)
 # Since we have disabled HSTS above we get a warning when running check --deploy
 # we are manually silencing this as we have verified apache is enforcing
 # https://docs.djangoproject.com/en/dev/ref/checks/#security
@@ -79,9 +75,7 @@
 # EMAIL
 # ------------------------------------------------------------------------------
 # https://docs.djangoproject.com/en/dev/ref/settings/#default-from-email
-DEFAULT_FROM_EMAIL = env(
-    "DJANGO_DEFAULT_FROM_EMAIL", default="gac-django <[email protected]>"
-)
+DEFAULT_FROM_EMAIL = env("DJANGO_DEFAULT_FROM_EMAIL", default="gac-django <[email protected]>")
 # https://docs.djangoproject.com/en/dev/ref/settings/#server-email
 SERVER_EMAIL = env("DJANGO_SERVER_EMAIL", default=DEFAULT_FROM_EMAIL)
 # https://docs.djangoproject.com/en/dev/ref/settings/#email-subject-prefix
@@ -130,12 +124,7 @@
             "()": "maintenance_mode.logging.RequireNotMaintenanceMode503",
         },
     },
-    "formatters": {
-        "verbose": {
-            "format": "%(levelname)s %(asctime)s %(module)s "
-            "%(process)d %(thread)d %(message)s"
-        }
-    },
+    "formatters": {"verbose": {"format": "%(levelname)s %(asctime)s %(module)s " "%(process)d %(thread)d %(message)s"}},
     "handlers": {
         "mail_admins": {
             "level": "ERROR",

diff --git a/config/urls.py b/config/urls.py
@@ -7,9 +7,7 @@
 
 urlpatterns = [
     path("", TemplateView.as_view(template_name="pages/home.html"), name="home"),
-    path(
-        "about/", TemplateView.as_view(template_name="pages/about.html"), name="about"
-    ),
+    path("about/", TemplateView.as_view(template_name="pages/about.html"), name="about"),
     # Django Admin, use {% url 'admin:index' %}
     path(settings.ADMIN_URL, admin.site.urls),
     # User management

diff --git a/config/wsgi.py b/config/wsgi.py
@@ -13,6 +13,7 @@
 framework.
 
 """
+
 import os
 import sys
 from pathlib import Path

diff --git a/gregor_django/__init__.py b/gregor_django/__init__.py
@@ -1,7 +1,2 @@
 __version__ = "0.1.0"
-__version_info__ = tuple(
-    [
-        int(num) if num.isdigit() else num
-        for num in __version__.replace("-", ".", 1).split(".")
-    ]
-)
+__version_info__ = tuple([int(num) if num.isdigit() else num for num in __version__.replace("-", ".", 1).split(".")])
diff --git a/gregor_django/drupal_oauth_provider/provider.py b/gregor_django/drupal_oauth_provider/provider.py
@@ -24,7 +24,6 @@ class CustomAccount(ProviderAccount):
 
 
 class CustomProvider(OAuth2Provider):
-
     id = DRUPAL_PROVIDER_ID
     name = OVERRIDE_NAME
     account_class = CustomAccount

diff --git a/gregor_django/drupal_oauth_provider/tests.py b/gregor_django/drupal_oauth_provider/tests.py
@@ -167,6 +167,4 @@ def test_custom_provider_has_scope(self):
             }
         ]
         with override_settings(SOCIALACCOUNT_PROVIDERS=custom_provider_settings):
-            CustomProvider(request).get_provider_managed_scope_status(
-                scopes_granted=["X"]
-            )
+            CustomProvider(request).get_provider_managed_scope_status(scopes_granted=["X"])
diff --git a/gregor_django/drupal_oauth_provider/views.py b/gregor_django/drupal_oauth_provider/views.py
@@ -50,12 +50,9 @@ def _get_public_key_jwk(self, headers):
             return keys[0]
 
     def get_public_key(self, headers):
-
         public_key_jwk = self._get_public_key_jwk(headers)
         try:
-            public_key = jwt.algorithms.RSAAlgorithm.from_jwk(
-                json.dumps(public_key_jwk)
-            )
+            public_key = jwt.algorithms.RSAAlgorithm.from_jwk(json.dumps(public_key_jwk))
         except Exception as e:
             logger.error(f"[get_public_key] failed to convert jwk to public key {e}")
         else:
@@ -83,9 +80,7 @@ def get_scopes_from_token(self, id_token, headers):
             logger.error(f"Invalid id_token {e} {id_token.token}")
             raise OAuth2Error("Invalid id_token") from e
         except Exception as e:
-            logger.error(
-                f"Other exception parsing token {e} header {unverified_header} token {id_token}"
-            )
+            logger.error(f"Other exception parsing token {e} header {unverified_header} token {id_token}")
             raise OAuth2Error("Error when decoding token {e}")
         else:
             scopes = token_payload.get("scope")
@@ -96,9 +91,7 @@ def complete_login(self, request, app, token, **kwargs):
         headers = {"Authorization": "Bearer {0}".format(token.token)}
 
         scopes_granted = self.get_scopes_from_token(token, headers)
-        managed_scope_status = self.get_provider().get_provider_managed_scope_status(
-            scopes_granted
-        )
+        managed_scope_status = self.get_provider().get_provider_managed_scope_status(scopes_granted)
 
         resp = requests.get(self.profile_url, headers=headers)
         resp.raise_for_status()
@@ -110,9 +103,7 @@ def complete_login(self, request, app, token, **kwargs):
         )
         extra_data["scopes_granted"] = scopes_granted
         extra_data["managed_scope_status"] = managed_scope_status
-        social_login = self.get_provider().sociallogin_from_response(
-            request, extra_data
-        )
+        social_login = self.get_provider().sociallogin_from_response(request, extra_data)
 
         return social_login
 

diff --git a/gregor_django/gregor_anvil/adapters.py b/gregor_django/gregor_anvil/adapters.py
@@ -15,9 +15,7 @@ class AccountAdapter(BaseAccountAdapter):
     def get_autocomplete_queryset(self, queryset, q):
         """Filter to Accounts where the email or the associated user name matches the query `q`."""
         if q:
-            queryset = queryset.filter(
-                Q(email__icontains=q) | Q(user__name__icontains=q)
-            )
+            queryset = queryset.filter(Q(email__icontains=q) | Q(user__name__icontains=q))
         return queryset
 
     def get_autocomplete_label(self, account):
@@ -78,7 +76,9 @@ class ResourceWorkspaceAdapter(BaseWorkspaceAdapter):
 
     type = "resource"
     name = "Resource workspace"
-    description = "Workspaces that contain general Consortium resources (e.g., examples of using AnVIL, working with data, etc.)"  # noqa: E501
+    description = (
+        "Workspaces that contain general Consortium resources (e.g., examples of using AnVIL, working with data, etc.)"  # noqa: E501
+    )
     list_table_class_view = tables.DefaultWorkspaceTable
     list_table_class_staff_view = tables.DefaultWorkspaceTable
     workspace_data_model = models.ResourceWorkspace
@@ -111,9 +111,7 @@ class CombinedConsortiumDataWorkspaceAdapter(BaseWorkspaceAdapter):
     list_table_class_staff_view = tables.CombinedConsortiumDataWorkspaceTable
     workspace_data_model = models.CombinedConsortiumDataWorkspace
     workspace_data_form_class = forms.CombinedConsortiumDataWorkspaceForm
-    workspace_detail_template_name = (
-        "gregor_anvil/combinedconsortiumdataworkspace_detail.html"
-    )
+    workspace_detail_template_name = "gregor_anvil/combinedconsortiumdataworkspace_detail.html"
     workspace_form_class = WorkspaceForm
 
 
@@ -155,9 +153,7 @@ class DCCProcessedDataWorkspaceAdapter(BaseWorkspaceAdapter):
     list_table_class_staff_view = tables.DCCProcessedDataWorkspaceTable
     workspace_data_model = models.DCCProcessedDataWorkspace
     workspace_data_form_class = forms.DCCProcessedDataWorkspaceForm
-    workspace_detail_template_name = (
-        "gregor_anvil/dccprocesseddataworkspace_detail.html"
-    )
+    workspace_detail_template_name = "gregor_anvil/dccprocesseddataworkspace_detail.html"
     workspace_form_class = WorkspaceForm
 
 

diff --git a/gregor_django/gregor_anvil/forms.py b/gregor_django/gregor_anvil/forms.py
@@ -117,9 +117,7 @@ class Meta:
 class DCCProcessingWorkspaceForm(Bootstrap5MediaFormMixin, forms.ModelForm):
     """Form for a DCCProcessingWorkspace object."""
 
-    ERROR_UPLOAD_CYCLE = (
-        "upload_cycle must match upload_cycle of all upload_workspaces."
-    )
+    ERROR_UPLOAD_CYCLE = "upload_cycle must match upload_cycle of all upload_workspaces."
 
     class Meta:
         model = models.DCCProcessingWorkspace

diff --git a/gregor_django/gregor_anvil/models.py b/gregor_django/gregor_anvil/models.py
@@ -103,32 +103,28 @@ class Meta:
     def __str__(self):
         return "U{cycle:02d}".format(cycle=self.cycle)
 
+    def get_absolute_url(self):
+        """Return the absolute url for this object."""
+        return reverse("gregor_anvil:upload_cycles:detail", args=[self.cycle])
+
     def clean(self):
         """Custom cleaning methods."""
         # End date must be after start date.
         if self.start_date and self.end_date and self.start_date >= self.end_date:
             raise ValidationError("end_date must be after start_date!")
 
-    def get_absolute_url(self):
-        """Return the absolute url for this object."""
-        return reverse("gregor_anvil:upload_cycles:detail", args=[self.cycle])
-
     def get_partner_upload_workspaces(self):
         """Return a queryset of PartnerUploadWorkspace objects that are included in this upload cycle.
 
         For a given PartnerGroup and ConsentGroup, the workspace with the highest version that also has a date_completed
         that is before the end_date of this upload cycle is included.
         """
-        qs = PartnerUploadWorkspace.objects.filter(
-            date_completed__lte=self.end_date
-        ).order_by("-version")
+        qs = PartnerUploadWorkspace.objects.filter(date_completed__lte=self.end_date).order_by("-version")
         # This is not ideal, but we can't use .distinct on fields.
         pks_to_keep = []
         for partner_group in PartnerGroup.objects.all():
             for consent_group in ConsentGroup.objects.all():
-                instance = qs.filter(
-                    partner_group=partner_group, consent_group=consent_group
-                ).first()
+                instance = qs.filter(partner_group=partner_group, consent_group=consent_group).first()
                 if instance:
                     pks_to_keep.append(instance.pk)
         return qs.filter(pk__in=pks_to_keep)
@@ -216,9 +212,7 @@ class ReleaseWorkspace(TimeStampedModel, BaseWorkspaceData):
         on_delete=models.PROTECT,
     )
     upload_cycle = models.ForeignKey(UploadCycle, on_delete=models.PROTECT)
-    full_data_use_limitations = models.TextField(
-        help_text="The full data use limitations for this workspace."
-    )
+    full_data_use_limitations = models.TextField(help_text="The full data use limitations for this workspace.")
     dbgap_version = models.IntegerField(
         verbose_name=" dbGaP version",
         validators=[MinValueValidator(1)],
@@ -245,21 +239,16 @@ class Meta:
         ]
 
     def get_dbgap_accession(self):
-        return "phs{phs:06d}.v{v}.p{p}".format(
-            phs=self.phs, v=self.dbgap_version, p=self.dbgap_participant_set
-        )
+        return "phs{phs:06d}.v{v}.p{p}".format(phs=self.phs, v=self.dbgap_version, p=self.dbgap_participant_set)
 
 
 class DCCProcessingWorkspace(TimeStampedModel, BaseWorkspaceData):
-
     upload_cycle = models.ForeignKey(
         UploadCycle,
         on_delete=models.PROTECT,
         help_text="Upload cycle associated with this workspace.",
     )
-    purpose = models.TextField(
-        help_text="The type of processing that is done in this workspace."
-    )
+    purpose = models.TextField(help_text="The type of processing that is done in this workspace.")
 
 
 class DCCProcessedDataWorkspace(TimeStampedModel, BaseWorkspaceData):

diff --git a/gregor_django/gregor_anvil/tables.py b/gregor_django/gregor_anvil/tables.py
@@ -95,16 +95,12 @@ def render_consortium_access(self, record):
         except ManagedGroup.DoesNotExist:
             has_consortium_access = False
         else:
-            has_consortium_access = record.is_in_authorization_domain(
-                group
-            ) and record.is_shared(group)
+            has_consortium_access = record.is_in_authorization_domain(group) and record.is_shared(group)
 
         if has_consortium_access:
             icon = "check-circle-fill"
             color = "green"
-            value = format_html(
-                """<i class="bi bi-{}" style="color: {};"></i>""".format(icon, color)
-            )
+            value = format_html("""<i class="bi bi-{}" style="color: {};"></i>""".format(icon, color))
         else:
             value = ""
         return value
@@ -187,9 +183,7 @@ class WorkspaceReportTable(tables.Table):
 
     workspace_type = tables.columns.Column(orderable=False)
     n_total = tables.columns.Column(verbose_name="Total number", orderable=False)
-    n_shared = tables.columns.Column(
-        verbose_name="Number shared with consortium", orderable=False
-    )
+    n_shared = tables.columns.Column(verbose_name="Number shared with consortium", orderable=False)
 
     class Meta:
         model = Workspace
@@ -200,9 +194,7 @@ def render_workspace_type(self, value):
         return adapter_names[value] + "s"
 
 
-class CombinedConsortiumDataWorkspaceTable(
-    WorkspaceConsortiumAccessTable, tables.Table
-):
+class CombinedConsortiumDataWorkspaceTable(WorkspaceConsortiumAccessTable, tables.Table):
     """A table for Workspaces that includes fields from CombinedConsortiumDataWorkspace."""
 
     name = tables.columns.Column(linkify=True)