Merge pull request #550 from UW-GAC/maint/use-ruff

Switch to ruff

.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

.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 = ["primed", "config", ]

add_cdsa_example_data.py

@@ -29,12 +29,8 @@
 major_version = factories.AgreementMajorVersionFactory.create(version=1)
 
 # Create some agreement versions
-v10 = factories.AgreementVersionFactory.create(
-    major_version=major_version, minor_version=0
-)
-v11 = factories.AgreementVersionFactory.create(
-    major_version=major_version, minor_version=1
-)
+v10 = factories.AgreementVersionFactory.create(major_version=major_version, minor_version=0)
+v11 = factories.AgreementVersionFactory.create(major_version=major_version, minor_version=1)
 
 # Create a couple signed CDSAs.
 dup = DataUsePermission.objects.get(abbreviation="GRU")
@@ -57,9 +53,7 @@
     signed_agreement__version=v10,
     study_site=StudySite.objects.get(short_name="CC"),
 )
-GroupGroupMembershipFactory.create(
-    parent_group=cdsa_group, child_group=cdsa_1001.signed_agreement.anvil_access_group
-)
+GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1001.signed_agreement.anvil_access_group)
 
 cdsa_1002 = factories.MemberAgreementFactory.create(
     signed_agreement__cc_id=1002,
@@ -70,9 +64,7 @@
     signed_agreement__version=v10,
     study_site=StudySite.objects.get(short_name="CARDINAL"),
 )
-GroupGroupMembershipFactory.create(
-    parent_group=cdsa_group, child_group=cdsa_1002.signed_agreement.anvil_access_group
-)
+GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1002.signed_agreement.anvil_access_group)
 
 cdsa_1003 = factories.MemberAgreementFactory.create(
     signed_agreement__cc_id=1003,
@@ -83,9 +75,7 @@
     signed_agreement__version=v10,
     study_site=StudySite.objects.get(short_name="CARDINAL"),
 )
-GroupGroupMembershipFactory.create(
-    parent_group=cdsa_group, child_group=cdsa_1003.signed_agreement.anvil_access_group
-)
+GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1003.signed_agreement.anvil_access_group)
 
 cdsa_1004 = factories.MemberAgreementFactory.create(
     signed_agreement__cc_id=1004,
@@ -96,9 +86,7 @@
     signed_agreement__version=v11,
     study_site=StudySite.objects.get(short_name="CARDINAL"),
 )
-GroupGroupMembershipFactory.create(
-    parent_group=cdsa_group, child_group=cdsa_1004.signed_agreement.anvil_access_group
-)
+GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1004.signed_agreement.anvil_access_group)
 
 cdsa_1005 = factories.DataAffiliateAgreementFactory.create(
     signed_agreement__cc_id=1005,
@@ -108,9 +96,7 @@
     study=Study.objects.get(short_name="Amish"),
     signed_agreement__version=v10,
 )
-GroupGroupMembershipFactory.create(
-    parent_group=cdsa_group, child_group=cdsa_1005.signed_agreement.anvil_access_group
-)
+GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1005.signed_agreement.anvil_access_group)
 
 cdsa_1006 = factories.DataAffiliateAgreementFactory.create(
     signed_agreement__cc_id=1006,
@@ -122,9 +108,7 @@
     additional_limitations="This data can only be used for testing the app.",
     requires_study_review=True,
 )
-GroupGroupMembershipFactory.create(
-    parent_group=cdsa_group, child_group=cdsa_1006.signed_agreement.anvil_access_group
-)
+GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1006.signed_agreement.anvil_access_group)
 
 cdsa_1007 = factories.DataAffiliateAgreementFactory.create(
     signed_agreement__cc_id=1007,
@@ -135,9 +119,7 @@
     study=Study.objects.get(short_name="MESA"),
     signed_agreement__version=v10,
 )
-GroupGroupMembershipFactory.create(
-    parent_group=cdsa_group, child_group=cdsa_1007.signed_agreement.anvil_access_group
-)
+GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1007.signed_agreement.anvil_access_group)
 
 cdsa_1008 = factories.DataAffiliateAgreementFactory.create(
     signed_agreement__cc_id=1008,
@@ -148,9 +130,7 @@
     study=Study.objects.get(short_name="MESA"),
     signed_agreement__version=v10,
 )
-GroupGroupMembershipFactory.create(
-    parent_group=cdsa_group, child_group=cdsa_1008.signed_agreement.anvil_access_group
-)
+GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1008.signed_agreement.anvil_access_group)
 
 cdsa_1009 = factories.NonDataAffiliateAgreementFactory.create(
     signed_agreement__cc_id=1009,
@@ -236,8 +216,6 @@
 cdsa_workspace_3 = factories.CDSAWorkspaceFactory.create(
     workspace__billing_project__name="demo-primed-cdsa",
     workspace__name="DEMO_PRIMED_CDSA_ARIC_1",
-    study=Study.objects.create(
-        short_name="ARIC", full_name="Atherosclerosis Risk in Communities"
-    ),
+    study=Study.objects.create(short_name="ARIC", full_name="Atherosclerosis Risk in Communities"),
     data_use_permission=dup,
 )

add_collaborative_analysis_example_data.py

@@ -55,27 +55,15 @@
 
 
 # Add accounts to the auth domains.
-account_1 = AccountFactory.create(
-    user__name="Adrienne", verified=True, email="[email protected]"
-)
-account_2 = AccountFactory.create(
-    user__name="Ben", verified=True, email="[email protected]"
-)
-account_3 = AccountFactory.create(
-    user__name="Matt", verified=True, email="[email protected]"
-)
-account_4 = AccountFactory.create(
-    user__name="Stephanie", verified=True, email="[email protected]"
-)
+account_1 = AccountFactory.create(user__name="Adrienne", verified=True, email="[email protected]")
+account_2 = AccountFactory.create(user__name="Ben", verified=True, email="[email protected]")
+account_3 = AccountFactory.create(user__name="Matt", verified=True, email="[email protected]")
+account_4 = AccountFactory.create(user__name="Stephanie", verified=True, email="[email protected]")
 
 # Set up collab analysis workspace one
 # analyst group
-GroupAccountMembershipFactory.create(
-    account=account_1, group=collaborative_analysis_workspace_1.analyst_group
-)
-GroupAccountMembershipFactory.create(
-    account=account_2, group=collaborative_analysis_workspace_1.analyst_group
-)
+GroupAccountMembershipFactory.create(account=account_1, group=collaborative_analysis_workspace_1.analyst_group)
+GroupAccountMembershipFactory.create(account=account_2, group=collaborative_analysis_workspace_1.analyst_group)
 # auth domains
 GroupAccountMembershipFactory.create(
     account=account_1,
@@ -84,12 +72,8 @@
 
 # Set up collab analysis workspace two
 # analyst group
-GroupAccountMembershipFactory.create(
-    account=account_3, group=collaborative_analysis_workspace_2.analyst_group
-)
-GroupAccountMembershipFactory.create(
-    account=account_4, group=collaborative_analysis_workspace_2.analyst_group
-)
+GroupAccountMembershipFactory.create(account=account_3, group=collaborative_analysis_workspace_2.analyst_group)
+GroupAccountMembershipFactory.create(account=account_4, group=collaborative_analysis_workspace_2.analyst_group)
 # auth domains
 GroupAccountMembershipFactory.create(
     account=account_3,

add_dbgap_example_data.py

@@ -10,23 +10,13 @@
 
 # Studies
 fhs = StudyFactory.create(short_name="FHS", full_name="Framingham Heart Study")
-mesa = StudyFactory.create(
-    short_name="MESA", full_name="Multi-Ethnic Study of Atherosclerosis"
-)
-aric = StudyFactory.create(
-    short_name="ARIC", full_name="Atherosclerosis Risk in Communities"
-)
+mesa = StudyFactory.create(short_name="MESA", full_name="Multi-Ethnic Study of Atherosclerosis")
+aric = StudyFactory.create(short_name="ARIC", full_name="Atherosclerosis Risk in Communities")
 
 # dbGaP study accessions
-dbgap_study_accession_fhs = factories.dbGaPStudyAccessionFactory.create(
-    dbgap_phs=7, studies=[fhs]
-)
-dbgap_study_accession_mesa = factories.dbGaPStudyAccessionFactory.create(
-    dbgap_phs=209, studies=[mesa]
-)
-dbgap_study_accession_aric = factories.dbGaPStudyAccessionFactory.create(
-    dbgap_phs=280, studies=[aric]
-)
+dbgap_study_accession_fhs = factories.dbGaPStudyAccessionFactory.create(dbgap_phs=7, studies=[fhs])
+dbgap_study_accession_mesa = factories.dbGaPStudyAccessionFactory.create(dbgap_phs=209, studies=[mesa])
+dbgap_study_accession_aric = factories.dbGaPStudyAccessionFactory.create(dbgap_phs=280, studies=[aric])
 
 
 # Create some dbGaP workspaces.
@@ -78,9 +68,7 @@
     dbgap_project_id=33119,
 )
 # Add a snapshot
-dar_snapshot_1 = factories.dbGaPDataAccessSnapshotFactory.create(
-    dbgap_application=dbgap_application_1
-)
+dar_snapshot_1 = factories.dbGaPDataAccessSnapshotFactory.create(dbgap_application=dbgap_application_1)
 # Add some data access requests.
 dar_1_1 = factories.dbGaPDataAccessRequestForWorkspaceFactory.create(
     dbgap_workspace=workspace_fhs_1,
@@ -112,9 +100,7 @@
     dbgap_project_id=33371,
 )
 # Add a snapshot
-dar_snapshot_2 = factories.dbGaPDataAccessSnapshotFactory.create(
-    dbgap_application=dbgap_application_2
-)
+dar_snapshot_2 = factories.dbGaPDataAccessSnapshotFactory.create(dbgap_application=dbgap_application_2)
 # Add some data access requests, only for FHS.
 dar_1_1 = factories.dbGaPDataAccessRequestForWorkspaceFactory.create(
     dbgap_workspace=workspace_fhs_1,

add_phenotype_inventory_input_example_data.py

@@ -39,12 +39,6 @@
 
 # Share workspaces with PRIMED_ALL
 primed_all = ManagedGroupFactory.create(name="PRIMED_ALL")
-WorkspaceGroupSharingFactory.create(
-    workspace=workspace_dbgap.workspace, group=primed_all
-)
-WorkspaceGroupSharingFactory.create(
-    workspace=workspace_cdsa.workspace, group=primed_all
-)
-WorkspaceGroupSharingFactory.create(
-    workspace=workspace_open_access.workspace, group=primed_all
-)
+WorkspaceGroupSharingFactory.create(workspace=workspace_dbgap.workspace, group=primed_all)
+WorkspaceGroupSharingFactory.create(workspace=workspace_cdsa.workspace, group=primed_all)
+WorkspaceGroupSharingFactory.create(workspace=workspace_open_access.workspace, group=primed_all)

config/settings/base.py

@@ -1,6 +1,7 @@
 """
 Base settings to build other settings files upon.
 """
+
 from pathlib import Path
 
 import environ
@@ -135,9 +136,7 @@
 ]
 # 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"},
@@ -264,12 +263,7 @@
 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",
@@ -407,9 +401,5 @@
 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")
-DRUPAL_DATA_AUDIT_DEACTIVATE_USERS = env(
-    "DRUPAL_DATA_AUDIT_DEACTIVATE_USERS", default=False
-)
-DRUPAL_DATA_AUDIT_REMOVE_USER_SITES = env(
-    "DRUPAL_DATA_AUDIT_REMOVE_USER_SITES", default=False
-)
+DRUPAL_DATA_AUDIT_DEACTIVATE_USERS = env("DRUPAL_DATA_AUDIT_DEACTIVATE_USERS", default=False)
+DRUPAL_DATA_AUDIT_REMOVE_USER_SITES = env("DRUPAL_DATA_AUDIT_REMOVE_USER_SITES", default=False)

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
 # ------------------------------------------------------------------------------
@@ -73,10 +71,6 @@
 # ANVIL_CDSA_GROUP_PREFIX = env(
 #     "ANVIL_CDSA_GROUP_PREFIX", default="DEV_PRIMED_CDSA_ACCESS"
 # )
-ANVIL_DATA_ACCESS_GROUP_PREFIX = env(
-    "ANVIL_DATA_ACCESS_GROUP_PREFIX", default="DEV_PRIMED"
-)
+ANVIL_DATA_ACCESS_GROUP_PREFIX = env("ANVIL_DATA_ACCESS_GROUP_PREFIX", default="DEV_PRIMED")
 ANVIL_CDSA_GROUP_NAME = env("ANVIL_CDSA_GROUP_NAME", default="DEV_PRIMED_CDSA")
-ANVIL_CC_ADMINS_GROUP_NAME = env(
-    "ANVIL_CC_ADMINS_GROUP_NAME", default="DEV_PRIMED_CC_ADMINS"
-)
+ANVIL_CC_ADMINS_GROUP_NAME = env("ANVIL_CC_ADMINS_GROUP_NAME", default="DEV_PRIMED_CC_ADMINS")

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",