make ruff stricter

bmds_ui/analysis/api.py

@@ -52,7 +52,7 @@ def patch_inputs(self, request, *args, **kwargs):
         try:
             validators.validate_input(data, partial=partial)
         except ValidationError as err:
-            raise exceptions.ValidationError(err.message)
+            raise exceptions.ValidationError(err.message) from None
 
         instance.reset_execution()
         instance.inputs = data
@@ -207,7 +207,7 @@ def _run_analysis(self, request) -> PolyKAdjustment:
         try:
             settings = pydantic_validate(request.data, schema.PolyKInput)
         except ValidationError as err:
-            raise exceptions.ValidationError(err.message)
+            raise exceptions.ValidationError(err.message) from None
         return settings.calculate()
 
     def create(self, request, *args, **kwargs):

bmds_ui/analysis/serializers.py

@@ -65,5 +65,5 @@ def validate_inputs(self, value):
         try:
             validators.validate_input(value)
         except ValueError as err:
-            raise serializers.ValidationError(err)
+            raise serializers.ValidationError("Validation failed") from err
         return value

bmds_ui/common/templatetags/bs4.py

@@ -8,8 +8,7 @@
 
 from django import template
 from django.utils import timezone
-from django.utils.html import escapejs
-from django.utils.safestring import mark_safe
+from django.utils.html import escapejs, format_html
 from plotly.graph_objs._figure import Figure
 
 register = template.Library()
@@ -39,7 +38,7 @@ def render(self, context):
 
 @register.simple_tag
 def icon(name: str):
-    return mark_safe(f'<span class="bi bi-{name}" aria-hidden="true"></span>')
+    return format_html('<span class="bi bi-{name}" aria-hidden="true"></span>', name=name)
 
 
 @register.simple_tag()
@@ -48,18 +47,18 @@ def plotly(fig: Figure) -> str | None:
     if fig is None:
         return ""
     id = uuid4()
-    return mark_safe(
-        dedent(
-            f"""
+    return format_html(
+        dedent("""
     <div id="{id}"><span class="text-muted">Loading...</span></div>
     <script>
         document.addEventListener("DOMContentLoaded", startup, false);
         function startup () {{
-            const data = JSON.parse("{escapejs(fig.to_json())}")
+            const data = JSON.parse("{json}")
             window.app.renderPlotlyFigure(document.getElementById("{id}"), data);
         }};
-    </script>"""
-        )
+    </script>"""),
+        id=id,
+        json=escapejs(fig.to_json()),
     )
 
 

bmds_ui/common/validation.py

@@ -23,4 +23,4 @@ def pydantic_validate(data: Any, model: type[T]) -> T:
     try:
         return model.model_validate(data)
     except PydanticValidationError as err:
-        raise ValidationError(err.json())
+        raise ValidationError(err.json()) from None

bmds_ui/common/views.py

@@ -214,11 +214,11 @@ def uuid_or_404(value: str) -> UUID:
     try:
         return UUID(value)
     except ValueError:
-        raise Http404()
+        raise Http404() from None
 
 
 def int_or_404(value: str) -> int:
     try:
         return int(value)
     except ValueError:
-        raise Http404()
+        raise Http404() from None

bmds_ui/desktop/components/database_form.py

@@ -43,14 +43,14 @@ def additional_path_checks(path: Path):
     try:
         path.exists()
     except PermissionError:
-        raise ValueError(f"Permission denied: {path}")
+        raise ValueError(f"Permission denied: {path}") from None
 
     # create parent path if it doesn't already exist
     if not path.parent.exists():
         try:
             path.parent.mkdir(parents=True)
         except Exception:
-            raise ValueError(f"Cannot create path {path.parent}")
+            raise ValueError(f"Cannot create path {path.parent}") from None
 
     # check path is writable
     if not path.exists():
@@ -59,7 +59,7 @@ def additional_path_checks(path: Path):
                 f.write("test")
                 f.flush()
         except Exception:
-            raise ValueError(f"Cannot write to {path.parent}")
+            raise ValueError(f"Cannot write to {path.parent}") from None
 
     # check existing database is loadable and writeable
     if path.exists():
@@ -70,7 +70,7 @@ def additional_path_checks(path: Path):
             conn.commit()
             conn.close()
         except (sqlite3.DatabaseError, sqlite3.OperationalError):
-            raise ValueError(f"Cannot edit database {path}. Is this a sqlite database?")
+            raise ValueError(f"Cannot edit database {path}. Is this a sqlite database?") from None
 
 
 class NullWidget(Widget):

bmds_ui/desktop/config.py

@@ -159,9 +159,7 @@ def get(cls) -> DesktopConfig:
         try:
             cls._config = DesktopConfig.model_validate_json(cls._config_path.read_text())
         except ValidationError as err:
-            raise DesktopException(
-                f"Cannot parse configuration: {cls._config_path}\n\nSpecific error:{err}"
-            )
+            raise DesktopException(f"Cannot parse configuration: {cls._config_path}") from err
         return cls._config
 
     @classmethod

pyproject.toml

@@ -112,16 +112,12 @@ omit = [
 ]
 
 [tool.ruff]
+exclude = ["scripts"]
 line-length = 100
-target-version = "py311"
-
-[tool.ruff.lint]
-select = ["F", "E", "W", "I", "UP", "S", "B", "T20", "RUF"]
-ignore = ["E501", "B904", "B007", "S308", "S113", "S314"]
-unfixable = ["F401", "F841"]
-
-[tool.ruff.lint.isort]
-known-first-party = ["bmds_ui", "pybmds"]
+lint.select = ["F", "E", "W", "I", "UP", "S", "B", "T20", "ERA", "NPY", "RUF", "PTH"]
+lint.ignore = ["E501"]
+lint.unfixable = ["F401", "F841"]
+lint.isort.known-first-party = ["bmds_ui", "pybmds"]
 
 [tool.ruff.lint.per-file-ignores]
 "test_*.py" = ["S101", "S106"]

tests/analysis/test_executor.py

@@ -72,14 +72,14 @@ def _expected_degree(session, n: int):
             degrees = set([model.settings.degree for model in session.frequentist.models])
             assert degrees == set(list(range(1, n + 1)))
 
-        # degree = 1
+        # check when degree = 1
         data = deepcopy(complete_dichotomous)
         data["models"] = {"frequentist_restricted": ["Multistage"]}
         data["dataset_options"][0]["degree"] = 1
         session = AnalysisSession.create(data, 0, 0)
         _expected_degree(session, 1)
 
-        # degree = 2
+        # check when degree = 2
         data = deepcopy(complete_dichotomous)
         data["models"] = {"frequentist_restricted": ["Multistage"]}
         data["dataset_options"][0]["degree"] = 2

tests/common/test_api.py

@@ -45,7 +45,7 @@ def test_throttle(self):
 
         # success - admin
         url = reverse("api:healthcheck-throttle")
-        for i in range(5):
+        for _ in range(5):
             resp = admin.get(url)
             assert resp.status_code == 200
             assert "identity" in resp.data

tests/common/test_diagnostics.py

@@ -6,7 +6,6 @@
 
 
 @pytest.fixture
-@pytest.mark.django_db
 def admin_client():
     client = Client()
     client.login(username="[email protected]", password="pw")

tests/common/test_worker_health.py

@@ -19,7 +19,7 @@ def test_worker_healthcheck():
 
     # has recent data; should be healthy
     worker.MAX_SIZE = 5
-    for i in range(worker.MAX_SIZE + 2):
+    for _ in range(worker.MAX_SIZE + 2):
         worker.push()
     assert worker.healthy() is True
     assert worker.series().size == worker.MAX_SIZE

tests/desktop/test_config.py

@@ -14,4 +14,4 @@ def test_get_version_path():
 
 def test_get_app_home():
     assert "bmds" in str(config.get_app_home())
-    assert Path(".") == config.get_app_home(path_str=".")
+    assert Path() == config.get_app_home(path_str=".")