mid ruff linting

Author: sneakers-the-rat

linkml_runtime/linkml_model/__init__.py

@@ -3,6 +3,11 @@
 from .meta import (
     AltDescription,
     AltDescriptionSource,
+    AnonymousClassExpression,
+    AnonymousEnumExpression,
+    AnonymousExpression,
+    AnonymousSlotExpression,
+    AnonymousTypeExpression,
     ClassDefinition,
     ClassDefinitionName,
     Definition,
@@ -90,4 +95,9 @@
     "AltDescription",
     "PermissibleValue",
     "PvFormulaOptions",
+    "AnonymousClassExpression",
+    "AnonymousEnumExpression",
+    "AnonymousExpression",
+    "AnonymousSlotExpression",
+    "AnonymousTypeExpression",
 ]

linkml_runtime/utils/permissiblevalueimpl.py

@@ -2,9 +2,9 @@
 from typing import Any, ClassVar, Optional, Union
 
 from rdflib import URIRef
-from utils.enumerations import EnumDefinitionImpl
 
 from linkml_runtime.utils.curienamespace import CurieNamespace
+from linkml_runtime.utils.enumerations import EnumDefinitionImpl
 from linkml_runtime.utils.metamodelcore import URI, URIorCURIE, empty_list
 from linkml_runtime.utils.yamlutils import YAMLRoot, extended_str
 

linkml_runtime/utils/ruleutils.py

@@ -136,12 +136,12 @@ def subclass_to_rules(
 
 
 def rule_subsumed_by_class(view: SchemaView, rule, cls: ClassDefinition):
-    induced_slots = view.class_induced_slots(cls.name)
+    # induced_slots = view.class_induced_slots(cls.name)
     return False
 
 
 def remove_redundant_rules(view: SchemaView, class_name: ClassDefinitionName):
-    induced_slots = view.class_induced_slots(class_name)
+    # induced_slots = view.class_induced_slots(class_name)
     cls = view.get_class(class_name)
     redundant_rules = []
     for rule in cls.rules:

linkml_runtime/utils/schemaops.py

@@ -22,7 +22,6 @@ def roll_up(sv: SchemaView, classes: CLASS_NAME_OR_LIST = None, mixins=True, is_
     dels = set()
     for cn in classes:
         c = sv.get_class(cn)
-        slots = []
         for d in sv.class_descendants(cn, reflexive=False, mixins=mixins, is_a=is_a):
             for sn in sv.class_slots(d):
                 s = sv.induced_slot(sn, class_name=d)
@@ -54,7 +53,6 @@ def roll_down(sv: SchemaView, classes: list[CLASS_NAME] = None, mixins=True, is_
     dels = set()
     for cn in classes:
         c = sv.get_class(cn)
-        slots = []
         for d in sv.class_ancestors(cn, reflexive=False, mixins=mixins, is_a=is_a):
             for sn in sv.class_slots(d):
                 s = sv.induced_slot(sn, class_name=d)
@@ -74,6 +72,5 @@ def roll_down(sv: SchemaView, classes: list[CLASS_NAME] = None, mixins=True, is_
             if is_a and c.is_a is not None:
                 del c.is_a
     for d in dels:
-        d_cls = sv.get_class(d)
         sv.delete_class(d)
     sv.set_modified()

linkml_runtime/utils/schemaview.py

@@ -6,17 +6,38 @@
 from collections import defaultdict, deque
 from collections.abc import Mapping
 from copy import copy, deepcopy
+from dataclasses import dataclass
 from enum import Enum
 from functools import lru_cache
 from pathlib import Path
-from typing import Optional, TypeVar
+from typing import Any, Optional, TypeVar, Union
 
 from deprecated.classic import deprecated
 
 from linkml_runtime.exceptions import OrderingError
-from linkml_runtime.linkml_model.meta import *
+from linkml_runtime.linkml_model import (
+    AnonymousSlotExpression,
+    ClassDefinition,
+    ClassDefinitionName,
+    Definition,
+    DefinitionName,
+    Element,
+    ElementName,
+    EnumDefinition,
+    EnumDefinitionName,
+    PermissibleValueText,
+    SchemaDefinition,
+    SchemaDefinitionName,
+    SlotDefinition,
+    SlotDefinitionName,
+    SubsetDefinition,
+    SubsetDefinitionName,
+    TypeDefinition,
+    TypeDefinitionName,
+)
 from linkml_runtime.utils.context_utils import map_import, parse_import_map
 from linkml_runtime.utils.formatutils import camelcase, is_empty, underscore
+from linkml_runtime.utils.metamodelcore import URIorCURIE
 from linkml_runtime.utils.namespaces import Namespaces
 from linkml_runtime.utils.pattern import PatternResolver
 
@@ -1117,7 +1138,7 @@ def get_uri(self, element: Union[ElementName, Element], imports=True, expand=Fal
         if uri is None or native:
             if e.from_schema is not None:
                 schema = next(sc for sc in self.schema_map.values() if sc.id == e.from_schema)
-                if schema == None:
+                if schema is None:
                     raise ValueError(f"Cannot find {e.from_schema} in schema_map")
             else:
                 schema = self.schema_map[self.in_schema(e.name)]

linkml_runtime/utils/yamlutils.py

@@ -12,7 +12,7 @@
 from yaml.constructor import ConstructorError
 
 from linkml_runtime.utils.context_utils import CONTEXTS_PARAM_TYPE, merge_contexts
-from linkml_runtime.utils.formatutils import is_empty, items
+from linkml_runtime.utils.formatutils import is_empty
 
 YAMLObjTypes = Union[JsonObjTypes, "YAMLRoot"]
 
@@ -229,16 +229,20 @@ def _normalize_inlined_slot(
                 self.<slot> = []
             if not isinstance(self.<slot>, list):
                 self.extensions = [self.<slot>]
-            self._normalize_inlined_slot(slot_name="<slot>", slot_type=<type>, key_name="<key>", inlined_as_list=True, keyed=...)
+            self._normalize_inlined_slot(
+                slot_name="<slot>", slot_type=<type>, key_name="<key>", inlined_as_list=True, keyed=...
+            )
         or
             if self.<slot> is None:
                 self.<slot> = []
             if not isinstance(self.<slot>, (list, dict)):
                 self.local_names = [self.<slot>]
-            self._normalize_inlined_slot(slot_name="<slot>", slot_type=<type>, key_name="<key>", inlined_as_list=None, keyed=...)
+            self._normalize_inlined_slot(
+                slot_name="<slot>", slot_type=<type>, key_name="<key>", inlined_as_list=None, keyed=...
+            )
 
-        The above pattern broke when the new jsonasobj was introduced, which is why we have the normalization above.  The code
-        below reverse engineers the above and invokes the new form
+        The above pattern broke when the new jsonasobj was introduced, which is why we have the normalization above.
+        The code below reverse engineers the above and invokes the new form
 
         """
         if inlined_as_list:
@@ -305,7 +309,8 @@ def _pformat(fields: dict, cls_name: str, indent: str = "  ") -> str:
         # pformat handles everything else that isn't a YAMLRoot object, but it sure does look ugly
         # use it to split lines and as the thing of last resort, but otherwise indent = 0, we'll do that
         val_str = pformat(val, indent=0, compact=True, sort_dicts=False)
-        # now we indent everything except the first line by indenting and then using regex to remove just the first indent
+        # now we indent everything except the first line by indenting
+        # and then using regex to remove just the first indent
         val_str = re.sub(rf"\A{re.escape(indent)}", "", textwrap.indent(val_str, indent))
         # now recombine with the key in a format that can be re-eval'd into an object if indent is just whitespace
         val_str = f"'{key}': " + val_str

pyproject.toml

@@ -100,7 +100,10 @@ select = [
   "UP", # pyupgrade
 ]
 force-exclude = true
-extend-ignore = ["E203"]
+extend-ignore = [
+    "E203",
+    "UP007", # until we drop 3.9
+]
 
 # -- Exclude files --
 extend-exclude = [
@@ -110,6 +113,9 @@ extend-exclude = [
     "notebooks/"
 ]
 
+[tool.ruff.per-file-ignores]
+"tests/**/**.py" = ["F841", "E501", "F842", "E741"] # I ain't fixing all that
+
 [tool.codespell]
 skip = '.git,*.pdf,*.svg,./tests,pyproject.toml,*.dill,poetry.lock'
 # Ignore table where words could be split across rows

tests/__init__.py

@@ -1,11 +1,14 @@
 import configparser
-import logging
 
 # Global testing control variables
 import os
 
 from tests.support.test_environment import MismatchAction
 
+__all__ = [
+    "MismatchAction",
+]
+
 # ---------------------------------------------------------------
 #                DO NOT change this file.
 # To change the default test harness settings:

tests/support/test_environment.py

@@ -22,7 +22,7 @@ def no_click_exit(_self, code=0):
 
 
 # This import has to occur here
-import click
+import click  # noqa: E402
 
 click.core.Context.exit = no_click_exit
 
@@ -209,8 +209,9 @@ def generate_single_file(
         :return: the generator output
         """
         # If no filter, default to identity function
-        if not filtr:
-            filtr = lambda s: s
+        if filtr is None:
+            def filtr(s):
+                return s
         filename = filename if isinstance(filename, list) else [filename]
         actual_file = self.root_temp_file_path(*filename) if use_testing_root else self.actual_path(*filename)
         expected_file = self.root_expected_path(*filename) if use_testing_root else self.expected_path(*filename)

tests/test_issues/test_linkml_runtime_issue_68.py

@@ -107,7 +107,7 @@ def test_issue_68(self):
 
         s3_induced_c2 = view.induced_slot("slot3", "class2")
         assert not s3_induced_c2.required
-        assert s3_induced_c2.description == None
+        assert s3_induced_c2.description is None
         assert s3_induced_c2.range == "class0"
 
         # mixins take priority over is-a