Consolidate test cases from triplet to single-file format

Author: nikolay-e

.gitleaks.toml

@@ -4,11 +4,16 @@ useDefault = true
 [allowlist]
 paths = [
     '''\.secrets\.baseline''',
-    '''tests/cases/diff/kubernetes/k8s_406_secret_reference\.yaml''',
-    '''tests/cases/diff/kubernetes/k8s_418_image_pull_secret\.yaml''',
-    '''tests/cases/diff/algorithm/algorithm_004_fragment_markdown_section_diffctx\.yaml''',
-    '''tests/cases/diff/docker/docker_039_compose_secrets_before\.yaml''',
-    '''tests/cases/diff/docker/docker_039_compose_secrets_after\.yaml''',
-    '''tests/cases/diff/fragments/fragments_018_config_yaml_top_level_keys_before\.yaml''',
-    '''tests/cases/diff/fragments/fragments_018_config_yaml_top_level_keys_after\.yaml''',
+    '''tests/cases/diff/algorithm/algorithm_004_fragment_markdown_section\.yaml''',
+    '''tests/cases/diff/docker/docker_039_compose_secrets\.yaml''',
+    '''tests/cases/diff/fragments/fragments_018_config_yaml_top_level_keys\.yaml''',
+    '''tests/cases/diff/kubernetes/kubernetes_006_secret_reference\.yaml''',
+    '''tests/cases/diff/kubernetes/kubernetes_018_image_pull_secret\.yaml''',
+    '''tests/cases/diff/kubernetes/kubernetes_029_network_policy_ingress\.yaml''',
+    '''tests/cases/diff/python/python_018_dunder_add_operator\.yaml''',
+    '''tests/cases/diff/terraform/terraform_079_kms_key\.yaml''',
+    '''tests/cases/diff/fragments/fragments_019_config_toml_sections\.yaml''',
+    '''tests/cases/diff/fragments/fragments_020_config_json_top_level_keys\.yaml''',
+    '''tests/cases/diff/helm/helm_025_template_secret\.yaml''',
+    '''tests/cases/diff/kubernetes/kubernetes_002_replicas_change\.yaml''',
 ]

.treemapper/review-cicd.whitelist

@@ -0,0 +1,7 @@
+# CI/CD Pipeline Review
+# Workflows, pyproject.toml, pre-commit
+
+.github/workflows/*.yml
+pyproject.toml
+.pre-commit-config.yaml
+treemapper.spec

.treemapper/review-core.whitelist

@@ -0,0 +1,12 @@
+# Core Tree Mapping Review
+# Filesystem walker, ignore/whitelist logic, output writers, CLI
+
+src/treemapper/treemapper.py
+src/treemapper/cli.py
+src/treemapper/tree.py
+src/treemapper/writer.py
+src/treemapper/ignore.py
+src/treemapper/tokens.py
+src/treemapper/clipboard.py
+src/treemapper/logger.py
+src/treemapper/version.py

.treemapper/review-diffctx.whitelist

@@ -0,0 +1,4 @@
+# Diff Context Mode Review
+# Semantic analysis, graph, PPR, fragment selection
+
+src/treemapper/diffctx/**/*.py

.treemapper/review-edges.whitelist

@@ -0,0 +1,7 @@
+# Edge System Review
+# Graph edges: semantic, structural, similarity, history, document
+
+src/treemapper/diffctx/edges/**/*.py
+src/treemapper/diffctx/graph.py
+src/treemapper/diffctx/ppr.py
+src/treemapper/diffctx/embeddings.py

.treemapper/review-parsers.whitelist

@@ -0,0 +1,8 @@
+# Language Parsers Review
+# Tree-sitter parsers, generic/HTML/K8s/Markdown/Python parsers
+
+src/treemapper/diffctx/parsers/**/*.py
+src/treemapper/diffctx/parsers/**/*.yaml
+src/treemapper/diffctx/python_semantics.py
+src/treemapper/diffctx/javascript_semantics.py
+src/treemapper/diffctx/languages.py

tests/cases/diff/algorithm/algorithm_001_fragment_class_decorator_included.yaml

@@ -0,0 +1,252 @@
+initial:
+  models/user.py: |
+    from dataclasses import dataclass, field
+    from typing import Optional, List
+    from datetime import datetime
+
+    @dataclass
+    class Address:
+        street: str
+        city: str
+        country: str
+        postal_code: str
+
+        def format(self) -> str:
+            return f"{self.street}, {self.city}, {self.postal_code}"
+
+    @dataclass
+    class User:
+        id: int
+        username: str
+        email: str
+        created_at: datetime = field(default_factory=datetime.now)
+        address: Optional[Address] = None
+        roles: List[str] = field(default_factory=list)
+
+        def is_admin(self) -> bool:
+            return "admin" in self.roles
+
+        def has_address(self) -> bool:
+            return self.address is not None
+  services/user_service.py: |
+    from models.user import User, Address
+
+    class UserService:
+        def __init__(self, repository):
+            self.repository = repository
+
+        def create_user(self, username: str, email: str) -> User:
+            user = User(
+                id=self.repository.next_id(),
+                username=username,
+                email=email
+            )
+            self.repository.save(user)
+            return user
+
+        def add_role(self, user: User, role: str) -> None:
+            if role not in user.roles:
+                user.roles.append(role)
+                self.repository.save(user)
+
+        def set_address(self, user: User, address: Address) -> None:
+            user.address = address
+            self.repository.save(user)
+
+  # --- Tricky garbage: shares "display_name" identifier with the diff ---
+  garbage_display_config.py: |
+    GARBAGE_ALGO_001_DISPLAY_CONFIG_G = "display_settings"
+    GARBAGE_ALGO_001_THEME_MARKER_H = True
+
+    class DisplayConfig:
+        display_name = "Default Theme"
+        display_mode = "dark"
+        GARBAGE_ALGO_001_RENDER_MARKER_I = 42
+
+        def get_display_name(self) -> str:
+            return self.display_name
+
+        def set_theme(self, theme: str) -> None:
+            self.display_name = theme
+
+  # --- Tricky garbage: imports User but is completely unrelated ---
+  garbage_user_export.py: |
+    from models.user import User
+    GARBAGE_ALGO_001_EXPORT_MARKER_J = "csv_export"
+    GARBAGE_ALGO_001_FORMAT_MARKER_K = "xlsx"
+
+    class UserExporter:
+        GARBAGE_ALGO_001_BATCH_MARKER_L = 1000
+
+        def export_users(self, users: list) -> bytes:
+            return b""
+
+        def schedule_export(self, cron: str) -> None:
+            pass
+
+  # --- Plain garbage: no overlap at all ---
+  garbage_analytics.py: |
+    GARBAGE_ALGO_001_ANALYTICS_MARKER_A = "analytics"
+    GARBAGE_ALGO_001_TRACKER_MARKER_B = True
+
+    class AnalyticsTracker:
+        GARBAGE_ALGO_001_CLASS_MARKER_C = "tracker"
+
+        def track(self, event: str) -> None:
+            pass
+  garbage_notifications.py: |
+    GARBAGE_ALGO_001_NOTIFY_MARKER_D = "notify"
+    GARBAGE_ALGO_001_PUSH_MARKER_E = 42
+
+    class PushService:
+        GARBAGE_ALGO_001_PUSH_CLASS_F = True
+
+        def send(self, token: str, message: str) -> bool:
+            return True
+
+changed:
+  models/user.py: |
+    from dataclasses import dataclass, field
+    from typing import Optional, List
+    from datetime import datetime
+
+    @dataclass
+    class Address:
+        street: str
+        city: str
+        country: str
+        postal_code: str
+
+        def format(self) -> str:
+            return f"{self.street}, {self.city}, {self.postal_code}"
+
+    @dataclass
+    class User:
+        id: int
+        username: str
+        email: str
+        display_name: Optional[str] = None
+        created_at: datetime = field(default_factory=datetime.now)
+        address: Optional[Address] = None
+        roles: List[str] = field(default_factory=list)
+
+        def is_admin(self) -> bool:
+            return "admin" in self.roles
+
+        def has_address(self) -> bool:
+            return self.address is not None
+
+        def get_display_name(self) -> str:
+            return self.display_name or self.username
+  services/user_service.py: |
+    from models.user import User, Address
+
+    class UserService:
+        def __init__(self, repository):
+            self.repository = repository
+
+        def create_user(self, username: str, email: str) -> User:
+            user = User(
+                id=self.repository.next_id(),
+                username=username,
+                email=email
+            )
+            self.repository.save(user)
+            return user
+
+        def add_role(self, user: User, role: str) -> None:
+            if role not in user.roles:
+                user.roles.append(role)
+                self.repository.save(user)
+
+        def set_address(self, user: User, address: Address) -> None:
+            user.address = address
+            self.repository.save(user)
+  garbage_display_config.py: |
+    GARBAGE_ALGO_001_DISPLAY_CONFIG_G = "display_settings"
+    GARBAGE_ALGO_001_THEME_MARKER_H = True
+
+    class DisplayConfig:
+        display_name = "Default Theme"
+        display_mode = "dark"
+        GARBAGE_ALGO_001_RENDER_MARKER_I = 42
+
+        def get_display_name(self) -> str:
+            return self.display_name
+
+        def set_theme(self, theme: str) -> None:
+            self.display_name = theme
+  garbage_user_export.py: |
+    from models.user import User
+    GARBAGE_ALGO_001_EXPORT_MARKER_J = "csv_export"
+    GARBAGE_ALGO_001_FORMAT_MARKER_K = "xlsx"
+
+    class UserExporter:
+        GARBAGE_ALGO_001_BATCH_MARKER_L = 1000
+
+        def export_users(self, users: list) -> bytes:
+            return b""
+
+        def schedule_export(self, cron: str) -> None:
+            pass
+  garbage_analytics.py: |
+    GARBAGE_ALGO_001_ANALYTICS_MARKER_A = "analytics"
+    GARBAGE_ALGO_001_TRACKER_MARKER_B = True
+
+    class AnalyticsTracker:
+        GARBAGE_ALGO_001_CLASS_MARKER_C = "tracker"
+
+        def track(self, event: str) -> None:
+            pass
+  garbage_notifications.py: |
+    GARBAGE_ALGO_001_NOTIFY_MARKER_D = "notify"
+    GARBAGE_ALGO_001_PUSH_MARKER_E = 42
+
+    class PushService:
+        GARBAGE_ALGO_001_PUSH_CLASS_F = True
+
+        def send(self, token: str, message: str) -> bool:
+            return True
+
+# === Assertions ===
+
+must_include_files:
+- models/user.py
+
+must_include_content_from:
+  models/user.py:
+    # Added symbols — the actual diff content
+    - 'def get_display_name(self) -> str:'
+    - return self.display_name or self.username
+    - 'display_name: Optional[str] = None'
+    # Class context — fragment should include enough surrounding code
+    - 'class User:'
+    - 'def is_admin(self) -> bool:'
+
+must_not_include:
+# Plain garbage markers
+- GARBAGE_ALGO_001_ANALYTICS_MARKER_A
+- GARBAGE_ALGO_001_CLASS_MARKER_C
+- GARBAGE_ALGO_001_NOTIFY_MARKER_D
+- GARBAGE_ALGO_001_PUSH_CLASS_F
+- GARBAGE_ALGO_001_PUSH_MARKER_E
+- GARBAGE_ALGO_001_TRACKER_MARKER_B
+# Tricky: shares "display_name" and "get_display_name" identifiers
+- GARBAGE_ALGO_001_DISPLAY_CONFIG_G
+- GARBAGE_ALGO_001_THEME_MARKER_H
+- GARBAGE_ALGO_001_RENDER_MARKER_I
+# Tricky: imports User directly
+- GARBAGE_ALGO_001_EXPORT_MARKER_J
+- GARBAGE_ALGO_001_FORMAT_MARKER_K
+- GARBAGE_ALGO_001_BATCH_MARKER_L
+
+must_not_include_files:
+- garbage_analytics.py
+- garbage_notifications.py
+- garbage_display_config.py
+- garbage_user_export.py
+
+max_fragments: 6
+max_files: 3
+add_garbage_files: false
+skip_garbage_check: true