Merge branch 'main' into gpu-flag

Author: KRRT7

.github/workflows/claude-code-review.yml

@@ -1,6 +1,8 @@
 name: Claude Code
 
 on:
+  pull_request:
+    types: [opened, synchronize, ready_for_review, reopened]
   issue_comment:
     types: [created]
   pull_request_review_comment:
@@ -11,19 +13,154 @@ on:
     types: [submitted]
 
 jobs:
-  claude:
+  # Automatic PR review (can fix linting issues and push)
+  # Blocked for fork PRs to prevent malicious code execution
+  pr-review:
     if: |
-      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) ||
-      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) ||
-      (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) ||
-      (github.event_name == 'issues' && (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude')))
+      github.event_name == 'pull_request' &&
+      github.actor != 'claude[bot]' &&
+      github.event.pull_request.head.repo.full_name == github.repository
     runs-on: ubuntu-latest
     permissions:
       contents: write
       pull-requests: write
       issues: read
       id-token: write
-      actions: read # Required for Claude to read CI results on PRs
+      actions: read
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          ref: ${{ github.event.pull_request.head.ref }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Install dependencies
+        run: |
+          uv venv --seed
+          uv sync
+
+      - name: Run Claude Code
+        id: claude
+        uses: anthropics/claude-code-action@v1
+        with:
+          use_foundry: "true"
+          use_sticky_comment: true
+          allowed_bots: "claude[bot]"
+          prompt: |
+            REPO: ${{ github.repository }}
+            PR NUMBER: ${{ github.event.pull_request.number }}
+            EVENT: ${{ github.event.action }}
+
+            ## STEP 1: Run pre-commit checks and fix issues
+
+            First, run `uv run prek run --from-ref origin/main` to check for linting/formatting issues on files changed in this PR.
+
+            If there are any issues:
+            - For SAFE auto-fixable issues (formatting, import sorting, trailing whitespace, etc.), run `uv run prek run --from-ref origin/main` again to auto-fix them
+            - Stage the fixed files with `git add`
+            - Commit with message "style: auto-fix linting issues"
+            - Push the changes with `git push`
+
+            Do NOT attempt to fix:
+            - Type errors that require logic changes
+            - Complex refactoring suggestions
+            - Anything that could change behavior
+
+            ## STEP 2: Review the PR
+
+            ${{ github.event.action == 'synchronize' && 'This is a RE-REVIEW after new commits. First, get the list of changed files in this latest push using `gh pr diff`. Review ONLY the changed files. Check ALL existing review comments and resolve ones that are now fixed.' || 'This is the INITIAL REVIEW.' }}
+
+            Review this PR focusing ONLY on:
+            1. Critical bugs or logic errors
+            2. Security vulnerabilities
+            3. Breaking API changes
+            4. Test failures (methods with typos that wont run)
+
+            IMPORTANT:
+            - First check existing review comments using `gh api repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/comments`. For each existing comment, check if the issue still exists in the current code.
+            - If an issue is fixed, use `gh api --method PATCH repos/${{ github.repository }}/pulls/comments/COMMENT_ID -f body="✅ Fixed in latest commit"` to resolve it.
+            - Only create NEW inline comments for HIGH-PRIORITY issues found in changed files.
+            - Limit to 5-7 NEW comments maximum per review.
+            - Use CLAUDE.md for project-specific guidance.
+            - Use `gh pr comment` for summary-level feedback.
+            - Use `mcp__github_inline_comment__create_inline_comment` sparingly for critical code issues only.
+
+            ## STEP 3: Coverage analysis
+
+            Analyze test coverage for changed files:
+
+            1. Get the list of Python files changed in this PR (excluding tests):
+               `git diff --name-only origin/main...HEAD -- '*.py' | grep -v test`
+
+            2. Run tests with coverage on the PR branch:
+               `uv run coverage run -m pytest tests/ -q --tb=no`
+               `uv run coverage json -o coverage-pr.json`
+
+            3. Get coverage for changed files only:
+               `uv run coverage report --include="<changed_files_comma_separated>"`
+
+            4. Compare with main branch coverage:
+               - Checkout main: `git checkout origin/main`
+               - Run coverage: `uv run coverage run -m pytest tests/ -q --tb=no && uv run coverage json -o coverage-main.json`
+               - Checkout back: `git checkout -`
+
+            5. Analyze the diff to identify:
+               - NEW FILES: Files that don't exist on main (require good test coverage)
+               - MODIFIED FILES: Files with changes (changes must be covered by tests)
+
+            6. Report in PR comment with a markdown table:
+               - Coverage % for each changed file (PR vs main)
+               - Overall coverage change
+               - For NEW files: Flag if coverage is below 75%
+               - For MODIFIED files: Flag if the changed lines are not covered by tests
+               - Flag if overall coverage decreased
+
+            Coverage requirements:
+            - New implementations/files: Must have ≥75% test coverage
+            - Modified code: Changed lines should be exercised by existing or new tests
+            - No coverage regressions: Overall coverage should not decrease
+          claude_args: '--allowedTools "mcp__github_inline_comment__create_inline_comment,Bash(gh pr comment:*),Bash(gh pr diff:*),Bash(gh pr view:*),Bash(gh pr list:*),Bash(gh issue view:*),Bash(gh issue list:*),Bash(gh api:*),Bash(uv run prek *),Bash(uv run coverage *),Bash(uv run pytest *),Bash(git status*),Bash(git add *),Bash(git commit *),Bash(git push*),Bash(git diff *),Bash(git checkout *),Read,Glob,Grep"'
+          additional_permissions: |
+            actions: read
+        env:
+          ANTHROPIC_FOUNDRY_API_KEY: ${{ secrets.AZURE_ANTHROPIC_API_KEY }}
+          ANTHROPIC_FOUNDRY_BASE_URL: ${{ secrets.AZURE_ANTHROPIC_ENDPOINT }}
+
+  # @claude mentions (can edit and push) - restricted to maintainers only
+  claude-mention:
+    if: |
+      (
+        github.event_name == 'issue_comment' &&
+        contains(github.event.comment.body, '@claude') &&
+        (github.event.comment.author_association == 'OWNER' || github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'COLLABORATOR')
+      ) ||
+      (
+        github.event_name == 'pull_request_review_comment' &&
+        contains(github.event.comment.body, '@claude') &&
+        (github.event.comment.author_association == 'OWNER' || github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'COLLABORATOR') &&
+        github.event.pull_request.head.repo.full_name == github.repository
+      ) ||
+      (
+        github.event_name == 'pull_request_review' &&
+        contains(github.event.review.body, '@claude') &&
+        (github.event.review.author_association == 'OWNER' || github.event.review.author_association == 'MEMBER' || github.event.review.author_association == 'COLLABORATOR') &&
+        github.event.pull_request.head.repo.full_name == github.repository
+      ) ||
+      (
+        github.event_name == 'issues' &&
+        (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude')) &&
+        (github.event.issue.author_association == 'OWNER' || github.event.issue.author_association == 'MEMBER' || github.event.issue.author_association == 'COLLABORATOR')
+      )
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+      issues: read
+      id-token: write
+      actions: read
     steps:
       - name: Get PR head ref
         id: pr-ref
@@ -44,15 +181,22 @@ jobs:
           fetch-depth: 0
           ref: ${{ steps.pr-ref.outputs.ref }}
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Install dependencies
+        run: |
+          uv venv --seed
+          uv sync
+
       - name: Run Claude Code
         id: claude
         uses: anthropics/claude-code-action@v1
         with:
           use_foundry: "true"
-          claude_args: '--allowedTools "Read,Edit,Write,Glob,Grep,Bash(git status*),Bash(git diff*),Bash(git add *),Bash(git commit *),Bash(git push*),Bash(git log*),Bash(uv run pre-commit *),Bash(uv run ruff *),Bash(uv run pytest *),Bash(uv run mypy *),Bash(uv run coverage *),Bash(gh pr comment*),Bash(gh pr view*),Bash(gh pr diff*)"'
+          claude_args: '--allowedTools "Read,Edit,Write,Glob,Grep,Bash(git status*),Bash(git diff*),Bash(git add *),Bash(git commit *),Bash(git push*),Bash(git log*),Bash(git merge*),Bash(git fetch*),Bash(git checkout*),Bash(git branch*),Bash(uv run prek *),Bash(prek *),Bash(uv run ruff *),Bash(uv run pytest *),Bash(uv run mypy *),Bash(uv run coverage *),Bash(gh pr comment*),Bash(gh pr view*),Bash(gh pr diff*),Bash(gh pr merge*),Bash(gh pr close*)"'
           additional_permissions: |
             actions: read
         env:
           ANTHROPIC_FOUNDRY_API_KEY: ${{ secrets.AZURE_ANTHROPIC_API_KEY }}
           ANTHROPIC_FOUNDRY_BASE_URL: ${{ secrets.AZURE_ANTHROPIC_ENDPOINT }}
-

.github/workflows/claude.yml

@@ -0,0 +1,18 @@
+name: Lint
+on: [pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref_name }}
+  cancel-in-progress: true
+
+jobs:
+    prek:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@v4
+              with:
+                fetch-depth: 0
+            - uses: astral-sh/setup-uv@v6
+            - uses: j178/prek-action@v1
+              with:
+                extra-args: '--from-ref origin/${{ github.base_ref }} --to-ref ${{ github.sha }}'

.github/workflows/pre-commit.yaml

@@ -1429,7 +1429,9 @@ def _collect_numerical_imports(tree: ast.Module) -> tuple[set[str], set[str]]:
     numerical_names: set[str] = set()
     modules_used: set[str] = set()
 
-    for node in ast.walk(tree):
+    stack: list[ast.AST] = [tree]
+    while stack:
+        node = stack.pop()
         if isinstance(node, ast.Import):
             for alias in node.names:
                 # import numpy or import numpy as np
@@ -1451,6 +1453,8 @@ def _collect_numerical_imports(tree: ast.Module) -> tuple[set[str], set[str]]:
                         name = alias.asname or alias.name
                         numerical_names.add(name)
                 modules_used.add(module_root)
+        else:
+            stack.extend(ast.iter_child_nodes(node))
 
     return numerical_names, modules_used
 

.github/workflows/prek.yaml

@@ -746,7 +746,11 @@ def get_external_base_class_inits(code_context: CodeStringsMarkdown, project_roo
         return CodeStringsMarkdown(code_strings=[])
 
     imported_names: dict[str, str] = {}
-    external_bases: list[tuple[str, str]] = []
+    # Use a set to deduplicate external base entries to avoid repeated expensive checks/imports.
+    external_bases_set: set[tuple[str, str]] = set()
+    # Local cache to avoid repeated _is_project_module calls for the same module_name.
+    is_project_cache: dict[str, bool] = {}
+
     for node in ast.walk(tree):
         if isinstance(node, ast.ImportFrom) and node.module:
             for alias in node.names:
@@ -763,21 +767,31 @@ def get_external_base_class_inits(code_context: CodeStringsMarkdown, project_roo
 
                 if base_name and base_name in imported_names:
                     module_name = imported_names[base_name]
-                    if not _is_project_module(module_name, project_root_path):
-                        external_bases.append((base_name, module_name))
-
-    if not external_bases:
+                    # Check cache first to avoid repeated expensive checks.
+                    cached = is_project_cache.get(module_name)
+                    if cached is None:
+                        is_project = _is_project_module(module_name, project_root_path)
+                        is_project_cache[module_name] = is_project
+                    else:
+                        is_project = cached
+
+                    if not is_project:
+                        external_bases_set.add((base_name, module_name))
+
+    if not external_bases_set:
         return CodeStringsMarkdown(code_strings=[])
 
     code_strings: list[CodeString] = []
-    extracted: set[tuple[str, str]] = set()
-
-    for base_name, module_name in external_bases:
-        if (module_name, base_name) in extracted:
-            continue
+    # Cache imported modules to avoid repeated importlib.import_module calls.
+    imported_module_cache: dict[str, object] = {}
 
+    for base_name, module_name in external_bases_set:
         try:
-            module = importlib.import_module(module_name)
+            module = imported_module_cache.get(module_name)
+            if module is None:
+                module = importlib.import_module(module_name)
+                imported_module_cache[module_name] = module
+
             base_class = getattr(module, base_name, None)
             if base_class is None:
                 continue
@@ -799,7 +813,6 @@ def get_external_base_class_inits(code_context: CodeStringsMarkdown, project_roo
 
             class_source = f"class {base_name}:\n" + textwrap.indent(init_source, "    ")
             code_strings.append(CodeString(code=class_source, file_path=class_file))
-            extracted.add((module_name, base_name))
 
         except (ImportError, ModuleNotFoundError, AttributeError):
             logger.debug(f"Failed to extract __init__ for {module_name}.{base_name}")
@@ -854,12 +867,13 @@ def extract_imports_for_class(module_tree: ast.Module, class_node: ast.ClassDef,
                 needed_names.add(decorator.func.value.id)
 
     # Get type annotation names from class body (for dataclass fields)
-    for item in ast.walk(class_node):
+    for item in class_node.body:
         if isinstance(item, ast.AnnAssign) and item.annotation:
             collect_names_from_annotation(item.annotation, needed_names)
         # Also check for field() calls which are common in dataclasses
-        if isinstance(item, ast.Call) and isinstance(item.func, ast.Name):
-            needed_names.add(item.func.id)
+        elif isinstance(item, ast.Assign) and isinstance(item.value, ast.Call):
+            if isinstance(item.value.func, ast.Name):
+                needed_names.add(item.value.func.id)
 
     # Find imports that provide these names
     import_lines: list[str] = []