scitex-linter 0.1.0__tar.gz → 0.1.2__tar.gz

{scitex_linter-0.1.0/src/scitex_linter.egg-info → scitex_linter-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scitex-linter
-Version: 0.1.0
+Version: 0.1.2
 Summary: AST-based linter enforcing SciTeX reproducible research patterns
 Author: ywatanabe
 License: AGPL-3.0
@@ -70,20 +70,21 @@ pip install scitex-linter
 
 ```bash
 # Lint a file
-scitex-linter lint script.py
+scitex-linter check script.py
 
 # Lint then execute
 scitex-linter python experiment.py --strict
 
 # List all 35 rules
-scitex-linter list-rules
+scitex-linter rule
 ```
 
-## Four Interfaces
+## Five Interfaces
 
 | Interface | For | Description |
 |-----------|-----|-------------|
-| 🖥️ **CLI** | Terminal users | `scitex-linter lint`, `scitex-linter python` |
+| 🖥️ **CLI** | Terminal users | `scitex-linter check`, `scitex-linter python` |
+| ✨ **Format** | Auto-fix | `scitex-linter format` — auto-fix SciTeX issues |
 | 🐍 **Python API** | Programmatic use | `from scitex_linter.checker import lint_file` |
 | 🔌 **flake8 Plugin** | CI pipelines | `flake8 --select STX` |
 | 🔧 **MCP Server** | AI agents | 3 tools for Claude/GPT integration |
@@ -97,12 +98,18 @@ scitex-linter list-rules
 scitex-linter --help                              # Show all commands
 scitex-linter --help-recursive                    # Show help for all subcommands
 
-# Lint - Check for SciTeX pattern violations
-scitex-linter lint script.py                      # Lint a file
-scitex-linter lint ./src/                         # Lint a directory
-scitex-linter lint script.py --severity error     # Only errors
-scitex-linter lint script.py --category path      # Only path rules
-scitex-linter lint script.py --json               # JSON output for CI
+# Check - Check for SciTeX pattern violations
+scitex-linter check script.py                      # Check a file
+scitex-linter check ./src/                         # Check a directory
+scitex-linter check script.py --severity error     # Only errors
+scitex-linter check script.py --category path      # Only path rules
+scitex-linter check script.py --json               # JSON output for CI
+
+# Format - Auto-fix SciTeX pattern issues
+scitex-linter format script.py                     # Fix in place
+scitex-linter format script.py --check             # Dry run (exit 1 if changes needed)
+scitex-linter format script.py --diff              # Show diff of changes
+scitex-linter format ./src/                        # Format a directory
 
 # Python - Lint then execute
 scitex-linter python experiment.py                # Lint and run
@@ -110,9 +117,9 @@ scitex-linter python experiment.py --strict       # Abort on errors
 scitex-linter python experiment.py -- --lr 0.001  # Pass script args
 
 # Rules - Browse available rules
-scitex-linter list-rules                          # List all 35 rules
-scitex-linter list-rules --category stats         # Filter by category
-scitex-linter list-rules --json                   # JSON output
+scitex-linter rule                          # List all 35 rules
+scitex-linter rule --category stats         # Filter by category
+scitex-linter rule --json                   # JSON output
 
 # MCP - AI agent server
 scitex-linter mcp start                           # Start MCP server (stdio)
@@ -165,7 +172,7 @@ Integrates with existing flake8 workflows, pre-commit hooks, and CI pipelines.
 
 | Tool | Description |
 |------|-------------|
-| `linter_lint` | Lint a Python file for SciTeX compliance |
+| `linter_check` | Check a Python file for SciTeX compliance |
 | `linter_list_rules` | List all available rules |
 | `linter_check_source` | Lint source code string |
 
@@ -238,6 +245,37 @@ SciTeX Linter works as a **post-tool-use hook** for Claude Code, automatically l
 
 This ensures AI-generated code follows SciTeX patterns from the start.
 
+## Configuration
+
+<details>
+<summary><strong>Configure via pyproject.toml or environment variables</strong></summary>
+
+<br>
+
+```toml
+[tool.scitex-linter]
+severity = "info"                    # Minimum severity: error, warning, info
+disable = ["STX-P004", "STX-I003"]   # Disable specific rules
+exclude-dirs = ["venv", ".venv"]     # Directories to skip
+library-dirs = ["src"]               # Exempt from script-only rules
+
+[tool.scitex-linter.per-rule-severity]
+STX-S003 = "warning"                 # Downgrade argparse rule
+
+[tool.scitex-linter.session]
+required-injected = ["CONFIG", "plt", "COLORS", "rngg", "logger"]
+```
+
+Environment variables (highest priority):
+```bash
+SCITEX_LINTER_SEVERITY=error
+SCITEX_LINTER_DISABLE=STX-P004,STX-I003
+```
+
+Priority: CLI flags > env vars > pyproject.toml > defaults
+
+</details>
+
 ## What a Clean Script Looks Like
 
 ```python

{scitex_linter-0.1.0 → scitex_linter-0.1.2}/README.md

@@ -41,20 +41,21 @@ pip install scitex-linter
 
 ```bash
 # Lint a file
-scitex-linter lint script.py
+scitex-linter check script.py
 
 # Lint then execute
 scitex-linter python experiment.py --strict
 
 # List all 35 rules
-scitex-linter list-rules
+scitex-linter rule
 ```
 
-## Four Interfaces
+## Five Interfaces
 
 | Interface | For | Description |
 |-----------|-----|-------------|
-| 🖥️ **CLI** | Terminal users | `scitex-linter lint`, `scitex-linter python` |
+| 🖥️ **CLI** | Terminal users | `scitex-linter check`, `scitex-linter python` |
+| ✨ **Format** | Auto-fix | `scitex-linter format` — auto-fix SciTeX issues |
 | 🐍 **Python API** | Programmatic use | `from scitex_linter.checker import lint_file` |
 | 🔌 **flake8 Plugin** | CI pipelines | `flake8 --select STX` |
 | 🔧 **MCP Server** | AI agents | 3 tools for Claude/GPT integration |
@@ -68,12 +69,18 @@ scitex-linter list-rules
 scitex-linter --help                              # Show all commands
 scitex-linter --help-recursive                    # Show help for all subcommands
 
-# Lint - Check for SciTeX pattern violations
-scitex-linter lint script.py                      # Lint a file
-scitex-linter lint ./src/                         # Lint a directory
-scitex-linter lint script.py --severity error     # Only errors
-scitex-linter lint script.py --category path      # Only path rules
-scitex-linter lint script.py --json               # JSON output for CI
+# Check - Check for SciTeX pattern violations
+scitex-linter check script.py                      # Check a file
+scitex-linter check ./src/                         # Check a directory
+scitex-linter check script.py --severity error     # Only errors
+scitex-linter check script.py --category path      # Only path rules
+scitex-linter check script.py --json               # JSON output for CI
+
+# Format - Auto-fix SciTeX pattern issues
+scitex-linter format script.py                     # Fix in place
+scitex-linter format script.py --check             # Dry run (exit 1 if changes needed)
+scitex-linter format script.py --diff              # Show diff of changes
+scitex-linter format ./src/                        # Format a directory
 
 # Python - Lint then execute
 scitex-linter python experiment.py                # Lint and run
@@ -81,9 +88,9 @@ scitex-linter python experiment.py --strict       # Abort on errors
 scitex-linter python experiment.py -- --lr 0.001  # Pass script args
 
 # Rules - Browse available rules
-scitex-linter list-rules                          # List all 35 rules
-scitex-linter list-rules --category stats         # Filter by category
-scitex-linter list-rules --json                   # JSON output
+scitex-linter rule                          # List all 35 rules
+scitex-linter rule --category stats         # Filter by category
+scitex-linter rule --json                   # JSON output
 
 # MCP - AI agent server
 scitex-linter mcp start                           # Start MCP server (stdio)
@@ -136,7 +143,7 @@ Integrates with existing flake8 workflows, pre-commit hooks, and CI pipelines.
 
 | Tool | Description |
 |------|-------------|
-| `linter_lint` | Lint a Python file for SciTeX compliance |
+| `linter_check` | Check a Python file for SciTeX compliance |
 | `linter_list_rules` | List all available rules |
 | `linter_check_source` | Lint source code string |
 
@@ -209,6 +216,37 @@ SciTeX Linter works as a **post-tool-use hook** for Claude Code, automatically l
 
 This ensures AI-generated code follows SciTeX patterns from the start.
 
+## Configuration
+
+<details>
+<summary><strong>Configure via pyproject.toml or environment variables</strong></summary>
+
+<br>
+
+```toml
+[tool.scitex-linter]
+severity = "info"                    # Minimum severity: error, warning, info
+disable = ["STX-P004", "STX-I003"]   # Disable specific rules
+exclude-dirs = ["venv", ".venv"]     # Directories to skip
+library-dirs = ["src"]               # Exempt from script-only rules
+
+[tool.scitex-linter.per-rule-severity]
+STX-S003 = "warning"                 # Downgrade argparse rule
+
+[tool.scitex-linter.session]
+required-injected = ["CONFIG", "plt", "COLORS", "rngg", "logger"]
+```
+
+Environment variables (highest priority):
+```bash
+SCITEX_LINTER_SEVERITY=error
+SCITEX_LINTER_DISABLE=STX-P004,STX-I003
+```
+
+Priority: CLI flags > env vars > pyproject.toml > defaults
+
+</details>
+
 ## What a Clean Script Looks Like
 
 ```python

{scitex_linter-0.1.0 → scitex_linter-0.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "scitex-linter"
-version = "0.1.0"
+version = "0.1.2"
 description = "AST-based linter enforcing SciTeX reproducible research patterns"
 readme = "README.md"
 license = {text = "AGPL-3.0"}

{scitex_linter-0.1.0 → scitex_linter-0.1.2}/src/scitex_linter/__init__.py

@@ -1,3 +1,3 @@
 """SciTeX Linter — enforce reproducible research patterns via AST analysis."""
 
-__version__ = "0.1.0"
+__version__ = "0.1.2"

scitex_linter-0.1.2/src/scitex_linter/_cmd_format.py

@@ -0,0 +1,70 @@
+"""CLI handler for the 'format' subcommand."""
+
+import difflib
+import sys
+from pathlib import Path
+
+from .fixer import fix_source
+
+
+def register(subparsers) -> None:
+    p = subparsers.add_parser(
+        "format",
+        help="Auto-fix SciTeX pattern issues",
+        description="Auto-fix SciTeX pattern issues (e.g. insert missing INJECTED parameters).",
+    )
+    p.add_argument("path", help="Python file or directory to format")
+    p.add_argument(
+        "--check",
+        action="store_true",
+        help="Check if changes needed without writing (exit 1 if changes needed)",
+    )
+    p.add_argument("--diff", action="store_true", help="Show diff of changes")
+    p.set_defaults(func=cmd_format)
+
+
+def cmd_format(args) -> int:
+    from .cli import _collect_files
+    from .config import load_config
+
+    config = load_config(args.path)
+    target = Path(args.path)
+    if not target.exists():
+        print(f"Error: {args.path} not found", file=sys.stderr)
+        return 2
+
+    files = _collect_files(target, config=config)
+    if not files:
+        print(f"No Python files found in {args.path}", file=sys.stderr)
+        return 0
+
+    changed_count = 0
+    for f in files:
+        original = f.read_text(encoding="utf-8")
+        fixed = fix_source(original, filepath=str(f), config=config)
+        if fixed != original:
+            changed_count += 1
+            if args.diff:
+                diff = difflib.unified_diff(
+                    original.splitlines(keepends=True),
+                    fixed.splitlines(keepends=True),
+                    fromfile=str(f),
+                    tofile=str(f),
+                )
+                sys.stdout.writelines(diff)
+            if not args.check:
+                f.write_text(fixed, encoding="utf-8")
+                print(f"Fixed {f}")
+            else:
+                print(f"Would fix {f}")
+
+    if changed_count == 0:
+        print("All files clean")
+        return 0
+
+    if args.check:
+        print(f"\n{changed_count} file(s) would be changed")
+        return 1
+
+    print(f"\n{changed_count} file(s) fixed")
+    return 0

{scitex_linter-0.1.0 → scitex_linter-0.1.2}/src/scitex_linter/_mcp/tools/lint.py

@@ -7,15 +7,17 @@ def register_lint_tools(mcp) -> None:
     """Register lint-related MCP tools."""
 
     @mcp.tool()
-    def linter_lint(
+    def linter_check(
         path: str, severity: str = "info", category: Optional[str] = None
     ) -> dict:
-        """[linter] Lint a Python file for SciTeX pattern compliance."""
+        """[linter] Check a Python file for SciTeX pattern compliance."""
         from ...checker import lint_file
+        from ...config import load_config
         from ...formatter import to_json
         from ...rules import SEVERITY_ORDER
 
-        issues = lint_file(path)
+        config = load_config(path)
+        issues = lint_file(path, config=config)
         min_sev = SEVERITY_ORDER.get(severity, 0)
         categories = set(category.split(",")) if category else None
 
@@ -61,7 +63,9 @@ def register_lint_tools(mcp) -> None:
     def linter_check_source(source: str, filepath: str = "<stdin>") -> dict:
         """[linter] Lint Python source code string for SciTeX pattern compliance."""
         from ...checker import lint_source
+        from ...config import load_config
         from ...formatter import to_json
 
-        issues = lint_source(source, filepath=filepath)
+        config = load_config(filepath)
+        issues = lint_source(source, filepath=filepath, config=config)
         return to_json(issues, filepath)

{scitex_linter-0.1.0 → scitex_linter-0.1.2}/src/scitex_linter/_server.py

@@ -8,7 +8,7 @@ _INSTRUCTIONS = """\
 SciTeX Linter: AST-based linter enforcing reproducible research patterns.
 
 Tools:
-- linter_lint: Lint a Python file
+- linter_check: Check a Python file
 - linter_list_rules: List all lint rules
 - linter_check_source: Lint source code string
 """

{scitex_linter-0.1.0 → scitex_linter-0.1.2}/src/scitex_linter/checker.py

@@ -8,13 +8,8 @@ from . import rules
 from .rules import Rule
 
 # Shortcuts for Phase 1 rules
-S001, S002, S003, S004, S005 = (
-    rules.S001,
-    rules.S002,
-    rules.S003,
-    rules.S004,
-    rules.S005,
-)
+S001, S002, S003 = rules.S001, rules.S002, rules.S003
+S004, S005, S006 = rules.S004, rules.S005, rules.S006
 I001, I002, I003 = rules.I001, rules.I002, rules.I003
 I006, I007 = rules.I006, rules.I007
 
@@ -67,24 +62,42 @@ class Issue:
     source_line: str = ""
 
 
-def is_script(filepath: str) -> bool:
-    """Check if file is a script (not a library module)."""
-    name = Path(filepath).name
-    if name == "__init__.py":
-        return False
-    if name.startswith("test_") or name == "conftest.py":
-        return False
-    if name in ("setup.py", "manage.py"):
+def is_script(filepath: str, config=None) -> bool:
+    """Check if file is a script (not a library module).
+
+    Uses config.library_patterns and config.library_dirs to determine
+    which files are library modules (exempt from script-only rules).
+    """
+    from .config import LinterConfig, matches_library_pattern
+
+    if config is None:
+        config = LinterConfig()
+
+    path = Path(filepath)
+    name = path.name
+
+    # Check filename against library patterns (e.g., __*__.py, test_*.py)
+    if matches_library_pattern(name, config):
         return False
+
+    # Check if file is inside a library directory (e.g., src/)
+    parts = path.parts
+    for lib_dir in config.library_dirs:
+        if lib_dir in parts:
+            return False
+
     return True
 
 
 class SciTeXChecker(ast.NodeVisitor):
     """AST visitor detecting non-SciTeX patterns."""
 
-    def __init__(self, source_lines: list, filepath: str = "<stdin>"):
+    def __init__(self, source_lines: list, filepath: str = "<stdin>", config=None):
+        from .config import LinterConfig
+
         self.source_lines = source_lines
         self.filepath = filepath
+        self.config = config or LinterConfig()
         self.issues: list = []
 
         # Tracking state
@@ -93,7 +106,7 @@ class SciTeXChecker(ast.NodeVisitor):
         self._has_session_decorator = False
         self._session_func_returns_int = False
         self._imports: dict = {}  # alias -> full module path
-        self._is_script = is_script(filepath)
+        self._is_script = is_script(filepath, self.config)
 
     # -----------------------------------------------------------------
     # Import visitors
@@ -343,10 +356,15 @@ class SciTeXChecker(ast.NodeVisitor):
     # Function/decorator visitors
     # -----------------------------------------------------------------
 
+    @property
+    def _REQUIRED_INJECTED(self):
+        return set(self.config.required_injected)
+
     def visit_FunctionDef(self, node: ast.FunctionDef) -> None:
         if self._has_session_deco(node):
             self._has_session_decorator = True
             self._check_session_return(node)
+            self._check_injected_params(node)
         self.generic_visit(node)
 
     visit_AsyncFunctionDef = visit_FunctionDef
@@ -380,6 +398,25 @@ class SciTeXChecker(ast.NodeVisitor):
         line = self._get_source(node.lineno)
         self._add(S004, node.lineno, node.col_offset, line)
 
+    def _check_injected_params(self, node: ast.FunctionDef) -> None:
+        """Check that @stx.session function declares all INJECTED parameters."""
+        declared = {arg.arg for arg in node.args.args}
+        missing = sorted(self._REQUIRED_INJECTED - declared)
+        if missing:
+            line = self._get_source(node.lineno)
+            missing_str = ", ".join(missing)
+            dynamic_rule = Rule(
+                id=S006.id,
+                severity=S006.severity,
+                category=S006.category,
+                message=(
+                    f"@stx.session function missing INJECTED parameters: {missing_str}. "
+                    f"All 5 must be declared: CONFIG, COLORS, logger, plt, rngg"
+                ),
+                suggestion=S006.suggestion,
+            )
+            self._add(dynamic_rule, node.lineno, node.col_offset, line)
+
     # -----------------------------------------------------------------
     # Module-level checks (run after visiting entire tree)
     # -----------------------------------------------------------------
@@ -427,11 +464,12 @@ class SciTeXChecker(ast.NodeVisitor):
         self.issues.sort(key=lambda i: (-SEVERITY_ORDER[i.rule.severity], i.line))
         return self.issues
 
-    # -----------------------------------------------------------------
-    # Helpers
-    # -----------------------------------------------------------------
-
     def _add(self, rule: Rule, line: int, col: int, source_line: str) -> None:
+        if rule.id in self.config.disable:
+            return
+        sev = self.config.per_rule_severity.get(rule.id)
+        if sev:
+            rule = Rule(rule.id, sev, rule.category, rule.message, rule.suggestion)
         self.issues.append(
             Issue(rule=rule, line=line, col=col, source_line=source_line)
         )
@@ -447,7 +485,7 @@ class SciTeXChecker(ast.NodeVisitor):
 # =============================================================================
 
 
-def lint_source(source: str, filepath: str = "<stdin>") -> list:
+def lint_source(source: str, filepath: str = "<stdin>", config=None) -> list:
     """Lint Python source code and return list of Issues."""
     try:
         tree = ast.parse(source, filename=filepath)
@@ -455,15 +493,15 @@ def lint_source(source: str, filepath: str = "<stdin>") -> list:
         return []
 
     lines = source.splitlines()
-    checker = SciTeXChecker(lines, filepath=filepath)
+    checker = SciTeXChecker(lines, filepath=filepath, config=config)
     checker.visit(tree)
     return checker.get_issues()
 
 
-def lint_file(filepath: str) -> list:
+def lint_file(filepath: str, config=None) -> list:
     """Lint a Python file and return list of Issues."""
     path = Path(filepath)
     if not path.exists() or not path.is_file():
         return []
     source = path.read_text(encoding="utf-8")
-    return lint_source(source, filepath=str(path))
+    return lint_source(source, filepath=str(path), config=config)

{scitex_linter-0.1.0 → scitex_linter-0.1.2}/src/scitex_linter/cli.py

@@ -1,9 +1,10 @@
 """CLI entry point for scitex-linter.
 
 Usage:
-    scitex-linter lint <path> [--json] [--severity] [--category] [--no-color]
+    scitex-linter check <path> [--json] [--severity] [--category] [--no-color]
+    scitex-linter format <path> [--check] [--diff]
     scitex-linter python <script.py> [--strict] [-- script_args...]
-    scitex-linter list-rules [--json] [--category] [--severity]
+    scitex-linter rule [--json] [--category] [--severity]
     scitex-linter mcp start
     scitex-linter mcp list-tools
     scitex-linter --help-recursive
@@ -15,7 +16,9 @@ import sys
 from pathlib import Path
 
 from . import __version__
+from ._cmd_format import register as _register_format
 from .checker import lint_file
+from .config import load_config
 from .formatter import format_issue, format_summary, to_json
 from .rules import ALL_RULES, SEVERITY_ORDER
 
@@ -24,13 +27,17 @@ from .rules import ALL_RULES, SEVERITY_ORDER
 # =========================================================================
 
 
-def _collect_files(path: Path, recursive: bool = True) -> list:
+def _collect_files(path: Path, recursive: bool = True, config=None) -> list:
     """Collect Python files from a path."""
     if path.is_file():
         return [path]
     if path.is_dir():
         pattern = "**/*.py" if recursive else "*.py"
-        skip = {"__pycache__", ".git", "node_modules", ".tox", "venv", ".venv"}
+        skip = (
+            set(config.exclude_dirs)
+            if config
+            else {"__pycache__", ".git", "node_modules", ".tox", "venv", ".venv"}
+        )
         return sorted(
             p for p in path.glob(pattern) if not any(s in p.parts for s in skip)
         )
@@ -38,17 +45,17 @@ def _collect_files(path: Path, recursive: bool = True) -> list:
 
 
 # =========================================================================
-# Subcommand: lint
+# Subcommand: check
 # =========================================================================
 
 
-def _register_lint(subparsers) -> None:
+def _register_check(subparsers) -> None:
     p = subparsers.add_parser(
-        "lint",
-        help="Lint Python files for SciTeX pattern compliance",
-        description="Lint Python files for SciTeX pattern compliance.",
+        "check",
+        help="Check Python files for SciTeX pattern compliance",
+        description="Check Python files for SciTeX pattern compliance.",
     )
-    p.add_argument("path", help="Python file or directory to lint")
+    p.add_argument("path", help="Python file or directory to check")
     p.add_argument("--json", action="store_true", dest="as_json", help="Output as JSON")
     p.add_argument("--no-color", action="store_true", help="Disable colored output")
     p.add_argument(
@@ -61,10 +68,11 @@ def _register_lint(subparsers) -> None:
         "--category",
         help="Filter by category (comma-separated: structure,import,io,plot,stats)",
     )
-    p.set_defaults(func=_cmd_lint)
+    p.set_defaults(func=_cmd_check)
 
 
-def _cmd_lint(args) -> int:
+def _cmd_check(args) -> int:
+    config = load_config(args.path)
     use_color = not args.no_color and sys.stdout.isatty()
     min_sev = SEVERITY_ORDER[args.severity]
     categories = set(args.category.split(",")) if args.category else None
@@ -74,14 +82,14 @@ def _cmd_lint(args) -> int:
         print(f"Error: {args.path} not found", file=sys.stderr)
         return 2
 
-    files = _collect_files(target)
+    files = _collect_files(target, config=config)
     if not files:
         print(f"No Python files found in {args.path}", file=sys.stderr)
         return 0
 
     all_results = {}
     for f in files:
-        issues = lint_file(str(f))
+        issues = lint_file(str(f), config=config)
         issues = [
             i
             for i in issues
@@ -151,13 +159,13 @@ def _cmd_python(args) -> int:
 
 
 # =========================================================================
-# Subcommand: list-rules
+# Subcommand: rule
 # =========================================================================
 
 
-def _register_list_rules(subparsers) -> None:
+def _register_rule(subparsers) -> None:
     p = subparsers.add_parser(
-        "list-rules",
+        "rule",
         help="List all lint rules",
         description="List all available SciTeX lint rules.",
     )
@@ -171,10 +179,10 @@ def _register_list_rules(subparsers) -> None:
         choices=["error", "warning", "info"],
         help="Filter by severity",
     )
-    p.set_defaults(func=_cmd_list_rules)
+    p.set_defaults(func=_cmd_rule)
 
 
-def _cmd_list_rules(args) -> int:
+def _cmd_rule(args) -> int:
     categories = set(args.category.split(",")) if args.category else None
     rules_list = list(ALL_RULES.values())
 
@@ -272,7 +280,7 @@ def _cmd_mcp_start(args) -> int:
 
 def _cmd_mcp_list_tools(args) -> int:
     tools = [
-        ("linter_lint", "Lint a Python file for SciTeX pattern compliance"),
+        ("linter_check", "Check a Python file for SciTeX pattern compliance"),
         ("linter_list_rules", "List all available lint rules"),
         ("linter_check_source", "Lint Python source code string"),
     ]
@@ -364,7 +372,6 @@ def _cmd_mcp_installation(args) -> int:
 def _print_help_recursive(parser, subparsers_actions) -> None:
     """Print help for all commands recursively."""
     cyan = "\033[96m" if sys.stdout.isatty() else ""
-    bold = "\033[1m" if sys.stdout.isatty() else ""
     reset = "\033[0m" if sys.stdout.isatty() else ""
 
     bar = "\u2501" * 3
@@ -409,9 +416,10 @@ def main(argv: list = None) -> int:
 
     subparsers = parser.add_subparsers(dest="command")
 
-    _register_lint(subparsers)
+    _register_check(subparsers)
+    _register_format(subparsers)
     _register_python(subparsers)
-    _register_list_rules(subparsers)
+    _register_rule(subparsers)
     _register_mcp(subparsers)
 
     # Split on -- to capture script args for the 'python' subcommand