fix: formatting errors and failure to detect empty or missing __init__ modules

Author: bashandbone

src/exportify/pipeline.py

@@ -147,12 +147,6 @@ def _generate_code(
 
         for manifest in manifests.values():
             if not self._should_generate_init(manifest):
-                skipped_files.append(
-                    SkippedFile(
-                        path=Path(manifest.module_path),
-                        reason="Not a package or has no exports to generate",
-                    )
-                )
                 continue
 
             try:
@@ -174,15 +168,18 @@ def _should_generate_init(self, manifest: ExportManifest) -> bool:
         # It needs one if:
         # 1. It already has one (recorded in self._package_modules)
         # 2. It has exports (own or propagated) AND it has children (it's a directory)
-        # 3. It's the root package being processed (optional, but good for consistency)
+        # 3. It's a directory (parent) in our source tree
         is_existing_package = manifest.module_path in self._package_modules
         has_exports = len(manifest.all_exports) > 0
 
         # Use graph to check if it's a parent of other modules
         node = self.graph.modules.get(manifest.module_path)
         is_parent = bool(node and node.children)
 
-        return is_existing_package or (has_exports and is_parent)
+        # Generate if it exists OR if it is a parent (directory package)
+        # Even if it has no exports yet, a package usually needs an __init__.py
+        # but here we focus on those that are parents of our discovered modules.
+        return is_existing_package or is_parent
 
     def _process_manifest(
         self, manifest: ExportManifest, *, dry_run: bool
@@ -333,7 +330,7 @@ def _process_file(self, file_path: Path, source_root: Path) -> None:
             parts[-1] = relative.stem
             is_package = False
 
-        module_path = ".".join(parts) if parts else "root"
+        module_path = ".".join(parts) if parts else ""
 
         # Track package modules so the generator only writes __init__.py for them.
         if is_package:

src/exportify/utils.py

@@ -196,37 +196,43 @@ def _run_ruff_format(
     """Run ruff format via subprocess and return formatted content if successful."""
     import subprocess
 
-    ruff_binary = shutil.which("ruff") or f"{shutil.which('uvx')} ruff"
+    ruff_binary = shutil.which("ruff")
+    if not ruff_binary and shutil.which("uvx"):
+        ruff_binary = "uvx ruff"
+
     if not ruff_binary:
         return None
+
+    # 1. Run ruff format
+    # Use split() if ruff_binary is "uvx ruff"
+    cmd = ruff_binary.split() if " " in ruff_binary else [ruff_binary]
     result = subprocess.run(
-        [ruff_binary, "format", "--verbose" if verbose else "--quiet", *stdin_filename_args, "-"],
+        [*cmd, "format", "--quiet", *stdin_filename_args, "-"],
         input=content,
         capture_output=True,
         text=True,
         check=False,
     )
+    if result.returncode != 0:
+        return None
+
+    formatted_content = result.stdout
+
+    # 2. Run ruff check --fix on the formatted content
+    result = subprocess.run(
+        [*cmd, "check", "--fix", "--quiet", *stdin_filename_args, "-"],
+        input=formatted_content,
+        capture_output=True,
+        text=True,
+        check=False,
+    )
+
     if result.returncode == 0:
-        stdout_message = result.stdout.strip()
-        result = subprocess.run(
-            [
-                ruff_binary,
-                "check",
-                "--fix",
-                "--verbose" if verbose else "--quiet",
-                *stdin_filename_args,
-                "-",
-            ],
-            input=content,
-            capture_output=True,
-            text=True,
-            check=False,
-        )
-    if result.returncode == 0:
-        stdout_message += f"\n\n{result.stdout.strip()}"
-        stdout_message += "\nAll checks passed after formatting."
-        return stdout_message
-    return result.stderr.strip() if result.stderr else None
+        # Return the final content (from stdout if any, else use formatted_content)
+        # Note: ruff check --fix - usually outputs the fixed content to stdout
+        return result.stdout or formatted_content
+
+    return None
 
 
 def format_content(content: str, *, filename: Path | None = None, verbose: bool = False) -> str: