Fix pyproject.toml formatting when appending alembic config

alembic/script/base.py

@@ -554,13 +554,57 @@ def run_env(self) -> None:
     def env_py_location(self) -> str:
         return str(Path(self.dir, "env.py"))
 
-    def _append_template(self, src: Path, dest: Path, **kw: Any) -> None:
-        with util.status(
-            f"Appending to existing {dest.absolute()}",
-            **self.messaging_opts,
-        ):
+
+    def _append_template(
+        self, template_path: Path, output_path: Union[str, Path], **kw: Any
+    ) -> None:
+        """
+        Append content from a Mako template to an existing file.
+
+        Special handling for TOML files to ensure proper formatting between
+        sections, addressing issue #1679.
+
+        Args:
+            template_path: Path to the template file
+            output_path: Path to the output file to append to
+            **kw: Keyword arguments for template rendering
+        """
+        output_path = Path(output_path)
+
+        # For TOML files, we need special handling to ensure proper spacing
+        if output_path.suffix.lower() == '.toml' and output_path.exists():
+            # Read existing content
+            with open(output_path, 'r', encoding=self.output_encoding) as f:
+                existing_content = f.read()
+
+            # Check if we need to add newlines before appending
+            existing_content = existing_content.rstrip()
+
+            # Save the modified content back
+            with open(output_path, 'w', encoding=self.output_encoding) as f:
+                f.write(existing_content)
+
+                # TOML convention: ensure 2 newlines between top-level sections
+                # The template should start with [tool.alembic], so we need proper spacing
+                if existing_content:
+                    f.write('\n\n')
+
+            # Now append the template content
+            util.template_to_file(
+                template_path,
+                output_path,
+                self.output_encoding,
+                append=True,
+                **kw
+            )
+        else:
+            # For non-TOML files or new files, just use template_to_file directly
             util.template_to_file(
-                src, dest, self.output_encoding, append=True, **kw
+                template_path,
+                output_path,
+                self.output_encoding,
+                append=True,
+                **kw
             )
 
     def _generate_template(self, src: Path, dest: Path, **kw: Any) -> None:

tests/test_append_template.py

@@ -0,0 +1,41 @@
+"""Tests for pyproject.toml template functionality."""
+import os
+import tempfile
+from pathlib import Path
+
+from alembic import command
+from alembic.config import Config
+from alembic.testing import TestBase
+
+
+class TestPyprojectTemplate(TestBase):
+    """Test the pyproject template, particularly issue #1679."""
+
+    def test_init_pyproject_existing_file_formatting(self):
+        """Test that appending to existing pyproject.toml maintains proper spacing."""
+        with tempfile.TemporaryDirectory() as tmpdir:
+            os.chdir(tmpdir)
+
+            # Create existing pyproject.toml
+            pyproject_path = Path("pyproject.toml")
+            pyproject_path.write_text(
+                '[tool.black]\ntarget-version = [\'py37\']\n\n'
+                '[tool.mypy]\npython_version = "3.10"'
+            )
+
+            # Run init
+            config = Config("pyproject.toml")
+            command.init(config, "alembic", template="pyproject")
+
+            # Check result
+            result = pyproject_path.read_text()
+
+            # Verify no concatenation (issue #1679)
+            assert 'python_version = "3.10"[tool.alembic]' not in result
+
+            # Verify proper spacing
+            assert '\n\n[tool.alembic]' in result
+
+            # Verify content preserved
+            assert '[tool.black]' in result
+            assert '[tool.mypy]' in result