Deprecate dotted filenames for package qualified module names.

Close #2686.

CHANGES.rst

@@ -163,6 +163,10 @@ Other changes
 * The command line parser was rewritten and modernised using ``argparse``.
   Patch by Egor Dranischnikow.  (Github issue #2952, #3001)
 
+* Dotted filenames for qualified module names (``pkg.mod.pyx``) are deprecated.
+  Use the normal Python package directory layout instead.
+  (Github issue #2686)
+
 * Support for Python 2.6 was removed.
 
 

Cython/Compiler/Main.py

@@ -494,6 +494,12 @@ def run_pipeline(source, options, full_module_name=None, context=None):
         pipeline = Pipeline.create_pyx_pipeline(context, options, result)
 
     context.setup_errors(options, result)
+
+    if '.' in full_module_name and '.' in os.path.splitext(os.path.basename(abs_path))[0]:
+        warning((source_desc, 1, 0),
+                "Dotted filenames ('%s') are deprecated."
+                " Please use the normal Python package directory layout." % os.path.basename(abs_path), level=1)
+
     err, enddata = Pipeline.run_pipeline(pipeline, source)
     context.teardown_errors(err, options, result)
     return result
@@ -650,6 +656,8 @@ def search_include_directories(dirs, qualified_name, suffix, pos, include=False)
     for dirname in dirs:
         path = os.path.join(dirname, dotted_filename)
         if os.path.exists(path):
+            warning(pos, "Dotted filenames ('%s') are deprecated."
+                         " Please use the normal Python package directory layout." % dotted_filename, level=1)
             return path
 
     # search for filename in package structure e.g. <dir>/foo/bar.pxd or <dir>/foo/bar/__init__.pxd

tests/build/dotted.filename.modules.pyx

+# mode: compile
+# tag: warnings
+
+_WARNINGS="""
+1:0: Dotted filenames ('dotted.filename.modules.pxd') are deprecated. Please use the normal Python package directory layout.
+1:0: Dotted filenames ('dotted.filename.modules.pyx') are deprecated. Please use the normal Python package directory layout.
+"""