Fix submodule check out

repo2docker/contentproviders/git.py

@@ -23,7 +23,12 @@ class Git(ContentProvider):
         try:
             cmd = ["git", "clone", "--recursive"]
             if ref is None:
+                # check out of HEAD is performed after the clone is complete
                 cmd.extend(["--depth", "1"])
+            else:
+                # don't check out HEAD, the given ref will be checked out later
+                # this prevents HEAD's submodules to be cloned if ref doesn't have them
+                cmd.extend(["--no-checkout"])
             cmd.extend([repo, output_dir])
             for line in execute_cmd(cmd, capture=yield_output):
                 yield line
@@ -34,6 +39,11 @@ class Git(ContentProvider):
 
         # check out the specific ref given by the user
         if ref is not None:
+            # check out ref as it has not been done yet
+            for line in execute_cmd(
+                ["git", "checkout", ref], cwd=output_dir, capture=yield_output
+            ):
+                yield line
             hash = check_ref(ref, output_dir)
             if hash is None:
                 self.log.error(