Replace TaggedFilesHierarchy with os.walk and implement configure_directory entrypoint (#695)

This PR adds a configure_directory entry point, as well as tests. It
also removes TaggedFilesHierarchy and replaces it with os.walk. Finally,
the Generator tests have been refactored.

[ reviewed by @MattToast @mellis13 @juliaputko ]
[ committed by @amandarichardsonn ]

Author: amandarichardsonn

smartsim/_core/commands/command_list.py

@@ -34,9 +34,11 @@
 class CommandList(MutableSequence[Command]):
     """Container for a Sequence of Command objects"""
 
-    def __init__(self, commands: t.Union[Command, t.List[Command]]):
+    def __init__(self, commands: t.Optional[t.Union[Command, t.List[Command]]] = None):
         """CommandList constructor"""
-        if isinstance(commands, Command):
+        if commands is None:
+            commands = []
+        elif isinstance(commands, Command):
             commands = [commands]
         self._commands: t.List[Command] = list(commands)
 

smartsim/_core/entrypoints/file_operations.py

@@ -49,7 +49,7 @@ def _abspath(input_path: str) -> pathlib.Path:
     """Helper function to check that paths are absolute"""
     path = pathlib.Path(input_path)
     if not path.is_absolute():
-        raise ValueError(f"path `{path}` must be absolute")
+        raise ValueError(f"Path `{path}` must be absolute.")
     return path
 
 
@@ -62,6 +62,22 @@ def _make_substitution(
     )
 
 
+def _prepare_param_dict(param_dict: str) -> dict[str, t.Any]:
+    """Decode and deserialize a base64-encoded parameter dictionary.
+
+    This function takes a base64-encoded string representation of a dictionary,
+    decodes it, and then deserializes it using pickle. It performs validation
+    to ensure the resulting object is a non-empty dictionary.
+    """
+    decoded_dict = base64.b64decode(param_dict)
+    deserialized_dict = pickle.loads(decoded_dict)
+    if not isinstance(deserialized_dict, dict):
+        raise TypeError("param dict is not a valid dictionary")
+    if not deserialized_dict:
+        raise ValueError("param dictionary is empty")
+    return deserialized_dict
+
+
 def _replace_tags_in(
     item: str,
     substitutions: t.Sequence[Callable[[str], str]],
@@ -70,6 +86,23 @@ def _replace_tags_in(
     return functools.reduce(lambda a, fn: fn(a), substitutions, item)
 
 
+def _process_file(
+    substitutions: t.Sequence[Callable[[str], str]],
+    source: pathlib.Path,
+    destination: pathlib.Path,
+) -> None:
+    """
+    Process a source file by replacing tags with specified substitutions and
+    write the result to a destination file.
+    """
+    # Set the lines to iterate over
+    with open(source, "r+", encoding="utf-8") as file_stream:
+        lines = [_replace_tags_in(line, substitutions) for line in file_stream]
+    # write configured file to destination specified
+    with open(destination, "w+", encoding="utf-8") as file_stream:
+        file_stream.writelines(lines)
+
+
 def move(parsed_args: argparse.Namespace) -> None:
     """Move a source file or directory to another location. If dest is an
     existing directory or a symlink to a directory, then the srouce will
@@ -155,9 +188,9 @@ def symlink(parsed_args: argparse.Namespace) -> None:
 
 def configure(parsed_args: argparse.Namespace) -> None:
     """Set, search and replace the tagged parameters for the
-    configure operation within tagged files attached to an entity.
+    configure_file operation within tagged files attached to an entity.
 
-    User-formatted files can be attached using the `configure` argument.
+    User-formatted files can be attached using the `configure_file` argument.
     These files will be modified during ``Application`` generation to replace
     tagged sections in the user-formatted files with values from the `params`
     initializer argument used during ``Application`` creation:
@@ -166,39 +199,38 @@ def configure(parsed_args: argparse.Namespace) -> None:
     .. highlight:: bash
     .. code-block:: bash
             python -m smartsim._core.entrypoints.file_operations \
-                configure /absolute/file/source/pat /absolute/file/dest/path \
+                configure_file /absolute/file/source/path /absolute/file/dest/path \
                 tag_deliminator param_dict
 
     /absolute/file/source/path: The tagged files the search and replace operations
     to be performed upon
     /absolute/file/dest/path: The destination for configured files to be
     written to.
-    tag_delimiter: tag for the configure operation to search for, defaults to
+    tag_delimiter: tag for the configure_file operation to search for, defaults to
         semi-colon e.g. ";"
     param_dict: A dict of parameter names and values set for the file
 
     """
     tag_delimiter = parsed_args.tag_delimiter
-
-    decoded_dict = base64.b64decode(parsed_args.param_dict)
-    param_dict = pickle.loads(decoded_dict)
-
-    if not param_dict:
-        raise ValueError("param dictionary is empty")
-    if not isinstance(param_dict, dict):
-        raise TypeError("param dict is not a valid dictionary")
+    param_dict = _prepare_param_dict(parsed_args.param_dict)
 
     substitutions = tuple(
         _make_substitution(k, v, tag_delimiter) for k, v in param_dict.items()
     )
-
-    # Set the lines to iterate over
-    with open(parsed_args.source, "r+", encoding="utf-8") as file_stream:
-        lines = [_replace_tags_in(line, substitutions) for line in file_stream]
-
-    # write configured file to destination specified
-    with open(parsed_args.dest, "w+", encoding="utf-8") as file_stream:
-        file_stream.writelines(lines)
+    if parsed_args.source.is_dir():
+        for dirpath, _, filenames in os.walk(parsed_args.source):
+            new_dir_dest = dirpath.replace(
+                str(parsed_args.source), str(parsed_args.dest), 1
+            )
+            os.makedirs(new_dir_dest, exist_ok=True)
+            for file_name in filenames:
+                src_file = os.path.join(dirpath, file_name)
+                dst_file = os.path.join(new_dir_dest, file_name)
+                print(type(substitutions))
+                _process_file(substitutions, src_file, dst_file)
+    else:
+        dst_file = parsed_args.dest / os.path.basename(parsed_args.source)
+        _process_file(substitutions, parsed_args.source, dst_file)
 
 
 def get_parser() -> argparse.ArgumentParser: