Application.files refactor (CrayLabs#732)

This PR refactors how files are added to an Application.

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

conftest.py

@@ -40,6 +40,8 @@
 import typing as t
 import uuid
 import warnings
+from glob import glob
+from os import path as osp
 from collections import defaultdict
 from dataclasses import dataclass
 from subprocess import run
@@ -53,6 +55,8 @@
 from smartsim._core.config.config import Config
 from smartsim._core.launcher.dragon.dragon_connector import DragonConnector
 from smartsim._core.launcher.dragon.dragon_launcher import DragonLauncher
+from smartsim._core.generation.operations.operations import ConfigureOperation, CopyOperation, SymlinkOperation
+from smartsim._core.generation.generator import Generator
 from smartsim._core.utils.telemetry.telemetry import JobEntity
 from smartsim.database import FeatureStore
 from smartsim.entity import Application
@@ -469,6 +473,58 @@ def check_output_dir() -> None:
 def fsutils() -> t.Type[FSUtils]:
     return FSUtils
 
+@pytest.fixture
+def files(fileutils):
+    path_to_files = fileutils.get_test_conf_path(
+        osp.join("generator_files", "easy", "correct/")
+    )
+    list_of_files_strs = glob(path_to_files + "/*")
+    yield [pathlib.Path(str_path) for str_path in list_of_files_strs]
+
+
+@pytest.fixture
+def directory(fileutils):
+    directory = fileutils.get_test_conf_path(
+        osp.join("generator_files", "easy", "correct/")
+    )
+    yield [pathlib.Path(directory)]
+
+
+@pytest.fixture(params=["files", "directory"])
+def source(request):
+    yield request.getfixturevalue(request.param)
+
+
+@pytest.fixture
+def mock_src(test_dir: str):
+    """Fixture to create a mock source path."""
+    return pathlib.Path(test_dir) / pathlib.Path("mock_src")
+
+
+@pytest.fixture
+def mock_dest():
+    """Fixture to create a mock destination path."""
+    return pathlib.Path("mock_dest")
+
+
+@pytest.fixture
+def copy_operation(mock_src: pathlib.Path, mock_dest: pathlib.Path):
+    """Fixture to create a CopyOperation object."""
+    return CopyOperation(src=mock_src, dest=mock_dest)
+
+
+@pytest.fixture
+def symlink_operation(mock_src: pathlib.Path, mock_dest: pathlib.Path):
+    """Fixture to create a CopyOperation object."""
+    return SymlinkOperation(src=mock_src, dest=mock_dest)
+
+
+@pytest.fixture
+def configure_operation(mock_src: pathlib.Path, mock_dest: pathlib.Path):
+    """Fixture to create a Configure object."""
+    return ConfigureOperation(
+        src=mock_src, dest=mock_dest, file_parameters={"FOO": "BAR"}
+    )
 
 class FSUtils:
     @staticmethod

smartsim/_core/commands/command.py

@@ -35,6 +35,10 @@ class Command(MutableSequence[str]):
     """Basic container for command information"""
 
     def __init__(self, command: t.List[str]) -> None:
+        if not command:
+            raise TypeError("Command list cannot be empty")
+        if not all(isinstance(item, str) for item in command):
+            raise TypeError("All items in the command list must be strings")
         """Command constructor"""
         self._command = command
 
@@ -66,17 +70,15 @@ def __setitem__(
         """Set the command at the specified index."""
         if isinstance(idx, int):
             if not isinstance(value, str):
-                raise ValueError(
+                raise TypeError(
                     "Value must be of type `str` when assigning to an index"
                 )
             self._command[idx] = deepcopy(value)
             return
         if not isinstance(value, list) or not all(
             isinstance(item, str) for item in value
         ):
-            raise ValueError(
-                "Value must be a list of strings when assigning to a slice"
-            )
+            raise TypeError("Value must be a list of strings when assigning to a slice")
         self._command[idx] = (deepcopy(val) for val in value)
 
     def __delitem__(self, idx: t.Union[int, slice]) -> None:

smartsim/_core/commands/command_list.py

@@ -69,20 +69,20 @@ def __setitem__(
         """Set the Commands at the specified index."""
         if isinstance(idx, int):
             if not isinstance(value, Command):
-                raise ValueError(
+                raise TypeError(
                     "Value must be of type `Command` when assigning to an index"
                 )
             self._commands[idx] = deepcopy(value)
             return
         if not isinstance(value, list):
-            raise ValueError(
+            raise TypeError(
                 "Value must be a list of Commands when assigning to a slice"
             )
         for sublist in value:
             if not isinstance(sublist.command, list) or not all(
                 isinstance(item, str) for item in sublist.command
             ):
-                raise ValueError(
+                raise TypeError(
                     "Value sublists must be a list of Commands when assigning to a slice"
                 )
         self._commands[idx] = (deepcopy(val) for val in value)

smartsim/_core/entrypoints/file_operations.py

@@ -154,9 +154,9 @@ def copy(parsed_args: argparse.Namespace) -> None:
     /absolute/file/dest/path: Path to destination directory or path to
         destination file
     --dirs_exist_ok: if the flag is included, the copying operation will 
-        continue if the destination directory and files alrady exist, 
+        continue if the destination directory and files already exist, 
         and will be overwritten by corresponding files. If the flag is 
-        not includedm and the destination file already exists, a
+        not included and the destination file already exists, a
         FileExistsError will be raised
     """
     if os.path.isdir(parsed_args.source):
@@ -226,7 +226,6 @@ def configure(parsed_args: argparse.Namespace) -> None:
             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)