From 7c5ad60289dac53db72546adff70260b3a6b8b4e Mon Sep 17 00:00:00 2001
From: Adam Lamson <lamsoa729@gmail.com>
Date: Tue, 23 Jan 2024 09:49:38 -0500
Subject: [PATCH] Added nonyaml file testing

---
 chi_pet/chi_parse.py    | 11 +++++++++++
 tests/test_chi_parse.py | 39 ++++++++++++++++++++++++++++++++++++---
 tests/test_chi_run.py   |  3 ++-
 3 files changed, 49 insertions(+), 4 deletions(-)

diff --git a/chi_pet/chi_parse.py b/chi_pet/chi_parse.py
index b6fac3c..31b7745 100644
--- a/chi_pet/chi_parse.py
+++ b/chi_pet/chi_parse.py
@@ -76,6 +76,7 @@ def parse_chi_options():
 
     opts = parser.parse_args()
 
+    # General checking and options
     if not opts.workdir:
         opts.workdir = Path.cwd()
     elif not opts.workdir.exists():
@@ -87,11 +88,21 @@ def parse_chi_options():
 
         with opts.args_file.open('r') as f:
             opts.args_dict = clib.load_yaml_in_order(f)
+    else:
+        opts.args_dict = {}
 
+    # Create parsing
     if opts.command == 'create':
         if not opts.states:
             opts.states = list(opts.args_dict.keys())
 
+        if opts.non_yaml:
+            for ny in opts.non_yaml:
+                if not ny.exists():
+                    raise FileNotFoundError(
+                        f"Non-yaml file {ny} does not exist.")
+
+    # Run parsing
     elif opts.command == 'run':
         if opts.args_file is None:
             parser.error("'run' requires the '--args_file' option.")
diff --git a/tests/test_chi_parse.py b/tests/test_chi_parse.py
index ec1debd..05a2325 100644
--- a/tests/test_chi_parse.py
+++ b/tests/test_chi_parse.py
@@ -18,10 +18,9 @@
 
 def test_chi_create_argument_parsing(mock_root_dir):
     root_path = mock_root_dir
-    mock_args_path = mock_args_file(root_path)
     # Setup
     sys.argv = ['chi', 'create', 'param1.yaml',
-                'param2.yaml', '-a', f'{mock_args_path}']
+                'param2.yaml']
     # Test
     opts = parse_chi_options()
     # Assert
@@ -30,6 +29,29 @@ def test_chi_create_argument_parsing(mock_root_dir):
         assert Path(pf) in opts.param_files
 
 
+def test_chi_create_non_yaml_parsing(mock_root_dir):
+    root_path = mock_root_dir
+    ny_path_1 = (root_path / 'mock_non_yaml1.txt')
+    ny_path_2 = (root_path / 'mock_non_yaml2.txt')
+    ny_path_1.touch()
+    ny_path_2.touch()
+
+    # Setup
+    sys.argv = ['chi', 'create', 'param1.yaml', '-ny',
+                f'{ny_path_1}', f'{ny_path_2}']
+    opts = parse_chi_options()
+
+    assert opts.non_yaml == [ny_path_1, ny_path_2]
+    # Test that error is thrown
+    ny_path_2.unlink()
+
+    # Setup
+    sys.argv = ['chi', 'create', 'param1.yaml', '-ny',
+                f'{ny_path_1}', f'{ny_path_2}']
+    with pytest.raises(FileNotFoundError):
+        opts = parse_chi_options()
+
+
 def test_chi_run_argument_parsing(mock_root_dir):
     root_path = mock_root_dir
     mock_args_path = mock_args_file(root_path)
@@ -43,6 +65,17 @@ def test_chi_run_argument_parsing(mock_root_dir):
     with pytest.raises(SystemExit):
         opts = parse_chi_options()
 
-# TODO Add test for non-yaml files
 
 # TODO Add test for sim states
+
+
+# def test_chi_run_state(mock_root_dir):
+#     root_path = mock_root_dir
+#     mock_args_path = mock_args_file(root_path)
+
+#     (root_path / 'sim.touch1').touch()
+
+#     # Setup
+#     sys.argv = ['chi', 'run', '-a', f'{mock_args_path}', '--use-sim-states']
+#     opts = parse_chi_options()
+#     assert opts.states == ['touch1']
diff --git a/tests/test_chi_run.py b/tests/test_chi_run.py
index cdd4b4d..26fd70d 100644
--- a/tests/test_chi_run.py
+++ b/tests/test_chi_run.py
@@ -33,7 +33,7 @@ def test_chi_run_touch(mock_leaf_dir, mock_run_opts):
     assert (mock_leaf_path / 'mock_output2.txt').exists()
 
 
-def test_chi_run_only_one_touch(mock_leaf_dir, mock_run_opts):
+def test_chi_run_only_one_touch_with_opts(mock_leaf_dir, mock_run_opts):
     """Test chi_run."""
     mock_leaf_path = mock_leaf_dir
     # Create and modify run optoins
@@ -50,4 +50,5 @@ def test_chi_run_only_one_touch(mock_leaf_dir, mock_run_opts):
     assert (mock_leaf_path / 'mock_output1.txt').exists()
     assert not (mock_leaf_path / 'mock_output2.txt').exists()
 
+
 # TODO NEXT TEST test run args to make sure it always returns you to the right directory