update: restructure standata tests

tests/py/unit/test_cli.py

@@ -0,0 +1,101 @@
+import json
+import os
+from pathlib import Path
+from unittest.mock import patch
+
+import pytest
+import yaml
+from mat3ra.standata.build.cli import main
+
+# Test data
+SAMPLE_CONFIG = {
+    "categories": {"dimensionality": ["2D", "3D"], "type": ["metal", "semiconductor"]},
+    "entities": [
+        {"filename": "material1.json", "categories": ["2D", "metal"]},
+        {"filename": "material2.json", "categories": ["3D", "semiconductor"]},
+    ],
+}
+
+SAMPLE_ENTITY = {"name": "Test Material", "isNonPeriodic": False, "lattice": {"a": 1.0, "b": 1.0, "c": 1.0}}
+
+
+@pytest.fixture
+def temp_dir(tmp_path):
+    """Create a temporary directory with test files."""
+    # Create config file
+    config_path = tmp_path / "categories.yml"
+    with open(config_path, "w") as f:
+        yaml.dump(SAMPLE_CONFIG, f)
+
+    # Create entity files
+    for entity in SAMPLE_CONFIG["entities"]:
+        entity_path = tmp_path / entity["filename"]
+        with open(entity_path, "w") as f:
+            json.dump(SAMPLE_ENTITY, f)
+
+    return tmp_path
+
+
+def test_create_category_structure(temp_dir):
+    """Test creation of category structure."""
+    # Pass None as destination to avoid typer.Option issue
+    main(yaml_config=str(temp_dir / "categories.yml"), destination=None)
+
+    # Verify the structure was created correctly
+    categories_root = temp_dir / "by_category"
+    assert (categories_root / "dimensionality/2D").exists()
+    assert (categories_root / "dimensionality/3D").exists()
+    assert (categories_root / "type/metal").exists()
+    assert (categories_root / "type/semiconductor").exists()
+
+
+def test_custom_destination(temp_dir):
+    """Test creating category structure in custom destination."""
+    custom_dest = temp_dir / "custom_dest"
+    custom_dest.mkdir()
+
+    # Use explicit keyword arguments
+    main(yaml_config=str(temp_dir / "categories.yml"), destination=str(custom_dest))
+
+    # Verify the structure was created in custom destination
+    categories_root = custom_dest / "by_category"
+    assert (categories_root / "dimensionality/2D").exists()
+    assert (categories_root / "type/metal").exists()
+
+
+def test_symlink_creation(temp_dir):
+    """Test if symlinks are created correctly."""
+    main(yaml_config=str(temp_dir / "categories.yml"), destination=None)
+
+    # Verify symlinks
+    metal_link = temp_dir / "by_category/type/metal/material1.json"
+    assert metal_link.exists()
+    assert metal_link.is_symlink()
+    assert metal_link.resolve() == (temp_dir / "material1.json").resolve()
+
+
+@pytest.mark.skipif(os.name == "nt", reason="Symlinks might not work on Windows without admin privileges")
+def test_permission_error(temp_dir):
+    """Test handling of permission errors during symlink creation."""
+    with patch("pathlib.Path.symlink_to", side_effect=PermissionError):
+        with pytest.raises(PermissionError):
+            main(yaml_config=str(temp_dir / "categories.yml"), destination=None)
+
+
+def test_nonexistent_config(temp_dir):
+    """Test handling of non-existent config file."""
+    with pytest.raises(FileNotFoundError):
+        main(yaml_config=str(temp_dir / "nonexistent.yml"), destination=None)
+
+
+def test_duplicate_run(temp_dir):
+    """Test running the command twice (should handle existing symlinks)."""
+    # Run twice with explicit keyword arguments
+    main(yaml_config=str(temp_dir / "categories.yml"), destination=None)
+    main(yaml_config=str(temp_dir / "categories.yml"), destination=None)
+
+    # Verify structure is still correct
+    categories_root = temp_dir / "by_category"
+    assert (categories_root / "dimensionality/2D").exists()
+    metal_link = categories_root / "type/metal/material1.json"
+    assert metal_link.is_symlink()

tests/py/unit/materials/test_standata_build.py → tests/py/unit/test_standata_build.py

@@ -92,64 +92,3 @@ def test_load_invalid_yaml(temp_dir):
     assert isinstance(config, StandataConfig)
     assert len(config.categories) == 0
     assert len(config.entities) == 0
-
-
-# CLI Integration Tests
-@pytest.mark.integration
-def test_create_category_structure(temp_dir):
-    """Test creation of category structure."""
-    config = StandataBuilder.build_from_file(temp_dir / "categories.yml")
-
-    # Set up the category directory
-    categories_root = temp_dir / "by_category"
-    categories_root.mkdir(exist_ok=True)
-
-    # Create category directories and symlinks
-    for entity in config.entities:
-        categories = config.convert_tags_to_categories_list(*entity.categories)
-        entity_path = temp_dir / entity.filename
-
-        for category in categories:
-            category_dir = categories_root / category
-            category_dir.mkdir(parents=True, exist_ok=True)
-            linked_entity = category_dir / entity.filename
-            if not linked_entity.exists():
-                try:
-                    linked_entity.symlink_to(entity_path)
-                except PermissionError:
-                    pytest.skip("No permission to create symlinks")
-
-    # Verify the structure
-    assert (categories_root / "dimensionality/2D").exists()
-    assert (categories_root / "dimensionality/3D").exists()
-    assert (categories_root / "type/metal").exists()
-    assert (categories_root / "type/semiconductor").exists()
-
-
-@pytest.mark.integration
-def test_symlink_creation(temp_dir):
-    """Test symlink creation for materials."""
-    config = StandataBuilder.build_from_file(temp_dir / "categories.yml")
-    categories_root = temp_dir / "by_category"
-    categories_root.mkdir(exist_ok=True)
-
-    # Create symlinks for one material
-    entity = config.entities[0]  # First material
-    categories = config.convert_tags_to_categories_list(*entity.categories)
-    entity_path = temp_dir / entity.filename
-
-    for category in categories:
-        category_dir = categories_root / category
-        category_dir.mkdir(parents=True, exist_ok=True)
-        linked_entity = category_dir / entity.filename
-        if not linked_entity.exists():
-            try:
-                linked_entity.symlink_to(entity_path)
-            except PermissionError:
-                pytest.skip("No permission to create symlinks")
-
-    # Verify symlinks
-    metal_link = categories_root / "type/metal/material1.json"
-    if metal_link.exists():
-        assert metal_link.is_symlink()
-        assert metal_link.resolve() == (temp_dir / "material1.json").resolve()