Adjust file handling

janus_core/calculations/md.py

@@ -266,7 +266,7 @@ def __init__(  # pylint: disable=too-many-arguments,too-many-locals,too-many-sta
         self.ensemble = ensemble
         self.seed = seed
 
-        FileNameMixin.__init__(self, struct, struct_name, file_prefix, self.ensemble)
+        FileNameMixin.__init__(self, struct, struct_name, file_prefix, ensemble)
 
         self.log_kwargs = (
             log_kwargs if log_kwargs else {}

janus_core/calculations/single_point.py

@@ -338,7 +338,7 @@ def run(
 
         write_kwargs.setdefault(
             "filename",
-            Path(self._build_filename("results.xyz")).absolute(),
+            self._build_filename("results.xyz").absolute(),
         )
 
         if self.logger:

janus_core/helpers/utils.py

@@ -55,20 +55,11 @@ def __init__(
             Default prefix to use.
         *additional
             Components to add to file_prefix (joined by hyphens).
-
-        Methods
-        -------
-        _get_default_struct_name(struct, struct_name)
-             Return the name from the provided struct_name or generate from struct.
-        _get_default_prefix(file_prefix, struct_name)
-             Return a prefix from the provided file_prefix or from struct_name.
-        _build_filename(suffix, *additional, filename, prefix_override)
-             Return a standard format filename if filename not provided.
         """
         self.struct_name = self._get_default_struct_name(struct, struct_name)
 
-        self.file_prefix = "-".join(
-            (self._get_default_prefix(file_prefix, self.struct_name, *additional),)
+        self.file_prefix = Path(
+            self._get_default_prefix(file_prefix, self.struct_name, *additional)
         )
 
     @staticmethod
@@ -80,7 +71,7 @@ def _get_default_struct_name(struct: Atoms, struct_name: Optional[str]) -> str:
         ----------
         struct : Atoms
             Structure of system.
-        struct_name : str
+        struct_name : Optional[str]
             Name of structure.
 
         Returns
@@ -145,9 +136,11 @@ def _build_filename(
             Filename specified, or default filename.
         """
         if filename:
-            return filename
-        prefix = prefix_override if prefix_override is not None else self.file_prefix
-        return "-".join((prefix, *filter(None, additional), suffix))
+            return Path(filename)
+        prefix = (
+            prefix_override if prefix_override is not None else str(self.file_prefix)
+        )
+        return Path("-".join((prefix, *filter(None, additional), suffix)))
 
 
 def spacegroup(

tests/test_filenamemixin.py

@@ -0,0 +1,117 @@
+"""Test FileNameMixin functions."""
+
+from pathlib import Path
+
+from ase.io import read
+import pytest
+
+from janus_core.helpers.utils import FileNameMixin
+
+DATA_PATH = Path(__file__).parent / "data"
+STRUCT = read(DATA_PATH / "benzene.xyz")
+
+
+class DummyFileHandler(FileNameMixin):  # pylint: disable=too-few-public-methods
+    """
+    Used for testing FileNameMixin methods.
+    """
+
+    def build_filename(self, *args, **kwargs):
+        """
+        Expose _build_filename publicly.
+        """
+        return self._build_filename(*args, **kwargs)
+
+
+@pytest.mark.parametrize(
+    "params,struct_name,file_prefix",
+    (
+        # Defaults to structure atoms from ASE
+        ((STRUCT, None, None), "C6H6", "C6H6"),
+        # Passing structure name sets file_prefix
+        ((STRUCT, "benzene", None), "benzene", "benzene"),
+        # file_prefix just sets itself
+        ((STRUCT, None, "benzene"), "C6H6", "benzene"),
+        ((STRUCT, "benzene", "cake"), "benzene", "cake"),
+        # file_prefix ignores additional
+        ((STRUCT, "benzene", "benzene", "wowzers"), "benzene", "benzene"),
+        # Additional only applies where no file_prefix
+        ((STRUCT, "benzene", None, "wowzers"), "benzene", "benzene-wowzers"),
+        ((STRUCT, None, None, "wowzers"), "C6H6", "C6H6-wowzers"),
+    ),
+)
+def test_file_name_mixin_init(params, struct_name, file_prefix):
+    """
+    Test various options for initializing the mixin.
+    """
+    file_mix = DummyFileHandler(*params)
+
+    assert file_mix.struct_name == struct_name
+    assert file_mix.file_prefix == Path(file_prefix)
+
+
+@pytest.mark.parametrize(
+    "mixin_params,file_args,file_kwargs,file_name",
+    (
+        ((STRUCT, None, None), ("data.xyz",), {}, "C6H6-data.xyz"),
+        ((STRUCT, "benzene", None), ("data.xyz",), {}, "benzene-data.xyz"),
+        ((STRUCT, None, "benzene"), ("data.xyz",), {}, "benzene-data.xyz"),
+        ((STRUCT, "benzene", "benzene"), ("data.xyz",), {}, "benzene-data.xyz"),
+        ((STRUCT, "benzene", "benzene"), ("data.xyz",), {}, "benzene-data.xyz"),
+        (
+            (STRUCT, "benzene", "benzene", "wowzers"),
+            ("data.xyz",),
+            {},
+            "benzene-data.xyz",
+        ),
+        ((STRUCT, None, "benzene", "wowzers"), ("data.xyz",), {}, "benzene-data.xyz"),
+        ((STRUCT, None, None, "wowzers"), ("data.xyz",), {}, "C6H6-wowzers-data.xyz"),
+        # Additional stacks with base
+        (
+            (STRUCT, None, None, "wowzers"),
+            ("data.xyz", "beef"),
+            {},
+            "C6H6-wowzers-beef-data.xyz",
+        ),
+        # Prefix override ignores class options
+        (
+            (STRUCT, None, None, "wowzers"),
+            ("data.xyz",),
+            {"prefix_override": "beef"},
+            "beef-data.xyz",
+        ),
+        # But not additional
+        (
+            (STRUCT, None, None, "wowzers"),
+            ("data.xyz", "tasty"),
+            {"prefix_override": "beef"},
+            "beef-tasty-data.xyz",
+        ),
+        # Filename overrides everything
+        (
+            (STRUCT, None, None, "wowzers"),
+            ("data.xyz",),
+            {"filename": "hello.xyz"},
+            "hello.xyz",
+        ),
+        (
+            (STRUCT, None, None, "wowzers"),
+            ("data.xyz",),
+            {"prefix_override": "beef", "filename": "hello.xyz"},
+            "hello.xyz",
+        ),
+        (
+            (STRUCT, None, None, "wowzers"),
+            ("data.xyz", "tasty"),
+            {"prefix_override": "beef", "filename": "hello.xyz"},
+            "hello.xyz",
+        ),
+    ),
+)
+def test_file_name_mixin_build(mixin_params, file_args, file_kwargs, file_name):
+    """
+    Test building the filename for mixins
+    """
+    file_mix = DummyFileHandler(*mixin_params)
+
+    assert file_mix.build_filename(*file_args, **file_kwargs) == Path(file_name)