Merge pull request #185 from stevenhua0320/fix-load-structure

fix: fix load_structure method with loading Path object.

Author: sbillinge

news/fix-load-structure.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* Added method ``load_structure`` in ``__init__.py``
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* Deprecated method ``loadStructure`` in ``__init__.py`` for removal in version 4.0.0
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Fixed ``load_structure`` with successfully loading `Path` object
+
+**Security:**
+
+* <news item>

src/diffpy/structure/__init__.py

@@ -34,6 +34,7 @@
 """
 
 
+import os
 import sys
 
 import diffpy.structure as _structure
@@ -46,8 +47,17 @@
 
 # package version
 from diffpy.structure.version import __version__
+from diffpy.utils._deprecator import build_deprecation_message, deprecated
 
 # Deprecations -------------------------------------------------------
+base = "diffpy.structure"
+removal_version = "4.0.0"
+loadStructure_deprecation_msg = build_deprecation_message(
+    base,
+    "loadStructure",
+    "load_structure",
+    removal_version,
+)
 
 
 # @deprecated
@@ -72,7 +82,17 @@ def __getattr__(self, name):
 # top level routines
 
 
+@deprecated(loadStructure_deprecation_msg)
 def loadStructure(filename, fmt="auto", **kw):
+    """This function has been deprecated and will be removed in version
+    4.0.0.
+
+    Please use diffpy.structure.load_structure instead.
+    """
+    return load_structure(filename, fmt, **kw)
+
+
+def load_structure(filename, fmt="auto", **kw):
     """Load new structure object from the specified file.
 
     Parameters
@@ -96,7 +116,7 @@ def loadStructure(filename, fmt="auto", **kw):
         Return a more specific PDFFitStructure type for 'pdffit'
         and 'discus' formats.
     """
-
+    filename = os.fspath(filename)
     p = get_parser(fmt, **kw)
     rv = p.parse_file(filename)
     return rv

tests/test_loadstructure.py

@@ -6,7 +6,7 @@
 
 import pytest
 
-from diffpy.structure import PDFFitStructure, Structure, loadStructure
+from diffpy.structure import PDFFitStructure, Structure, load_structure, loadStructure
 from diffpy.structure.structureerrors import StructureFormatError
 
 
@@ -19,22 +19,22 @@ def prepare_fixture(self, datafile):
     def test_xcfg(self):
         """Check loading of atomeye xcfg format."""
         f = self.datafile("BubbleRaftShort.xcfg")
-        stru = loadStructure(f)
+        stru = load_structure(f)
         self.assertTrue(type(stru) is Structure)
-        self.assertRaises(StructureFormatError, loadStructure, f, "xyz")
+        self.assertRaises(StructureFormatError, load_structure, f, "xyz")
         return
 
     def test_discus(self):
         """Check loading of discus file format."""
         f = self.datafile("Ni-discus.stru")
-        stru = loadStructure(f)
+        stru = load_structure(f)
         self.assertTrue(type(stru) is PDFFitStructure)
         return
 
     def test_cif(self):
         """Check loading of CIF file format."""
         f = self.datafile("PbTe.cif")
-        stru = loadStructure(f)
+        stru = load_structure(f)
         self.assertTrue(isinstance(stru, Structure))
         self.assertFalse(isinstance(stru, PDFFitStructure))
         return
@@ -45,25 +45,51 @@ def test_badfile(self):
         self.assertRaises(StructureFormatError, loadStructure, f)
         return
 
+    def test_load_bad_file(self):
+        """Check loading of CIF file format."""
+        f = self.datafile("Ni-bad.stru")
+        self.assertRaises(StructureFormatError, load_structure, f)
+        return
+
     def test_goodkwarg(self):
         """Check loading of CIF file and passing of parser keyword
         argument."""
         f = self.datafile("graphite.cif")
-        stru = loadStructure(f, eps=1e-10)
+        stru = load_structure(f, eps=1e-10)
         self.assertEqual(8, len(stru))
         return
 
     def test_badkwarg(self):
         """Check loading of xyz file format with invalid keyword
         argument."""
         f = self.datafile("bucky.xyz")
-        self.assertRaises(TypeError, loadStructure, f, eps=1e-10)
+        self.assertRaises(TypeError, load_structure, f, eps=1e-10)
         return
 
 
 # End of class TestLoadStructure
 
+
 # ----------------------------------------------------------------------------
+@pytest.mark.parametrize(
+    "filename, expected",
+    [  # C1: Load the cif file in Path object, expected to load the Structure instance.
+        ("PbTe.cif", (True, False)),
+    ],
+)
+def test_load_structure_cif_in_path(datafile, filename, expected):
+    from pathlib import Path
+
+    f = datafile(filename)
+    f_path = Path(f)
+    stru = load_structure(f_path)
+    actual = (
+        isinstance(stru, Structure),
+        isinstance(stru, PDFFitStructure),
+    )
+
+    assert actual == expected
+
 
 if __name__ == "__main__":
     unittest.main()