Fix for incorrect file path in tests/io/test_zeopp.py (#3784)

* Fix filepaths to test files in zeopp tests

* format

* fix ruff 0.4.2: pymatgen/util/due.py:54:46: UP031 Use format specifiers instead of percent format

---------

Co-authored-by: Anthony <[email protected]>
Co-authored-by: Janosh Riebesell <[email protected]>

Author: 3 people

pymatgen/core/structure.py

@@ -4291,8 +4291,7 @@ def perturb(self, distance: float, min_distance: float | None = None) -> Self:
         symmetries. Modifies the structure in place.
 
         Args:
-            distance (float): Distance in angstroms by which to perturb each
-                site.
+            distance (float): Distance in angstroms by which to perturb each site.
             min_distance (None, int, or float): if None, all displacements will
                 be equal amplitude. If int or float, perturb each site a
                 distance drawn from the uniform distribution between

pymatgen/util/due.py

@@ -51,7 +51,7 @@ def _donothing_func(*args, **kwargs):
         raise RuntimeError("Imported due lacks .cite. DueCredit is now disabled")
 except Exception as exc:
     if not isinstance(exc, ImportError):
-        logging.getLogger("duecredit").error("Failed to import duecredit due to %s" % str(exc))
+        logging.getLogger("duecredit").error(f"Failed to import duecredit due to {exc}")
     # Initiate due stub
     due = InactiveDueCreditCollector()
     BibTeX = Doi = Url = Text = _donothing_func

tests/analysis/test_graphs.py

@@ -339,7 +339,8 @@ def test_mul(self):
             assert nio_struct_graph.get_coordination_of_site(n) == 6
 
     @pytest.mark.skipif(
-        pygraphviz is None or not (which("neato") and which("fdp")), reason="graphviz executables not present"
+        pygraphviz is None or not (which("neato") and which("fdp")),
+        reason="graphviz executables not present",
     )
     def test_draw(self):
         # draw MoS2 graph

tests/io/test_zeopp.py

@@ -32,7 +32,7 @@
 __date__ = "Aug 2, 2013"
 
 
-@pytest.mark.skipif(zeo is None, reason="zeo not present.")
+@pytest.mark.skipif(zeo is None, reason="zeo not present")
 class TestZeoCssr(TestCase):
     def setUp(self):
         filepath = f"{VASP_IN_DIR}/POSCAR"
@@ -70,12 +70,12 @@ def test_str(self):
         assert str(self.zeo_cssr) == expected_string
 
     def test_from_file(self):
-        filename = f"{TEST_FILES_DIR}/cssr/EDI.cssr"
+        filename = f"{TEST_FILES_DIR}/io/cssr/EDI.cssr"
         zeo_cssr = ZeoCssr.from_file(filename)
         assert isinstance(zeo_cssr.structure, Structure)
 
 
-@pytest.mark.skipif(zeo is None, reason="zeo not present.")
+@pytest.mark.skipif(zeo is None, reason="zeo not present")
 class TestZeoCssrOxi(TestCase):
     def setUp(self):
         filepath = f"{VASP_IN_DIR}/POSCAR"
@@ -114,12 +114,12 @@ def test_str(self):
         assert str(self.zeo_cssr) == expected_string
 
     def test_from_file(self):
-        filename = f"{TEST_FILES_DIR}/cssr/EDI_oxistate_decorated.cssr"
+        filename = f"{TEST_FILES_DIR}/io/cssr/EDI_oxistate_decorated.cssr"
         zeocssr = ZeoCssr.from_file(filename)
         assert isinstance(zeocssr.structure, Structure)
 
 
-@pytest.mark.skipif(zeo is None, reason="zeo not present.")
+@pytest.mark.skipif(zeo is None, reason="zeo not present")
 class TestZeoVoronoiXYZ(TestCase):
     def setUp(self):
         coords = [
@@ -150,7 +150,7 @@ def test_from_file(self):
         assert isinstance(voronoi.molecule, Molecule)
 
 
-@pytest.mark.skipif(zeo is None, reason="zeo not present.")
+@pytest.mark.skipif(zeo is None, reason="zeo not present")
 class TestGetVoronoiNodes(TestCase):
     def setUp(self):
         filepath = f"{VASP_IN_DIR}/POSCAR"
@@ -189,7 +189,7 @@ def test_get_free_sphere_params(self):
         assert free_sph_params["inc_sph_along_free_sph_path_max_dia"] == approx(2.58251, abs=1e-1)
 
 
-@pytest.mark.skipif(zeo is None, reason="zeo not present.")
+@pytest.mark.skipif(zeo is None, reason="zeo not present")
 class TestGetHighAccuracyVoronoiNodes(TestCase):
     def setUp(self):
         filepath = f"{VASP_IN_DIR}/POSCAR"
@@ -209,7 +209,7 @@ def test_get_voronoi_nodes(self):
         assert isinstance(vor_node_struct, Structure)
 
 
-@pytest.mark.skipif(zeo is None, reason="zeo not present.")
+@pytest.mark.skipif(zeo is None, reason="zeo not present")
 class TestGetVoronoiNodesMultiOxi(TestCase):
     def setUp(self):
         filepath = f"{VASP_IN_DIR}/POSCAR"