test_to_from_file_string() left tmp files lying around when crashing,…

… use monty ScratchDir to fix

pymatgen/core/tests/test_structure.py

@@ -10,6 +10,7 @@
 
 import numpy as np
 import pytest
+from monty.tempfile import ScratchDir
 
 from pymatgen.core.composition import Composition
 from pymatgen.core.lattice import Lattice
@@ -677,43 +678,41 @@ def test_get_dist_matrix(self):
         self.assertArrayAlmostEqual(self.struct.distance_matrix, ans)
 
     def test_to_from_file_string(self):
-        for fmt in ["cif", "json", "poscar", "cssr"]:
-            s = self.struct.to(fmt=fmt)
-            assert s is not None
-            ss = IStructure.from_str(s, fmt=fmt)
-            self.assertArrayAlmostEqual(ss.lattice.parameters, self.struct.lattice.parameters, decimal=5)
-            self.assertArrayAlmostEqual(ss.frac_coords, self.struct.frac_coords)
-            assert isinstance(ss, IStructure)
-
-        assert "Fd-3m" in self.struct.to(fmt="CIF", symprec=0.1)
-
-        self.struct.to(filename="POSCAR.testing")
-        assert os.path.exists("POSCAR.testing")
-        os.remove("POSCAR.testing")
-
-        self.struct.to(filename="Si_testing.yaml")
-        assert os.path.exists("Si_testing.yaml")
-        s = Structure.from_file("Si_testing.yaml")
-        assert s == self.struct
-        # Test Path support.
-        s = Structure.from_file(Path("Si_testing.yaml"))
-        assert s == self.struct
-
-        # Test .yml extension works too.
-        os.replace("Si_testing.yaml", "Si_testing.yml")
-        s = Structure.from_file("Si_testing.yml")
-        assert s == self.struct
-        os.remove("Si_testing.yml")
-
-        with pytest.raises(ValueError):
-            self.struct.to(filename="whatever")
-        with pytest.raises(ValueError):
-            self.struct.to(fmt="badformat")
-
-        self.struct.to(filename="POSCAR.testing.gz")
-        s = Structure.from_file("POSCAR.testing.gz")
-        assert s == self.struct
-        os.remove("POSCAR.testing.gz")
+        with ScratchDir("."):
+            for fmt in ["cif", "json", "poscar", "cssr"]:
+                s = self.struct.to(fmt=fmt)
+                assert s is not None
+                ss = IStructure.from_str(s, fmt=fmt)
+                self.assertArrayAlmostEqual(ss.lattice.parameters, self.struct.lattice.parameters, decimal=5)
+                self.assertArrayAlmostEqual(ss.frac_coords, self.struct.frac_coords)
+                assert isinstance(ss, IStructure)
+
+            assert "Fd-3m" in self.struct.to(fmt="CIF", symprec=0.1)
+
+            self.struct.to(filename="POSCAR.testing")
+            assert os.path.exists("POSCAR.testing")
+
+            self.struct.to(filename="Si_testing.yaml")
+            assert os.path.exists("Si_testing.yaml")
+            s = Structure.from_file("Si_testing.yaml")
+            assert s == self.struct
+            # Test Path support.
+            s = Structure.from_file(Path("Si_testing.yaml"))
+            assert s == self.struct
+
+            # Test .yml extension works too.
+            os.replace("Si_testing.yaml", "Si_testing.yml")
+            s = Structure.from_file("Si_testing.yml")
+            assert s == self.struct
+
+            with pytest.raises(ValueError):
+                self.struct.to(filename="whatever")
+            with pytest.raises(ValueError):
+                self.struct.to(fmt="badformat")
+
+            self.struct.to(filename="POSCAR.testing.gz")
+            s = Structure.from_file("POSCAR.testing.gz")
+            assert s == self.struct
 
     def test_pbc(self):
         self.assertArrayEqual(self.struct.pbc, (True, True, True))
@@ -1056,23 +1055,20 @@ def test_to_from_abivars(self):
         assert isinstance(s2, Structure)
 
     def test_to_from_file_string(self):
-        for fmt in ["cif", "json", "poscar", "cssr", "yaml", "xsf", "res"]:
-            s = self.structure.to(fmt=fmt)
-            assert s is not None
-            ss = Structure.from_str(s, fmt=fmt)
-            self.assertArrayAlmostEqual(ss.lattice.parameters, self.structure.lattice.parameters, decimal=5)
-            self.assertArrayAlmostEqual(ss.frac_coords, self.structure.frac_coords)
-            assert isinstance(ss, Structure)
-
-        self.structure.to(filename="POSCAR.testing")
-        assert os.path.exists("POSCAR.testing")
-        os.remove("POSCAR.testing")
-
-        self.structure.to(filename="structure_testing.json")
-        assert os.path.exists("structure_testing.json")
-        s = Structure.from_file("structure_testing.json")
-        assert s == self.structure
-        os.remove("structure_testing.json")
+        with ScratchDir("."):
+            for fmt in ["cif", "json", "poscar", "cssr", "yaml", "xsf", "res"]:
+                s = self.structure.to(fmt=fmt)
+                assert s is not None
+                ss = Structure.from_str(s, fmt=fmt)
+                self.assertArrayAlmostEqual(ss.lattice.parameters, self.structure.lattice.parameters, decimal=5)
+                self.assertArrayAlmostEqual(ss.frac_coords, self.structure.frac_coords)
+                assert isinstance(ss, Structure)
+
+            self.structure.to(filename="POSCAR.testing")
+            assert os.path.exists("POSCAR.testing")
+
+            self.structure.to(filename="structure_testing.json")
+            assert Structure.from_file("structure_testing.json") == self.structure
 
     def test_from_spacegroup(self):
         s1 = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Li", "O"], [[0.25, 0.25, 0.25], [0, 0, 0]])

pymatgen/io/tests/test_packmol.py

@@ -14,7 +14,7 @@
 
 
 # Just skip this whole test for now since packmol is problematic.
-if True:  # which("packmol") is None:
+if True:  # if which("packmol") is None:
     pytest.skip("packmol executable not present", allow_module_level=True)
 
 

pymatgen/util/provenance.py

@@ -5,12 +5,15 @@
 Classes and methods related to the Structure Notation Language (SNL)
 """
 
+from __future__ import annotations
+
 import datetime
 import json
 import re
 import sys
 from collections import namedtuple
 from io import StringIO
+from typing import Sequence
 
 from monty.json import MontyDecoder, MontyEncoder
 from monty.string import remove_non_ascii
@@ -34,7 +37,7 @@
 MAX_BIBTEX_CHARS = 20000  # maximum number of characters for BibTeX reference
 
 
-def is_valid_bibtex(reference):
+def is_valid_bibtex(reference: str) -> bool:
     """
     Use pybtex to validate that a reference is in proper BibTeX format
 
@@ -80,14 +83,14 @@ class HistoryNode(namedtuple("HistoryNode", ["name", "url", "description"])):
         Structure (dict).
     """
 
-    def as_dict(self):
+    def as_dict(self) -> dict[str, str]:
         """
         Returns: Dict
         """
         return {"name": self.name, "url": self.url, "description": self.description}
 
     @staticmethod
-    def from_dict(h_node):
+    def from_dict(h_node: dict[str, str]) -> HistoryNode:
         """
         Args:
             d (dict): Dict representation
@@ -181,7 +184,7 @@ def parse_author(author):
 
 class StructureNL:
     """
-    The Structure Notation Language (SNL, pronounced 'snail') is container
+    The Structure Notation Language (SNL, pronounced 'snail') is a container
     for a pymatgen Structure/Molecule object with some additional fields for
     enhanced provenance. It is meant to be imported/exported in a JSON file
     format with the following structure:
@@ -329,8 +332,8 @@ def from_dict(cls, d):
     @classmethod
     def from_structures(
         cls,
-        structures,
-        authors,
+        structures: Sequence[Structure],
+        authors: Sequence[dict[str, str]],
         projects=None,
         references="",
         remarks=None,