Unskip and fix packmol tests (#3195)

* don't use tempfile.TemporaryDirectory() in tests, prefer PymatgenTest.tmp_path auto-used fixture

* fix broken test_files paths in TestPackmolSet

* skip failing TestPackmolSet.test_random_seed due to openbabel not installed

pymatgen/io/tests/test_packmol.py:188:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

args = (<pymatgen.analysis.molecule_matcher.MoleculeMatcher object at 0x2aecc7bd0>,)
kwargs = {}

    @functools.wraps(_callable)
    def decorated(*args, **kwargs):
        if not self.condition:
>           raise RuntimeError(self.message)
E           RuntimeError: BabelMolAdaptor requires openbabel to be installed with Python bindings. Please get it at http://openbabel.org (version >=3.0.0).

* only skip pymatgen/io/tests/test_packmol.py if packmol not installed

was set to always skip

Author: janosh

pymatgen/core/tests/test_structure.py

@@ -6,7 +6,6 @@
 import warnings
 from pathlib import Path
 from shutil import which
-from tempfile import TemporaryDirectory
 from unittest import skipIf
 
 import numpy as np
@@ -1467,8 +1466,7 @@ def test_relax_ase_return_traj(self):
     def test_relax_ase_opt_kwargs(self):
         pytest.importorskip("ase")
         structure = self.cu_structure
-        tmp_dir = TemporaryDirectory()
-        traj_file = f"{tmp_dir.name}/testing.traj"
+        traj_file = f"{self.tmp_path}/testing.traj"
         relaxed, traj = structure.relax(
             calculator=EMT(), fmax=0.01, steps=2, return_trajectory=True, opt_kwargs={"trajectory": traj_file}
         )
@@ -2005,8 +2003,7 @@ def test_relax_ase_mol(self):
 
     def test_relax_ase_mol_return_traj(self):
         pytest.importorskip("ase")
-        tmp_dir = TemporaryDirectory()
-        traj_file = f"{tmp_dir.name}/testing.traj"
+        traj_file = f"{self.tmp_path}/testing.traj"
         relaxed, traj = self.mol.relax(
             calculator=EMT(), fmax=0.01, steps=2, return_trajectory=True, opt_kwargs={"trajectory": traj_file}
         )

pymatgen/io/lammps/tests/test_inputs.py

@@ -4,9 +4,7 @@
 import os
 import re
 import shutil
-import tempfile
 import unittest
-from pathlib import Path
 
 import pandas as pd
 import pytest
@@ -671,45 +669,43 @@ def tearDownClass(cls):
 
 class LammpsTemplateGenTest(PymatgenTest):
     def test_write_inputs(self):
-        with tempfile.TemporaryDirectory() as tmp_dir:
-            # simple script without data file
-            lis = LammpsTemplateGen().get_input_set(
-                script_template=f"{PymatgenTest.TEST_FILES_DIR}/lammps/kappa.txt",
-                settings={"method": "heat"},
-                data=None,
-                data_filename="data.peptide",
-            )
-            tmp_dir = Path(tmp_dir)
-            assert len(lis) == 1
-            lis.write_input(tmp_dir / "heat")
-
-            with open(tmp_dir / "heat" / "in.lammps") as f:
-                kappa_script = f.read()
-            fix_hot = re.search(r"fix\s+hot\s+all\s+([^\s]+)\s+", kappa_script)
-            # placeholders supposed to be filled
-            assert fix_hot.group(1) == "heat"
-            fix_cold = re.search(r"fix\s+cold\s+all\s+([^\s]+)\s+", kappa_script)
-            assert fix_cold.group(1) == "heat"
-            lattice = re.search(r"lattice\s+fcc\s+(.*)\n", kappa_script)
-            # parentheses not supposed to be filled
-            assert lattice.group(1) == "${rho}"
-            pair_style = re.search(r"pair_style\slj/cut\s+(.*)\n", kappa_script)
-            assert pair_style.group(1) == "${rc}"
-
-            # script with data file
-            obj = LammpsData.from_file(
-                os.path.join(PymatgenTest.TEST_FILES_DIR, "lammps", "data.quartz"), atom_style="atomic"
-            )
-            lis = LammpsTemplateGen().get_input_set(
-                script_template=f"{PymatgenTest.TEST_FILES_DIR}/lammps/in.peptide",
-                settings=None,
-                data=obj,
-                data_filename="data.peptide",
-            )
-            assert len(lis) == 2
-            assert isinstance(lis["data.peptide"], LammpsData)
-            lis.write_input(tmp_dir / "obj")
-
-            obj_read = LammpsData.from_file(str(tmp_dir / "obj" / "data.peptide"), atom_style="atomic")
-            pd.testing.assert_frame_equal(obj_read.masses, obj.masses)
-            pd.testing.assert_frame_equal(obj_read.atoms, obj.atoms)
+        # simple script without data file
+        lis = LammpsTemplateGen().get_input_set(
+            script_template=f"{PymatgenTest.TEST_FILES_DIR}/lammps/kappa.txt",
+            settings={"method": "heat"},
+            data=None,
+            data_filename="data.peptide",
+        )
+        assert len(lis) == 1
+        lis.write_input(self.tmp_path / "heat")
+
+        with open(self.tmp_path / "heat" / "in.lammps") as f:
+            kappa_script = f.read()
+        fix_hot = re.search(r"fix\s+hot\s+all\s+([^\s]+)\s+", kappa_script)
+        # placeholders supposed to be filled
+        assert fix_hot.group(1) == "heat"
+        fix_cold = re.search(r"fix\s+cold\s+all\s+([^\s]+)\s+", kappa_script)
+        assert fix_cold.group(1) == "heat"
+        lattice = re.search(r"lattice\s+fcc\s+(.*)\n", kappa_script)
+        # parentheses not supposed to be filled
+        assert lattice.group(1) == "${rho}"
+        pair_style = re.search(r"pair_style\slj/cut\s+(.*)\n", kappa_script)
+        assert pair_style.group(1) == "${rc}"
+
+        # script with data file
+        obj = LammpsData.from_file(
+            os.path.join(PymatgenTest.TEST_FILES_DIR, "lammps", "data.quartz"), atom_style="atomic"
+        )
+        lis = LammpsTemplateGen().get_input_set(
+            script_template=f"{PymatgenTest.TEST_FILES_DIR}/lammps/in.peptide",
+            settings=None,
+            data=obj,
+            data_filename="data.peptide",
+        )
+        assert len(lis) == 2
+        assert isinstance(lis["data.peptide"], LammpsData)
+        lis.write_input(self.tmp_path / "obj")
+
+        obj_read = LammpsData.from_file(str(self.tmp_path / "obj" / "data.peptide"), atom_style="atomic")
+        pd.testing.assert_frame_equal(obj_read.masses, obj.masses)
+        pd.testing.assert_frame_equal(obj_read.atoms, obj.atoms)