Merge pull request #42 from benrich37/setup_teardown_inputs

Changing all "zopen" to just "open" due to an error raised when monty…

src/pymatgen/io/jdftx/_output_utils.py

@@ -14,7 +14,6 @@
 from typing import TYPE_CHECKING, Any
 
 import numpy as np
-from monty.io import zopen
 
 if TYPE_CHECKING:
     from collections.abc import Callable
@@ -52,7 +51,7 @@ def read_file(file_name: str) -> list[str]:
     text: list[str]
         list of strings from file
     """
-    with zopen(file_name, "r") as f:
+    with open(file_name) as f:
         text = f.readlines()
     f.close()
     return text

src/pymatgen/io/jdftx/inputs.py

@@ -18,7 +18,6 @@ class is written.
 
 import numpy as np
 import scipy.constants as const
-from monty.io import zopen
 from monty.json import MSONable
 
 from pymatgen.core import Structure
@@ -185,7 +184,7 @@ def write_file(self, filename: PathLike) -> None:
         Args:
             filename (PathLike): Filename to write to.
         """
-        with zopen(filename, mode="wt") as file:
+        with open(filename, mode="w") as file:
             file.write(str(self))
 
     @classmethod
@@ -211,7 +210,7 @@ def from_file(
         path_parent = None
         if assign_path_parent:
             path_parent = Path(filename).parents[0]
-        with zopen(filename, mode="rt") as file:
+        with open(filename) as file:
             return cls.from_str(
                 file.read(),
                 dont_require_structure=dont_require_structure,
@@ -835,7 +834,7 @@ def write_file(self, filename: PathLike, **kwargs) -> None:
             filename (PathLike): Filename to write to.
             **kwargs: Kwargs to pass to JDFTXStructure.get_str.
         """
-        with zopen(filename, mode="wt") as file:
+        with open(filename, mode="w") as file:
             file.write(self.get_str(**kwargs))
 
     def as_dict(self) -> dict:

tests/io/jdftx/outputs_test_utils.py

@@ -21,14 +21,13 @@
     from collections.abc import Callable
 
 
-from .shared_test_utils import assert_same_value, dump_files_dir
+from .shared_test_utils import assert_same_value
 
-
-def write_mt_file(fname: str, write_dir: Path = dump_files_dir):
-    filepath = write_dir / fname
-    with open(filepath, "w") as f:
-        f.write("if you're reading this yell at ben")
-    f.close()
+# def write_mt_file(fname: str, write_dir: Path = dump_files_dir):
+#     filepath = write_dir / fname
+#     with open(filepath, "w") as f:
+#         f.write("if you're reading this yell at ben")
+#     f.close()
 
 
 def object_hasall_known_simple(obj: Any, knowndict: dict):

tests/io/jdftx/shared_test_utils.py

@@ -5,6 +5,8 @@
 
 from __future__ import annotations
 
+import os
+import shutil
 from pathlib import Path
 
 import pytest
@@ -31,3 +33,17 @@ def assert_same_value(testval, knownval):
         assert len(testval) == len(knownval)
         for i in range(len(testval)):
             assert_same_value(testval[i], knownval[i])
+
+
+@pytest.fixture(scope="module")
+def tmp_path():
+    os.mkdir(dump_files_dir)
+    yield dump_files_dir
+    shutil.rmtree(dump_files_dir)
+
+
+def write_mt_file(tmp_path: Path, fname: str):
+    filepath = tmp_path / fname
+    with open(filepath, "w") as f:
+        f.write("if you're reading this yell at ben")
+    f.close()

tests/io/jdftx/test_jdftxinfile.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import os
 import re
 from copy import deepcopy
 from typing import TYPE_CHECKING, Any
@@ -21,7 +20,7 @@
     ex_infile2_fname,
     ex_infile3_fname,
 )
-from .shared_test_utils import assert_same_value, dump_files_dir
+from .shared_test_utils import assert_same_value
 
 if TYPE_CHECKING:
     from collections.abc import Callable
@@ -47,6 +46,42 @@ def test_JDFTXInfile_known_lambda(infile_fname: str, bool_func: Callable[[JDFTXI
     assert bool_func(jif)
 
 
+def JDFTXInfile_self_consistency_tester(jif: JDFTXInfile, tmp_path: PathLike):
+    """Create an assortment of JDFTXinfile created from the same data but through different methods, and test that
+    they are all equivalent through "assert_idential_jif" """
+    dict_jif = jif.as_dict()
+    # # Commenting out tests with jif2 due to the list representation asserted
+    jif2 = JDFTXInfile.get_dict_representation(JDFTXInfile._from_dict(dict_jif))
+    str_list_jif = jif.get_text_list()
+    str_jif = "\n".join(str_list_jif)
+    jif3 = JDFTXInfile.from_str(str_jif)
+    tmp_fname = tmp_path / "tmp.in"
+    jif.write_file(tmp_fname)
+    jif4 = JDFTXInfile.from_file(tmp_fname)
+    jifs = [jif, jif2, jif3, jif4]
+    for i in range(len(jifs)):
+        for j in range(i + 1, len(jifs)):
+            print(f"{i}, {j}")
+            assert_idential_jif(jifs[i], jifs[j])
+
+
+def test_JDFTXInfile_from_dict(tmp_path) -> None:
+    jif = JDFTXInfile.from_file(ex_infile1_fname)
+    jif_dict = jif.as_dict()
+    # Test that dictionary can be modified and that _from_dict will fix set values
+    jif_dict["elec-cutoff"] = 20
+    jif2 = JDFTXInfile.from_dict(jif_dict)
+    JDFTXInfile_self_consistency_tester(jif2, tmp_path)
+
+
+@pytest.mark.parametrize("infile_fname", [ex_infile3_fname, ex_infile1_fname, ex_infile2_fname])
+def test_JDFTXInfile_self_consistency_fromfile(infile_fname: PathLike, tmp_path) -> None:
+    """Test that JDFTXInfile objects with different assortments of tags survive inter-conversion done within
+    "JDFTXInfile_self_consistency_tester"""
+    jif = JDFTXInfile.from_file(infile_fname)
+    JDFTXInfile_self_consistency_tester(jif, tmp_path)
+
+
 @pytest.mark.parametrize(
     ("val_key", "val"),
     [
@@ -63,22 +98,12 @@ def test_JDFTXInfile_known_lambda(infile_fname: str, bool_func: Callable[[JDFTXI
         ("elec-cutoff", 20),
     ],
 )
-def test_JDFTXInfile_set_values(val_key: str, val: Any):
+def test_JDFTXInfile_set_values(val_key: str, val: Any, tmp_path) -> None:
     """Test value setting for various tags"""
     jif = JDFTXInfile.from_file(ex_infile1_fname)
     jif[val_key] = val
     # Test that the JDFTXInfile object is still consistent
-    JDFTXInfile_self_consistency_tester(jif)
-
-
-def test_JDFTXInfile_from_dict():
-    """Test the from_dict method"""
-    jif = JDFTXInfile.from_file(ex_infile1_fname)
-    jif_dict = jif.as_dict()
-    # Test that dictionary can be modified and that _from_dict will fix set values
-    jif_dict["elec-cutoff"] = 20
-    jif2 = JDFTXInfile.from_dict(jif_dict)
-    JDFTXInfile_self_consistency_tester(jif2)
+    JDFTXInfile_self_consistency_tester(jif, tmp_path)
 
 
 @pytest.mark.parametrize(
@@ -91,15 +116,15 @@ def test_JDFTXInfile_from_dict():
         ("ion", "Fe 1 1 1 0"),
     ],
 )
-def test_JDFTXInfile_append_values(val_key: str, val: Any):
+def test_JDFTXInfile_append_values(val_key: str, val: Any, tmp_path) -> None:
     """Test the append_tag method"""
     jif = JDFTXInfile.from_file(ex_infile1_fname)
     val_old = None if val_key not in jif else deepcopy(jif[val_key])
     jif.append_tag(val_key, val)
     val_new = jif[val_key]
     assert val_old != val_new
     # Test that the append_tag does not break the JDFTXInfile object
-    JDFTXInfile_self_consistency_tester(jif)
+    JDFTXInfile_self_consistency_tester(jif, tmp_path)
 
 
 def test_JDFTXInfile_expected_exceptions():
@@ -217,34 +242,6 @@ def test_JDFTXInfile_knowns_simple(infile_fname: PathLike, knowns: dict):
         assert_same_value(jif[key], val)
 
 
-@pytest.mark.parametrize("infile_fname", [ex_infile3_fname, ex_infile1_fname, ex_infile2_fname])
-def test_JDFTXInfile_self_consistency(infile_fname: PathLike):
-    """Test that JDFTXInfile objects with different assortments of tags survive inter-conversion done within
-    "JDFTXInfile_self_consistency_tester"""
-    jif = JDFTXInfile.from_file(infile_fname)
-    JDFTXInfile_self_consistency_tester(jif)
-
-
-def JDFTXInfile_self_consistency_tester(jif: JDFTXInfile):
-    """Create an assortment of JDFTXinfile created from the same data but through different methods, and test that
-    they are all equivalent through "assert_idential_jif" """
-    dict_jif = jif.as_dict()
-    # # Commenting out tests with jif2 due to the list representation asserted
-    jif2 = JDFTXInfile.get_dict_representation(JDFTXInfile._from_dict(dict_jif))
-    str_list_jif = jif.get_text_list()
-    str_jif = "\n".join(str_list_jif)
-    jif3 = JDFTXInfile.from_str(str_jif)
-    tmp_fname = dump_files_dir / "tmp.in"
-    jif.write_file(tmp_fname)
-    jif4 = JDFTXInfile.from_file(tmp_fname)
-    jifs = [jif, jif2, jif3, jif4]
-    for i in range(len(jifs)):
-        for j in range(i + 1, len(jifs)):
-            print(f"{i}, {j}")
-            assert_idential_jif(jifs[i], jifs[j])
-    os.remove(tmp_fname)
-
-
 def test_jdftxstructure():
     """Test the JDFTXStructure object associated with the JDFTXInfile object"""
     jif = JDFTXInfile.from_file(ex_infile2_fname)

tests/io/jdftx/test_output_utils.py

@@ -10,8 +10,8 @@
 from pymatgen.io.jdftx.joutstructures import _get_joutstructures_start_idx
 from pymatgen.io.jdftx.outputs import _find_jdftx_out_file
 
-from .outputs_test_utils import noeigstats_outfile_path, write_mt_file
-from .shared_test_utils import dump_files_dir
+from .outputs_test_utils import noeigstats_outfile_path
+from .shared_test_utils import write_mt_file
 
 
 def test_get_start_lines():
@@ -66,26 +66,23 @@ def test_get_joutstructures_start_idx():
     assert _get_joutstructures_start_idx(["ken", "ken"], out_slice_start_flag=start_flag) is None
 
 
-def test_find_jdftx_out_file():
+def test_find_jdftx_out_file(tmp_path):
     """Test the _find_jdftx_out_file function.
 
     This function is used to find the JDFTx out file in a directory.
     It tests the behavior to make sure the correct errors are raised on directories without and out file
     and directories with multiple out files. And out file must match "*.out" or "out" exactly.
     """
     with pytest.raises(FileNotFoundError, match="No JDFTx out file found in directory."):
-        _find_jdftx_out_file(dump_files_dir)
-    write_mt_file("test.out")
-    assert _find_jdftx_out_file(dump_files_dir) == dump_files_dir / "test.out"
+        _find_jdftx_out_file(tmp_path)
+    write_mt_file(tmp_path, "test.out")
+    assert _find_jdftx_out_file(tmp_path) == tmp_path / "test.out"
     # out file has to match "*.out" or "out" exactly
-    write_mt_file("tinyout")
-    assert _find_jdftx_out_file(dump_files_dir) == dump_files_dir / "test.out"
-    remove(_find_jdftx_out_file(dump_files_dir))
-    write_mt_file("out")
-    assert _find_jdftx_out_file(dump_files_dir) == dump_files_dir / "out"
-    write_mt_file("tinyout.out")
+    write_mt_file(tmp_path, "tinyout")
+    assert _find_jdftx_out_file(tmp_path) == tmp_path / "test.out"
+    remove(_find_jdftx_out_file(tmp_path))
+    write_mt_file(tmp_path, "out")
+    assert _find_jdftx_out_file(tmp_path) == tmp_path / "out"
+    write_mt_file(tmp_path, "tinyout.out")
     with pytest.raises(FileNotFoundError, match="Multiple JDFTx out files found in directory."):
-        _find_jdftx_out_file(dump_files_dir)
-    # remove tmp files
-    for remaining in dump_files_dir.glob("*out"):
-        remove(remaining)
+        _find_jdftx_out_file(tmp_path)