Fix monty imports, enhance test for Outcar parser to cover uncompressed format

.github/workflows/test.yml

@@ -86,6 +86,9 @@ jobs:
 
           uv pip install --editable '.[${{ matrix.config.extras }}]' --resolution=${{ matrix.config.resolution }}
 
+          # TODO: test monty fix for reverse readline
+          uv pip install git+https://github.com/DanielYang59/monty.git@readline-line-ending
+
       - name: Install optional Ubuntu dependencies
         if: matrix.config.os == 'ubuntu-latest'
         run: |

dev_scripts/potcar_scrambler.py

@@ -7,8 +7,8 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
+from monty.io import zopen
 from monty.os.path import zpath
-from monty.serialization import zopen
 
 from pymatgen.core import SETTINGS
 from pymatgen.io.vasp import Potcar, PotcarSingle

src/pymatgen/io/adf.py

@@ -6,10 +6,9 @@
 import re
 from typing import TYPE_CHECKING
 
-from monty.io import reverse_readline
+from monty.io import reverse_readfile
 from monty.itertools import chunks
 from monty.json import MSONable
-from monty.serialization import zopen
 
 from pymatgen.core.structure import Molecule
 
@@ -645,16 +644,15 @@ def _parse_logfile(self, logfile):
         # The last non-empty line of the logfile must match the end pattern.
         # Otherwise the job has some internal failure. The TAPE13 part of the
         # ADF manual has a detailed explanation.
-        with zopen(logfile, mode="rt") as file:
-            for line in reverse_readline(file):
-                if line == "":
-                    continue
-                if end_patt.search(line) is None:
-                    self.is_internal_crash = True
-                    self.error = "Internal crash. TAPE13 is generated!"
-                    self.is_failed = True
-                    return
-                break
+        for line in reverse_readfile(logfile):
+            if line.strip() == "":
+                continue
+            if end_patt.search(line) is None:
+                self.is_internal_crash = True
+                self.error = "Internal crash. TAPE13 is generated!"
+                self.is_failed = True
+                return
+            break
 
         with open(logfile) as file:
             for line in file:

tests/core/test_tensors.py

@@ -4,7 +4,8 @@
 
 import numpy as np
 import pytest
-from monty.serialization import MontyDecoder, loadfn
+from monty.json import MontyDecoder
+from monty.serialization import loadfn
 from numpy.testing import assert_allclose
 from pytest import approx
 

tests/io/test_core.py

@@ -5,7 +5,7 @@
 from typing import TYPE_CHECKING
 
 import pytest
-from monty.serialization import MontyDecoder
+from monty.json import MontyDecoder
 
 from pymatgen.core.structure import Structure
 from pymatgen.io.cif import CifParser, CifWriter

tests/io/vasp/test_outputs.py

@@ -12,6 +12,8 @@
 import numpy as np
 import pytest
 from monty.io import zopen
+from monty.shutil import decompress_file
+from monty.tempfile import ScratchDir
 from numpy.testing import assert_allclose
 from pytest import approx
 
@@ -831,9 +833,20 @@ def test_parse_potcar_cwd_relative(self):
                 assert vrun.potcar_spec[ipot]["summary_stats"] == potcar[ipot]._summary_stats
 
 
-class TestOutcar(PymatgenTest):
-    def test_init(self):
-        outcar = Outcar(f"{VASP_OUT_DIR}/OUTCAR.gz")
+class TestOutcar:
+    @pytest.mark.parametrize("compressed", [True, False])
+    def test_init(self, compressed: bool):
+        """Test from both compressed and uncompressed versions,
+        as there was a bug in monty causing different behaviours.
+        """
+        with ScratchDir("."):
+            if compressed:
+                copyfile(f"{VASP_OUT_DIR}/OUTCAR.gz", "./OUTCAR.gz")
+                decompress_file("./OUTCAR.gz")
+                outcar = Outcar("./OUTCAR")
+            else:
+                outcar = Outcar(f"{VASP_OUT_DIR}/OUTCAR.gz")
+
         expected_mag = (
             {"d": 0.0, "p": 0.003, "s": 0.002, "tot": 0.005},
             {"d": 0.798, "p": 0.008, "s": 0.007, "tot": 0.813},