Test monty fix for reverse readline

.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
 
@@ -648,16 +647,15 @@ 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
 
@@ -799,7 +801,11 @@ def test_parse_potcar_cwd_relative(self):
 
 
 class TestOutcar(PymatgenTest):
-    def test_init(self):
+    def test_init_from_compressed(self):
+        """Test for both compressed and uncomressed versions,
+        because there was a bug in monty causing different
+        behaviour.
+        """
         outcar = Outcar(f"{VASP_OUT_DIR}/OUTCAR.gz")
         expected_mag = (
             {"d": 0.0, "p": 0.003, "s": 0.002, "tot": 0.005},
@@ -845,6 +851,38 @@ def test_init(self):
             toten += outcar.final_energy_contribs[k]
         assert toten == approx(outcar.final_energy, abs=1e-6)
 
+    def test_init_from_uncompressed(self):
+        """Test for both compressed and uncomressed versions,
+        because there was a bug in monty causing different
+        behaviour.
+        """
+        with ScratchDir("."):
+            copyfile(f"{VASP_OUT_DIR}/OUTCAR.gz", "./OUTCAR.gz")
+            decompress_file("./OUTCAR.gz")
+            outcar = Outcar("./OUTCAR")
+
+        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},
+            {"d": 0.798, "p": 0.008, "s": 0.007, "tot": 0.813},
+            {"d": 0.0, "p": -0.117, "s": 0.005, "tot": -0.112},
+            {"d": 0.0, "p": -0.165, "s": 0.004, "tot": -0.162},
+            {"d": 0.0, "p": -0.117, "s": 0.005, "tot": -0.112},
+            {"d": 0.0, "p": -0.165, "s": 0.004, "tot": -0.162},
+        )
+        expected_chg = (
+            {"p": 0.154, "s": 0.078, "d": 0.0, "tot": 0.232},
+            {"p": 0.707, "s": 0.463, "d": 8.316, "tot": 9.486},
+            {"p": 0.707, "s": 0.463, "d": 8.316, "tot": 9.486},
+            {"p": 3.388, "s": 1.576, "d": 0.0, "tot": 4.964},
+            {"p": 3.365, "s": 1.582, "d": 0.0, "tot": 4.947},
+            {"p": 3.388, "s": 1.576, "d": 0.0, "tot": 4.964},
+            {"p": 3.365, "s": 1.582, "d": 0.0, "tot": 4.947},
+        )
+
+        assert outcar.magnetization == approx(expected_mag, abs=1e-5), "Wrong magnetization read from Outcar"
+        assert outcar.charge == approx(expected_chg, abs=1e-5), "Wrong charge read from Outcar"
+
     def test_stopped_old(self):
         filepath = f"{VASP_OUT_DIR}/OUTCAR.stopped.gz"
         outcar = Outcar(filepath)