pymdkit 1.6.2__tar.gz → 1.6.3__tar.gz

{pymdkit-1.6.2 → pymdkit-1.6.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.6.2
+Version: 1.6.3
 Summary: A unified command-line toolkit for atomistic / MD structure workflows.
 Author-email: Yueda Wang <ydwang0608@ustc.edu.cn>
 License-Expression: GPL-3.0-or-later
@@ -336,8 +336,14 @@ CIF input with pymatgen rather than ASE. ASE interprets
 `_space_group_crystal_system` as a setting hint only for rhombohedral groups
 and emits a potentially misleading warning for other crystal systems. Using
 pymatgen avoids that ambiguity while PMK continues to use ASE for non-CIF
-formats. A partially occupied CIF must first be ordered with `convert -d2o`
-before it can be represented as an explicit atom list.
+formats. Pymatgen intentionally snaps fractional coordinates within its
+default `1e-4` tolerance to ideal values before applying symmetry. PMK keeps
+that corrective behavior but hides only its corresponding finite-precision
+notice; composition, occupancy, malformed-CIF, and all other warnings remain
+visible. See the
+[pymatgen CifParser documentation](https://pymatgen.org/pymatgen.io.html#pymatgen.io.cif.CifParser).
+A partially occupied CIF must first be ordered with `convert -d2o` before it
+can be represented as an explicit atom list.
 
 CIF `_atom_type_symbol` and `_atom_site_label` values use per-element
 inequivalent-site identifiers such as `Li1`, `Y1`, `Cl1`, and `Cl2`.

{pymdkit-1.6.2 → pymdkit-1.6.3}/README.md

@@ -309,8 +309,14 @@ CIF input with pymatgen rather than ASE. ASE interprets
 `_space_group_crystal_system` as a setting hint only for rhombohedral groups
 and emits a potentially misleading warning for other crystal systems. Using
 pymatgen avoids that ambiguity while PMK continues to use ASE for non-CIF
-formats. A partially occupied CIF must first be ordered with `convert -d2o`
-before it can be represented as an explicit atom list.
+formats. Pymatgen intentionally snaps fractional coordinates within its
+default `1e-4` tolerance to ideal values before applying symmetry. PMK keeps
+that corrective behavior but hides only its corresponding finite-precision
+notice; composition, occupancy, malformed-CIF, and all other warnings remain
+visible. See the
+[pymatgen CifParser documentation](https://pymatgen.org/pymatgen.io.html#pymatgen.io.cif.CifParser).
+A partially occupied CIF must first be ordered with `convert -d2o` before it
+can be represented as an explicit atom list.
 
 CIF `_atom_type_symbol` and `_atom_site_label` values use per-element
 inequivalent-site identifiers such as `Li1`, `Y1`, `Cl1`, and `Cl2`.

{pymdkit-1.6.2 → pymdkit-1.6.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pymdkit"
-version = "1.6.2"
+version = "1.6.3"
 description = "A unified command-line toolkit for atomistic / MD structure workflows."
 readme = "README.md"
 requires-python = ">=3.9"

{pymdkit-1.6.2 → pymdkit-1.6.3}/src/pymdkit/__init__.py

@@ -1,3 +1,3 @@
 """pymdkit -- a unified CLI for atomistic / MD structure workflows."""
 
-__version__ = "1.6.2"
+__version__ = "1.6.3"

{pymdkit-1.6.2 → pymdkit-1.6.3}/src/pymdkit/commands/_cifio.py

@@ -41,12 +41,31 @@ CIF_FLOAT_TAGS = {
 _CIF_DECIMAL_RE = re.compile(
     r"[-+]?(?:(?:\d+\.\d*|\.\d+)(?:[eE][-+]?\d+)?|\d+[eE][-+]?\d+)"
 )
+_BENIGN_FRACTIONAL_ROUNDING_WARNING = (
+    r"Issues encountered while parsing CIF:\s*\d+ fractional coordinates? "
+    r"rounded to ideal values to avoid issues with finite precision\.\s*$"
+)
 
 
 def is_cif(path):
     return Path(path).suffix.lower() == ".cif"
 
 
+def read_structure(path):
+    """Read with pymatgen, hiding only its benign CIF idealization notice."""
+    from pymatgen.core import Structure
+
+    if not is_cif(path):
+        return Structure.from_file(str(path))
+    with warnings.catch_warnings():
+        warnings.filterwarnings(
+            "ignore",
+            message=_BENIGN_FRACTIONAL_ROUNDING_WARNING,
+            category=UserWarning,
+        )
+        return Structure.from_file(str(path))
+
+
 def as_pymatgen_structure(structure):
     """Return a periodic pymatgen Structure from pymatgen or ASE input."""
     from pymatgen.core import Structure

{pymdkit-1.6.2 → pymdkit-1.6.3}/src/pymdkit/commands/_symmetry.py

@@ -36,11 +36,9 @@ DEFAULT_OXIDATION_STATES = {
 
 
 def load_structure(path):
-    from pymatgen.core import Structure
-
     path = Path(path)
     try:
-        return Structure.from_file(str(path))
+        return _cifio.read_structure(path)
     except Exception as pymatgen_error:
         if _cifio.is_cif(path):
             raise ValueError(

{pymdkit-1.6.2 → pymdkit-1.6.3}/src/pymdkit/commands/_vaspset.py

@@ -17,12 +17,12 @@ from __future__ import annotations
 
 import argparse
 import ast
-import warnings
 from pathlib import Path
 
 try:
-    from . import _lattice, _precision, _supercell
+    from . import _cifio, _lattice, _precision, _supercell
 except ImportError:
+    import _cifio
     import _lattice
     import _precision
     import _supercell
@@ -216,8 +216,6 @@ def _run_trajectory(args, set_cls, settings):
 def run_vasp_set(args, set_cls, default_settings):
     """Write *set_cls* input files for one structure (-i), a folder (-if), or a
     trajectory (-it). Defaults can be overridden via ``-custom-setting FILE``."""
-    warnings.filterwarnings("ignore", category=UserWarning, module="pymatgen")
-    from pymatgen.core import Structure
 
     settings = dict(default_settings)
     if args.custom_setting:
@@ -244,7 +242,7 @@ def run_vasp_set(args, set_cls, default_settings):
     written = 0
     for struct_file, out_dir in jobs:
         try:
-            structure = Structure.from_file(str(struct_file))
+            structure = _cifio.read_structure(struct_file)
         except Exception as e:  # noqa: BLE001 - report and continue in batch
             print(f"{struct_file}: cannot read ({e}) -> skipping")
             continue

{pymdkit-1.6.2 → pymdkit-1.6.3}/src/pymdkit/commands/compute_rmsd.py

@@ -11,8 +11,9 @@ from itertools import combinations
 from pathlib import Path
 
 try:
-    from . import _fileio
+    from . import _cifio, _fileio
 except ImportError:
+    import _cifio
     import _fileio
 
 COMMAND = "rmsd"
@@ -49,11 +50,9 @@ def create_matcher():
 
 
 def load_structure(path):
-    from pymatgen.core import Structure
-
     path = Path(path)
     try:
-        return Structure.from_file(str(path))
+        return _cifio.read_structure(path)
     except Exception as pymatgen_error:
         if path.suffix.lower() == ".cif":
             print(f"  [warn] pymatgen could not read CIF {path}: {pymatgen_error}")

{pymdkit-1.6.2 → pymdkit-1.6.3}/src/pymdkit/commands/convert.py

@@ -23,10 +23,9 @@ HELP = "Convert structures, refine CIF symmetry, or order disorder."
 
 def _read_cif(path):
     """Read CIF with pymatgen, avoiding ASE's setting-name ambiguity."""
-    from pymatgen.core import Structure
     from pymatgen.io.ase import AseAtomsAdaptor
 
-    structure = Structure.from_file(str(path))
+    structure = _cifio.read_structure(path)
     if not structure.is_ordered:
         raise ValueError(
             "partially occupied CIF cannot be converted to an explicit atom "
@@ -149,9 +148,7 @@ def _write(
             ) from pmg_error
 
 def _read_structure(path):
-    from pymatgen.core import Structure
-
-    return Structure.from_file(str(path))
+    return _cifio.read_structure(path)
 
 
 def _write_structure(

{pymdkit-1.6.2 → pymdkit-1.6.3}/src/pymdkit/commands/ewald.py

@@ -14,14 +14,17 @@ from __future__ import annotations
 import argparse
 from pathlib import Path
 
+try:
+    from . import _cifio
+except ImportError:
+    import _cifio
+
 COMMAND = "ewald"
 HELP = "Compute CIF electrostatic energy using pymatgen EwaldSummation."
 
 
 def read_charged_structure(path):
-    from pymatgen.core import Structure
-
-    structure = Structure.from_file(str(path))
+    structure = _cifio.read_structure(path)
     missing = []
     for site in structure:
         for specie in site.species:

{pymdkit-1.6.2 → pymdkit-1.6.3}/src/pymdkit/commands/realloc_occ.py

@@ -580,9 +580,7 @@ def _write_candidate(
     temporary = output.with_name(f".{output.stem}.base.cif")
     try:
         render_candidate(parsed, occupancies, target, target_counts, z, temporary)
-        from pymatgen.core import Structure
-
-        structure = Structure.from_file(temporary)
+        structure = _cifio.read_structure(temporary)
         structure.make_supercell(list(matrix))
         _cifio.write_cif(structure, output, data_name=output.stem, refine=False)
     finally:

{pymdkit-1.6.2 → pymdkit-1.6.3}/src/pymdkit/commands/substitute.py

@@ -207,11 +207,9 @@ def read_cif_labels(path):
 
 def read_structure(path):
     """Read any pymatgen-readable structure, falling back to ASE."""
-    from pymatgen.core import Structure
-
     path = Path(path)
     try:
-        return Structure.from_file(str(path))
+        return _cifio.read_structure(path)
     except Exception as pymatgen_error:
         if _cifio.is_cif(path):
             raise ValueError(

{pymdkit-1.6.2 → pymdkit-1.6.3}/src/pymdkit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.6.2
+Version: 1.6.3
 Summary: A unified command-line toolkit for atomistic / MD structure workflows.
 Author-email: Yueda Wang <ydwang0608@ustc.edu.cn>
 License-Expression: GPL-3.0-or-later
@@ -336,8 +336,14 @@ CIF input with pymatgen rather than ASE. ASE interprets
 `_space_group_crystal_system` as a setting hint only for rhombohedral groups
 and emits a potentially misleading warning for other crystal systems. Using
 pymatgen avoids that ambiguity while PMK continues to use ASE for non-CIF
-formats. A partially occupied CIF must first be ordered with `convert -d2o`
-before it can be represented as an explicit atom list.
+formats. Pymatgen intentionally snaps fractional coordinates within its
+default `1e-4` tolerance to ideal values before applying symmetry. PMK keeps
+that corrective behavior but hides only its corresponding finite-precision
+notice; composition, occupancy, malformed-CIF, and all other warnings remain
+visible. See the
+[pymatgen CifParser documentation](https://pymatgen.org/pymatgen.io.html#pymatgen.io.cif.CifParser).
+A partially occupied CIF must first be ordered with `convert -d2o` before it
+can be represented as an explicit atom list.
 
 CIF `_atom_type_symbol` and `_atom_site_label` values use per-element
 inequivalent-site identifiers such as `Li1`, `Y1`, `Cl1`, and `Cl2`.

{pymdkit-1.6.2 → pymdkit-1.6.3}/tests/test_lattice_symmetry.py

@@ -2,6 +2,7 @@ import math
 import sys
 import types
 import unittest
+import warnings
 from pathlib import Path
 from unittest.mock import patch
 
@@ -38,6 +39,39 @@ class FakeLattice:
         return math.degrees(math.acos(float(np.clip(cosine, -1.0, 1.0))))
 
 
+class CifReaderTests(unittest.TestCase):
+    def test_only_benign_fractional_rounding_warning_is_hidden(self):
+        structure = object()
+
+        class Structure:
+            @classmethod
+            def from_file(cls, path):
+                warnings.warn(
+                    "Issues encountered while parsing CIF: 4 fractional "
+                    "coordinates rounded to ideal values to avoid issues "
+                    "with finite precision.",
+                    UserWarning,
+                )
+                warnings.warn("CIF composition mismatch", UserWarning)
+                return structure
+
+        pymatgen = types.ModuleType("pymatgen")
+        core = types.ModuleType("pymatgen.core")
+        core.Structure = Structure
+        pymatgen.core = core
+        with patch.dict(sys.modules, {
+            "pymatgen": pymatgen,
+            "pymatgen.core": core,
+        }), warnings.catch_warnings(record=True) as caught:
+            warnings.simplefilter("always")
+            result = _cifio.read_structure("input.cif")
+
+        self.assertIs(result, structure)
+        self.assertEqual([str(item.message) for item in caught], [
+            "CIF composition mismatch"
+        ])
+
+
 class LatticeGeometryTests(unittest.TestCase):
     def test_gpumd_uses_pymatgen_lattice_row_vectors(self):
         pymatgen = types.ModuleType("pymatgen")