mdinterface 1.5.3__tar.gz → 1.5.4__tar.gz

{mdinterface-1.5.3/mdinterface.egg-info → mdinterface-1.5.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mdinterface
-Version: 1.5.3
+Version: 1.5.4
 Summary: Build Interface Systems for Molecular Dynamics Simulations
 Author-email: Fabrice Roncoroni <fabrice.roncoroni@gmail.com>
 License-Expression: Apache-2.0

{mdinterface-1.5.3 → mdinterface-1.5.4}/mdinterface/__init__.py

@@ -6,8 +6,8 @@ Initially developed to construct electrolyte/electrode interfaces, it is also we
 
 """
 
-__version__ = '1.5.3'
-__date__ = '09 Jul. 2026'
+__version__ = '1.5.4'
+__date__ = '12 Aug. 2026'
 __author__ = 'Fabrice Roncoroni'
 __all__ = ['SimulationBox', 'SimCell', 'BoxBuilder', "Specie", "Polymer"]
 

{mdinterface-1.5.3 → mdinterface-1.5.4}/mdinterface/core/topology.py

@@ -249,13 +249,14 @@ class Dihedral(Topology):
         return (self.values == other.values and
                 (self.symbols == other.symbols or self.symbols == other.symbols[::-1]))
 
-    def write(self, fout):
+    def write(self, fout, idx=None):
         atype = "{}-{}-{}-{}".format(*self.symbols)
         if self._values[-1] is not None:
             value = "{:>7.4f}  {:>7.4f}  {:>7.4f}  {:>7.4f}  {:>7.4f}".format(*self.values)
         else:
             value = "{:>7.4f}  {:>7.4f}  {:>7.4f}  {:>7.4f}".format(*self.values[:-1])
-        fout.write("{:>5}    {}  #  {:<8} | {}\n".format(self.id, value, atype, self.resname))
+        fout.write("{:>5}    {}  #  {:<8} | {}\n".format(
+            idx if idx is not None else self.id, value, atype, self.resname))
         
     def __bool__(self):
         return any([bool(val) for val in self.values])

{mdinterface-1.5.3 → mdinterface-1.5.4}/mdinterface/io/lammpswriter.py

@@ -25,6 +25,16 @@ btype_sections = {'bond':'Bonds', 'angle':'Angles',
                   'dihedral':'Dihedrals', 'improper':'Impropers'}
 
 
+def _renumber_bonded_types(raw_types):
+    """
+    Map raw per-item bond/angle/dihedral/improper type ids -- which may be
+    sparse or non-contiguous (e.g. when a Specie template is reused across
+    several layers) -- to a contiguous 1..N range ordered by numeric value.
+    """
+    unique_sorted = sorted({int(t) for t in raw_types})
+    return {t: i + 1 for i, t in enumerate(unique_sorted)}
+
+
 class DATAWriter(base.WriterBase):
     """Write out the current time step as a LAMMPS DATA file.
 
@@ -161,9 +171,14 @@ class DATAWriter(base.WriterBase):
         self.f.write('\n')
         self.f.write('{}\n'.format(btype_sections[bonds.btype]))
         self.f.write('\n')
+        try:
+            remap = _renumber_bonded_types(bond.type for bond in bonds)
+        except (TypeError, ValueError):
+            remap = None
         for bond, i in zip(bonds, range(1, len(bonds)+1)):
             try:
-                self.f.write('{:d} {:d} '.format(i, int(bond.type))+\
+                btype_id = remap[int(bond.type)] if remap is not None else int(bond.type)
+                self.f.write('{:d} {:d} '.format(i, btype_id)+\
                         ' '.join((bond.atoms.indices + 1).astype(str))+'\n')
             except TypeError:
                 errmsg = (f"LAMMPS DATAWriter: Trying to write bond, but bond "
@@ -337,18 +352,20 @@ def write_lammps_coefficients(
     # Write Pair Coefficients
     fout.write("Pair Coeffs\n\n")
 
-    idx = 1
+    present_types = list(np.unique(system.atoms.types))
     atom_types = sorted_attributes.get("atoms", [])
+    written = set()
     for atom in atom_types:
-        if atom.extended_label not in np.unique(system.atoms.types):
+        if atom.extended_label not in present_types or atom.extended_label in written:
             continue
+        written.add(atom.extended_label)
+        idx = present_types.index(atom.extended_label) + 1
 
         eps = atom.eps if atom.eps is not None else 0
         sig = atom.sig if atom.sig is not None else 0
 
         fout.write("{:>5}    {:>12.8f}    {:>12.8f}  # {}\n".format(
             idx, eps, sig, atom.extended_label))
-        idx += 1
 
     # Write Bond Coefficients
     bond_types = sorted_attributes.get("bonds", [])
@@ -356,9 +373,13 @@ def write_lammps_coefficients(
         fout.write("\n")
         fout.write("Bond Coeffs\n\n")
 
+    bond_remap = _renumber_bonded_types(system.bonds.types()) if len(system.bonds) else {}
+    written_bonds = set()
     for bond in bond_types:
-        if bond.id not in np.array(system.bonds.types(), dtype=int):
+        if int(bond.id) not in bond_remap or bond.id in written_bonds:
             continue
+        written_bonds.add(bond.id)
+        idx = bond_remap[int(bond.id)]
 
         kr = bond.kr if bond.kr is not None else 0
         r0 = bond.r0 if bond.r0 is not None else 0
@@ -366,7 +387,7 @@ def write_lammps_coefficients(
         btype = "{}-{}".format(*bond.symbols)
 
         fout.write("{:>5}    {:>10.6f}    {:>10.6f}  #  {:<5} | {}\n".format(
-            bond.id, kr, r0, btype, bond.resname))
+            idx, kr, r0, btype, bond.resname))
 
     # Write Angle Coefficients
     angle_types = sorted_attributes.get("angles", [])
@@ -374,9 +395,13 @@ def write_lammps_coefficients(
         fout.write("\n")
         fout.write("Angle Coeffs\n\n")
 
+    angle_remap = _renumber_bonded_types(system.angles.types()) if len(system.angles) else {}
+    written_angles = set()
     for angle in angle_types:
-        if angle.id not in np.array(system.angles.types(), dtype=int):
+        if int(angle.id) not in angle_remap or angle.id in written_angles:
             continue
+        written_angles.add(angle.id)
+        idx = angle_remap[int(angle.id)]
 
         kr = angle.kr if angle.kr is not None else 0
         theta0 = angle.theta0 if angle.theta0 is not None else 0
@@ -384,7 +409,7 @@ def write_lammps_coefficients(
         atype = "{}-{}-{}".format(*angle.symbols)
 
         fout.write("{:>5}    {:>10.6f}    {:>10.6f}  #  {:<8} | {}\n".format(
-            angle.id, kr, theta0, atype, angle.resname))
+            idx, kr, theta0, atype, angle.resname))
 
     # Write Dihedral Coefficients
     dihedral_types = sorted_attributes.get("dihedrals", [])
@@ -392,26 +417,33 @@ def write_lammps_coefficients(
         fout.write("\n")
         fout.write("Dihedral Coeffs\n\n")
 
+    dihedral_remap = _renumber_bonded_types(system.dihedrals.types()) if len(system.dihedrals) else {}
+    written_dihedrals = set()
     for dihedral in dihedral_types:
-        if dihedral.id not in np.array(system.dihedrals.types(), dtype=int):
+        if int(dihedral.id) not in dihedral_remap or dihedral.id in written_dihedrals:
             continue
+        written_dihedrals.add(dihedral.id)
 
-        dihedral.write(fout)
+        dihedral.write(fout, idx=dihedral_remap[int(dihedral.id)])
 
     # Write Improper Coefficients
     improper_types = sorted_attributes.get("impropers", [])
     if improper_types and system.impropers.types():
         fout.write("\n")
         fout.write("Improper Coeffs\n\n")
-        
+
+    improper_remap = _renumber_bonded_types(system.impropers.types()) if len(system.impropers) else {}
+    written_impropers = set()
     for improper in improper_types:
-        if improper.id not in np.array(system.impropers.types(), dtype=int):
+        if int(improper.id) not in improper_remap or improper.id in written_impropers:
             continue
+        written_impropers.add(improper.id)
+        idx = improper_remap[int(improper.id)]
 
         atype = "{}-{}-{}-{}".format(*improper.symbols)
         value = "{:>7.4f}    {:>2d}    {:>2d}".format(*improper.values)
 
-        fout.write("{:>5}    {}  #  {:<2} | {}\n".format(improper.id, value, atype, improper.resname))
+        fout.write("{:>5}    {}  #  {:<2} | {}\n".format(idx, value, atype, improper.resname))
 
     fout.write("\n")
 

{mdinterface-1.5.3 → mdinterface-1.5.4}/mdinterface/simulationbox.py

@@ -22,7 +22,6 @@ import numpy as np
 
 import shutil
 import warnings
-warnings.filterwarnings('ignore')
 
 #%%
 
@@ -56,7 +55,14 @@ class SimulationBox():
     def __init__(self, solvent: Optional[Any] = None, solute: Optional[Union[Any, List[Any]]] = None,
                  interface: Optional[Any] = None, enderface: Optional[Any] = None,
                  miderface: Optional[Any] = None) -> None:
-        
+
+        warnings.warn(
+            "SimulationBox is deprecated and will be removed in a future version. "
+            "Use SimCell instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+
         # start species
         self._setup_species(solvent, solute, interface, enderface, miderface)
         
@@ -367,7 +373,7 @@ class SimulationBox():
                 ion_pos  = layer["ion_pos"]
 
                 # make solvent box
-                solvent = make_solvent_box(self.species, self.solvent, self._solute,
+                solvent = make_solvent_box(self.species, self._solvent, self._solute,
                                            [xsize, ysize, zsize], solv_rho,
                                            nions, concentration, conmodel, ion_pos, nsolvent)
 

{mdinterface-1.5.3 → mdinterface-1.5.4/mdinterface.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mdinterface
-Version: 1.5.3
+Version: 1.5.4
 Summary: Build Interface Systems for Molecular Dynamics Simulations
 Author-email: Fabrice Roncoroni <fabrice.roncoroni@gmail.com>
 License-Expression: Apache-2.0

{mdinterface-1.5.3 → mdinterface-1.5.4}/mdinterface.egg-info/SOURCES.txt

@@ -83,9 +83,11 @@ mdinterface/utils/map.py
 mdinterface/utils/poisson.py
 mdinterface/utils/rings.py
 mdinterface/utils/units.py
+scripts/extract_changelog_summary.py
 tests/__init__.py
 tests/test_auxiliary.py
 tests/test_builder.py
+tests/test_changelog_summary.py
 tests/test_database.py
 tests/test_solvent.py
 tests/test_specie.py

{mdinterface-1.5.3 → mdinterface-1.5.4}/mdinterface.egg-info/top_level.txt

@@ -3,4 +3,5 @@ dist
 docs
 examples
 mdinterface
+scripts
 tests

mdinterface-1.5.4/scripts/extract_changelog_summary.py

@@ -0,0 +1,78 @@
+#!/usr/bin/env python3
+"""Extract a version's summary paragraph from CHANGELOG.md.
+
+Usage: python scripts/extract_changelog_summary.py VERSION
+
+Prints the summary paragraph to stdout and exits 0 on success. Exits 1 with
+an error on stderr if the version's changelog header, or its summary
+paragraph, is missing.
+"""
+import sys
+from pathlib import Path
+
+
+def extract_summary(changelog_text: str, version: str) -> str:
+    """Return the summary paragraph for `## [version]` in changelog_text.
+
+    The summary is every non-blank line immediately following the header
+    (after skipping any blank lines right after it), stopping at the next
+    blank line or the next '## '/'### ' header — i.e. exactly one paragraph.
+    """
+    header = f"## [{version}]"
+    lines = changelog_text.splitlines()
+
+    header_idx = None
+    for i, line in enumerate(lines):
+        if line.startswith(header):
+            header_idx = i
+            break
+
+    if header_idx is None:
+        raise ValueError(
+            f"No changelog header found for version {version!r} "
+            f"(expected a line starting with {header!r})"
+        )
+
+    i = header_idx + 1
+    while i < len(lines) and lines[i].strip() == "":
+        i += 1
+
+    summary_lines = []
+    while i < len(lines):
+        line = lines[i]
+        if line.strip() == "" or line.startswith("## ") or line.startswith("### "):
+            break
+        summary_lines.append(line)
+        i += 1
+
+    summary = "\n".join(summary_lines).strip()
+    if not summary:
+        raise ValueError(
+            f"No summary paragraph found under {header!r} in CHANGELOG.md - "
+            "add one before the first '### ' group"
+        )
+
+    return summary
+
+
+def main(argv):
+    if len(argv) != 2:
+        print("Usage: extract_changelog_summary.py VERSION", file=sys.stderr)
+        return 1
+
+    version = argv[1]
+    changelog_path = Path(__file__).resolve().parent.parent / "CHANGELOG.md"
+    changelog_text = changelog_path.read_text()
+
+    try:
+        summary = extract_summary(changelog_text, version)
+    except ValueError as exc:
+        print(f"ERROR: {exc}", file=sys.stderr)
+        return 1
+
+    print(summary)
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main(sys.argv))

mdinterface-1.5.4/tests/test_changelog_summary.py

@@ -0,0 +1,91 @@
+import importlib.util
+from pathlib import Path
+
+import pytest
+
+_SCRIPT_PATH = Path(__file__).resolve().parent.parent / "scripts" / "extract_changelog_summary.py"
+_spec = importlib.util.spec_from_file_location("extract_changelog_summary", _SCRIPT_PATH)
+_module = importlib.util.module_from_spec(_spec)
+_spec.loader.exec_module(_module)
+extract_summary = _module.extract_summary
+
+
+def test_extract_summary_found():
+    changelog = """# Changelog
+
+## [Unreleased]
+
+---
+
+## [1.5.4] - 2026-08-11
+
+Fixes a silent LAMMPS output corruption bug.
+
+### Fixed
+- Something
+"""
+    assert extract_summary(changelog, "1.5.4") == "Fixes a silent LAMMPS output corruption bug."
+
+
+def test_extract_summary_multiline():
+    changelog = """## [1.5.4] - 2026-08-11
+
+Fixes a silent LAMMPS output corruption bug affecting systems that reuse
+the same Specie template across multiple layers.
+
+### Fixed
+- Something
+"""
+    expected = (
+        "Fixes a silent LAMMPS output corruption bug affecting systems that reuse\n"
+        "the same Specie template across multiple layers."
+    )
+    assert extract_summary(changelog, "1.5.4") == expected
+
+
+def test_missing_version_header_raises():
+    changelog = """## [1.5.3] - 2026-07-09
+
+Some summary.
+
+### Fixed
+- Something
+"""
+    with pytest.raises(ValueError, match="No changelog header found"):
+        extract_summary(changelog, "1.5.4")
+
+
+def test_missing_summary_paragraph_raises():
+    changelog = """## [1.5.4] - 2026-08-11
+
+### Fixed
+- Something
+"""
+    with pytest.raises(ValueError, match="No summary paragraph found"):
+        extract_summary(changelog, "1.5.4")
+
+
+def test_second_paragraph_not_included():
+    changelog = """## [1.5.4] - 2026-08-11
+
+First paragraph only.
+
+Second paragraph should not be included.
+
+### Fixed
+- Something
+"""
+    assert extract_summary(changelog, "1.5.4") == "First paragraph only."
+
+
+def test_header_prefix_does_not_match_longer_version():
+    # "## [1.5.4]" must not match when looking for "1.5" or "1.5.40"
+    changelog = """## [1.5.40] - 2026-08-11
+
+Wrong version's summary.
+
+### Fixed
+- Something
+"""
+    with pytest.raises(ValueError, match="No changelog header found"):
+        extract_summary(changelog, "1.5.4")