pymdkit 1.2.4__tar.gz → 1.2.5__tar.gz

{pymdkit-1.2.4/src/pymdkit.egg-info → pymdkit-1.2.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.2.4
+Version: 1.2.5
 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

{pymdkit-1.2.4 → pymdkit-1.2.5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pymdkit"
-version = "1.2.4"
+version = "1.2.5"
 description = "A unified command-line toolkit for atomistic / MD structure workflows."
 readme = "README.md"
 requires-python = ">=3.9"

{pymdkit-1.2.4 → pymdkit-1.2.5}/src/pymdkit/__init__.py

@@ -1,3 +1,3 @@
 """pymdkit -- a unified CLI for atomistic / MD structure workflows."""
 
-__version__ = "1.2.4"
+__version__ = "1.2.5"

{pymdkit-1.2.4 → pymdkit-1.2.5}/src/pymdkit/commands/stable_entry.py

@@ -14,19 +14,38 @@ def safe_formula(formula):
     return re.sub(r"[^A-Za-z0-9_.-]+", "", str(formula))
 
 
+def mpid_text(value):
+    if value is None:
+        return ""
+    if isinstance(value, dict):
+        for key in ("material_id", "task_id", "entry_id", "id", "identifier"):
+            if value.get(key):
+                return mpid_text(value[key])
+        return "-".join(f"{k}-{v}" for k, v in sorted(value.items()))
+    for attr in ("string", "identifier"):
+        text = getattr(value, attr, None)
+        if text:
+            return str(text)
+    text = str(value)
+    match = re.search(r"mp-\d+", text)
+    if match:
+        return match.group(0)
+    match = re.search(r"identifier=['\"]?(mp-[A-Za-z0-9]+)", text)
+    if match:
+        return match.group(1)
+    return text
+
+
 def entry_id_text(entry):
-    entry_id = getattr(entry, "entry_id", "")
-    if isinstance(entry_id, dict):
-        for key in ("material_id", "task_id", "entry_id", "id"):
-            if entry_id.get(key):
-                return str(entry_id[key])
-        return "-".join(f"{k}-{v}" for k, v in sorted(entry_id.items()))
-    if entry_id:
-        return str(entry_id)
+    entry_id = getattr(entry, "entry_id", None)
+    text = mpid_text(entry_id)
+    if text:
+        return text
     data = getattr(entry, "data", {}) or {}
     for key in ("material_id", "task_id", "entry_id", "id"):
-        if data.get(key):
-            return str(data[key])
+        text = mpid_text(data.get(key))
+        if text:
+            return text
     return "unknown"
 
 
@@ -43,20 +62,21 @@ def add_arguments(parser: argparse.ArgumentParser) -> None:
 
 
 def fetch_stable_entries(elements, api_key=None):
-    """Fetch stable thermo entries matching the Materials Project phase diagram."""
+    """Fetch entries and keep only entries stable on the full MP phase diagram."""
+    from pymatgen.analysis.phase_diagram import PhaseDiagram
     from pymatgen.ext.matproj import MPRester
 
     with MPRester(api_key) as mpr:
         entries = mpr.get_entries_in_chemsys(
             elements,
             inc_structure=True,
-            additional_criteria={
-                "thermo_types": ["GGA_GGA+U"],
-                "is_stable": True,
-            },
+            additional_criteria={"thermo_types": ["GGA_GGA+U"]},
         )
+    phase_diagram = PhaseDiagram(entries)
+    stable_entries = list(phase_diagram.stable_entries)
+    print(f"Fetched {len(entries)} MP thermo entries; {len(stable_entries)} are stable on the full phase diagram.")
     by_mpid = {}
-    for entry in entries:
+    for entry in stable_entries:
         by_mpid[entry_id_text(entry)] = entry
     return list(by_mpid.values())
 

{pymdkit-1.2.4 → pymdkit-1.2.5/src/pymdkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.2.4
+Version: 1.2.5
 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