pymdkit 1.2.9__tar.gz → 1.2.11__tar.gz

{pymdkit-1.2.9/src/pymdkit.egg-info → pymdkit-1.2.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.2.9
+Version: 1.2.11
 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-1.2.9 → pymdkit-1.2.11}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pymdkit"
-version = "1.2.9"
+version = "1.2.11"
 description = "A unified command-line toolkit for atomistic / MD structure workflows."
 readme = "README.md"
 requires-python = ">=3.9"

{pymdkit-1.2.9 → pymdkit-1.2.11}/src/pymdkit/__init__.py

@@ -1,3 +1,3 @@
 """pymdkit -- a unified CLI for atomistic / MD structure workflows."""
 
-__version__ = "1.2.9"
+__version__ = "1.2.11"

{pymdkit-1.2.9 → pymdkit-1.2.11}/src/pymdkit/commands/stable_entry.py

@@ -3,10 +3,7 @@
 from __future__ import annotations
 
 import argparse
-import json
 import re
-from urllib.parse import quote
-from urllib.request import Request, urlopen
 from pathlib import Path
 
 COMMAND = "stable-entry"
@@ -99,20 +96,28 @@ def resolve_public_material_ids(entries, api_key=None):
                     is_stable=True,
                     fields=["material_id", "formula_pretty", "structure"],
                 )
+            candidates = []
             for doc in cache[formula]:
                 structure = doc_get(doc, "structure")
                 material_id = mpid_text(doc_get(doc, "material_id"))
                 if not structure or not is_public_mpid(material_id):
                     continue
-                if str(structure.composition.reduced_formula) != formula:
-                    continue
-                if matcher.fit(entry.structure, structure):
-                    data = getattr(entry, "data", None)
-                    if data is None:
-                        entry.data = {}
-                        data = entry.data
-                    data["material_id"] = material_id
-                    break
+                if str(structure.composition.reduced_formula) == formula:
+                    candidates.append((doc, structure, material_id))
+            chosen = None
+            if len(candidates) == 1:
+                chosen = candidates[0][2]
+            else:
+                for _, structure, material_id in candidates:
+                    if matcher.fit(entry.structure, structure):
+                        chosen = material_id
+                        break
+            if chosen:
+                data = getattr(entry, "data", None)
+                if data is None:
+                    entry.data = {}
+                    data = entry.data
+                data["material_id"] = chosen
 
 
 def fetch_stable_entries(elements, api_key=None):
@@ -144,65 +149,44 @@ def fetch_stable_entries(elements, api_key=None):
     return list(by_mpid.values())
 
 
-def api_key_value(api_key=None):
-    if api_key:
-        return api_key
-    try:
-        from pymatgen.ext.matproj import MPRester
-        return getattr(MPRester(), "api_key", None)
-    except Exception:
-        return None
+def get_api_structure(material_id, api_key=None):
+    """Return the MP API structure for a public material_id."""
+    from mp_api.client import MPRester as MPApiRester
 
+    with MPApiRester(api_key) as mpr:
+        if hasattr(mpr, "get_structure_by_material_id"):
+            try:
+                return mpr.get_structure_by_material_id(
+                    material_id,
+                    conventional_unit_cell=True,
+                )
+            except TypeError:
+                return mpr.get_structure_by_material_id(material_id)
+
+        docs = mpr.materials.summary.search(
+            material_ids=[material_id],
+            fields=["material_id", "structure"],
+        )
+    if not docs:
+        raise RuntimeError(f"no MP summary structure found for {material_id}")
+    return doc_get(docs[0], "structure")
+
+
+def write_mp_symmetrized_cif(material_id, fallback_structure, path, api_key=None):
+    """Write an MP API structure as a symmetrized CIF."""
+    from pymatgen.io.cif import CifWriter
 
-def extract_cif_text(text):
-    stripped = text.lstrip()
-    if not stripped.startswith(("{", "[")):
-        if "_symmetry_space_group_name_H-M" in text or stripped.startswith(("data_", "#")):
-            return text
     try:
-        payload = json.loads(text)
-    except json.JSONDecodeError:
-        return None
-    candidates = []
-    if isinstance(payload, dict):
-        candidates.extend(payload.get("response", []) or [])
-        candidates.extend(payload.get("data", []) or [])
-        candidates.append(payload)
-    for item in candidates:
-        if isinstance(item, dict):
-            cif = item.get("cif") or item.get("cif_symmetrized") or item.get("symmetrized_cif")
-            if cif:
-                return cif
-    return None
-
-
-def download_mp_symmetrized_cif(material_id, path, api_key=None):
-    """Download the Materials Project CIF (Symmetrized) file for material_id."""
-    key = api_key_value(api_key)
-    headers = {"Accept": "text/plain", "User-Agent": "pymdkit"}
-    if key:
-        headers["X-API-KEY"] = key
-    quoted = quote(material_id, safe="")
-    urls = [
-        f"https://materialsproject.org/materials/{quoted}/cif?download=true&symmetrized=true",
-        f"https://materialsproject.org/materials/{quoted}/cif?symmetrized=true",
-        f"https://www.materialsproject.org/rest/v2/materials/{quoted}/cif",
-    ]
-    errors = []
-    for url in urls:
-        try:
-            req = Request(url, headers=headers)
-            with urlopen(req, timeout=60) as response:
-                text = response.read().decode("utf-8")
-            cif_text = extract_cif_text(text)
-            if cif_text:
-                Path(path).write_text(cif_text, encoding="utf-8")
-                return
-            errors.append(f"{url}: response did not contain CIF text")
-        except Exception as exc:  # noqa: BLE001 - try alternate MP endpoints
-            errors.append(f"{url}: {type(exc).__name__}: {exc}")
-    raise RuntimeError("Could not download MP CIF (Symmetrized): " + " | ".join(errors))
+        structure = get_api_structure(material_id, api_key)
+    except Exception as exc:  # noqa: BLE001 - keep command useful if MP API changes
+        structure = fallback_structure
+        print(f"  ! {material_id}: MP API structure fetch failed ({type(exc).__name__}); "
+              "using thermo structure fallback.")
 
+    try:
+        CifWriter(structure, symprec=0.1, refine_struct=True).write_file(str(path))
+    except TypeError:
+        CifWriter(structure, symprec=0.1).write_file(str(path))
 
 def run(args) -> int:
 
@@ -227,7 +211,7 @@ def run(args) -> int:
         mpid = safe_formula(entry_id_text(entry).split(" ")[0])
         formula = safe_formula(entry.composition.reduced_formula)
         path = out_dir / f"{mpid}-{formula}.cif"
-        download_mp_symmetrized_cif(mpid, path, args.mp_api_key)
+        write_mp_symmetrized_cif(mpid, entry.structure, path, args.mp_api_key)
         print(f"{mpid}\t{entry.composition.reduced_formula}\t-> {path}")
         written += 1
 

{pymdkit-1.2.9 → pymdkit-1.2.11/src/pymdkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pymdkit
-Version: 1.2.9
+Version: 1.2.11
 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