GraphAtoms 2.3.1__tar.gz → 2.3.2__tar.gz

{graphatoms-2.3.1 → graphatoms-2.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: graphatoms
-Version: 2.3.1
+Version: 2.3.2
 Summary: The Chemical Core Class for Graph Theory Analysis.
 Keywords: chemistry,graph theory,reaction,event,KMC
 Author: LiuGaoyong

{graphatoms-2.3.1 → graphatoms-2.3.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "graphatoms"
-version = "2.3.1"
+version = "2.3.2"
 readme = "README.md"
 description = "The Chemical Core Class for Graph Theory Analysis."
 license-files = ["src/LICENSE"]

{graphatoms-2.3.1 → graphatoms-2.3.2}/pyproject.toml.orig

@@ -12,7 +12,7 @@ graphatoms-network = "graphatoms.enterpoint.network:main"
 graphatoms-run = "graphatoms.enterpoint.runner:run"
 [project]
 name = "graphatoms"
-version = "2.3.1"
+version = "2.3.2"
 readme = "README.md"
 description = "The Chemical Core Class for Graph Theory Analysis."
 authors = [{ name = "LiuGaoyong", email = "liugaoyong_88@163.com" }]

{graphatoms-2.3.1 → graphatoms-2.3.2}/src/graphatoms/dataclasses/_pydanticMixin.py

@@ -229,7 +229,11 @@ class __Json(PydanticConvertFactoryMixin):
                 indent=indent,
             )
         )
-        filename.write_text(self.to_str(**kwargs), "utf-8")
+        bytesutils.atomic_write_text(
+            target=filename,
+            text=self.to_str(**kwargs),
+            encoding="utf-8",
+        )
         return filename
 
     @classmethod
@@ -260,13 +264,15 @@ class __Toml(PydanticConvertFactoryMixin):
                 numpy_ndarray_compatible=True,
             )
         )
-        with filename.open("wb") as f:
-            toml_w.dump(
+        bytesutils.atomic_write_text(
+            target=filename,
+            text=toml_w.dumps(
                 self.to_dict(**kwargs),
-                f,
                 indent=indent,
                 multiline_strings=True,
-            )
+            ),
+            encoding="utf-8",
+        )
         return filename
 
     @classmethod
@@ -301,16 +307,17 @@ class __Yaml(PydanticConvertFactoryMixin):
                 numpy_ndarray_compatible=True,
             )
         )
-        with filename.open("w", encoding="utf-8") as f:
-            f.write(
-                OmegaConf.to_yaml(
-                    self.to_dict(**kwargs),
-                    # f,
-                    # encoding="utf-8",
-                    # # default_flow_style=False,
-                    # indent=4,
-                )
-            )
+        bytesutils.atomic_write_text(
+            target=filename,
+            text=OmegaConf.to_yaml(
+                self.to_dict(**kwargs),
+                # f,
+                # encoding="utf-8",
+                # # default_flow_style=False,
+                # indent=4,
+            ),
+            encoding="utf-8",
+        )
         return filename
 
     @classmethod
@@ -345,10 +352,14 @@ class __Npz(PydanticConvertFactoryMixin):
                 numpy_ndarray_compatible=True,
             )
         )
-        (np.savez_compressed if compress else np.savez)(
-            filename,
-            allow_pickle=False,
-            **self.to_dict(**kwargs),
+        func = np.savez_compressed if compress else np.savez
+        bytesutils.atomic_write(
+            target=filename,
+            writer=lambda p: func(
+                p,
+                allow_pickle=False,
+                **self.to_dict(**kwargs),
+            ),
         )
         return filename
 
@@ -411,7 +422,14 @@ class __Pickle(PydanticConvertFactoryMixin):
                 numpy_ndarray_compatible=True,
             )
         )
-        dump(self.to_dict(**kwargs), filename, compress=compress)
+        bytesutils.atomic_write(
+            target=filename,
+            writer=lambda p: dump(
+                value=self.to_dict(**kwargs),
+                filename=p,
+                compress=compress,  # type: ignore
+            ),
+        )
         return filename
 
     @classmethod

{graphatoms-2.3.1 → graphatoms-2.3.2}/src/graphatoms/enterpoint/network/_clsnetwork.py

@@ -27,6 +27,7 @@ from graphatoms.reaction import (
 )
 from graphatoms.system import Cluster, Gas, SysGraph, System
 from graphatoms.system.database import DatabaseABC, get_db
+from graphatoms.utils.bytestool import atomic_write, atomic_write_text
 
 __all__ = [
     "MetaData",
@@ -88,8 +89,9 @@ class ReactionNetwork(Mapping[str, tuple[EventInfo, EventBase]]):
                 + " Please delete it or use `restart=True`."
             )
             self.__path.mkdir(parents=True, exist_ok=True)
-            self.__path_exploration_recorder.write_text(
-                RecorderInfo.get_csv_title() + "\n"
+            atomic_write_text(
+                self.__path_exploration_recorder,
+                RecorderInfo.get_csv_title() + "\n",
             )
             self.__recorder = Recorder()
             self.__scheduler = Scheduler()
@@ -130,6 +132,7 @@ class ReactionNetwork(Mapping[str, tuple[EventInfo, EventBase]]):
         config: Config,
         *args,
         restart: bool | None = None,
+        remote_retry_times: float = 2.0,
         remote_mode: bool = False,
         **kwargs,
     ) -> Self:  # type: ignore
@@ -152,7 +155,7 @@ class ReactionNetwork(Mapping[str, tuple[EventInfo, EventBase]]):
                     )
                     break
                 except Exception as e:
-                    time.sleep(0.5)
+                    time.sleep(abs(remote_retry_times))
                     err = e
             if err is not None:
                 raise RuntimeError(
@@ -535,8 +538,11 @@ class ReactionNetwork(Mapping[str, tuple[EventInfo, EventBase]]):
                     msg = f"Event {event._string()} failed "
                     msg += f"to simplify. because of {e}"
                     fname = self.__path / "event-simplify-fail.pkl"
-                    fname.with_suffix(".err").write_text(msg)
-                    fname.write_bytes(pickle.dumps(event))
+                    atomic_write_text(fname.with_suffix(".err"), msg)
+                    atomic_write(
+                        fname,
+                        writer=lambda p: p.write_bytes(pickle.dumps(event)),
+                    )
                     event.R.write_npz(fname.with_suffix(".R.npz"))
                     event.P.write_npz(fname.with_suffix(".P.npz"))
                     if event.G is not None:
@@ -789,8 +795,10 @@ if __name__ == "__main__":
         if "merge" not in zzzz_path.name:
             p = zzzz_path / "event"
             (p / "recorder.json").unlink(missing_ok=True)
-            with open(p / "recorder.json", "w") as f:
-                json.dump({}, f, indent=4)
+            atomic_write_text(
+                p / "recorder.json",
+                json.dumps({}, indent=4),
+            )
             network_lst.append(
                 ReactionNetwork(
                     zzzz_path / "event",

{graphatoms-2.3.1 → graphatoms-2.3.2}/src/graphatoms/enterpoint/network/_metadata.py

@@ -10,6 +10,7 @@ from graphatoms.dataclasses import OurBaseModel
 from graphatoms.enterpoint.config import Config, EventConfig
 from graphatoms.reaction import EventBase, EventInfo
 from graphatoms.system.bonds import matchmode2nmatch
+from graphatoms.utils.bytestool import atomic_write
 
 __all__ = ["MetaData"]
 
@@ -187,7 +188,10 @@ class MetaData(BaseModel):
 
     def persistence(self, path: Path | str) -> None:
         self.basic.write_json(Path(path) / "metadata-basic.json")
-        self.table.dataframe.to_feather(Path(path) / "metadata-table.feather")
+        atomic_write(
+            Path(path) / "metadata-table.feather",
+            writer=lambda p: self.table.dataframe.to_feather(p),
+        )
 
     @classmethod
     def from_storage(cls, path: Path | str) -> Self:

{graphatoms-2.3.1 → graphatoms-2.3.2}/src/graphatoms/enterpoint/network/_scheduler.py

@@ -9,6 +9,7 @@ from sklearn.metrics.pairwise import cosine_similarity
 
 from graphatoms.dataclasses._numpydantic import NDArray
 from graphatoms.system import SysGraph  # type: ignore
+from graphatoms.utils.bytestool import atomic_write
 
 
 class Scheduler(BaseModel):
@@ -35,7 +36,10 @@ class Scheduler(BaseModel):
         save: Callable = np.savez_compressed if compress else np.savez
         dct = {f"{k}_is_fixed": v for k, v in self.is_fixed.items()}
         dct = {f"{k}_dR": v for k, v in self.dR.items()} | dct
-        save(filename, allow_pickle=False, **dct)
+        atomic_write(
+            target=filename,
+            writer=lambda p: save(p, allow_pickle=False, **dct),
+        )
         return filename
 
     @classmethod
@@ -151,5 +155,8 @@ if __name__ == "__main__":
     plt.title("Blue: Keep; Red: Skip")
 
     p = Path(__file__).with_suffix(".png")
-    plt.savefig(p)
+    atomic_write(
+        p,
+        writer=lambda p: plt.savefig(p),
+    )
     obj.write_npz(p.with_suffix(".npz"))

{graphatoms-2.3.1 → graphatoms-2.3.2}/src/graphatoms/enterpoint/runner/common/_base.py

@@ -26,6 +26,7 @@ from graphatoms.enterpoint.config.atoms import AseReadAtomsConfig
 from graphatoms.enterpoint.network import ReactionNetwork
 from graphatoms.enterpoint.parallel import get_executor
 from graphatoms.system import Cluster, Gas, System
+from graphatoms.utils.bytestool import atomic_write_text
 from graphatoms.utils.parser import hydra_parse
 
 from ._helper import helper_optimization
@@ -241,8 +242,10 @@ class RunnerABC:
 
     def persist_gas_number_dct(self) -> None:
         """Persist the gas number dct to file."""
-        with open(self.__gas_number_path, "w") as f:
-            json.dump(self.gas_number_dct, f, indent=4)
+        atomic_write_text(
+            self.__gas_number_path,
+            json.dumps(self.gas_number_dct, indent=4),
+        )
 
     def load_gas_number_dct(self) -> None:
         """Load the gas number dct from file."""
@@ -376,7 +379,7 @@ class RunnerABC:
         values: list[Cluster] = []
         keys: list[tuple[bool, int, str]] = []
         for core in system.get_site_core(max_ncore=max_ncore):  # type: ignore
-            idx_core = np.unique(np.where(core)).astype(int)
+            idx_core = np.unique(np.where(core)).astype(int)  # type: ignore
             values.append(
                 Cluster.from_select(
                     system,

{graphatoms-2.3.1 → graphatoms-2.3.2}/src/graphatoms/enterpoint/runner/common/_helper.py

@@ -4,12 +4,14 @@ These helper functions only run calculation, and check the result.
 They do not check whether the calculation is necessary and output logger.
 """
 
+from pathlib import Path
 from time import perf_counter
 from typing import Any, Literal
 
 import numpy as np
 from ase import Atoms
 from ase.calculators.calculator import Calculator
+from ase.io.extxyz import write_xyz as write_extxyz
 
 from graphatoms.enterpoint.config import Config
 from graphatoms.enterpoint.network import ReactionNetwork
@@ -18,6 +20,7 @@ from graphatoms.system import Cluster, Gas, SysGraph, System
 from graphatoms.system.atoms import Structure
 from graphatoms.utils import asetools
 from graphatoms.utils.adsorption import Helper
+from graphatoms.utils.bytestool import atomic_write
 from graphatoms.utils.parser import hydra_parse
 
 from ._errors import CheckVibrationFailed, HelperException, OptimizationFailed
@@ -178,11 +181,10 @@ def helper_optimization(
             deep=deep_copy,
         )
     except Exception as e:
-        lst[0].write(f"debug-{graph_label}.xyz", format="extxyz", append=False)
-        for i in range(1, len(lst)):
-            lst[i].write(
-                f"debug-{graph_label}.xyz", format="extxyz", append=True
-            )
+        atomic_write(
+            Path(f"debug-{graph_label}.xyz"),
+            writer=lambda p: write_extxyz(p, lst),
+        )
         raise e
     if (not allow_not_connected) and (not result.is_connected):
         e = HelperException(

{graphatoms-2.3.1 → graphatoms-2.3.2}/src/graphatoms/enterpoint/runner/general/otfkmc.py

@@ -17,6 +17,7 @@ from graphatoms.enterpoint.runner.common._helper import (
     helper_match,
 )
 from graphatoms.reaction import Adsorption, Desorption, Reaction
+from graphatoms.utils.bytestool import atomic_write
 
 from ._expl import ExplorationBase
 
@@ -92,7 +93,10 @@ class OTFKMC(ExplorationBase):
             # -------------------------------------------
             system = self.get_system_for(atoms)
             data = [i.model_dump() for i in df_data]
-            pd.DataFrame(data).to_csv(self.__info_path)
+            atomic_write(
+                self.__info_path,
+                writer=lambda p: pd.DataFrame(data).to_csv(p),
+            )
             self.__traj.write(system.to_ase())
             if df_data[-1].time > float(self.config.max_times):
                 self.logger.info(

{graphatoms-2.3.1 → graphatoms-2.3.2}/src/graphatoms/geometry/sample.py

@@ -56,6 +56,8 @@ if __name__ == "__main__":
     from matplotlib import pyplot as plt
     from matplotlib.axes import Axes
 
+    from graphatoms.utils.bytestool import atomic_write
+
     N = 100
 
     fig, axes = plt.subplots(1, 2, figsize=(8, 4.5), dpi=150)
@@ -76,4 +78,8 @@ if __name__ == "__main__":
         ax.set_xticks([])
         ax.set_yticks([])
     plt.tight_layout()
-    fig.savefig(Path(__file__).with_suffix(".png"))
+
+    atomic_write(
+        Path(__file__).with_suffix(".png"),
+        writer=lambda p: fig.savefig(p),
+    )

{graphatoms-2.3.1 → graphatoms-2.3.2}/src/graphatoms/system/database/abc.py

@@ -1,11 +1,14 @@
 from abc import abstractmethod
 from collections.abc import Mapping, MutableSet
+from pathlib import Path
 from typing import override
 
 import numpy as np
 from ase import Atoms
+from ase.io.extxyz import write_xyz as write_extxyz
 
 from graphatoms.system import SysGraph
+from graphatoms.utils.bytestool import atomic_write
 
 
 class DatabaseABC(Mapping[str, Atoms], MutableSet[str]):
@@ -63,11 +66,11 @@ class DatabaseABC(Mapping[str, Atoms], MutableSet[str]):
                 if not np.all(np.abs(vdiff) < check_threshold):
                     # Save some files for debug.
                     old = SysGraph.from_ase(old_value)
-                    for v, append in [
-                        (old_value, False),
-                        (value.to_ase(), True),
-                    ]:
-                        v.write(f"{key}-debug.xyz", "extxyz", append=append)
+                    lst = [old_value, value.to_ase()]
+                    atomic_write(
+                        Path(f"{key}-debug.xyz"),
+                        writer=lambda p: write_extxyz(p, lst),
+                    )
                     value.write_npz(f"{key}-new.npz")  # type: ignore
                     old.write_npz(f"{key}-old.npz")  # type: ignore
                     raise ValueError(

{graphatoms-2.3.1 → graphatoms-2.3.2}/src/graphatoms/utils/adsorption.py

@@ -23,10 +23,11 @@ from scipy.spatial.transform import Rotation
 from graphatoms.geometry import neighbor_list
 from graphatoms.geometry.sample import fibonacci_lattice
 from graphatoms.system import Cluster, Gas, System
+from graphatoms.utils.asetools import call_optimization as optimize
+from graphatoms.utils.bytestool import atomic_write
 from graphatoms.utils.rdutils import rdmol2ase, smiles2rdmol
 
 matplotlib.use("Agg")
-from .asetools import call_optimization as optimize
 
 
 #########################################
@@ -786,5 +787,8 @@ def plot(atoms: Atoms, pngfname: Path) -> None:
         )
         ax.set_xticks([])
         ax.set_yticks([])
-    fig.savefig(pngfname.with_suffix(".png"))
+    atomic_write(
+        pngfname.with_suffix(".png"),
+        writer=lambda p: fig.savefig(p),
+    )
     plt.close(fig)

{graphatoms-2.3.1 → graphatoms-2.3.2}/src/graphatoms/utils/bytestool.py

@@ -2,11 +2,14 @@
 
 import gzip
 import hashlib
+import os
 import string
+import uuid
 import zlib
 from collections.abc import Callable
 from functools import partial
-from typing import Annotated
+from pathlib import Path
+from typing import Annotated, Any
 
 from numpy.random import choice
 from pydantic import Field, validate_call
@@ -179,6 +182,54 @@ def random_string(n: int) -> str:
     return "".join(choice(pool, size=int(n)))
 
 
+def _fsync_dir(path: Path) -> None:
+    """Best-effort fsync of a directory so a rename is durable (POSIX)."""
+    try:
+        fd = os.open(str(path), os.O_RDONLY)
+    except OSError:
+        return
+    try:
+        os.fsync(fd)
+    except OSError:
+        pass
+    finally:
+        os.close(fd)
+
+
+def atomic_write(target: Path, writer: Callable[[Path], Any]) -> None:
+    """Write `target` atomically.
+
+    The `writer` callback receives a temporary path in the same
+    directory and must create/write the file there. The temp file is
+    fsynced and then os.replace()d onto `target`. Because both paths
+    live in the same directory, os.replace is atomic on POSIX.
+
+    The temp file keeps `target.suffix`, so callers such as
+    ``np.savez`` that auto-append ".npz" behave correctly.
+    """
+    target = Path(target)
+    target.parent.mkdir(parents=True, exist_ok=True)
+    file_stem = f".{target.stem}.tmp.{os.getpid()}{uuid.uuid4().hex}"
+    tmp = target.parent / f"{file_stem}{target.suffix}"
+    try:
+        writer(tmp)
+        # ensure the file is synced to disk
+        with open(tmp, "rb") as f:
+            os.fsync(f.fileno())
+        os.replace(tmp, target)
+        _fsync_dir(target.parent)
+    except Exception:
+        try:
+            tmp.unlink()
+        except FileNotFoundError:
+            pass
+        raise
+
+
+def atomic_write_text(target: Path, text: str, encoding="utf-8") -> None:
+    atomic_write(target, lambda p: p.write_text(text, encoding=encoding))
+
+
 #######################################################################
 #                                   Test
 #######################################################################