fix: fix DPOSPath.save_numpy, DPH5Path.is_file, DPH5Path.is_dir (#3631)

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

deepmd/utils/path.py

@@ -11,6 +11,8 @@
     Path,
 )
 from typing import (
+    ClassVar,
+    Dict,
     List,
     Optional,
 )
@@ -200,7 +202,8 @@ def save_numpy(self, arr: np.ndarray) -> None:
         """
         if self.mode == "r":
             raise ValueError("Cannot save to read-only path")
-        np.save(str(self.path), arr)
+        with self.path.open("wb") as f:
+            np.save(f, arr)
 
     def glob(self, pattern: str) -> List["DPPath"]:
         """Search path using the glob pattern.
@@ -354,6 +357,7 @@ def save_numpy(self, arr: np.ndarray) -> None:
             del self.root[self._name]
         self.root.create_dataset(self._name, data=arr)
         self.root.flush()
+        self._new_keys.append(self._name)
 
     def glob(self, pattern: str) -> List["DPPath"]:
         """Search path using the glob pattern.
@@ -396,6 +400,14 @@ def _keys(self) -> List[str]:
         """Walk all groups and dataset."""
         return self._file_keys(self.root)
 
+    __file_new_keys: ClassVar[Dict[h5py.File, List[str]]] = {}
+
+    @property
+    def _new_keys(self):
+        """New keys that haven't been cached."""
+        self.__file_new_keys.setdefault(self.root, [])
+        return self.__file_new_keys[self.root]
+
     @classmethod
     @lru_cache(None)
     def _file_keys(cls, file: h5py.File) -> List[str]:
@@ -406,15 +418,15 @@ def _file_keys(cls, file: h5py.File) -> List[str]:
 
     def is_file(self) -> bool:
         """Check if self is file."""
-        if self._name not in self._keys:
+        if self._name not in self._keys and self._name not in self._new_keys:
             return False
         return isinstance(self.root[self._name], h5py.Dataset)
 
     def is_dir(self) -> bool:
         """Check if self is directory."""
         if self._name == "/":
             return True
-        if self._name not in self._keys:
+        if self._name not in self._keys and self._name not in self._new_keys:
             return False
         return isinstance(self.root[self._name], h5py.Group)
 
@@ -461,3 +473,4 @@ def mkdir(self, parents: bool = False, exist_ok: bool = False) -> None:
             self.root.require_group(self._name)
         else:
             self.root.create_group(self._name)
+        self._new_keys.append(self._name)

source/tests/common/test_path.py

@@ -0,0 +1,53 @@
+# SPDX-License-Identifier: LGPL-3.0-or-later
+import tempfile
+import unittest
+from pathlib import (
+    Path,
+)
+
+import h5py
+import numpy as np
+
+from deepmd.utils.path import (
+    DPPath,
+)
+
+
+class PathTest:
+    path: DPPath
+
+    def test_numpy(self):
+        numpy_path = self.path / "testcase"
+        arr1 = np.ones(3)
+        self.assertFalse(numpy_path.is_file())
+        numpy_path.save_numpy(arr1)
+        self.assertTrue(numpy_path.is_file())
+        arr2 = numpy_path.load_numpy()
+        np.testing.assert_array_equal(arr1, arr2)
+
+    def test_dir(self):
+        dir_path = self.path / "testcase"
+        self.assertFalse(dir_path.is_dir())
+        dir_path.mkdir()
+        self.assertTrue(dir_path.is_dir())
+
+
+class TestOSPath(PathTest, unittest.TestCase):
+    def setUp(self):
+        self.tempdir = tempfile.TemporaryDirectory()
+        self.path = DPPath(self.tempdir.name, "a")
+
+    def tearDown(self):
+        self.tempdir.cleanup()
+
+
+class TestH5Path(PathTest, unittest.TestCase):
+    def setUp(self):
+        self.tempdir = tempfile.TemporaryDirectory()
+        h5file = str((Path(self.tempdir.name) / "testcase.h5").resolve())
+        with h5py.File(h5file, "w") as f:
+            pass
+        self.path = DPPath(h5file, "a")
+
+    def tearDown(self):
+        self.tempdir.cleanup()