Merge pull request #1606 from pyiron/dependabot/pip/h5io-browser-0.0.18

Bump h5io-browser from 0.0.17 to 0.0.18

.ci_support/environment-docs.yml

@@ -9,7 +9,7 @@ dependencies:
 - conda_subprocess =0.0.4
 - cloudpickle =3.0.0
 - gitpython =3.1.43
-- h5io_browser =0.0.17
+- h5io_browser =0.0.18
 - h5py =3.11.0
 - jinja2 =3.1.4
 - monty =2024.7.30

.ci_support/environment-mini.yml

@@ -2,7 +2,7 @@ channels:
 - conda-forge
 dependencies:
 - cloudpickle =3.0.0
-- h5io_browser =0.0.17
+- h5io_browser =0.0.18
 - h5py =3.11.0
 - monty =2024.7.30
 - numpy =2.0.1

.ci_support/environment.yml

@@ -7,7 +7,7 @@ dependencies:
 - conda_subprocess =0.0.4
 - cloudpickle =3.0.0
 - gitpython =3.1.43
-- h5io_browser =0.0.17
+- h5io_browser =0.0.18
 - h5py =3.11.0
 - jinja2 =3.1.4
 - monty =2024.7.30

binder/environment.yml

@@ -6,7 +6,7 @@ dependencies:
 - conda_subprocess =0.0.4
 - cloudpickle =3.0.0
 - gitpython =3.1.43
-- h5io_browser =0.0.17
+- h5io_browser =0.0.18
 - h5py =3.11.0
 - jinja2 =3.1.4
 - monty =2024.7.30

pyproject.toml

@@ -26,7 +26,7 @@ classifiers = [
 dependencies = [
     "cloudpickle==3.0.0",
     "executorlib==0.0.1",
-    "h5io_browser==0.0.17",
+    "h5io_browser==0.0.18",
     "h5py==3.11.0",
     "numpy==2.0.1",
     "monty==2024.7.30",

tests/unit/storage/test_helper_functions.py

@@ -1,5 +1,6 @@
 import os
 import posixpath
+import numpy as np
 import h5py
 from unittest import TestCase
 from pyiron_base.storage.hdfio import _list_groups_and_nodes
@@ -23,58 +24,65 @@ class TestWriteHdfIO(TestCase):
     def setUp(self):
         self.file_name = "test_write_hdf5.h5"
         self.h5_path = "data_hierarchical"
-        self.data_hierarchical = {"a": [1, 2], "b": 3, "c": {"d": 4, "e": {"f": 5}}}
-        _write_hdf(
-            hdf_filehandle=self.file_name,
-            data=self.data_hierarchical,
-            h5_path=self.h5_path,
+        self.data_hierarchical = {
+            "a": np.array([1, 2]),
+            "b": 3,
+            "c": {"d": np.array([4, 5]), "e": np.array([6, 7])},
+        }
+        write_dict_to_hdf(
+            file_name=self.file_name,
+            data_dict={
+                posixpath.join(self.h5_path, "a"): self.data_hierarchical["a"],
+                posixpath.join(self.h5_path, "b"): self.data_hierarchical["b"],
+                posixpath.join(self.h5_path, "c", "d"): self.data_hierarchical["c"][
+                    "d"
+                ],
+                posixpath.join(self.h5_path, "c", "e"): self.data_hierarchical["c"][
+                    "e"
+                ],
+            },
         )
 
     def tearDown(self):
         os.remove(self.file_name)
 
-    def test_read_hierarchical(self):
-        self.assertEqual(
-            self.data_hierarchical,
-            _read_hdf(hdf_filehandle=self.file_name, h5_path=self.h5_path),
-        )
-
     def test_read_dict_hierarchical(self):
-        self.assertEqual(
-            {"key_b": 3},
-            read_nested_dict_from_hdf(file_name=self.file_name, h5_path=self.h5_path),
+        output = read_nested_dict_from_hdf(
+            file_name=self.file_name, h5_path=self.h5_path
         )
-        self.assertEqual(
-            {"key_a": {"idx_0": 1, "idx_1": 2}, "key_b": 3, "key_c": {"key_d": 4}},
-            read_nested_dict_from_hdf(
-                file_name=self.file_name,
-                h5_path=self.h5_path,
-                group_paths=["key_a", "key_c"],
-            ),
+        self.assertTrue(
+            np.all(np.equal(output["a"], np.array([1, 2]))),
         )
-        self.assertEqual(
-            {
-                "key_a": {"idx_0": 1, "idx_1": 2},
-                "key_b": 3,
-                "key_c": {"key_d": 4, "key_e": {"key_f": 5}},
-            },
-            read_nested_dict_from_hdf(
-                file_name=self.file_name,
-                h5_path=self.h5_path,
-                group_paths=["key_a", "key_c", "key_c/key_e"],
-            ),
+        self.assertEqual(output["b"], 3)
+        output = read_nested_dict_from_hdf(
+            file_name=self.file_name,
+            h5_path=self.h5_path,
+            group_paths=["c"],
         )
-        self.assertEqual(
-            {
-                "key_a": {"idx_0": 1, "idx_1": 2},
-                "key_b": 3,
-                "key_c": {"key_d": 4, "key_e": {"key_f": 5}},
-            },
-            read_nested_dict_from_hdf(
-                file_name=self.file_name,
-                h5_path=self.h5_path,
-                recursive=True,
-            ),
+        self.assertTrue(
+            np.all(np.equal(output["a"], np.array([1, 2]))),
+        )
+        self.assertEqual(output["b"], 3)
+        self.assertTrue(
+            np.all(np.equal(output["c"]["d"], np.array([4, 5]))),
+        )
+        self.assertTrue(
+            np.all(np.equal(output["c"]["e"], np.array([6, 7]))),
+        )
+        output = read_nested_dict_from_hdf(
+            file_name=self.file_name,
+            h5_path=self.h5_path,
+            recursive=True,
+        )
+        self.assertTrue(
+            np.all(np.equal(output["a"], np.array([1, 2]))),
+        )
+        self.assertEqual(output["b"], 3)
+        self.assertTrue(
+            np.all(np.equal(output["c"]["d"], np.array([4, 5]))),
+        )
+        self.assertTrue(
+            np.all(np.equal(output["c"]["e"], np.array([6, 7]))),
         )
 
     def test_write_overwrite_error(self):
@@ -90,23 +98,20 @@ def test_hdf5_structure(self):
         self.assertEqual(
             get_hdf5_raw_content(file_name=self.file_name),
             [
-                {"data_hierarchical": {"TITLE": "dict"}},
-                {"data_hierarchical/key_a": {"TITLE": "list"}},
-                {"data_hierarchical/key_a/idx_0": {"TITLE": "int"}},
-                {"data_hierarchical/key_a/idx_1": {"TITLE": "int"}},
-                {"data_hierarchical/key_b": {"TITLE": "int"}},
-                {"data_hierarchical/key_c": {"TITLE": "dict"}},
-                {"data_hierarchical/key_c/key_d": {"TITLE": "int"}},
-                {"data_hierarchical/key_c/key_e": {"TITLE": "dict"}},
-                {"data_hierarchical/key_c/key_e/key_f": {"TITLE": "int"}},
+                {"data_hierarchical": {}},
+                {"data_hierarchical/a": {"TITLE": "ndarray"}},
+                {"data_hierarchical/b": {"TITLE": "int"}},
+                {"data_hierarchical/c": {}},
+                {"data_hierarchical/c/d": {"TITLE": "ndarray"}},
+                {"data_hierarchical/c/e": {"TITLE": "ndarray"}},
             ],
         )
 
     def test_list_groups(self):
         with h5py.File(self.file_name, "r") as f:
             groups, nodes = _list_groups_and_nodes(hdf=f, h5_path="data_hierarchical")
-        self.assertEqual(list(sorted(groups)), ["key_a", "key_c"])
-        self.assertEqual(nodes, ["key_b"])
+        self.assertEqual(list(sorted(groups)), ["c"])
+        self.assertEqual(list(sorted(nodes)), ["a", "b"])
 
 
 class TestWriteDictHdfIO(TestCase):