Merge branch 'dev' into add/read_nwb_func

.readthedocs.yaml

@@ -6,9 +6,9 @@
 version: 2
 
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
-    python: '3.9'
+    python: '3.12'
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

CHANGELOG.md

@@ -1,5 +1,10 @@
 # HDMF-ZARR Changelog
 
+## 1.0.0 (Upcoming)
+### Enhancements
+* Added support for Pathlib paths. @mavaylon1 [#212](https://github.com/hdmf-dev/hdmf-zarr/pull/212)
+* Updated packages used for testing and readthedocs configuration. @mavaylon1, @rly [#214](https://github.com/hdmf-dev/hdmf-zarr/pull/214)
+
 ## 0.9.0 (September 16, 2024)
 ### Enhancements
 * Added support for appending a dataset of references. @mavaylon1 [#203](https://github.com/hdmf-dev/hdmf-zarr/pull/203)

requirements-dev.txt

@@ -12,4 +12,4 @@ pytest==7.4.3
 pytest-cov==4.1.0
 python-dateutil==2.8.2
 ruff==0.1.3
-tox==4.11.3
+tox==4.11.3

requirements-opt.txt

@@ -1,3 +1,3 @@
-tqdm==4.66.4
-fsspec==2024.6.0
-s3fs==2024.6.0
+tqdm==4.67.0
+fsspec==2024.10.0
+s3fs==2024.10.0

requirements.txt

@@ -1,7 +1,7 @@
 # pinned dependencies to reproduce an entire development environment to use HDMF-ZARR
-hdmf==3.14.2
-zarr==2.16.1
-pynwb==2.5.0
-numpy==2.0.0
-numcodecs==0.12.1
-threadpoolctl==3.2.0
+hdmf==3.14.5
+zarr==2.18.3
+pynwb==2.8.2
+numpy==2.1.3
+numcodecs==0.13.1
+threadpoolctl==3.5.0

src/hdmf_zarr/backend.py

@@ -48,6 +48,9 @@
 from hdmf.query import HDMFDataset
 from hdmf.container import Container
 
+from pathlib import Path
+
+
 # Module variables
 ROOT_NAME = 'root'
 """
@@ -84,7 +87,7 @@ def can_read(path):
             return False
 
     @docval({'name': 'path',
-             'type': (str, *SUPPORTED_ZARR_STORES),
+             'type': (str, Path, *SUPPORTED_ZARR_STORES),
              'doc': 'the path to the Zarr file or a supported Zarr store'},
             {'name': 'manager', 'type': BuildManager, 'doc': 'the BuildManager to use for I/O', 'default': None},
             {'name': 'mode', 'type': str,
@@ -115,6 +118,8 @@ def __init__(self, **kwargs):
         else:
             self.__synchronizer = synchronizer
         self.__mode = mode
+        if isinstance(path, Path):
+            path = str(path)
         self.__path = path
         self.__file = None
         self.__storage_options = storage_options
@@ -195,7 +200,7 @@ def is_remote(self):
              'type': (NamespaceCatalog, TypeMap),
              'doc': 'the NamespaceCatalog or TypeMap to load namespaces into'},
             {'name': 'path',
-             'type': (str, *SUPPORTED_ZARR_STORES),
+             'type': (str, Path, *SUPPORTED_ZARR_STORES),
              'doc': 'the path to the Zarr file or a supported Zarr store'},
             {'name': 'storage_options', 'type': dict,
              'doc': 'Zarr storage options to read remote folders',

tests/unit/test_zarrio.py

@@ -24,6 +24,7 @@
 import os
 import shutil
 import warnings
+import pathlib
 
 
 CUR_DIR = os.path.dirname(os.path.realpath(__file__))
@@ -136,6 +137,16 @@ def setUp(self):
         self.store = [NestedDirectoryStore(p) for p in self.store_path]
 
 
+#########################################
+#  Pathlib Tests
+#########################################
+class TestPathlib(BaseTestZarrWriter):
+    """Test writing of builder with Zarr using a custom DirectoryStore"""
+    def setUp(self):
+        super().setUp()
+        self.store = pathlib.Path(self.store_path)
+
+
 #########################################
 #  Consolidate Metadata tests
 #########################################
@@ -195,7 +206,7 @@ class TestDimensionLabels(BuildDatasetShapeMixin):
     Workflow:
     i) We need to define a `get_dataset_inc_spec` to set the dim in the spec (via BuildDatasetShapeMixin)
     ii) Create and write a BarDataHolder with a BarData.
-    iii) Read and check that the _ARRAY_DIMENSIONS attribute is set. 
+    iii) Read and check that the _ARRAY_DIMENSIONS attribute is set.
     """
     def tearDown(self):
         shutil.rmtree(self.store)