Remove zarr.Array monkey-patches, use ndim-based detection

.github/workflows/HDMF_dev.yaml

@@ -21,7 +21,7 @@ jobs:
 
       - name: Install HDMF_Zarr Requirements
         run: |
-          python -m pip install ".[test]"
+          python -m pip install --group test "."
 
       - name: Clone and Install HDMF Dev Branch
         run: |

.github/workflows/check_external_links.yml

@@ -23,7 +23,7 @@ jobs:
       - name: Install Sphinx dependencies and package
         run: |
           python -m pip install --upgrade pip
-          python -m pip install ".[test,docs,full]"
+          python -m pip install --group docs ".[full]"
 
       - name: Check Sphinx external links
         run: sphinx-build -W -b linkcheck ./docs/source ./test_build

.github/workflows/run_coverage.yml

@@ -44,15 +44,16 @@ jobs:
       - name: Upgrade pip
         run: |
           python -m pip install --upgrade pip
+          python -m pip --version
 
       - name: Install package
         if: ${{ ! matrix.opt_req }}
         run: |
-          python -m pip install ".[test]"
+          python -m pip install --group test "."
 
       - name: Install package with optional dependencies
         if: ${{ matrix.opt_req }}
-        run: python -m pip install ".[test,full]"
+        run: python -m pip install --group test ".[full]"
 
       - name: Run tests and generate coverage report
         run: |

.readthedocs.yaml

@@ -9,15 +9,14 @@ build:
   os: ubuntu-24.04
   tools:
     python: '3.14'
+  jobs:
+    install:
+      - pip install -U pip
+      - pip install --group docs ".[full]"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/source/conf.py
 
 # Optionally build your docs in additional formats such as PDF and ePub
 formats: all
-
-# Optionally set the version of Python and requirements required to build your docs
-python:
-  install:
-    - path: .[docs,full] # path to the package relative to the root

CHANGELOG.md

@@ -11,8 +11,11 @@
 - Fixed bug where the cached spec was not included in consolidated metadata when exporting using `ZarrIO`. @rly [#315](https://github.com/hdmf-dev/hdmf-zarr/pull/315)
 - Fixed bug where consolidated metadata was always written by `ZarrIO`. @rly [#315](https://github.com/hdmf-dev/hdmf-zarr/pull/315)
 - Fixed bug where the `specifications` group and its contents were read during `ZarrIO.read_builder`. @rly [#322](https://github.com/hdmf-dev/hdmf-zarr/pull/322)
+- Fixed issue with `tox.ini` configuration. @rly [#326](https://github.com/hdmf-dev/hdmf-zarr/pull/326)
+- Fixed `ZarrIO.is_remote()` returning `False` for remote stores using consolidated metadata, which caused `resolve_ref` to mangle HTTPS URLs and fail with `PathNotFoundError` when reading links. @rly [#328](https://github.com/hdmf-dev/hdmf-zarr/pull/328)
 
 ### Changed
+- Replaced `requirements-min.txt` with `uv pip install --resolution lowest-direct` in tox and converted `test` and `docs` from optional dependencies to dependency groups (PEP 735), making the project compatible with uv. @h-mayorquin [#327](https://github.com/hdmf-dev/hdmf-zarr/pull/327)
 - Updated documentation about how the `zarr_dtype` attribute is used to specify a compound dtype (structured array) for a dataset. @rly [#313](https://github.com/hdmf-dev/hdmf-zarr/pull/313)
 - Dropped testing for Python 3.9. @rly [#298](https://github.com/hdmf-dev/hdmf-zarr/pull/298)
 - Added support for Python 3.14. @rly [#298](https://github.com/hdmf-dev/hdmf-zarr/pull/298)

pyproject.toml

@@ -30,7 +30,7 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Medical Science Apps."
 ]
 dependencies = [
-    "hdmf>=4.2.0",
+    "hdmf @ git+https://github.com/hdmf-dev/hdmf.git@remove_duck_typing_for_type",
     "zarr>=3.1.3",
     "numpy>=1.26.0",
     "numcodecs>=0.14.0",
@@ -47,6 +47,10 @@ full = [
     "s3fs",
 ]
 
+# all runtime optional dependencies
+all = ["hdmf-zarr[full]"]
+
+[dependency-groups]
 # development dependencies
 test = [
     "black",
@@ -57,28 +61,31 @@ test = [
     "pytest-cov",
     "python-dateutil",  # used in some tests
     "ruff",
-    "scipy",  # used in some tests
+    "scipy>=1.7",  # used in some tests
     "tox",
 ]
 
 # documentation dependencies
 docs = [
-    "matplotlib",
-    "scipy",  # used in some docs
+    "matplotlib>=3.6",
+    "scipy>=1.7",  # used in some docs
     "sphinx>=4",  # improved support for docutils>=0.17
     "sphinx_rtd_theme>=1",  # <1 does not work with docutils>=0.17
-    "sphinx-gallery",
-    "sphinx-copybutton",
+    "sphinx-gallery>=0.16",
+    "sphinx-copybutton>=0.5",
 ]
 
-# all possible dependencies
-all = ["hdmf-zarr[full,test,docs]"]
-
 
 [project.urls]
 "Homepage" = "https://github.com/hdmf-dev/hdmf-zarr"
 "Bug Tracker" = "https://github.com/hdmf-dev/hdmf-zarr/issues"
 
+[tool.uv.sources]
+hdmf = { git = "https://github.com/hdmf-dev/hdmf.git", branch = "remove_duck_typing_for_type" }
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
 [tool.hatch.version]
 source = "vcs"
 

src/hdmf_zarr/backend.py

@@ -36,24 +36,6 @@
 
 from pathlib import Path
 
-# zarr v3 Array does not implement __len__; add it for compatibility with array-like interfaces
-if not hasattr(Array, "__len__"):
-    Array.__len__ = lambda self: self.shape[0]
-
-# zarr v3 Array scalar indexing returns 0-d ndarrays instead of numpy scalars;
-# patch to match zarr v2 / numpy behavior expected by hdmf type checks
-_zarr_array_original_getitem = Array.__getitem__
-
-
-def _zarr_array_getitem_scalar_fix(self, key):
-    result = _zarr_array_original_getitem(self, key)
-    if isinstance(result, np.ndarray) and result.ndim == 0:
-        return result[()]
-    return result
-
-
-Array.__getitem__ = _zarr_array_getitem_scalar_fix
-
 
 # Module variables
 ROOT_NAME = "root"
@@ -1400,7 +1382,7 @@ def write_dataset(self, **kwargs):  # noqa: C901
             )
             self._written_builders.set_written(builder)  # record that the builder has been written
             dset.attrs["zarr_dtype"] = type_str
-            if hasattr(refs, "__len__") and not isinstance(refs, dict):
+            if self._is_collection(refs) and not isinstance(refs, dict):
                 json_refs = [json.dumps(dict(r)) for r in refs]
                 for i, jr in enumerate(json_refs):
                     dset[i] = jr
@@ -1414,7 +1396,7 @@ def write_dataset(self, **kwargs):  # noqa: C901
             elif isinstance(data, AbstractDataChunkIterator):
                 dset = self.__setup_chunked_dataset__(parent, name, data, options)
                 self.__dci_queue.append(dataset=dset, data=data)
-            elif hasattr(data, "__len__"):
+            elif self._is_collection(data):
                 dset = self.__list_fill__(parent, name, data, options)
             else:
                 dset = self.__scalar_fill__(parent, name, data, options)
@@ -1506,13 +1488,39 @@ def get_type(cls, data):
             return cls.__dtypes.get("str")
         elif isinstance(data, bytes):
             return cls.__dtypes.get("bytes")
-        elif not hasattr(data, "__len__"):
+        elif isinstance(data, np.ndarray) and data.ndim == 0:
+            return type(data.item())
+        elif not cls._is_collection(data):
             return type(data)
         else:
-            if len(data) == 0:
+            if cls._get_length(data) == 0:
                 raise ValueError("cannot determine type for empty data")
             return cls.get_type(data[0])
 
+    @staticmethod
+    def _is_collection(data):
+        """Check if data is a collection (array-like with elements) vs a scalar.
+
+        Uses ndim for array-like objects (numpy, zarr, h5py, dask) and falls back
+        to __len__ for plain Python containers (list, tuple). Strings and bytes
+        are treated as scalars.
+        """
+        if isinstance(data, (str, bytes)):
+            return False
+        if hasattr(data, "ndim"):
+            return data.ndim > 0
+        return hasattr(data, "__len__")
+
+    @staticmethod
+    def _get_length(data):
+        """Get the length of the first dimension of a collection.
+
+        Uses shape[0] for array-like objects and len() for plain containers.
+        """
+        if hasattr(data, "shape") and data.shape is not None:
+            return data.shape[0]
+        return len(data)
+
     __reserve_attribute = ("zarr_dtype", "zarr_link", SPEC_LOC_ATTR)
 
     def __list_fill__(self, parent, name, data, options=None):  # noqa: C901

tests/unit/test_fsspec_streaming.py

@@ -40,6 +40,20 @@ def test_s3_open_with_consolidated_(self):
             read_io.open()
             self.assertIsNotNone(read_io._file)
 
+    @unittest.skipIf(not HAVE_FSSPEC, "fsspec not installed")
+    def test_is_remote_with_consolidated(self):
+        """Test that is_remote() returns True for remote HTTPS stores with consolidated metadata."""
+        with NWBZarrIO(self.https_s3_path, mode="r") as read_io:
+            read_io.open()
+            self.assertTrue(read_io.is_remote())
+
+    @unittest.skipIf(not HAVE_FSSPEC, "fsspec not installed")
+    def test_is_remote_without_consolidated(self):
+        """Test that is_remote() returns True for remote HTTPS stores without consolidated metadata."""
+        with NWBZarrIO(self.https_s3_path, mode="-r") as read_io:
+            read_io.open()
+            self.assertTrue(read_io.is_remote())
+
     @unittest.skipIf(not HAVE_FSSPEC, "fsspec not installed")
     def test_fsspec_streaming_via_read_nwb(self):
         """

tests/unit/test_zarrio.py

@@ -198,6 +198,20 @@ def test_force_open_without_consolidated_fails(self):
             except ValueError as e:
                 self.fail("ZarrIO.__open_file_consolidated raised an unexpected ValueError: {}".format(e))
 
+    def test_is_remote_local_with_consolidated(self):
+        """Test that is_remote() returns False for local stores with consolidated metadata."""
+        self.create_zarr(consolidate_metadata=True)
+        with ZarrIO(self.store_path, mode="r") as read_io:
+            read_io.open()
+            self.assertFalse(read_io.is_remote())
+
+    def test_is_remote_local_without_consolidated(self):
+        """Test that is_remote() returns False for local stores without consolidated metadata."""
+        self.create_zarr()
+        with ZarrIO(self.store_path, mode="r-") as read_io:
+            read_io.open()
+            self.assertFalse(read_io.is_remote())
+
 
 class TestOverwriteExistingFile(ZarrStoreTestCase):
     def test_force_overwrite_when_file_exists(self):

tox.ini

@@ -16,7 +16,7 @@ setenv =
   PYTHONDONTWRITEBYTECODE = 1
 install_command =
     python -m pip install -U {opts} {packages}
-extras = test
+dependency_groups = test
 commands =
     python -m pip list
     python -m pip check
@@ -37,34 +37,41 @@ commands = {[testenv]commands}
 
 # Test with python 3.13 and all optional dependencies
 [testenv:py313-optional]
-extras = {[testenv]extras}, full
+extras = full
+dependency_groups = {[testenv]dependency_groups}
 commands = {[testenv]commands}
 
 # Test with python 3.13 and all optional dependencies, using pre-release versions
 [testenv:py313-prerelease]
 install_command =
     python -m pip install -U --pre {opts} {packages}
-extras = {[testenv]extras}, full
+extras = full
+dependency_groups = {[testenv]dependency_groups}
 commands = {[testenv]commands}
 
 # Test with python 3.14 and all optional dependencies
 [testenv:py314-optional]
-extras = {[testenv]extras}, full
+extras = full
+dependency_groups = {[testenv]dependency_groups}
 commands = {[testenv]commands}
 
 # Test with python 3.14 and all optional dependencies, using pre-release versions
 [testenv:py314-prerelease]
 install_command =
     python -m pip install -U --pre {opts} {packages}
-extras = {[testenv]extras}, full
+extras = full
+dependency_groups = {[testenv]dependency_groups}
 commands = {[testenv]commands}
 
-# Test with python 3.10 and minimum dependencies
+# Test with python 3.11 and minimum dependencies
+# Uses uv with --resolution lowest-direct to install the lowest compatible
+# versions of direct dependencies, replacing the old requirements-min.txt approach.
 [testenv:py311-minimum]
-install_command =
-    python -m pip install {opts} {packages}
-deps =
-    -r requirements-min.txt
+skip_install = True
+dependency_groups = test
+commands_pre =
+    python -m pip install uv
+    python -m uv pip install --resolution lowest-direct -e .
 commands = {[testenv]commands}
 
 
@@ -99,32 +106,37 @@ commands = {[testenv:gallery]commands}
 
 # Test with python 3.13 and all optional dependencies
 [testenv:gallery-py313-optional]
-extras = {[testenv:gallery]extras}, full
+extras = full
+dependency_groups = docs
 commands = {[testenv:gallery]commands}
 
 # Test with python 3.13 and all optional dependencies, using pre-release versions
 [testenv:gallery-py313-prerelease]
 install_command =
     python -m pip install -U --pre {opts} {packages}
-extras = {[testenv:gallery]extras}, full
+extras = full
+dependency_groups = docs
 commands = {[testenv:gallery]commands}
 
 # Test with python 3.14 and all optional dependencies
 [testenv:gallery-py314-optional]
-extras = {[testenv:gallery]extras}, full
+extras = full
+dependency_groups = docs
 commands = {[testenv:gallery]commands}
 
 # Test with python 3.14 and all optional dependencies, using pre-release versions
 [testenv:gallery-py314-prerelease]
 install_command =
     python -m pip install -U --pre {opts} {packages}
-extras = {[testenv:gallery]extras}, full
+extras = full
+dependency_groups = docs
 commands = {[testenv:gallery]commands}
 
-# Test with python 3.10 and minimum dependencies
+# Test with python 3.11 and minimum dependencies
 [testenv:gallery-py311-minimum]
-install_command =
-    python -m pip install {opts} {packages}
-deps =
-    -r requirements-min.txt
+skip_install = True
+dependency_groups = test
+commands_pre =
+    python -m pip install uv
+    python -m uv pip install --resolution lowest-direct --group docs -e .
 commands = {[testenv:gallery]commands}