rename classes

README.md

@@ -47,7 +47,7 @@ with open("example.zarr.json", "w") as f:
     json.dump(rfs, f, indent=2)
 
 # Create the h5py-like client from the reference file system
-client = lindi.LindiH5pyFile.from_reference_file_system(rfs)
+client = lindi.LindiZarrWrapper.from_reference_file_system(rfs)
 
 # Try to read using pynwb
 # (This part does not work yet)

devel/old_tests/test_lindi_client.py

@@ -1,8 +1,8 @@
-from lindi import LindiH5pyFile, LindiGroup, LindiDataset
+from lindi import LindiZarrWrapper, LindiZarrWrapperGroup, LindiZarrWrapperDataset
 
 
 def test_lindi_client():
-    client = LindiH5pyFile.from_file("example_0.zarr.json")
+    client = LindiZarrWrapper.from_file("example_0.zarr.json")
 
     for k, v in client.attrs.items():
         print(f"{k}: {v}")
@@ -11,23 +11,23 @@ def test_lindi_client():
         print(k)
 
     acquisition = client["acquisition"]
-    assert isinstance(acquisition, LindiGroup)
+    assert isinstance(acquisition, LindiZarrWrapperGroup)
     for k in acquisition.keys():
         print(k)
 
     aa = client["acquisition/ElectricalSeriesAp"]
-    assert isinstance(aa, LindiGroup)
+    assert isinstance(aa, LindiZarrWrapperGroup)
     x = aa["data"]
-    assert isinstance(x, LindiDataset)
+    assert isinstance(x, LindiZarrWrapperDataset)
 
     print(x.shape)
     print(x[:5])
 
     general = client["general"]
-    assert isinstance(general, LindiGroup)
+    assert isinstance(general, LindiZarrWrapperGroup)
     for k in general.keys():
         a = general[k]
-        if isinstance(a, LindiDataset):
+        if isinstance(a, LindiZarrWrapperDataset):
             print(f"{k}: {a.shape}")
             print(a[()])
 

devel/old_tests/tests.py

@@ -1,7 +1,7 @@
 import tempfile
 import numpy as np
 import h5py
-from lindi import LindiH5ZarrStore, LindiH5pyFile, LindiGroup, LindiDataset
+from lindi import LindiH5ZarrStore, LindiZarrWrapper, LindiZarrWrapperGroup, LindiZarrWrapperDataset
 
 
 def test_scalar_dataset():
@@ -15,12 +15,12 @@ def test_scalar_dataset():
                 filename, url=filename
             ) as store:  # set url so that a reference file system can be created
                 rfs = store.to_reference_file_system()
-                client = LindiH5pyFile.from_reference_file_system(rfs)
+                client = LindiZarrWrapper.from_reference_file_system(rfs)
                 h5f = h5py.File(filename, "r")
                 X1 = h5f["X"]
                 assert isinstance(X1, h5py.Dataset)
                 X2 = client["X"]
-                assert isinstance(X2, LindiDataset)
+                assert isinstance(X2, LindiZarrWrapperDataset)
                 if not _check_equal(X1[()], X2[()]):
                     print(f"WARNING: {X1} ({type(X1)}) != {X2} ({type(X2)})")
 
@@ -73,12 +73,12 @@ def test_numpy_array():
                 filename, url=filename
             ) as store:  # set url so that a reference file system can be created
                 rfs = store.to_reference_file_system()
-                client = LindiH5pyFile.from_reference_file_system(rfs)
+                client = LindiZarrWrapper.from_reference_file_system(rfs)
                 h5f = h5py.File(filename, "r")
                 X1 = h5f["X"]
                 assert isinstance(X1, h5py.Dataset)
                 X2 = client["X"]
-                assert isinstance(X2, LindiDataset)
+                assert isinstance(X2, LindiZarrWrapperDataset)
                 if not _check_equal(X1[:], X2[:]):
                     print("WARNING. Arrays are not equal")
                     print(X1[:])
@@ -94,11 +94,11 @@ def test_numpy_array_of_strings():
         h5f = h5py.File(filename, "r")
         with LindiH5ZarrStore.from_file(filename, url=filename) as store:
             rfs = store.to_reference_file_system()
-            client = LindiH5pyFile.from_reference_file_system(rfs)
+            client = LindiZarrWrapper.from_reference_file_system(rfs)
             X1 = h5f["X"]
             assert isinstance(X1, h5py.Dataset)
             X2 = client["X"]
-            assert isinstance(X2, LindiDataset)
+            assert isinstance(X2, LindiZarrWrapperDataset)
             if not _check_equal(X1[:], X2[:]):
                 print("WARNING. Arrays are not equal")
                 print(X1[:])
@@ -122,11 +122,11 @@ def test_attributes():
         h5f = h5py.File(filename, "r")
         with LindiH5ZarrStore.from_file(filename, url=filename) as store:
             rfs = store.to_reference_file_system()
-            client = LindiH5pyFile.from_reference_file_system(rfs)
+            client = LindiZarrWrapper.from_reference_file_system(rfs)
             X1 = h5f["X"]
             assert isinstance(X1, h5py.Dataset)
             X2 = client["X"]
-            assert isinstance(X2, LindiDataset)
+            assert isinstance(X2, LindiZarrWrapperDataset)
             if X1.attrs["foo"] != X2.attrs["foo"]:
                 print("WARNING. Attributes are not equal")
                 print(X1.attrs["foo"])
@@ -138,7 +138,7 @@ def test_attributes():
             group1 = h5f["group"]
             assert isinstance(group1, h5py.Group)
             group2 = client["group"]
-            assert isinstance(group2, LindiGroup)
+            assert isinstance(group2, LindiZarrWrapperGroup)
             if group1.attrs["foo"] != group2.attrs["foo"]:
                 print("WARNING. Attributes are not equal")
                 print(group1.attrs["foo"])

examples/example1.py

@@ -2,7 +2,7 @@
 import h5py
 import tempfile
 import lindi
-from lindi import LindiH5ZarrStore, LindiH5pyFile, LindiDataset
+from lindi import LindiH5ZarrStore, LindiZarrWrapper, LindiZarrWrapperDataset
 from _check_equal import _check_equal
 
 
@@ -11,9 +11,9 @@ def example1():
     # datasets, groups, and attributes. We then load that file using
     # LindiH5ZarrStore which is a zarr storage backend providing read-only view of
     # that hdf5 file. We then create a reference file system and use that to
-    # create a LindiH5pyFile, which mimics the h5py API. We then compare the
+    # create a LindiZarrWrapper, which mimics the h5py API. We then compare the
     # datasets, groups, and attributes of the original hdf5 file with those of
-    # the LindiH5pyFile.
+    # the LindiZarrWrapper.
 
     with tempfile.TemporaryDirectory() as tmpdir:
         print("Creating an example hdf5 file")
@@ -39,14 +39,14 @@ def example1():
             rfs_fname = f"{tmpdir}/example.zarr.json"
             store.to_file(rfs_fname)
 
-            print("Creating a LindiH5pyFile from the reference file system")
-            client = LindiH5pyFile.from_file(rfs_fname)
+            print("Creating a LindiZarrWrapper from the reference file system")
+            client = LindiZarrWrapper.from_file(rfs_fname)
 
             print("Comparing dataset: X")
             X1 = h5f["X"]
             assert isinstance(X1, h5py.Dataset)
             X2 = client["X"]
-            assert isinstance(X2, LindiDataset)
+            assert isinstance(X2, LindiZarrWrapperDataset)
             assert len(X1) == len(X2)
             assert X1.shape == X2.shape
             assert X1.dtype == X2.dtype
@@ -70,14 +70,14 @@ def example1():
             scalar_dataset1 = h5f["scalar_dataset"]
             assert isinstance(scalar_dataset1, h5py.Dataset)
             scalar_dataset2 = client["scalar_dataset"]
-            assert isinstance(scalar_dataset2, LindiDataset)
+            assert isinstance(scalar_dataset2, LindiZarrWrapperDataset)
             assert scalar_dataset1[()] == scalar_dataset2[()]
 
             print("Comparing group: group")
             G1 = h5f["group"]
             G2 = client["group"]
             for k, v in G1.attrs.items():
-                if not isinstance(G2, lindi.LindiReference):
+                if not isinstance(G2, lindi.LindiZarrWrapperReference):
                     assert k in G2.attrs
                     assert _check_equal(v, G2.attrs[k])
 

examples/try_pynwb.py

@@ -19,7 +19,7 @@ def try_pynwb():
         json.dump(rfs, f, indent=2)
 
     # Create the client from the reference file system
-    client = lindi.LindiH5pyFile.from_reference_file_system(rfs)
+    client = lindi.LindiZarrWrapper.from_reference_file_system(rfs)
 
     # Try to read using pynwb
     with pynwb.NWBHDF5IO(file=client, mode="r") as io:

lindi/LindiH5ZarrStore/LindiH5ZarrStore.py

@@ -397,7 +397,7 @@ def listdir(self, path: str = "") -> List[str]:
     def to_file(self, file_name: str, *, file_type: Literal["zarr.json"] = "zarr.json"):
         """Write a reference file system cooresponding to this store to a file.
 
-        This can then be loaded using LindiH5pyFile.from_file(fname)
+        This can then be loaded using LindiZarrWrapper.from_file(fname)
         """
         if file_type != "zarr.json":
             raise Exception(f"Unsupported file type: {file_type}")
@@ -410,7 +410,7 @@ def to_reference_file_system(self) -> dict:
         """Create a reference file system cooresponding to this store.
 
         This can then be loaded using
-        LindiH5pyFile.from_reference_file_system(obj)
+        LindiZarrWrapper.from_reference_file_system(obj)
         """
         if self._h5f is None:
             raise Exception("Store is closed")

lindi/LindiH5pyFile/LindiH5pyFile.py → lindi/LindiZarrWrapper/LindiZarrWrapper.py

@@ -7,11 +7,11 @@
 import urllib.request
 from fsspec.implementations.reference import ReferenceFileSystem
 from zarr.storage import Store
-from .LindiGroup import LindiGroup
-from .LindiReference import LindiReference
+from .LindiZarrWrapperGroup import LindiZarrWrapperGroup
+from .LindiZarrWrapperReference import LindiZarrWrapperReference
 
 
-class LindiH5pyFile(LindiGroup):
+class LindiZarrWrapper(LindiZarrWrapperGroup):
     def __init__(
         self,
         *,
@@ -25,38 +25,38 @@ def filename(self):
         return ''
 
     @staticmethod
-    def from_zarr_store(zarr_store: Union[Store, FSMap]) -> "LindiH5pyFile":
+    def from_zarr_store(zarr_store: Union[Store, FSMap]) -> "LindiZarrWrapper":
         zarr_group = zarr.open(store=zarr_store, mode="r")
         assert isinstance(zarr_group, zarr.Group)
-        return LindiH5pyFile.from_zarr_group(zarr_group)
+        return LindiZarrWrapper.from_zarr_group(zarr_group)
 
     @staticmethod
     def from_file(
         json_file: str, file_type: Literal["zarr.json"] = "zarr.json"
-    ) -> "LindiH5pyFile":
+    ) -> "LindiZarrWrapper":
         if file_type == "zarr.json":
             if json_file.startswith("http") or json_file.startswith("https"):
                 with tempfile.TemporaryDirectory() as tmpdir:
                     filename = f"{tmpdir}/temp.zarr.json"
                     _download_file(json_file, filename)
                     with open(filename, "r") as f:
                         data = json.load(f)
-                    return LindiH5pyFile.from_reference_file_system(data)
+                    return LindiZarrWrapper.from_reference_file_system(data)
             else:
                 with open(json_file, "r") as f:
                     data = json.load(f)
-                return LindiH5pyFile.from_reference_file_system(data)
+                return LindiZarrWrapper.from_reference_file_system(data)
         else:
             raise ValueError(f"Unknown file_type: {file_type}")
 
     @staticmethod
-    def from_zarr_group(zarr_group: zarr.Group) -> "LindiH5pyFile":
-        return LindiH5pyFile(_zarr_group=zarr_group)
+    def from_zarr_group(zarr_group: zarr.Group) -> "LindiZarrWrapper":
+        return LindiZarrWrapper(_zarr_group=zarr_group)
 
     @staticmethod
-    def from_reference_file_system(data: dict) -> "LindiH5pyFile":
+    def from_reference_file_system(data: dict) -> "LindiZarrWrapper":
         fs = ReferenceFileSystem(data).get_mapper(root="")
-        return LindiH5pyFile.from_zarr_store(fs)
+        return LindiZarrWrapper.from_zarr_store(fs)
 
     def get(self, key, default=None, getlink: bool = False):
         try:
@@ -66,7 +66,7 @@ def get(self, key, default=None, getlink: bool = False):
         if getlink:
             return ret
         else:
-            if isinstance(ret, LindiReference):
+            if isinstance(ret, LindiZarrWrapperReference):
                 return self[ret]
             else:
                 return ret
@@ -83,7 +83,7 @@ def __getitem__(self, key):  # type: ignore
                 for part in parts:
                     g = g[part]
                 return g
-        elif isinstance(key, LindiReference):
+        elif isinstance(key, LindiZarrWrapperReference):
             if key._source != '.':
                 raise Exception(f'For now, source of reference must be ".", got "{key._source}"')
             if key._source_object_id is not None:
@@ -95,7 +95,7 @@ def __getitem__(self, key):  # type: ignore
                     raise Exception(f'Mismatch in object_id: "{key._object_id}" and "{target.attrs.get("object_id")}"')
             return target
         else:
-            raise Exception(f'Cannot use key "{key}" of type "{type(key)}" to index into a LindiH5pyFile')
+            raise Exception(f'Cannot use key "{key}" of type "{type(key)}" to index into a LindiZarrWrapper')
 
 
 def _download_file(url: str, filename: str) -> None:

lindi/LindiH5pyFile/LindiAttributes.py → lindi/LindiZarrWrapper/LindiZarrWrapperAttributes.py

@@ -1,9 +1,9 @@
 from typing import Union
 import zarr
-from .LindiReference import LindiReference
+from .LindiZarrWrapperReference import LindiZarrWrapperReference
 
 
-class LindiAttributes:
+class LindiZarrWrapperAttributes:
     def __init__(self, *, _object: Union[zarr.Group, zarr.Array]):
         self._object = _object
 
@@ -16,7 +16,7 @@ def get(self, key, default=None):
     def __getitem__(self, key):
         val = self._object.attrs[key]
         if isinstance(val, dict) and "_REFERENCE" in val:
-            return LindiReference(val["_REFERENCE"])
+            return LindiZarrWrapperReference(val["_REFERENCE"])
         return self._object.attrs[key]
 
     def __setitem__(self, key, value):

lindi/LindiH5pyFile/LindiDataset.py → lindi/LindiZarrWrapper/LindiZarrWrapperDataset.py

@@ -3,11 +3,11 @@
 import zarr
 import h5py
 import remfile
-from .LindiAttributes import LindiAttributes
-from .LindiReference import LindiReference
+from .LindiZarrWrapperAttributes import LindiZarrWrapperAttributes
+from .LindiZarrWrapperReference import LindiZarrWrapperReference
 
 
-class LindiDataset:
+class LindiZarrWrapperDataset:
     def __init__(self, *, _zarr_array: zarr.Array, _client):
         self._zarr_array = _zarr_array
         self._is_scalar = self._zarr_array.attrs.get("_SCALAR", False)
@@ -41,7 +41,7 @@ def name(self):
     @property
     def attrs(self):
         """Attributes attached to this object"""
-        return LindiAttributes(_object=self._zarr_array)
+        return LindiZarrWrapperAttributes(_object=self._zarr_array)
 
     @property
     def ndim(self):
@@ -115,7 +115,7 @@ def __getitem__(self, selection):
                     dtype = np.dtype(dt)
                 # Return a new object that can be sliced further
                 # It's important that the return type is Any here, because otherwise we get linter problems
-                ret: Any = LindiDatasetCompoundFieldSelection(
+                ret: Any = LindiZarrWrapperDatasetCompoundFieldSelection(
                     dataset=self, ind=ind, dtype=dtype
                 )
                 return ret
@@ -139,14 +139,14 @@ def _get_external_hdf5_client(self, url: str) -> h5py.File:
         return self._external_hdf5_clients[url]
 
 
-class LindiDatasetCompoundFieldSelection:
+class LindiZarrWrapperDatasetCompoundFieldSelection:
     """
     This class is returned when a compound dataset is indexed with a field name.
     For example, if the dataset has dtype [('x', 'f4'), ('y', 'f4')], then we
     can do dataset['x'][0] to get the first x value. The dataset['x'] returns an
     object of this class.
     """
-    def __init__(self, *, dataset: LindiDataset, ind: int, dtype: np.dtype):
+    def __init__(self, *, dataset: LindiZarrWrapperDataset, ind: int, dtype: np.dtype):
         self._dataset = dataset  # The parent dataset
         self._ind = ind  # The index of the field in the compound dtype
         self._dtype = dtype  # The dtype of the field
@@ -159,8 +159,8 @@ def __init__(self, *, dataset: LindiDataset, ind: int, dtype: np.dtype):
         za = self._dataset._zarr_array
         d = [za[i][self._ind] for i in range(len(za))]
         if self._dtype == h5py.Reference:
-            # Convert to LindiReference
-            d = [LindiReference(x['_REFERENCE']) for x in d]
+            # Convert to LindiZarrWrapperReference
+            d = [LindiZarrWrapperReference(x['_REFERENCE']) for x in d]
         self._data = np.array(d, dtype=self._dtype)
 
     def __len__(self):