rename classes

.vscode/tasks/quick_test.sh

@@ -2,6 +2,10 @@
 set -ex
 
 # black --check .
+
+cd lindi
 flake8 .
 # pyright
+cd ..
+
 pytest --cov=lindi --cov-report=xml --cov-report=term -m "not slow" tests/

.vscode/tasks/test.sh

@@ -2,6 +2,10 @@
 set -ex
 
 # black --check .
+
+cd lindi
 flake8 .
 pyright
+cd ..
+
 pytest --cov=lindi --cov-report=xml --cov-report=term tests/

README.md

@@ -37,7 +37,7 @@ h5_url = "https://api.dandiarchive.org/api/assets/3d12a902-139a-4c1a-8fd0-0a7faf
 
 
 # Create the read-only Zarr store for the h5 file
-store = lindi.LindiH5Store.from_file(h5_url)
+store = lindi.LindiH5ZarrStore.from_file(h5_url)
 
 # Create the reference file system object
 rfs = store.to_reference_file_system()
@@ -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.LindiClient.from_reference_file_system(rfs)
+client = lindi.LindiH5pyFile.from_reference_file_system(rfs)
 
 # Try to read using pynwb
 # (This part does not work yet)

devel/old_tests/old_tests.py

@@ -4,7 +4,7 @@
 import h5py
 import zarr
 import kerchunk.hdf  # type: ignore
-from lindi import LindiH5Store
+from lindi import LindiH5ZarrStore
 from fsspec.implementations.reference import ReferenceFileSystem
 
 
@@ -88,7 +88,7 @@ def test_numpy_array_of_strings():
 
 
 def _get_lindi_zarr(filename):
-    store = LindiH5Store.from_file(filename, url='.')  # use url='.' so that a reference file system can be created
+    store = LindiH5ZarrStore.from_file(filename, url='.')  # use url='.' so that a reference file system can be created
     root = zarr.open(store)
     return root, store
 

devel/old_tests/test_lindi_client.py

@@ -1,8 +1,8 @@
-from lindi import LindiClient, LindiGroup, LindiDataset
+from lindi import LindiH5pyFile, LindiGroup, LindiDataset
 
 
 def test_lindi_client():
-    client = LindiClient.from_file("example_0.zarr.json")
+    client = LindiH5pyFile.from_file("example_0.zarr.json")
 
     for k, v in client.attrs.items():
         print(f"{k}: {v}")

devel/old_tests/test_with_real_data.py

@@ -3,7 +3,7 @@
 import zarr
 import h5py
 import remfile
-from lindi import LindiH5Store
+from lindi import LindiH5ZarrStore
 
 examples = []
 
@@ -40,7 +40,7 @@ def do_compare(example_num: int):
     h5_url = example["h5_url"]
     print(f"Running comparison for {h5_url}")
     h5f = h5py.File(remfile.File(h5_url), "r")
-    with LindiH5Store.from_file(h5_url) as store:
+    with LindiH5ZarrStore.from_file(h5_url) as store:
         root = zarr.open(store)
         assert isinstance(root, zarr.Group)
 

devel/old_tests/tests.py

@@ -1,7 +1,7 @@
 import tempfile
 import numpy as np
 import h5py
-from lindi import LindiH5Store, LindiClient, LindiGroup, LindiDataset
+from lindi import LindiH5ZarrStore, LindiH5pyFile, LindiGroup, LindiDataset
 
 
 def test_scalar_dataset():
@@ -11,11 +11,11 @@ def test_scalar_dataset():
             filename = f"{tmpdir}/test.h5"
             with h5py.File(filename, "w") as f:
                 f.create_dataset("X", data=val)
-            with LindiH5Store.from_file(
+            with LindiH5ZarrStore.from_file(
                 filename, url=filename
             ) as store:  # set url so that a reference file system can be created
                 rfs = store.to_reference_file_system()
-                client = LindiClient.from_reference_file_system(rfs)
+                client = LindiH5pyFile.from_reference_file_system(rfs)
                 h5f = h5py.File(filename, "r")
                 X1 = h5f["X"]
                 assert isinstance(X1, h5py.Dataset)
@@ -69,11 +69,11 @@ def test_numpy_array():
             filename = f"{tmpdir}/test.h5"
             with h5py.File(filename, "w") as f:
                 f.create_dataset("X", data=array, chunks=chunks)
-            with LindiH5Store.from_file(
+            with LindiH5ZarrStore.from_file(
                 filename, url=filename
             ) as store:  # set url so that a reference file system can be created
                 rfs = store.to_reference_file_system()
-                client = LindiClient.from_reference_file_system(rfs)
+                client = LindiH5pyFile.from_reference_file_system(rfs)
                 h5f = h5py.File(filename, "r")
                 X1 = h5f["X"]
                 assert isinstance(X1, h5py.Dataset)
@@ -92,9 +92,9 @@ def test_numpy_array_of_strings():
         with h5py.File(filename, "w") as f:
             f.create_dataset("X", data=["abc", "def", "ghi"])
         h5f = h5py.File(filename, "r")
-        with LindiH5Store.from_file(filename, url=filename) as store:
+        with LindiH5ZarrStore.from_file(filename, url=filename) as store:
             rfs = store.to_reference_file_system()
-            client = LindiClient.from_reference_file_system(rfs)
+            client = LindiH5pyFile.from_reference_file_system(rfs)
             X1 = h5f["X"]
             assert isinstance(X1, h5py.Dataset)
             X2 = client["X"]
@@ -120,9 +120,9 @@ def test_attributes():
             f["group"].attrs["foo"] = "bar2"
             f["group"].attrs["baz"] = 3.15
         h5f = h5py.File(filename, "r")
-        with LindiH5Store.from_file(filename, url=filename) as store:
+        with LindiH5ZarrStore.from_file(filename, url=filename) as store:
             rfs = store.to_reference_file_system()
-            client = LindiClient.from_reference_file_system(rfs)
+            client = LindiH5pyFile.from_reference_file_system(rfs)
             X1 = h5f["X"]
             assert isinstance(X1, h5py.Dataset)
             X2 = client["X"]

examples/example1.py

@@ -2,18 +2,18 @@
 import h5py
 import tempfile
 import lindi
-from lindi import LindiH5Store, LindiClient, LindiDataset
+from lindi import LindiH5ZarrStore, LindiH5pyFile, LindiDataset
 from _check_equal import _check_equal
 
 
 def example1():
     # In this example, we create a temporary hdf5 file, with some sample
     # datasets, groups, and attributes. We then load that file using
-    # LindiH5Store which is a zarr storage backend providing read-only view of
+    # 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 LindiClient, which mimics the h5py API. We then compare the
+    # create a LindiH5pyFile, which mimics the h5py API. We then compare the
     # datasets, groups, and attributes of the original hdf5 file with those of
-    # the LindiClient.
+    # the LindiH5pyFile.
 
     with tempfile.TemporaryDirectory() as tmpdir:
         print("Creating an example hdf5 file")
@@ -31,16 +31,16 @@ def example1():
             f["group"].attrs["baz"] = 3.15
         h5f = h5py.File(filename, "r")
 
-        print("Creating a LindiH5Store from the hdf5 file")
+        print("Creating a LindiH5ZarrStore from the hdf5 file")
         # We set url to filename so that the references can point to a local file
         # but normally, this would be a remote URL
-        with LindiH5Store.from_file(filename, url=filename) as store:
-            print("Creating a reference file system from the LindiH5Store")
+        with LindiH5ZarrStore.from_file(filename, url=filename) as store:
+            print("Creating a reference file system from the LindiH5ZarrStore")
             rfs_fname = f"{tmpdir}/example.zarr.json"
             store.to_file(rfs_fname)
 
-            print("Creating a LindiClient from the reference file system")
-            client = LindiClient.from_file(rfs_fname)
+            print("Creating a LindiH5pyFile from the reference file system")
+            client = LindiH5pyFile.from_file(rfs_fname)
 
             print("Comparing dataset: X")
             X1 = h5f["X"]

examples/try_pynwb.py

@@ -9,7 +9,7 @@
 
 def try_pynwb():
     # Create the read-only store for the h5 file
-    store = lindi.LindiH5Store.from_file(h5_url)
+    store = lindi.LindiH5ZarrStore.from_file(h5_url)
 
     # Create the reference file system object
     rfs = store.to_reference_file_system()
@@ -19,7 +19,7 @@ def try_pynwb():
         json.dump(rfs, f, indent=2)
 
     # Create the client from the reference file system
-    client = lindi.LindiClient.from_reference_file_system(rfs)
+    client = lindi.LindiH5pyFile.from_reference_file_system(rfs)
 
     # Try to read using pynwb
     with pynwb.NWBHDF5IO(file=client, mode="r") as io:

lindi/LindiH5Store/LindiH5Store.py → lindi/LindiH5ZarrStore/LindiH5ZarrStore.py

@@ -18,30 +18,30 @@
 
 
 @dataclass
-class LindiH5StoreOpts:
+class LindiH5ZarrStoreOpts:
     num_dataset_chunks_threshold: Union[int, None] = 1000
 
 
-class LindiH5Store(Store):
+class LindiH5ZarrStore(Store):
     """A zarr store that provides a read-only view of an HDF5 file.
 
     Do not call the constructor directly. Instead do one of the following:
 
-    store = LindiH5Store.from_file(hdf5_file_name)
+    store = LindiH5ZarrStore.from_file(hdf5_file_name)
     # do stuff with store
     store.close()
 
     or
 
-    with LindiH5Store.from_file(hdf5_file_name) as store:
+    with LindiH5ZarrStore.from_file(hdf5_file_name) as store:
         # do stuff with store
     """
 
     def __init__(
         self,
         *,
         _file: Union[IO, Any],
-        _opts: LindiH5StoreOpts,
+        _opts: LindiH5ZarrStoreOpts,
         _url: Union[str, None] = None,
     ):
         """
@@ -76,17 +76,17 @@ def close(self):
     def from_file(
         hdf5_file_name_or_url: str,
         *,
-        opts: LindiH5StoreOpts = LindiH5StoreOpts(),
+        opts: LindiH5ZarrStoreOpts = LindiH5ZarrStoreOpts(),
         url: Union[str, None] = None,
     ):
         """
-        Create a LindiH5Store from a file or url.
+        Create a LindiH5ZarrStore from a file or url.
 
         Parameters
         ----------
         hdf5_file_name_or_url : str
             The name of the HDF5 file or a URL to the HDF5 file.
-        opts : LindiH5StoreOpts
+        opts : LindiH5ZarrStoreOpts
             Options for the store.
         url : str or None
             If hdf5_file_name_or_url is a local file name, then this can
@@ -100,10 +100,10 @@ def from_file(
             "http://"
         ) or hdf5_file_name_or_url.startswith("https://"):
             remf = remfile.File(hdf5_file_name_or_url, verbose=False)
-            return LindiH5Store(_file=remf, _url=hdf5_file_name_or_url, _opts=opts)
+            return LindiH5ZarrStore(_file=remf, _url=hdf5_file_name_or_url, _opts=opts)
         else:
             f = open(hdf5_file_name_or_url, "rb")
-            return LindiH5Store(_file=f, _url=url, _opts=opts)
+            return LindiH5ZarrStore(_file=f, _url=url, _opts=opts)
 
     def __getitem__(self, key):
         """Get an item from the store (required by base class)."""
@@ -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 LindiClient.from_file(fname)
+        This can then be loaded using LindiH5pyFile.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
-        LindiClient.from_reference_file_system(obj)
+        LindiH5pyFile.from_reference_file_system(obj)
         """
         if self._h5f is None:
             raise Exception("Store is closed")

lindi/LindiH5ZarrStore/__init__.py

@@ -0,0 +1 @@
+from .LindiH5ZarrStore import LindiH5ZarrStore, LindiH5ZarrStoreOpts  # noqa: F401

lindi/LindiH5Store/_h5_attr_to_zarr_attr.py → lindi/LindiH5ZarrStore/_h5_attr_to_zarr_attr.py

@@ -74,7 +74,7 @@ def _h5_ref_to_zarr_attr(ref: h5py.Reference, *, label: str = '', h5f: h5py.File
     object_id = dref_obj.attrs.get("object_id", None)
 
     # Here we assume that the file has a top-level attribute called "object_id".
-    # This will be the case for files created by the LindiH5Store class.
+    # This will be the case for files created by the LindiH5ZarrStore class.
     file_object_id = h5f.attrs.get("object_id", None)
 
     # See https://hdmf-zarr.readthedocs.io/en/latest/storage.html#storing-object-references-in-attributes

lindi/LindiH5Store/_zarr_info_for_h5_dataset.py → lindi/LindiH5ZarrStore/_zarr_info_for_h5_dataset.py

@@ -24,7 +24,7 @@ class ZarrInfoForH5Dataset:
 def _zarr_info_for_h5_dataset(h5_dataset: h5py.Dataset) -> ZarrInfoForH5Dataset:
     """Get the information needed to create a zarr dataset from an h5py dataset.
 
-    This is the main workhorse function for LindiH5Store. It takes an h5py
+    This is the main workhorse function for LindiH5ZarrStore. It takes an h5py
     dataset and returns a ZarrInfoForH5Dataset object.
 
     It handles the following cases:

lindi/LindiClient/LindiClient.py → lindi/LindiH5pyFile/LindiH5pyFile.py

@@ -11,7 +11,7 @@
 from .LindiReference import LindiReference
 
 
-class LindiClient(LindiGroup):
+class LindiH5pyFile(LindiGroup):
     def __init__(
         self,
         *,
@@ -25,38 +25,38 @@ def filename(self):
         return ''
 
     @staticmethod
-    def from_zarr_store(zarr_store: Union[Store, FSMap]) -> "LindiClient":
+    def from_zarr_store(zarr_store: Union[Store, FSMap]) -> "LindiH5pyFile":
         zarr_group = zarr.open(store=zarr_store, mode="r")
         assert isinstance(zarr_group, zarr.Group)
-        return LindiClient.from_zarr_group(zarr_group)
+        return LindiH5pyFile.from_zarr_group(zarr_group)
 
     @staticmethod
     def from_file(
         json_file: str, file_type: Literal["zarr.json"] = "zarr.json"
-    ) -> "LindiClient":
+    ) -> "LindiH5pyFile":
         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 LindiClient.from_reference_file_system(data)
+                    return LindiH5pyFile.from_reference_file_system(data)
             else:
                 with open(json_file, "r") as f:
                     data = json.load(f)
-                return LindiClient.from_reference_file_system(data)
+                return LindiH5pyFile.from_reference_file_system(data)
         else:
             raise ValueError(f"Unknown file_type: {file_type}")
 
     @staticmethod
-    def from_zarr_group(zarr_group: zarr.Group) -> "LindiClient":
-        return LindiClient(_zarr_group=zarr_group)
+    def from_zarr_group(zarr_group: zarr.Group) -> "LindiH5pyFile":
+        return LindiH5pyFile(_zarr_group=zarr_group)
 
     @staticmethod
-    def from_reference_file_system(data: dict) -> "LindiClient":
+    def from_reference_file_system(data: dict) -> "LindiH5pyFile":
         fs = ReferenceFileSystem(data).get_mapper(root="")
-        return LindiClient.from_zarr_store(fs)
+        return LindiH5pyFile.from_zarr_store(fs)
 
     def get(self, key, default=None, getlink: bool = False):
         try:
@@ -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 LindiClient')
+            raise Exception(f'Cannot use key "{key}" of type "{type(key)}" to index into a LindiH5pyFile')
 
 
 def _download_file(url: str, filename: str) -> None:

lindi/LindiClient/__init__.py → lindi/LindiH5pyFile/__init__.py

@@ -1,4 +1,4 @@
-from .LindiClient import LindiClient  # noqa: F401
+from .LindiH5pyFile import LindiH5pyFile  # noqa: F401
 from .LindiGroup import LindiGroup  # noqa: F401
 from .LindiDataset import LindiDataset  # noqa: F401
 from .LindiAttributes import LindiAttributes  # noqa: F401

lindi/__init__.py

@@ -1,2 +1,2 @@
-from .LindiClient import LindiClient, LindiGroup, LindiDataset, LindiAttributes, LindiReference  # noqa: F401
-from .LindiH5Store import LindiH5Store, LindiH5StoreOpts  # noqa: F401
+from .LindiH5pyFile import LindiH5pyFile, LindiGroup, LindiDataset, LindiAttributes, LindiReference  # noqa: F401
+from .LindiH5ZarrStore import LindiH5ZarrStore, LindiH5ZarrStoreOpts  # noqa: F401