refresh of front docs page

.readthedocs.yaml

@@ -20,3 +20,4 @@ python:
       path: .
       extra_requirements:
         - docs
+        - arrays

docs/api/dtype.md

@@ -0,0 +1 @@
+# DType

docs/api/interface/dask.md

@@ -0,0 +1,6 @@
+# Dask
+
+```{eval-rst}
+.. automodule:: numpydantic.interface.dask
+    :members:
+```

docs/api/interface/hdf5.md

@@ -0,0 +1,6 @@
+# HDF5
+
+```{eval-rst}
+.. automodule:: numpydantic.interface.hdf5
+    :members:
+```

docs/api/interface/index.md

@@ -0,0 +1,13 @@
+# Interfaces
+
+```{eval-rst}
+.. automodule:: numpydantic.interface.interface
+    :members:
+```
+
+```{toctree}
+dask
+hdf5
+numpy
+zarr
+```

docs/api/interface/numpy.md

@@ -0,0 +1,6 @@
+# Numpy
+
+```{eval-rst}
+.. automodule:: numpydantic.interface.numpy
+    :members:
+```

docs/api/interface/zarr.md

@@ -0,0 +1,6 @@
+# Zarr
+
+```{eval-rst}
+.. automodule:: numpydantic.interface.zarr
+    :members:
+```

docs/api/proxy.md

@@ -1,6 +0,0 @@
-# proxy
-
-```{eval-rst}
-.. automodule:: numpydantic.proxy
-    :members:
-```

docs/api/types.md

@@ -0,0 +1 @@
+# Types

docs/conf.py

@@ -19,6 +19,7 @@ extensions = [
     "sphinx.ext.autodoc",
     "sphinxcontrib.autodoc_pydantic",
     "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
     "sphinx_design",
     "myst_parser",
     "sphinx.ext.todo",
@@ -48,12 +49,7 @@ html_static_path = ["_static"]
 # autodoc
 autodoc_pydantic_model_show_json_error_strategy = "coerce"
 autodoc_pydantic_model_show_json = False
-autodoc_mock_imports = [
-    "dask",
-    "h5py",
-    "linkml",
-    "linkml-runtime",
-]
+
 autoclass_content = "both"
 autodoc_member_order = "bysource"
 add_module_names = False

docs/index.md

@@ -1,9 +1,166 @@
 # numpydantic
 
-Type and shape validation and serialization for numpy arrays in pydantic models
+A python package for array types in pydantic.
+
+## Features:
+- **Types** - Annotations (based on [npytyping](https://github.com/ramonhagenaars/nptyping))
+  for specifying arrays in pydantic models
+- **Validation** - Shape, dtype, and other array validations
+- **Seralization** - JSON-Schema List-of-list schema generation
+- **Interfaces** - Works with numpy, dask, HDF5, zarr, and a simple extension system to make it work with
+  whatever else you want!
+
+Coming soon:
+- **Metadata** - This package was built to be used with [linkml arrays](https://linkml.io/linkml/schemas/arrays.html),
+  so we will be extending it to include any metadata included in the type annotation object in the JSON schema representation.
+- (see [todo](./todo.md))
+
+## Usage
+
+Specify an array using [nptyping syntax](https://github.com/ramonhagenaars/nptyping/blob/master/USERDOCS.md)
+and use it with your favorite array library :)
+
+```{todo}
+We will be moving away from using nptyping in v2.0.0.
+
+It was written for an older era in python before the dramatic changes in the Python
+type system and is no longer actively maintained. We will be reimplementing a syntax
+that extends its array specification syntax to include things like ranges and extensible
+dtypes with varying precision (and is much less finnicky to deal with).
+```
+
+Use the {class}`~numpydantic.NDArray` class like you would any other python type,
+combine it with {class}`typing.Union`, make it {class}`~typing.Optional`, etc.
+
+```python
+from typing import Union
+from pydantic import BaseModel
+import numpy as np
+
+from numpydantic import NDArray, Shape
+
+class Image(BaseModel):
+    """
+    Images: grayscale, RGB, RGBA, and videos too!
+    """
+    array: Union[
+        NDArray[Shape["* x, * y"], np.uint8],
+        NDArray[Shape["* x, * y, 3 rgb"], np.uint8],
+        NDArray[Shape["* x, * y, 4 rgba"], np.uint8],
+        NDArray[Shape["* t, * x, * y, 3 rgb"], np.uint8],
+        NDArray[Shape["* t, * x, * y, 4 rgba"], np.float64]
+    ]
+```
+
+And then use that as a transparent interface to your favorite array library!
+
+### Numpy
+
+The Coca-Cola of array libraries
+
+```python
+import numpy as np
+# works
+frame_gray = Image(array=np.ones((1280, 720), dtype=np.uint8))
+frame_rgb  = Image(array=np.ones((1280, 720, 3), dtype=np.uint8))
+frame_rgba = Image(array=np.ones((1280, 720, 4), dtype=np.uint8))
+video_rgb  = Image(array=np.ones((100, 1280, 720, 3), dtype=np.uint8))
+
+# fails
+wrong_n_dimensions = Image(array=np.ones((1280,), dtype=np.uint8))
+wrong_shape = Image(array=np.ones((1280,720,10), dtype=np.uint8))
+wrong_type = Image(array=np.ones((1280,720,3), dtype=np.float64))
+
+# shapes and types are checked together, so..
+# this works
+float_video = Image(array=np.ones((100, 1280, 720, 4), dtype=float))
+# this doesn't
+wrong_shape_float_video = Image(array=np.ones((100, 1280, 720, 3), dtype=float))
+```
+
+### Dask
+
+High performance chunked arrays! The backend for many new array libraries! 
+
+Works exactly the same as numpy arrays
+
+```python
+import dask.array as da
+
+# validate a huge video
+video_array = da.zeros(shape=(1920,1080,1000000,3), dtype=np.uint8)
+
+# this works
+dask_video = Image(array=video_array)
+```
+
+### HDF5
+
+Array work increasingly can't fit on memory, but dealing with arrays on disk 
+can become a pain in concurrent applications. Numpydantic allows you to 
+specify the location of an array within an hdf5 file on disk and use it just like
+any other array!
+
+eg. Make an array on disk...
+
+```python
+from pathlib import Path
+import h5py
+from numpydantic.interface.hdf5 import H5ArrayPath
+
+h5f_file = Path('my_file.h5')
+array_path = "/nested/array"
+
+# make an HDF5 array
+h5f = h5py.File(h5f_file, "w")
+array = np.random.random((1920,1080,3)).astype(np.uint8)
+h5f.create_dataset(array_path, data=array)
+h5f.close()
+```
+
+Then use it in your model! numpydantic will only open the file as long as it's needed
+
+```python
+>>> h5f_image = Image(array=H5ArrayPath(file=h5f_file, path=array_path))
+>>> h5f_image.array[0:5,0:5,0]
+array([[0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0]], dtype=uint8)
+>>> h5f_image.array[0:2,0:2,0] = 1
+>>> h5f_image.array[0:5,0:5,0]
+array([[1, 1, 0, 0, 0],
+       [1, 1, 0, 0, 0],
+       [0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0],
+       [0, 0, 0, 0, 0]], dtype=uint8)
+```
+
+Numpydantic tries to be a smart but transparent proxy, exposing the methods and attributes
+of the source type even when we aren't directly using them, like when dealing with on-disk HDF5 arrays.
+
+If you want, you can take full control and directly interact with the underlying :class:`h5py.Dataset`
+object and leave the file open between calls:
+
+```python
+>>> dataset = h5f_image.array.open()
+>>> # do some stuff that requires the datset to be held open
+>>> h5f_image.array.close()
+```
+
+### Zarr
+
+Zarr works similarly!
+
+Use it with any of Zarr's backends: Nested, Zipfile, S3, it's all the same!
+
+```{todo}
+Add the zarr examples!
+```
+
+
 
-- **Provide types** - Annotations (based on [npytyping](https://github.com/ramonhagenaars/nptyping))
-  for specifying numpy arrays in pydantic models, and
 
 ```{toctree}
 :maxdepth: 2
@@ -21,12 +178,13 @@ todo
 :caption: API
 :hidden: true
 
+api/interface/index
 api/index
+api/dtype
 api/ndarray
-api/proxy
-api/linkml/index
 api/maps
 api/monkeypatch
+api/types
 
 ```
 

docs/linkml.md

@@ -1,2 +0,0 @@
-# LinkML Generation
-