docs

simple old style nwb-linkml test

docs/api/index.md

@@ -0,0 +1,9 @@
+# numpydantic
+
+Top-level API contents
+
+```{eval-rst}
+.. automodule:: numpydantic
+    :members:
+    :imported-members:
+``` 

docs/api/linkml/index.md

@@ -0,0 +1,10 @@
+# linkml
+
+```{toctree}
+:caption: LinkML
+
+ndarraygen
+pydanticgen
+template
+```
+

docs/api/linkml/ndarraygen.md

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

docs/api/linkml/pydanticgen.md

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

docs/api/linkml/template.md

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

docs/api/maps.md

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

docs/api/monkeypatch.md

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

docs/api/ndarray.md

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

docs/api/proxy.md

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

docs/conf.py

@@ -6,48 +6,53 @@
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'numpydantic'
+project = "numpydantic"
-copyright = '2024, Jonny Saunders'
+copyright = "2024, Jonny Saunders"
-author = 'Jonny Saunders'
+author = "Jonny Saunders"
-release = 'v0.0.0'
+release = "v0.0.0"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = [
-    'sphinx.ext.napoleon',
+    "sphinx.ext.napoleon",
-    'sphinx.ext.autodoc',
+    "sphinx.ext.autodoc",
-    'sphinxcontrib.autodoc_pydantic',
+    "sphinxcontrib.autodoc_pydantic",
-    'sphinx.ext.intersphinx',
+    "sphinx.ext.intersphinx",
     "sphinx_design",
-    'myst_parser',
+    "myst_parser",
-    'sphinx.ext.todo'
+    "sphinx.ext.todo",
 ]
 
-templates_path = ['_templates']
+templates_path = ["_templates"]
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/3', None),
+    "python": ("https://docs.python.org/3", None),
-    'numpy': ('https://numpy.org/doc/stable/', None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
-    'pydantic': ('https://docs.pydantic.dev/latest/', None),
+    "pydantic": ("https://docs.pydantic.dev/latest/", None),
-    'linkml': ('https://linkml.io/linkml/', None),
+    "linkml": ("https://linkml.io/linkml/", None),
-    'linkml_runtime': ('https://linkml.io/linkml/', None),
+    "linkml_runtime": ("https://linkml.io/linkml/", None),
-    'linkml-runtime': ('https://linkml.io/linkml/', None)
+    "linkml-runtime": ("https://linkml.io/linkml/", None),
 }
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'furo'
+html_theme = "furo"
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # autodoc
-autodoc_pydantic_model_show_json_error_strategy = 'coerce'
+autodoc_pydantic_model_show_json_error_strategy = "coerce"
 autodoc_pydantic_model_show_json = False
-autodoc_mock_imports = []
+autodoc_mock_imports = [
+    "dask",
+    "h5py",
+    "linkml",
+    "linkml-runtime",
+]
 autoclass_content = "both"
-autodoc_member_order='bysource'
+autodoc_member_order = "bysource"
 add_module_names = False
 
 # Napoleon settings

docs/hooks.md

@@ -1,5 +1,11 @@
 # Hooks
 
-## TODO
+What hooks do we want to expose to downstream users so they can use this without needing
+to override everything?
 
-- nwb compatibility: allowable precision map in dtype check
+```{todo} 
+**NWB Compatibility**
+
+**Precision:** NWB allows for a sort of hierarchy of type specification - 
+a less precise type also allows the data to be specified in a more precise type
+```

docs/index.md

@@ -14,30 +14,32 @@ It does two primary things:
 - **Generate models from LinkML** - extend the LinkML pydantic generator to create models that 
   that use the [linkml-arrays](https://github.com/linkml/linkml-arrays) syntax
 
-## Overview
 
-The Python type annotation system is weird and not like the rest of Python! 
-(at least until [PEP 0649](https://peps.python.org/pep-0649/) gets mainlined).
-Similarly, Pydantic 2's core_schema system is wonderful but still relatively poorly
-documented for custom types! This package does the work of plugging them in
-together to make some kind of type validation frankenstein.
-
-The first problem is that type annotations are evaluated statically by python, mypy,
-etc. This means you can't use typical python syntax for declaring types - it has to
-be present at the time `__new__` is called, rather than `__init__`. 
-
-- pydantic schema
-- validation
-- serialization
-- lazy loading
-- compression
 
  
 ```{toctree}
 :maxdepth: 2
-:caption: Contents:
+:caption: Contents
-:hidden:
+:hidden: true
 
+overview
+ndarray
+linkml
 hooks
+todo
+```
+
+```{toctree}
+:maxdepth: 2
+:caption: API
+:hidden: true
+
+api/index
+api/ndarray
+api/proxy
+api/linkml/index
+api/maps
+api/monkeypatch
+
 ```
 

docs/linkml.md

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

docs/ndarray.md

@@ -0,0 +1,134 @@
+# Constrained Arrays
+
+## Implementation details
+
+```{todo}
+**Docs:**
+
+Describe implementation details!
+```
+
+## Examples
+
+### Declaration
+
+Type with a single {class}`~numpydantic.NDArray` class, or use a {class}`~typing.Union`
+to express more complex array constraints.
+
+This package is effectively a Pydantic interface to [nptyping](https://github.com/ramonhagenaars/nptyping),
+so any array syntax is valid there. (see [TODO](todo) for caveats)
+
+```python
+from typing import Union
+from pydantic import BaseModel
+from numpydantic import NDArray, Shape, UInt8, Float, Int
+
+class Image(BaseModel):
+    """
+    Data values. Data can be in 1-D, 2-D, 3-D, or 4-D. The first dimension should always represent time. This can also be used to store binary data (e.g., image frames). This can also be a link to data stored in an external file.
+    """
+    array: Union[
+        NDArray[Shape["* x, * y"], UInt8],
+        NDArray[Shape["* x, * y, 3 rgb"], UInt8],
+        NDArray[Shape["* x, * y, 4 rgba"], UInt8],
+        NDArray[Shape["* t, * x, * y, 3 rgb"], UInt8],
+        NDArray[Shape["* t, * x, * y, 4 rgba"], Float]
+    ]
+```
+
+### Validation:
+
+```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
+float_video = Image(array=np.ones((100, 1280, 720, 4),dtype=float))
+wrong_shape_float_video = Image(array=np.ones((100, 1280, 720, 3),dtype=float))
+```
+
+### JSON schema generation:
+
+```python
+class MyArray(BaseModel):
+  array: NDArray[Shape["2 x, * y, 4 z"], Float]
+```
+
+```python
+>>> print(json.dumps(MyArray.model_json_schema(), indent=2))
+```
+
+```json
+{
+  "properties": {
+    "array": {
+      "items": {
+        "items": {
+          "items": {
+            "type": "number"
+          },
+          "maxItems": 4,
+          "minItems": 4,
+          "type": "array"
+        },
+        "type": "array"
+      },
+      "maxItems": 2,
+      "minItems": 2,
+      "title": "Array",
+      "type": "array"
+    }
+  },
+  "required": [
+    "array"
+  ],
+  "title": "MyArray",
+  "type": "object"
+}
+```
+
+### Serialization
+
+```python
+class SmolArray(BaseModel):
+    array: NDArray[Shape["2 x, 2 y"], Int]
+
+class BigArray(BaseModel):
+    array: NDArray[Shape["1000 x, 1000 y"], Int]
+```
+
+Serialize small arrays as lists of lists, and big arrays as a b64-encoded blosc compressed string
+
+```python
+>>> smol = SmolArray(array=np.array([[1,2],[3,4]], dtype=int))
+>>> big = BigArray(array=np.random.randint(0,255,(1000,1000),int))
+
+>>> print(smol.model_dump_json())
+{"array":[[1,2],[3,4]]}
+>>> print(big.model_dump_json())
+{
+  "array": "( long b64 encoded string )",
+  "shape": [1000, 1000],
+  "dtype": "int64",
+  "unpack_fns": ["base64.b64decode", "blosc2.unpack_array2"],
+}
+```
+
+## TODO
+
+```{todo}
+Implement structured arrays
+```
+
+```{todo}
+Implement pandas dataframe validation?
+```

docs/overview.md

@@ -0,0 +1,17 @@
+# Overview
+
+The Python type annotation system is weird and not like the rest of Python! 
+(at least until [PEP 0649](https://peps.python.org/pep-0649/) gets mainlined).
+Similarly, Pydantic 2's core_schema system is wonderful but still relatively poorly
+documented for custom types! This package does the work of plugging them in
+together to make some kind of type validation frankenstein.
+
+The first problem is that type annotations are evaluated statically by python, mypy,
+etc. This means you can't use typical python syntax for declaring types - it has to
+be present at the time `__new__` is called, rather than `__init__`. 
+
+- pydantic schema
+- validation
+- serialization
+- lazy loading
+- compression

docs/todo.md

@@ -0,0 +1,5 @@
+# TODO
+
+```{todolist}
+
+``` 

numpydantic/__init__.py

@@ -1,12 +1,13 @@
 # ruff: noqa: E402
 # ruff: noqa: F401
+# ruff: noqa: I001
 from numpydantic.monkeypatch import apply_patches
 
 apply_patches()
 
+from numpydantic.ndarray import NDArray
+
 # convenience imports for typing - finish this!
 from typing import Any
 
 from nptyping import Float, Int, Number, Shape, UInt8
-
-from numpydantic.ndarray import NDArray

numpydantic/linkml/__init__.py

@@ -0,0 +1,8 @@
+# ruff: noqa: E402
+# ruff: noqa: F401
+from numpydantic.linkml.ndarraygen import (
+    ArrayFormat,
+    LinkMLDataArray,
+    LinkMLNDArray,
+    NWBLinkMLArraylike,
+)

tests/fixtures.py

@@ -2,6 +2,7 @@ import shutil
 from pathlib import Path
 
 import pytest
+from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition
 
 
 @pytest.fixture(scope="session")
@@ -38,3 +39,36 @@ def tmp_output_dir_mod(tmp_output_dir) -> Path:
         shutil.rmtree(str(subpath))
     subpath.mkdir()
     return subpath
+
+
+@pytest.fixture()
+def nwb_linkml_array() -> tuple[ClassDefinition, str]:
+    classdef = ClassDefinition(
+        name="NWB_Linkml Array",
+        description="Main class's array",
+        is_a="Arraylike",
+        attributes=[
+            SlotDefinition(name="x", range="numeric", required=True),
+            SlotDefinition(name="y", range="numeric", required=True),
+            SlotDefinition(
+                name="z",
+                range="numeric",
+                required=False,
+                maximum_cardinality=3,
+                minimum_cardinality=3,
+            ),
+            SlotDefinition(
+                name="a",
+                range="numeric",
+                required=False,
+                minimum_cardinality=4,
+                maximum_cardinality=4,
+            ),
+        ],
+    )
+    generated = """Union[
+        NDArray[Shape["* x, * y"], Number],
+        NDArray[Shape["* x, * y, 3 z"], Number],
+        NDArray[Shape["* x, * y, 3 z, 4 a"], Number]
+    ]"""
+    return classdef, generated

tests/test_linkml/test_ndarraygen.py

@@ -0,0 +1,14 @@
+import pytest
+
+from numpydantic.linkml import ArrayFormat, NWBLinkMLArraylike
+
+from ..fixtures import nwb_linkml_array
+
+
+def test_nwb_linkml_array(nwb_linkml_array):
+    classdef, generated = nwb_linkml_array
+
+    assert ArrayFormat.is_array(classdef)
+    assert NWBLinkMLArraylike.check(classdef)
+    assert ArrayFormat.get(classdef) is NWBLinkMLArraylike
+    assert generated == NWBLinkMLArraylike.make(classdef)