docs, but need to sleep, come back in morning

This commit is contained in:
sneakers-the-rat 2023-10-19 02:52:15 -07:00
parent dd956b35c3
commit 2276a7b501
12 changed files with 956 additions and 40 deletions

3
.gitignore vendored
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@ -161,4 +161,5 @@ cython_debug/
nwb.schema.json
__tmp__
prof
prof
jupyter_execute

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@ -16,9 +16,11 @@ build:
jobs:
post_create_environment:
- pip install poetry
- pip install poetry-kernel
- poetry config virtualenvs.create false
post_install:
- poetry install --no-root
- poetry run python -m ipykernel install --name nwb-linkml_docs
# Optionally build your docs in additional formats such as PDF and ePub
# formats:

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@ -16,7 +16,10 @@ help:
serve:
# env variable that makes it so we don't build all the models while in dev mode
SPHINX_MINIMAL="True" sphinx-autobuild "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) --watch ../nwb_linkml/src/nwb_linkml --watch ../nwb_schema_language/src/nwb_schema_language
SPHINX_MINIMAL="True" sphinx-autobuild "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) \
--watch ../nwb_linkml/src/nwb_linkml \
--watch ../nwb_schema_language/src/nwb_schema_language \
--re-ignore ".*jupyter_execute.*"
serve_fast:
sphinx-autobuild -a "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) --watch ../nwb_linkml/src/nwb_linkml --watch ../nwb_schema_language/src/nwb_schema_language

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@ -4,4 +4,19 @@
color: #1a1c1e;
font-style: italic;
border-radius: 4px;
}
/* make cell outputs brighter */
.cell_output.docutils.container {
filter: brightness(0.4) invert() saturate(5);
z-index: 999;
position:relative;
}
pre {
font-size: 0.8em;
}
.hide.below-input span {
color: var(--color-background-secondary);
}

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@ -7,4 +7,10 @@ dataset
group
namespaces
schema
```
```{eval-rst}
.. automodule:: nwb_linkml.adapters
:members:
:undoc-members:
```

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@ -27,7 +27,8 @@ extensions = [
'sphinx.ext.intersphinx',
'sphinx.ext.doctest',
"sphinx_design",
'myst_parser',
#'myst_parser',
"myst_nb",
'sphinx_togglebutton'
]
@ -59,8 +60,10 @@ intersphinx_mapping = {
'pandas': ('https://pandas.pydata.org/docs/', None),
'pydantic': ('https://docs.pydantic.dev/latest/', None),
'h5py': ('https://docs.h5py.org/en/stable/', None),
'dask': ('https://docs.dask.org/en/stable/', None)
'dask': ('https://docs.dask.org/en/stable/', None),
'linkml': ('https://linkml.io/linkml/', None),
'linkml_runtime': ('https://linkml.io/linkml/', None),
'linkml-runtime': ('https://linkml.io/linkml/', None)
}
@ -92,9 +95,12 @@ add_module_names = False
autodoc_default_options = {
'exclude-members': 'NDArray,Shape',
}
# --------------------------------------------------
# myst-nb
nb_render_markdown_format = 'myst'
nb_append_css = False
# doctest

107
docs/guide/quickstart.md Normal file
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@ -0,0 +1,107 @@
---
file_format: mystnb
kernelspec:
name: nwb-linkml_docs
mystnb:
output_stderr: 'remove-warn'
---
# Quickstart
## Reading Data
To get the fun part out of the way, you can read ur data:
```{code-cell}
:tags: [hide-output]
from pathlib import Path
from rich.pretty import pprint, pretty_repr
from rich.console import Console
from nwb_linkml.io import HDF5IO
# set up for pprinting in notebooks
console = Console(width=100)
print = console.print
# find sample data file and read
nwb_file = Path('../../nwb_linkml/tests/data/aibs.nwb')
data = HDF5IO(nwb_file).read()
print(data)
```
## Load and manipulate NWB schemas
A {mod}`~nwb_linkml.providers.git` provider module can manage a repository to
provide a given NWB namespace at a given version, and cast the
schema into Pydantic models from {mod}`nwb_schema_language`.
For the nwb-core schema, loading first just the namespaces file (without
adjoining schema):
```{code-cell}
:tags: [hide-output]
from nwb_linkml.providers.git import NWB_CORE_REPO
from nwb_linkml.io.schema import load_namespaces
namespace_file: 'Path' = NWB_CORE_REPO.provide_from_git('2.6.0')
core_namespaces = load_namespaces(namespace_file)
print(core_namespaces)
```
Or for a schema file...
```{code-cell}
:tags: [hide-output]
from nwb_linkml.io.schema import load_schema_file
base_schema_file = namespace_file.parent / 'nwb.base.yaml'
nwb_core_base = load_schema_file(base_schema_file)
print(nwb_core_base)
```
And additional {mod}`~nwb_linkml.adapters` are used to handle some of the
implicit behavior in nwb schema files, like importing other namespaces
at a specific version, and inter-schema class imports. Eg. the
{class}`~nwb_linkml.adapters.NamespacesAdapter` finds the implicitly
imported `hdmf-common` namespace (again provided by the git schema provider).
```{code-cell}
:tags: [hide-output]
from nwb_linkml.adapters import NamespacesAdapter
core_ns = NamespacesAdapter.from_yaml(namespace_file)
print(core_ns.imported)
```
The classes in {mod}`nwb_schema_language` are just pydantic models, so they
can be used like any other to create new, validated schemas.
## Translating to LinkML
{mod}`~nwb_linkml.adapters` handle the conversion from NWB schema language to
LinkML.
```{code-cell}
:tags: [hide-output]
core_linkml = core_ns.build()
print(core_linkml)
```
The {class}`~nwb_linkml.adapters.BuildResult` class holds the LinkML representation
of each of the schemas and their classes, which are now in {class}`linkml_runtime.linkml_model.SchemaDefinition`
and `ClassDefinition` classes:
```{code-cell}
:tags: [hide-output]
print(core_linkml.schemas[0])
```

View file

@ -7,9 +7,10 @@ A translation of the [Neurodata Without Borders](https://www.nwb.org/) standard
to [LinkML](https://linkml.io/).
```{admonition} Quick Links
* [Purpose](purpose) - Why this package exists
* [Overview](overview) - Overview of how it works
* [API Docs](api) - Ok *really* how it works
* [Quickstart](guide/quickstart) - Some stuff this package does
* [Purpose](intro/purpose) - Why this package exists
* [Overview](guide/overview) - Overview of how it works
* [API Docs](api/nwb_linkml/index) - Ok *really* how it works
```
`nwb-linkml` is an independent implementation of the standard capable of:
@ -22,31 +23,10 @@ to [LinkML](https://linkml.io/).
* {feature}`Coming Soon` Export NWB to a Relational Database
* {feature}`Coming Soon` Export NWB to a Triple Store
## Samples
### Reading
```python
from pathlib import Path
from rich import print
from nwb_linkml.io import HDF5IO
# find sample data file and read
nwb_file = Path('../nwb_linkml/tests/data/aibs.nwb')
data = HDF5IO(nwb_file).read()
print(data)
```
````{admonition} Model Print Output
:class: dropdown
```{literalinclude} read_output.txt
:language: python
```
````
## Example Translation
### TimeSeries
## TimeSeries
(Abbreviated for clarity)
@ -254,11 +234,8 @@ class TimeSeriesData(ConfiguredBaseModel):
```
````
`````
```{toctree}
:caption: Intro
:maxdepth: 3
@ -274,6 +251,7 @@ intro/translation
:maxdepth: 1
:hidden:
guide/quickstart
guide/overview
```
@ -302,6 +280,19 @@ api/nwb_linkml/schema/index
```
````
````{only} minimal
```{toctree}
:caption: Notes
:maxdepth: 3
:hidden:
_notes/linkml
_notes/pynwb
_notes/schema
_notes/translation
```
````
```{toctree}
:caption: Meta
:hidden:

View file

@ -17,4 +17,9 @@ NWB is
## Core Schema
### Special Cases
- `NWBFile` defines the storage layout
- `hdmf-common` defines the base data types, which effectively are all special cases
## PyNWB

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@ -21,7 +21,7 @@ def load_yaml(path:Path) -> dict:
ns_dict = apply_postload(ns_dict)
return ns_dict
def _load_namespaces(path:Path|NamespaceRepo) -> Namespaces:
def load_namespaces(path:Path|NamespaceRepo) -> Namespaces:
"""Loads the NWB SCHEMA LANGUAGE namespaces (not the namespacesadapter)"""
if isinstance(path, NamespaceRepo):
path = path.provide_from_git()
@ -32,6 +32,17 @@ def _load_namespaces(path:Path|NamespaceRepo) -> Namespaces:
return namespaces
def load_schema_file(path:Path, yaml:Optional[dict] = None) -> SchemaAdapter:
"""
Load a single schema file within an NWB namespace.
.. note::
This needs to be a separate function from loading a namespace because NWB
doesn't define a schema file per se in its spec, aside from having
a ``datasets`` and ``groups`` dictionary. We wanted to be as faithful to
the spec as possible in that package, and so that's picked up here.
"""
if yaml is not None:
source = yaml
source = apply_postload(source)
@ -81,20 +92,21 @@ def load_namespace_adapter(
"""
if path is None:
path = Path('..')
elif isinstance(path, str):
path = Path(path)
if isinstance(namespace, Path):
path = namespace
namespaces = _load_namespaces(path)
namespaces = load_namespaces(path)
elif isinstance(namespace, NamespaceRepo):
path = namespace.provide_from_git(commit=version)
namespaces = _load_namespaces(path)
namespaces = load_namespaces(path)
elif isinstance(namespace, Namespaces):
namespaces = namespace
else:
raise ValueError(f"Namespace must be a path, namespace repo, or already loaded namespaces")
if path.is_file():
# given the namespace file itself, so find paths relative to its directory
path = path.parent

769
poetry.lock generated
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@ -32,6 +32,17 @@ files = [
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]
[[package]]
name = "appnope"
version = "0.1.3"
description = "Disable App Nap on macOS >= 10.9"
optional = false
python-versions = "*"
files = [
{file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"},
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]
[[package]]
name = "arrow"
version = "1.3.0"
@ -51,6 +62,23 @@ types-python-dateutil = ">=2.8.10"
doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", "sphinx-autodoc-typehints", "sphinx_rtd_theme (>=1.3.0)"]
test = ["dateparser (==1.*)", "pre-commit", "pytest", "pytest-cov", "pytest-mock", "pytz (==2021.1)", "simplejson (==3.*)"]
[[package]]
name = "asttokens"
version = "2.4.0"
description = "Annotate AST trees with source code positions"
optional = false
python-versions = "*"
files = [
{file = "asttokens-2.4.0-py2.py3-none-any.whl", hash = "sha256:cf8fc9e61a86461aa9fb161a14a0841a03c405fa829ac6b202670b3495d2ce69"},
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]
[package.dependencies]
six = ">=1.12.0"
[package.extras]
test = ["astroid", "pytest"]
[[package]]
name = "attrs"
version = "23.1.0"
@ -105,6 +133,17 @@ files = [
[package.extras]
dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
[[package]]
name = "backcall"
version = "0.2.0"
description = "Specifications for callback functions passed in to an API"
optional = false
python-versions = "*"
files = [
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]
[[package]]
name = "beautifulsoup4"
version = "4.12.2"
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]
[[package]]
name = "cffi"
version = "1.16.0"
description = "Foreign Function Interface for Python calling C code."
optional = false
python-versions = ">=3.8"
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content-hash = "6e7b415ca1cd1531804b1879fe7a1296d35546a80e5eba89bc19ce83450d07e0"

View file

@ -22,6 +22,7 @@ nwb-linkml = { path = './nwb_linkml', develop = true }
nwb_schema_language = { path = './nwb_schema_language', develop = true }
sphinx-design = "^0.5.0"
sphinx-togglebutton = "^0.3.2"
myst-nb = { git = "https://github.com/executablebooks/MyST-NB.git" }
[build-system]