docs, but need to sleep, come back in morning

2024-11-12 17:54:29 +00:00 · 2023-10-19 02:52:15 -07:00 · 2023-10-19 02:52:15 -07:00 · 2276a7b501
commit 2276a7b501
parent dd956b35c3
12 changed files with 956 additions and 40 deletions
--- a/.gitignore
+++ b/.gitignore
@ -161,4 +161,5 @@ cython_debug/

 nwb.schema.json
 __tmp__
-prof
+prof
+jupyter_execute
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@ -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:
--- a/docs/Makefile
+++ b/docs/Makefile
@ -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
--- a/docs/_static/css/custom.css
+++ b/docs/_static/css/custom.css
@ -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);
 }
--- a/docs/api/nwb_linkml/adapters/index.md
+++ b/docs/api/nwb_linkml/adapters/index.md
@ -7,4 +7,10 @@ dataset
 group
 namespaces
 schema
+```
+
+```{eval-rst}
+.. automodule:: nwb_linkml.adapters
+    :members:
+    :undoc-members:
 ```
--- a/docs/conf.py
+++ b/docs/conf.py
@ -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
--- a/docs/guide/quickstart.md
+++ b/docs/guide/quickstart.md
@ -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])
+```
+
+
+
+
+
--- a/docs/index.md
+++ b/docs/index.md
@ -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:
--- a/docs/intro/nwb.md
+++ b/docs/intro/nwb.md
@ -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
--- a/nwb_linkml/src/nwb_linkml/io/schema.py
+++ b/nwb_linkml/src/nwb_linkml/io/schema.py
@ -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
--- a/poetry.lock
+++ b/poetry.lock
@ -32,6 +32,17 @@ files = [
    {file = "antlr4-python3-runtime-4.9.3.tar.gz", hash = "sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b"},
 ]

+[[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"},
+    {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"},
+]
+
 [[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"},
+    {file = "asttokens-2.4.0.tar.gz", hash = "sha256:2e0171b991b2c959acc6c49318049236844a5da1d65ba2672c4880c1c894834e"},
+]
+
+[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 = [
+    {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"},
+    {file = "backcall-0.2.0.tar.gz", hash = "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e"},
+]
+
 [[package]]
 name = "beautifulsoup4"
 version = "4.12.2"
@ -178,6 +217,70 @@ files = [
    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
 ]

+[[package]]
+name = "cffi"
+version = "1.16.0"
+description = "Foreign Function Interface for Python calling C code."
+optional = false
+python-versions = ">=3.8"
+files = [
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+    {file = "pyzmq-25.1.1-pp39-pypy39_pp73-win_amd64.whl", hash = "sha256:61706a6b6c24bdece85ff177fec393545a3191eeda35b07aaa1458a027ad1304"},
+    {file = "pyzmq-25.1.1.tar.gz", hash = "sha256:259c22485b71abacdfa8bf79720cd7bcf4b9d128b30ea554f01ae71fdbfdaa23"},
+]
+
+[package.dependencies]
+cffi = {version = "*", markers = "implementation_name == \"pypy\""}
+
 [[package]]
 name = "rdflib"
 version = "7.0.0"
@ -2488,6 +3196,39 @@ postgresql-psycopgbinary = ["psycopg[binary] (>=3.0.7)"]
 pymysql = ["pymysql"]
 sqlcipher = ["sqlcipher3-binary"]

+[[package]]
+name = "stack-data"
+version = "0.6.3"
+description = "Extract data from python stack frames and tracebacks for informative displays"
+optional = false
+python-versions = "*"
+files = [
+    {file = "stack_data-0.6.3-py3-none-any.whl", hash = "sha256:d5558e0c25a4cb0853cddad3d77da9891a08cb85dd9f9f91b9f8cd66e511e695"},
+    {file = "stack_data-0.6.3.tar.gz", hash = "sha256:836a778de4fec4dcd1dcd89ed8abff8a221f58308462e1c4aa2a3cf30148f0b9"},
+]
+
+[package.dependencies]
+asttokens = ">=2.1.0"
+executing = ">=1.2.0"
+pure-eval = "*"
+
+[package.extras]
+tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
+
+[[package]]
+name = "tabulate"
+version = "0.9.0"
+description = "Pretty-print tabular data"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "tabulate-0.9.0-py3-none-any.whl", hash = "sha256:024ca478df22e9340661486f85298cff5f6dcdba14f3813e8830015b9ed1948f"},
+    {file = "tabulate-0.9.0.tar.gz", hash = "sha256:0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c"},
+]
+
+[package.extras]
+widechars = ["wcwidth"]
+
 [[package]]
 name = "toolz"
 version = "0.12.0"
@ -2539,6 +3280,21 @@ notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]

+[[package]]
+name = "traitlets"
+version = "5.11.2"
+description = "Traitlets Python configuration system"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "traitlets-5.11.2-py3-none-any.whl", hash = "sha256:98277f247f18b2c5cabaf4af369187754f4fb0e85911d473f72329db8a7f4fae"},
+    {file = "traitlets-5.11.2.tar.gz", hash = "sha256:7564b5bf8d38c40fa45498072bf4dc5e8346eb087bbf1e2ae2d8774f6a0f078e"},
+]
+
+[package.extras]
+docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
+test = ["argcomplete (>=3.0.3)", "mypy (>=1.5.1)", "pre-commit", "pytest (>=7.0,<7.5)", "pytest-mock", "pytest-mypy-testing"]
+
 [[package]]
 name = "types-python-dateutil"
 version = "2.8.19.14"
@ -2631,6 +3387,17 @@ files = [
 [package.extras]
 watchmedo = ["PyYAML (>=3.10)"]

+[[package]]
+name = "wcwidth"
+version = "0.2.8"
+description = "Measures the displayed width of unicode strings in a terminal"
+optional = false
+python-versions = "*"
+files = [
+    {file = "wcwidth-0.2.8-py2.py3-none-any.whl", hash = "sha256:77f719e01648ed600dfa5402c347481c0992263b81a027344f3e1ba25493a704"},
+    {file = "wcwidth-0.2.8.tar.gz", hash = "sha256:8705c569999ffbb4f6a87c6d1b80f324bd6db952f5eb0b95bc07517f4c1813d4"},
+]
+
 [[package]]
 name = "webcolors"
 version = "1.13"
@ -2762,4 +3529,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.11,<3.13"
-content-hash = "ff4389164e6c41667acfe292fb4898303c356cf07d1dfb0d3ac6d6a29da8a738"
+content-hash = "6e7b415ca1cd1531804b1879fe7a1296d35546a80e5eba89bc19ce83450d07e0"
--- a/pyproject.toml
+++ b/pyproject.toml
@ -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]