docs: update docs and add deps

Author: synchon

docs/api/onthefly.rst

@@ -5,5 +5,5 @@ On-the-fly
    :members:
    :imported-members:
 
-.. automodule:: junifer.onthefly.brainprint
+.. automodule:: junifer.onthefly._brainprint
    :members:

docs/builtin.rst

@@ -158,16 +158,16 @@ Available
        | (subject-native or other template spaces)
      - Done
      - 0.0.4
-   * - ``Smoothing``
+   * - :class:`.Smoothing`
      - | Apply smoothing to data, particularly useful when dealing with
        | ``fMRIPrep``-ed data
      - In Progress
      - :gh:`161`
-   * - ``TemporalSlicer``
+   * - :class:`.TemporalSlicer`
      - Slice ``BOLD`` data temporally
      - | Done
      - :gh:`443`
-   * - ``TemporalFilter``
+   * - :class:`.TemporalFilter`
      - Filter (clean) ``BOLD`` data temporally
      - | Done
      - :gh:`432`

docs/conf.py

@@ -65,6 +65,8 @@
     "sphinx_copybutton",  # copy button for code blocks
     "sphinxcontrib.mermaid",  # mermaid support
     "sphinxcontrib.towncrier.ext",  # towncrier fragment support
+    "sphinxcontrib.autodoc_pydantic",  # autodoc support for pydantic models
+    "enum_tools.autoenum",  # enum support
 ]
 
 if use_multiversion:
@@ -97,6 +99,8 @@
     ("py:class", "pipeline.Pipeline"),  # nilearn
     ("py:obj", "neurokit2.*"),  # ignore neurokit2
     ("py:obj", "datalad.*"),  # ignore datalad
+    ("py:obj", "junifer.*"),  # ignore junifer internal
+    ("py:class", "annotated_types.*")  # ignore pydantic annotated types
 ]
 
 # -- Options for HTML output -------------------------------------------------
@@ -154,6 +158,7 @@
     "pandas": ("https://pandas.pydata.org/pandas-docs/dev", None),
     # "sqlalchemy": ("https://docs.sqlalchemy.org/en/20/", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+    "pydantic": ("https://docs.pydantic.dev/latest/", None),
 }
 
 # -- sphinx.ext.extlinks configuration ---------------------------------------

docs/whats_new.rst

@@ -146,7 +146,7 @@ Features
 ^^^^^^^^
 
 - Introduce :func:`.normalize` and :func:`.reweight` functions for downstream
-  BrainPrint analysis in :mod:`.onthefly.brainprint` by `Synchon Mandal`_
+  BrainPrint analysis in :mod:`.onthefly._brainprint` by `Synchon Mandal`_
   (:gh:`354`)
 - Introduce :class:`junifer.pipeline.PipelineComponentRegistry` to centralise
   pipeline component management by `Synchon Mandal`_ (:gh:`362`)

pyproject.toml

@@ -96,6 +96,8 @@ docs = [
     "sphinxcontrib-mermaid>=0.8.1,<0.10",
     "sphinxcontrib-towncrier==0.4.0a0",
     "setuptools-scm>=8",
+    "autodoc_pydantic>=2.0.0",
+    "enum-tools[sphinx]>=0.13.0,<0.14.0",
 ]
 
 ################