Update docstrings for readthedocs

- Add numpydoc
- Split submodule pages and add overview page
- Update afids_utils.io
- Update afids_utils.transforms

.readthedocs.yml

@@ -1,27 +1,23 @@
+---
 # .readthedocs.yml
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
 # Required
 version: 2
-
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/conf.py
-
 # Build documentation with MkDocs
-#mkdocs:
+# mkdocs:
 #  configuration: mkdocs.yml
 
 # Optionally build your docs in additional formats such as PDF
-formats:
-  - pdf
-
+formats: [pdf]
 build:
-  os: 'ubuntu-20.04'
+  os: ubuntu-20.04
   tools:
     python: '3.10'
-
 python:
   install:
     - requirements: docs/requirements.txt

afids_utils/io.py

@@ -1,4 +1,4 @@
-"""Methods for loading and saving nifti files"""
+"""Methods for loading and saving files associated with AFIDs"""
 from __future__ import annotations
 
 import csv
@@ -34,12 +34,20 @@ def get_afid(
 ) -> NDArray[np.single]:
     """
     Extract specific fiducial's spatial coordinates
-    
+
+    Parameters
+    ----------
+    fcsv_path : os.PathLike[str] | str
+        Path to .fcsv file to extract AFID coordinates from
+
+    fid_num : int
+        Unique fiducial number to extract from .fcsv file
+
     Returns
     -------
-    NDArray[np.single]
-        Floating-point array containing spatial coordinates (x, y, z) of single
-        AFID. 
+    numpy.ndarray[shape=(3,), dtype=np.single]
+        NumPy array containing spatial coordinates (x, y, z) of single AFID
+        coordinate
     """
     if fid_num < 1 or fid_num > 32:
         raise InvalidFiducialNumberError(fid_num)
@@ -59,7 +67,19 @@ def afids_to_fcsv(
     afid_coords: NDArray[np.single],
     fcsv_output: PathLike[str] | str,
 ) -> None:
-    """AFIDS to Slicer-compatible .fcsv file"""
+    """
+    Save AFIDS to Slicer-compatible .fcsv file
+
+    Parameters
+    ----------
+    afid_coords : numpy.ndarray[shape=(N, 3), dtype=np.single]
+        Floating-point NumPy array containing spatial coordinates (x, y, z) of
+        `N` AFIDs
+
+    fcsv_output : os.PathLike[str] | str
+        Path of file (including filename and extension) to save AFIDs to
+
+    """
     # Read in fcsv template
     with resources.open_text(
         "afids_utils.resources", "template.fcsv"

afids_utils/transforms.py

@@ -9,7 +9,25 @@ def afid_world2voxel(
     afid_world: NDArray[np.float_],
     nii_affine: NDArray[np.float_],
 ) -> NDArray[np.int_]:
-    """Transform fiducials in world coordinates to voxel coordinates"""
+    """
+    Transform fiducials from world coordinates to voxel coordinates
+
+    Parameters
+    ----------
+    afid_world : numpy.ndarray[shape=(3,), dtype=numpy.float_]
+        NumPy array containing floating-point spatial coordinates (x, y, z) to
+        transform
+
+    nii_affine : numpy.ndarray[shape=(4, 4), dtype=numpy.float_]
+        NumPy array containing affine transformation associated with
+        NifTI image
+
+    Returns
+    -------
+    numpy.ndarray[shape=(3,), dtype=numpy.float_]
+        NumPy array containing indices corresponding to voxel location along
+        spatial dimensions
+    """
 
     # Translation
     afid_voxel = afid_world.T - nii_affine[:3, 3:4]

docs/api/io.md

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

docs/api/main.md → docs/api/transform.md

@@ -1,12 +1,3 @@
-# API
-
-## afids_utils.io
-
-```{eval-rst}
-    .. automodule:: afids_utils.io
-        :members:
-```
-
 ## afids_utils.transforms
 
 ```{eval-rst}

docs/conf.py

@@ -22,6 +22,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "AFIDs Utils"
+release = ilm.version("afids_utils")
 copyright = f"{datetime.date.today().year}, Anatomical Fiducials"
 author = "Anatomical Fiducials Contributors"
 
@@ -32,15 +33,15 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
+    "sphinx_copybutton",
+    "sphinx_design",
+    "sphinx_reredirects",
     "sphinxarg.ext",
+    "sphinx.ext.autodoc",
     "sphinx.ext.intersphinx",
     "sphinx.ext.napoleon",
-    "sphinx.ext.autodoc",
-    "sphinxcontrib.asciinema",
     "myst_parser",
-    "sphinx_copybutton",
-    "sphinx_reredirects",
-    "sphinx_design",
+    "numpydoc",
 ]
 
 
@@ -62,15 +63,10 @@
 
 autodoc_member_order = "bysource"
 autodoc_typehints = "description"
-# autodoc_type_aliases = {
-#     "ZipList": "snakebids.types.ZipList",
-#     "ZipListLike": "snakebids.types.ZipListLike",
-#     "InputsConfig": "snakebids.types.InputsConfig",
-# }
+# autodoc_type_aliases = {}
 autodoc_typehints_format = "short"
 autosummary_imported_members = True
 
-
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
@@ -84,6 +80,7 @@
 
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/1.24", None),
 }
 
 
@@ -110,9 +107,3 @@
 # redirects = {
 #     "migration/0.5_to_0.6.md": "migration/0.5_to_0.8.html",
 # }
-
-# sphinxcontrib_asciinema_defaults = {
-#     "preload": 1,
-#     "rows": 24,
-#     "speed": 3,
-# }

docs/general/main.md

@@ -0,0 +1,33 @@
+# Overview
+
+The purpose of the `afids_utils` package is to provide commonly used utility 
+functions (written in Python) that is applicable to a various anatomical
+fiducial (AFIDS) projects.  The `afids_utils` documentation provides a 
+comprehensive reference guide designed to assist users and developers in 
+effectively utilizing the functionalities  provided by the package's 
+application programming interface (API). It serves as a centralized resource 
+that offers detailed information about the various modules, classes, functions, 
+and constants available within the `afids_utils` package.
+
+Following the introduction, the API Reference pages provide a structured 
+organization of the package's modules and classes. Each module is described, explaining its role and the specific functionalities it offers. Detailed 
+information is provided for each class, including its methods, attributes, and 
+inheritance hierarchy, along with explanations of their purposes and usage.
+
+Additionally, the API page includes comprehensive documentation for the 
+functions and constants within the package. It describes the parameters 
+expected by each function, their data types, and their respective return 
+values. The documentation also highlights any optional parameters, default 
+values, and notable exceptions that may be raised.
+
+To assist developers in understanding and effectively utilizing the 
+`afids_utils` package, the API page may include code examples that 
+demonstrate the practical usage of the various modules, classes, functions, 
+and constants. These examples showcase common use cases, allowing developers 
+to grasp the concepts quickly and integrate them into their own projects.
+
+Furthermore, the API page may provide guidelines and best practices specific to 
+the `afids_utils` package. It may include recommendations on code structure, 
+error handling, performance optimization, and any other considerations that can 
+enhance the developer experience and ensure reliable and efficient usage of the 
+package.

docs/index.md

@@ -2,9 +2,20 @@
 ```
 
 ```{toctree}
-:caption: Reference
+:caption: General
+:name: general
+:hidden:
+:maxdepth: 2
+
+general/main
+```
+
+```{toctree}
+:caption: API Reference
+:name: api_reference
 :hidden:
 :maxdepth: 1
 
-api/main
+api/io
+api/transform
 ```

docs/requirements.txt

@@ -1,7 +1,7 @@
 sphinx-argparse>=0.4.0,<0.5
-sphinxcontrib-asciinema>=0.3.7,<0.4
-myst-parser>=1.0.0,<2.0
-furo>=2023.3.23,<2024
-sphinx_copybutton>=0.5.1,<0.6
+sphinx-copybutton>=0.5.1,<0.6
+sphinx-design>=0.4.1,<0.5.0
 sphinx-reredirects>=0.1,<0.2
-sphinx_design>=0.4.1,<0.5.0
+furo>=2023.3.23,<2024
+myst-parser>=1.0.0,<2.0
+numpydoc>=1.5.0,<1.6