Merge pull request #8 from kaitj/docs/readthedocs

Documentation Page

.readthedocs.yml

@@ -0,0 +1,25 @@
+---
+# .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:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF
+formats: [pdf]
+build:
+  os: ubuntu-20.04
+  tools:
+    python: '3.10'
+python:
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .

README.md

@@ -1 +1,8 @@
 # Anatomical Fiducials (AFIDs) Utility Tools
+
+[![Documentation Status](https://readthedocs.org/projects/afids-utils/badge/?version=latest)](https://afids-utils.readthedocs.io/en/latest/?badge=latest)
+
+The `afids_utils` package provides common utilities for projects involving 
+anatomical fiducials (AFIDs). For a comprehensive list of available utilities 
+refer to the [documentation](https://afids-utils.readthedocs.io/en/stable) 
+page.

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
@@ -32,7 +32,23 @@
 def get_afid(
     fcsv_path: PathLike[str] | str, fid_num: int
 ) -> NDArray[np.single]:
-    """Extract specific fiducial's spatial coordinates"""
+    """
+    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
+    -------
+    numpy.ndarray[shape=(3,), dtype=numpy.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)
     fcsv_df = pl.scan_csv(
@@ -51,7 +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=numpy.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/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/api/io.md

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

docs/api/transform.md

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

docs/conf.py

@@ -0,0 +1,109 @@
+# flake8: noqa
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+import datetime
+import importlib.metadata as ilm
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath("../"))
+
+# -- Project information -----------------------------------------------------
+
+project = "AFIDs Utils"
+release = ilm.version("afids_utils")
+copyright = f"{datetime.date.today().year}, Anatomical Fiducials"
+author = "Anatomical Fiducials Contributors"
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# 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",
+    "myst_parser",
+    "numpydoc",
+]
+
+
+myst_enable_extensions = [
+    "attrs_block",
+]
+myst_enable_extensions = [
+    "attrs_block",
+    "attrs_inline",
+    "tasklist",
+    "deflist",
+    "fieldlist",
+]
+myst_number_code_blocks = ["python", "yaml"]
+
+
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+
+autodoc_member_order = "bysource"
+autodoc_typehints = "description"
+# 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"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+
+master_doc = "index"
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/1.24", None),
+}
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "furo"
+html_theme_options = {
+    "source_repository": "https://github.com/afids/afids-utils",
+    "source_branch": "main",
+    "source_directory": "docs/",
+}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+# templates_path = ["_templates"]
+
+html_css_files = ["css/typealiases.css"]
+
+# redirects = {
+#     "migration/0.5_to_0.6.md": "migration/0.5_to_0.8.html",
+# }

docs/index.md

@@ -0,0 +1,12 @@
+```{include} ../README.md
+```
+
+```{toctree}
+:caption: API Reference
+:name: api_reference
+:hidden:
+:maxdepth: 1
+
+api/io
+api/transform
+```

docs/requirements.txt

@@ -0,0 +1,7 @@
+sphinx-argparse>=0.4.0,<0.5
+sphinx-copybutton>=0.5.1,<0.6
+sphinx-design>=0.4.1,<0.5.0
+sphinx-reredirects>=0.1,<0.2
+furo>=2023.3.23,<2024
+myst-parser>=1.0.0,<2.0
+numpydoc>=1.5.0,<1.6