init readthedocs

- Set up configuration files
- Set up autodoc to get io and transform modules
- Add badge to documentation on README

.readthedocs.yml

@@ -0,0 +1,29 @@
+# .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 +1,3 @@
 # 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)

docs/Makefile

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+# 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/main.md

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+# API
+
+## afids_utils.io
+
+```{eval_rst}
+    .. automodule:: afids_utils.io
+        :members:
+```
+
+## afids_utils.transforms
+
+```{eval_rst}
+    .. automodule:: afids_utils.transforms
+        :members:
+```

docs/conf.py

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+# 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"
+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 = [
+    "sphinxarg.ext",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autodoc",
+    "sphinxcontrib.asciinema",
+    "myst_parser",
+    "sphinx_copybutton",
+    "sphinx_reredirects",
+    "sphinx_design",
+]
+
+
+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 = {
+#     "ZipList": "snakebids.types.ZipList",
+#     "ZipListLike": "snakebids.types.ZipListLike",
+#     "InputsConfig": "snakebids.types.InputsConfig",
+# }
+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),
+}
+
+
+# -- 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",
+# }
+
+# sphinxcontrib_asciinema_defaults = {
+#     "preload": 1,
+#     "rows": 24,
+#     "speed": 3,
+# }

docs/index.md

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+```{include} ../README.md
+```
+
+```{toctree}
+:caption: Reference
+:hidden:
+:maxdepth: 1
+
+api/main
+```

docs/requirements.txt

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+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-reredirects>=0.1,<0.2
+sphinx_design>=0.4.1,<0.5.0