started sphinx documentation. doesnt work yet

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = python -msphinx
+SPHINXPROJ    = nbiatoolkit
+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/changelog.md

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+```{include} ../CHANGELOG.md
+```

docs/conduct.md

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+```{include} ../CONDUCT.md
+```

docs/conf.py

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+# 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
+
+# -- Project information -----------------------------------------------------
+
+project = u"nbiatoolkit"
+copyright = u"2023, Jermiah Joseph"
+author = u"Jermiah Joseph"
+
+# -- 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 = [
+    "myst_nb",
+    "autoapi.extension",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.viewcode",
+]
+autoapi_dirs = ["../src"]
+
+# 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"]
+
+# -- 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 = "sphinx_rtd_theme"

docs/contributing.md

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+```{include} ../CONTRIBUTING.md
+```

docs/example.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Example Usage: python3 examples.ipynb\n",
+    "### Description: \n",
+    "This is a simple example of how to use the `nbiatoolkit` package."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Setup \n",
+    "\n",
+    "By default the client will use the Public API with the Guest Login credentials.\n",
+    "from the nbia which has access to all public data. \n",
+    "\n",
+    "To use your own credentials you can pass them in as parameters to the client using:\n",
+    "\n",
+    " `NBIAClient(username=\"YOUR_USERNAME\", password=\"YOUR_PASSWORD\")`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "2023-11-19 17:45:24,124 | NBIAClient | INFO | Setting up OAuth2 client... with username nbia_guest\n",
+      "2023-11-19 17:45:24,124 | NBIAClient | INFO | Setting up OAuth2 client... with username nbia_guest\n"
+     ]
+    }
+   ],
+   "source": [
+    "from nbiatoolkit import NBIAClient\n",
+    "\n",
+    "# Instantiate the client. \n",
+    "client = NBIAClient()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# import nbiatoolkit \n",
+    "# TODO::implement method forprint(nbiatoolkit.__version__)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Get Collection Methods"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Counts of Patients grouped by Body Parts\n",
+    "`getBodyPartCounts(collection: str = \"\", modality: str = \"\")`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "2023-11-19 17:42:42,892 | NBIAClient | INFO | Querying API endpoint: https://services.cancerimagingarchive.net/nbia-api/services/getBodyPartValuesAndCounts\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Total Number of Collections:98\n",
+      "First 5 body parts:\n",
+      "[{'BodyPartExamined': 'NOT SPECIFIED', 'Count': '8490'},\n",
+      " {'BodyPartExamined': 'ABDOMEN', 'Count': '2968'},\n",
+      " {'BodyPartExamined': 'ABDOMEN CAVIT', 'Count': '2'},\n",
+      " {'BodyPartExamined': 'ABDOMENPELVIC', 'Count': '2'},\n",
+      " {'BodyPartExamined': 'ABDOMENPELVIS', 'Count': '51'}]\n"
+     ]
+    }
+   ],
+   "source": [
+    "from pprint import pprint\n",
+    "bodypart_count = client.getBodyPartCounts()\n",
+    "print(\"Total Number of Collections:\" + str(len(bodypart_count)))\n",
+    "\n",
+    "print(\"First 5 body parts:\")\n",
+    "pprint(bodypart_count[0:5])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

docs/index.md

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+```{include} ../README.md
+```
+
+```{toctree}
+:maxdepth: 1
+:hidden:
+
+example.ipynb
+changelog.md
+contributing.md
+conduct.md
+autoapi/index
+```

docs/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=python -msphinx
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+set SPHINXPROJ=nbiatoolkit
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The Sphinx module was not found. Make sure you have Sphinx installed,
+	echo.then set the SPHINXBUILD environment variable to point to the full
+	echo.path of the 'sphinx-build' executable. Alternatively you may add the
+	echo.Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

docs/requirements.txt

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+myst-nb
+sphinx-autoapi
+sphinx-rtd-theme