Merge pull request #5 from jjjermiah/development

Development

.github/workflows/main.yml

@@ -1,4 +1,4 @@
-name: Unit Testsfrom nbiatoolkit import NBIAClient 
+name: Unit Tests
 
 on: [push]  
 

.gitignore

@@ -133,4 +133,8 @@ dmypy.json
 # Any Data
 tciaDownload*
 sandbox*
-old_src
+old_src
+resources/*
+dicomsort.py
+NBIA-toolkit.code-workspace
+docs/data/*

.readthedocs.yml

@@ -1,4 +1,4 @@
-# Required
+https://github.com/jjjermiah/NBIA-toolkit/tree/main# Required
 version: 2
 
 # Image to use

README.md

@@ -1,13 +1,11 @@
 [![PyTests](https://github.com/jjjermiah/NBIA-toolkit/actions/workflows/main.yml/badge.svg)](https://github.com/jjjermiah/NBIA-toolkit/actions/workflows/main.yml)
 
+# none of this works yet lol but it will soon
 # NBIA Toolkit 
 - Packaged code to access the NBIA REST API 
 
 See the [Wiki](https://github.com/jjjermiah/NBIA-toolkit/wiki) for more information.
 
-
-
-### none of this works yet lol but it will soon
 # nbiatoolkit
 
 A python package to query the National Biomedical Imaging Archive (NBIA) database.

docs/Makefile

@@ -0,0 +1,19 @@
+# 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

@@ -0,0 +1,2 @@
+```{include} ../CHANGELOG.md
+```

docs/conduct.md

@@ -0,0 +1,2 @@
+```{include} ../CONDUCT.md
+```

docs/conf.py

@@ -0,0 +1,36 @@
+# 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

@@ -0,0 +1,2 @@
+```{include} ../CONTRIBUTING.md
+```