added documentation (#6)

* added read the docs * added documentation
BIH-CEI · Sep 28, 2024 · d157604 · d157604
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,33 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+Optional but recommended, declare the Python requirements required
+to build your documentation
+See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+   - requirements: docs/requirements.tx
+
diff --git a/README.md b/README.md
@@ -3,15 +3,13 @@
 An ontology-based Rare Disease Common Data Model (RD CDM) to enable 
 international registry use, HL7 FHIR, and GA4GH Phenopackets.
 
-<!-- Python CI Badge -->
-![Python CI](https://github.com/{OWNER}/{REPO}/actions/workflows/python_ci.yml/badge.svg)
-
-<!-- JSON Creation Badge -->
-![RD CDM v2.0.0 JSON Creation](https://img.shields.io/badge/RD%20CDM%20v2.0.0-JSON%20Created%20Successfully-brightgreen)
-
-<!-- Validation Badge -->
-![RD CDM v2.0.0 Validation](https://img.shields.io/badge/RD%20CDM%20v2.0.0-Validation)
+<!-- Python CI and Documentation Status Badges -->
+[![Python CI](https://github.com/{OWNER}/{REPO}/actions/workflows/python_ci.yml/badge.svg)](https://github.com/{OWNER}/{REPO}/actions/workflows/python_ci.yml)
+[![Documentation Status](https://readthedocs.org/projects/rd-cdm/badge/?version=latest)](https://rd-cdm.readthedocs.io/en/latest/?badge=latest)
 
+<!-- JSON Creation and Validation Badges -->
+![RD CDM v2.0.0 JSON Creation](https://img.shields.io/badge/RD%20CDM%20v2.0.0-JSON%20Created%20Successfully-blue)
+![RD CDM v2.0.0 Validation](https://img.shields.io/badge/RD%20CDM%20v2.0.0-Validation%20Successful-brightgreen)
 
 ## Table of Contents
 

diff --git a/docs/background/background_file.rst b/docs/background/background_file.rst
@@ -0,0 +1,2 @@
+RD CDM Background
+=================
diff --git a/docs/changelog.rst b/docs/changelog.rst
@@ -0,0 +1,2 @@
+RD CDM Changelog
+================
diff --git a/docs/conf.py b/docs/conf.py
@@ -14,10 +14,10 @@
 src_path = os.path.abspath(os.path.join('..', 'src'))
 sys.path.insert(0, src_path)
 
-project = 'template_for_python_projects'
-copyright = '2024, test'
-author = 'test'
-release = '0.0.1'
+project = 'Ontology-Based Rare Disease Common Data Model (RD CDM)'
+copyright = 'Berlin Institute of Health, Charité Universitätsmedizin Berlin'
+author = 'Adam SL Graefe'
+release = '2.0.0'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -35,6 +35,7 @@
 
 templates_path = ['_templates']
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+html_static_path = ['_static']
 
 pygments_style = 'sphinx'
 

diff --git a/docs/contributing.rst b/docs/contributing.rst
@@ -0,0 +1,2 @@
+RD CDM contributing
+===================
diff --git a/docs/index.rst b/docs/index.rst
@@ -3,13 +3,20 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to template_for_python_projects's documentation!
-=================================
+Welcome to the RD CDM documentation!
+====================================
 
 .. toctree::
    :maxdepth: 2
    :caption: Contents:
 
+   background/background_file
+   resources/resources_file
+   usage/usage_file
+   contributing
+   license
+   changelog
+
 
 
 Indices and tables

diff --git a/docs/license.rst b/docs/license.rst
@@ -0,0 +1,2 @@
+RD CDM license
+==============
diff --git a/docs/resources/resources_file.rst b/docs/resources/resources_file.rst
@@ -0,0 +1,2 @@
+RD CDM resources
+=================
diff --git a/docs/usage/usage_file.rst b/docs/usage/usage_file.rst
@@ -0,0 +1,2 @@
+RD CDM Usage
+============
diff --git a/pyproject.toml b/pyproject.toml
@@ -8,9 +8,12 @@ description = "TODO"
 readme = "README.md"
 requires-python = ">=3.10"
 keywords = [
-    "Test",
-    "TODO",
-    "ETC",
+    "Rare Diseases",
+    "Ontology",
+    "GA4GH Phenopacket Schema",
+    "HL7 FHIR",
+    "Inernational Patient Summary",
+
 ]
 license = { file = "LICENSE" }
 classifiers = [
@@ -34,10 +37,10 @@ test = ["pytest>=7.0.0,<8.0.0"]
 docs = ["sphinx>=7.0.0", "sphinx-rtd-theme>=1.3.0", "sphinx-copybutton>=0.5.0"]
 
 [project.urls]
-homepage = "https://github.com/frehburg/template_for_python_projects"
-repository = "https://github.com/frehburg/template_for_python_projects.git"
+homepage = "https://github.com/BIH-CEI/rd-cdm"
+repository = "https://github.com/BIH-CEI/rd-cdm"
 documentation = "https://frehburg.github.io/template_for_python_projects/stable"
-bugtracker = "https://github.com/frehburg/template_for_python_projects/issues"
+bugtracker = "https://github.com/BIH-CEI/rd-cdm/issues"
 
 [tool.setuptools]
 package-dir = { "" = "src" }