Fix docs structure (#398)

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "docs/cyclops-webpage"]
 	path = docs/cyclops-webpage
-	url = git@github.com:amrit110/cyclops-webpage.git
+	url = git@github.com:VectorInstitute/cyclops-webpage.git

docs/source/api.rst

@@ -2,6 +2,6 @@ API Reference
 =============
 
 .. toctree::
-   :glob:
 
-   reference/api/*
+   reference/api/cyclops.query.rst
+   reference/api/cyclops.evaluate.rst

docs/source/tutorials.rst

@@ -3,7 +3,4 @@ Tutorials
 
 .. toctree::
 
-    tutorials/mimiciii/query_api.ipynb
-    tutorials/mimiciv/query_api.ipynb
-    tutorials/synthea/query_api.ipynb
-    tutorials/eicu/query_api.ipynb
+   tutorials_query

docs/source/tutorials/synthea/query_api.ipynb → docs/source/tutorials/omop/query_api.ipynb

@@ -5,18 +5,20 @@
    "id": "e337389b-1cfe-4796-a846-b4e1ba5690d6",
    "metadata": {},
    "source": [
-    "# Synthea query API tutorial"
+    "# OMOP query API tutorial"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "1efffc64",
    "metadata": {},
    "source": [
-    "This notebook shows examples of how to use the cyclops.query API on [Synthea](https://github.com/synthetichealth/synthea) in OMOP format.\n",
+    "This notebook shows examples of how to use the cyclops.query API to query EHR databases that follow the OMOP common data model. We showcase the examples on:\n",
     "\n",
-    "* First, generate synthea data using their releases. We used [v2.7.0](https://github.com/synthetichealth/synthea/releases/tag/v2.7.0) to generate data .\n",
-    "* Follow instructions provided in [ETL-Synthea](https://github.com/OHDSI/ETL-Synthea) to load the CSV data into a postgres database, and perform ETL to load the data into OMOP format."
+    "1. [Synthea](https://github.com/synthetichealth/synthea) in OMOP format.\n",
+    "\n",
+    "    * First, generate synthea data using their releases. We used [v2.7.0](https://github.com/synthetichealth/synthea/releases/tag/v2.7.0) to generate data .\n",
+    "    * Follow instructions provided in [ETL-Synthea](https://github.com/OHDSI/ETL-Synthea) to load the CSV data into a postgres database, and perform ETL to load the data into OMOP format."
    ]
   },
   {

docs/source/tutorials_query.rst

@@ -0,0 +1,15 @@
+query API
+=========
+
+The query API allows you to query EHR databases. It is a Python API that
+that communicates with postgresql databases. It is a wrapper around the
+SQLAlchemy ORM and uses SQLAlchemy query objects and functions to build
+queries.
+
+
+.. toctree::
+
+    tutorials/mimiciii/query_api.ipynb
+    tutorials/mimiciv/query_api.ipynb
+    tutorials/eicu/query_api.ipynb
+    tutorials/omop/query_api.ipynb