Merge pull request #2 from ArpiarSaundersLab/dev

Major Feature updates

Author: kennypavan

.gitignore

@@ -1,6 +1,7 @@
 data/
 db/
 env/
+env2/
 __pycache__/
 rdata/
 *.pyc
@@ -14,4 +15,5 @@ build_doc.sh
 build_wheel.sh
 .DS_Store
 /**/__pycache__/
-/**/.pytest_cache/
+/**/.pytest_cache/
+site/

README.md

@@ -1,11 +1,9 @@
-########################################################
-# Annsql uses the duckdb api to build the database and 
-# perform operations. You can access the .asql file in
-# R by simply installing the duckdb package and loading
-# the library and database. Once you've loaded the db
-# you can run any query you'd like.
-########################################################
+# Opening AnnSQL Databases in R
+Annsql uses the duckdb api to build the database and perform operations. You can access the .asql file in R by simply installing the duckdb package and loading the library and database. Once you've loaded the db you can run any query your heart desires.
+<br>
+<br>
 
+```
 #install the duckdb api dependency and load the library
 if (!requireNamespace("duckdb", quietly = TRUE)) {
 	install.packages("duckdb")
@@ -25,7 +23,7 @@ print(results)
 
 #don't forget to close the door
 dbDisconnect(con)
+```
+<br>
 
-
-
-
+While extended functionality in our Python based package is not currently implemented in R. AnnSQL databases can be opened, queried, and explored in R. 

examples/inteRoperability.R docs/R_usage.mdexamples/inteRoperability.R renamed to docs/R_usage.md

@@ -0,0 +1,4 @@
+# AnnSQL Class API
+
+::: src.AnnSQL.AnnSQL
+    handler: python

docs/api_annsql.md

@@ -0,0 +1,7 @@
+# BuildDb Class API
+**Note** This class is accessed by the `MakeDb` class for building an on-disk database. It is also used by the `AnnSQL` class to build an in-memory database. Generally, users shouldn't instantiate this class unless they pass their own database connection when instantiating the class. 
+
+<br>
+
+::: src.AnnSQL.BuildDb
+    handler: python

docs/api_builddb.md

@@ -0,0 +1,4 @@
+# MakeDb Class API
+
+::: src.AnnSQL.MakeDb
+    handler: python

docs/api_makedb.md

@@ -5,7 +5,7 @@
    "metadata": {},
    "source": [
     "# Basic Usage\n",
-    "Below, we give the the most streamlined example of how to use AnnSQL for a smaller datasets. This notebook shows how to use the in-memory querying capabilities of AnnSql. Depending on your system memory and the AnnData filesize, you may want to consider building local database using AnnSQL; however, if your dataset contains fewer than around 30k libraries, then this approach should work well."
+    "Below, we give the the most streamlined example of how to use AnnSQL for a smaller datasets. This notebook shows how to use the in-memory querying capabilities of AnnSql. Depending on your system memory and the AnnData filesize, you may want to consider building local database using AnnSQL; however, if your dataset contains fewer than around 30k cells, then this approach should work well."
    ]
   },
   {
@@ -72,7 +72,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Pass the adata object to the AnnSQL class.\n",
+    "### Pass the adata object to the AnnSQL class\n",
     "Below, we simply instantiate AnnSQL class with the adata object from above. Alternatively, you may pass a filepath to a h5ad file."
    ]
   },
@@ -99,7 +99,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Explore the data using SQL!\n",
+    "### Explore the data using SQL\n",
     "AnnSQL wraps around the powerful DuckDb SQL engine, you're now capable of running simple or complex queries on the dataset.\n",
     "\n",
     "### SELECT Example"
@@ -615,7 +615,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Filter by cell type (bulk_labels)"
+    "### Filter by cell type"
    ]
   },
   {
@@ -966,7 +966,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Count total cells by cell type (bulk_labels)"
+    "### Count total cells by cell type"
    ]
   },
   {
@@ -1077,6 +1077,13 @@
     "asql.query(\"SELECT bulk_labels, COUNT(*) as total FROM obs GROUP BY bulk_labels ORDER BY total DESC\")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Show all tables in the database"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 8,