diff --git a/.gitignore b/.gitignore
index 4d04522..1070006 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,8 +1,10 @@
 test-results.xml
 
-# ASTERIA User areas
+# ASTERIA User areas, ignore all files in these directories other than the gitignores
 scratch/*
+!scratch/.gitignore
 data/processed/*
+!data/processed/.gitignore
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
diff --git a/data/processed/.gitignore b/data/processed/.gitignore
new file mode 100644
index 0000000..f5b0070
--- /dev/null
+++ b/data/processed/.gitignore
@@ -0,0 +1,5 @@
+# Ignore all files in this directory
+*
+
+# Do not ignore this .gitignore
+!.gitignore
\ No newline at end of file
diff --git a/python/asteria/IO.py b/python/asteria/IO.py
index 72464e3..a135db1 100644
--- a/python/asteria/IO.py
+++ b/python/asteria/IO.py
@@ -1,4 +1,4 @@
-from os.path import isfile
+from os.path import isfile, isdir, dirname
 from .neutrino import Flavor
 
 import numpy as np
@@ -197,7 +197,10 @@ def find(group, Interactions, Hierarchy, Flavors, Enu, time):
     
 def save(config, Interactions, Hierarchy, Flavors, Enu, time, result, force=False):
     h5path = '/'.join([config.abs_base_path, config.IO.table.path])
-    
+
+    if not isdir(dirname(h5path)):
+        raise NotADirectoryError('Directory {0} not found, aborting.'.format(dirname(h5path)))
+
     # Test file existence 
     if not isfile(h5path):
         print('Creating file: {}'.format(h5path))
diff --git a/python/asteria/__init__.py b/python/asteria/__init__.py
index 394ccc8..0b6f69d 100644
--- a/python/asteria/__init__.py
+++ b/python/asteria/__init__.py
@@ -9,18 +9,3 @@
 """
 from __future__ import absolute_import
 from ._version import __version__
-import os
-
-
-src_path = os.path.realpath(__path__[0])
-base_path = os.sep.join(src_path.split(os.sep)[:-2])
-
-# Test for existence of scratch directory
-scratch_path = os.path.join(base_path, 'scratch')
-if not os.path.isdir(scratch_path):
-    os.mkdir(scratch_path)
-
-# Test for existence of processed directory
-processed_path = os.path.join(base_path, 'data', 'processed')
-if not os.path.isdir(processed_path):
-    os.mkdir(processed_path)
diff --git a/scratch/.gitignore b/scratch/.gitignore
new file mode 100644
index 0000000..f5b0070
--- /dev/null
+++ b/scratch/.gitignore
@@ -0,0 +1,5 @@
+# Ignore all files in this directory
+*
+
+# Do not ignore this .gitignore
+!.gitignore
\ No newline at end of file