diff --git a/scripts/update_README.py b/scripts/update_README.py
index c530ae58..652d5904 100755
--- a/scripts/update_README.py
+++ b/scripts/update_README.py
@@ -136,10 +136,15 @@ def update_documentation(data):
         
   
   items = []
+  dirname = os.path.basename(os.getcwd())
   command = "git ls-tree --full-tree --name-only HEAD:src/%s"
-  command = command%(os.path.basename(os.getcwd()))
+  command = command%(dirname)
   try:
-    tracked_files = subprocess.check_output(command.split())
+    if dirname != 'src':
+      p = subprocess.Popen(command.split(),stdout=subprocess.PIPE)
+      tracked_files = p.stdout.read()
+    else:
+      tracked_files = ""
     tracked_files = tracked_files.splitlines()
   except:
     tracked_files = []
diff --git a/src/README.rst b/src/README.rst
index d7d9b4f9..6cacb87a 100644
--- a/src/README.rst
+++ b/src/README.rst
@@ -108,37 +108,6 @@ should be always checked. For example, when creating a directory the existence
 of the directory has to be checked.
 
 
-Needed Modules
-==============
-
-.. Do not edit this section. It was auto-generated from the
-.. NEEDED_MODULES file.
-
-* `AOs <http://github.com/LCPQ/quantum_package/tree/master/src/AOs>`_
-* `BiInts <http://github.com/LCPQ/quantum_package/tree/master/src/BiInts>`_
-* `Bitmask <http://github.com/LCPQ/quantum_package/tree/master/src/Bitmask>`_
-* `CISD <http://github.com/LCPQ/quantum_package/tree/master/src/CISD>`_
-* `CISD_SC2_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_SC2_selected>`_
-* `CISD_selected <http://github.com/LCPQ/quantum_package/tree/master/src/CISD_selected>`_
-* `DensityMatrix <http://github.com/LCPQ/quantum_package/tree/master/src/DensityMatrix>`_
-* `Dets <http://github.com/LCPQ/quantum_package/tree/master/src/Dets>`_
-* `Electrons <http://github.com/LCPQ/quantum_package/tree/master/src/Electrons>`_
-* `Ezfio_files <http://github.com/LCPQ/quantum_package/tree/master/src/Ezfio_files>`_
-* `Full_CI <http://github.com/LCPQ/quantum_package/tree/master/src/Full_CI>`_
-* `Generators_full <http://github.com/LCPQ/quantum_package/tree/master/src/Generators_full>`_
-* `Hartree_Fock <http://github.com/LCPQ/quantum_package/tree/master/src/Hartree_Fock>`_
-* `MOGuess <http://github.com/LCPQ/quantum_package/tree/master/src/MOGuess>`_
-* `MonoInts <http://github.com/LCPQ/quantum_package/tree/master/src/MonoInts>`_
-* `MOs <http://github.com/LCPQ/quantum_package/tree/master/src/MOs>`_
-* `MP2 <http://github.com/LCPQ/quantum_package/tree/master/src/MP2>`_
-* `Nuclei <http://github.com/LCPQ/quantum_package/tree/master/src/Nuclei>`_
-* `Output <http://github.com/LCPQ/quantum_package/tree/master/src/Output>`_
-* `Perturbation <http://github.com/LCPQ/quantum_package/tree/master/src/Perturbation>`_
-* `SC2 <http://github.com/LCPQ/quantum_package/tree/master/src/SC2>`_
-* `Selectors_full <http://github.com/LCPQ/quantum_package/tree/master/src/Selectors_full>`_
-* `SingleRefMethod <http://github.com/LCPQ/quantum_package/tree/master/src/SingleRefMethod>`_
-* `Utils <http://github.com/LCPQ/quantum_package/tree/master/src/Utils>`_
-
 Documentation
 =============