fixing copy bug

.docs/apidoc.sh

@@ -4,11 +4,6 @@
 #
 # sphinx-apidoc -o source/ ../spython
 
-function rename_folder() {
-    name=$1
-
-}
-
 HERE="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 BASE=$(dirname $HERE)
 cd $HERE

.docs/source/spython.client.rst

@@ -1,20 +1,27 @@
-spython.client package
-======================
-
+spython\.client package
+=======================
 
 Submodules
 ----------
 
-spython.client.shell module
----------------------------
+spython\.client\.recipe module
+------------------------------
+
+.. automodule:: spython.client.recipe
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+spython\.client\.shell module
+-----------------------------
 
 .. automodule:: spython.client.shell
     :members:
     :undoc-members:
     :show-inheritance:
 
-spython.client.test module
---------------------------
+spython\.client\.test module
+----------------------------
 
 .. automodule:: spython.client.test
     :members:

.docs/source/spython.image.cmd.rst

@@ -0,0 +1,46 @@
+spython\.image\.cmd package
+===========================
+
+Submodules
+----------
+
+spython\.image\.cmd\.create module
+----------------------------------
+
+.. automodule:: spython.image.cmd.create
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+spython\.image\.cmd\.export module
+----------------------------------
+
+.. automodule:: spython.image.cmd.export
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+spython\.image\.cmd\.importcmd module
+-------------------------------------
+
+.. automodule:: spython.image.cmd.importcmd
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+spython\.image\.cmd\.utils module
+---------------------------------
+
+.. automodule:: spython.image.cmd.utils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: spython.image.cmd
+    :members:
+    :undoc-members:
+    :show-inheritance:

.docs/source/spython.image.rst

@@ -1,41 +1,12 @@
-spython.image package
-=====================
+spython\.image package
+======================
 
-Submodules
-----------
+Subpackages
+-----------
 
-spython.image.base module
--------------------------
-
-.. automodule:: spython.image.base
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-spython.image.binary module
----------------------------
-
-.. automodule:: spython.image.binary
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-spython.image.instance module
------------------------------
-
-.. automodule:: spython.image.instance
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-spython.image.regexp module
----------------------------
-
-.. automodule:: spython.image.regexp
-    :members:
-    :undoc-members:
-    :show-inheritance:
+.. toctree::
 
+    spython.image.cmd
 
 Module contents
 ---------------

.docs/source/spython.instance.cmd.rst

@@ -0,0 +1,38 @@
+spython\.instance\.cmd package
+==============================
+
+Submodules
+----------
+
+spython\.instance\.cmd\.iutils module
+-------------------------------------
+
+.. automodule:: spython.instance.cmd.iutils
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+spython\.instance\.cmd\.start module
+------------------------------------
+
+.. automodule:: spython.instance.cmd.start
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+spython\.instance\.cmd\.stop module
+-----------------------------------
+
+.. automodule:: spython.instance.cmd.stop
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: spython.instance.cmd
+    :members:
+    :undoc-members:
+    :show-inheritance:

.docs/source/spython.instance.rst

@@ -0,0 +1,17 @@
+spython\.instance package
+=========================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    spython.instance.cmd
+
+Module contents
+---------------
+
+.. automodule:: spython.instance
+    :members:
+    :undoc-members:
+    :show-inheritance:

.docs/source/spython.logger.rst

@@ -1,27 +1,27 @@
-spython.logger package
-======================
+spython\.logger package
+=======================
 
 Submodules
 ----------
 
-spython.logger.message module
------------------------------
+spython\.logger\.message module
+-------------------------------
 
 .. automodule:: spython.logger.message
     :members:
     :undoc-members:
     :show-inheritance:
 
-spython.logger.progress module
-------------------------------
+spython\.logger\.progress module
+--------------------------------
 
 .. automodule:: spython.logger.progress
     :members:
     :undoc-members:
     :show-inheritance:
 
-spython.logger.spinner module
------------------------------
+spython\.logger\.spinner module
+-------------------------------
 
 .. automodule:: spython.logger.spinner
     :members:

.docs/source/spython.main.base.rst

@@ -1,27 +1,43 @@
-Singularity Python API Main
+spython\.main\.base package
 ===========================
 
 Submodules
 ----------
 
-spython.main.base.command module
---------------------------------
+spython\.main\.base\.command module
+-----------------------------------
 
 .. automodule:: spython.main.base.command
     :members:
     :undoc-members:
     :show-inheritance:
 
-spython.main.base.logger module
--------------------------------
+spython\.main\.base\.flags module
+---------------------------------
+
+.. automodule:: spython.main.base.flags
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+spython\.main\.base\.generate module
+------------------------------------
+
+.. automodule:: spython.main.base.generate
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+spython\.main\.base\.logger module
+----------------------------------
 
 .. automodule:: spython.main.base.logger
     :members:
     :undoc-members:
     :show-inheritance:
 
-spython.main.base.sutils module
--------------------------------
+spython\.main\.base\.sutils module
+----------------------------------
 
 .. automodule:: spython.main.base.sutils
     :members:

.docs/source/spython.main.parse.rst

@@ -0,0 +1,54 @@
+spython\.main\.parse package
+============================
+
+Submodules
+----------
+
+spython\.main\.parse\.converters module
+---------------------------------------
+
+.. automodule:: spython.main.parse.converters
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+spython\.main\.parse\.docker module
+-----------------------------------
+
+.. automodule:: spython.main.parse.docker
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+spython\.main\.parse\.environment module
+----------------------------------------
+
+.. automodule:: spython.main.parse.environment
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+spython\.main\.parse\.recipe module
+-----------------------------------
+
+.. automodule:: spython.main.parse.recipe
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+spython\.main\.parse\.singularity module
+----------------------------------------
+
+.. automodule:: spython.main.parse.singularity
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: spython.main.parse
+    :members:
+    :undoc-members:
+    :show-inheritance: