diff --git a/data_specification/__init__.py b/data_specification/__init__.py
index 7036e32..7b4eb69 100644
--- a/data_specification/__init__.py
+++ b/data_specification/__init__.py
@@ -16,50 +16,51 @@
 """ Used to generate memory images for a SpiNNaker CPU core from a set of \
     instructions.
 
-The main part of this package is the \
-:py:class:`DataSpecificationGenerator` \
-class. This is used to generate a "Data Specification", which can then be \
-executed to produce a memory image.  This package also handles this function \
-if required, through the \
+The main part of this package is the
+:py:class:`DataSpecificationGenerator`
+class. This is used to generate a "Data Specification", which can then be
+executed to produce a memory image.  This package also handles this function
+if required, through the
 :py:class:`DataSpecificationExecutor` class.
 
 Functional Requirements
 =======================
 
-Creation of a Data Specification Language file which can be executed to \
+Creation of a Data Specification Language file which can be executed to
 produce a memory image.
 
-   * Any errors that can be checked during the creation of the \
-     specification should throw an exception.
+* Any errors that can be checked during the creation of the specification
+  should throw an exception.
 
-   * It will be impossible to detect all errors at creation time.
+* It will be impossible to detect all errors at creation time.
 
-   * There should be no assumption of where the data specification will \
-     be stored, although a default provision of a way to write the \
-     specification to a file is acceptable.
+* There should be no assumption of where the data specification will be
+  stored, although a default provision of a way to write the specification to
+  a file is acceptable.
 
 Execution of a Data Specification Language file, producing a memory image.
 
-   * This should detect any errors during execution and report them, \
-     halting the execution.
+* This should detect any errors during execution and report them, halting the
+  execution.
 
-   * There should be no assumption of where the data specification is \
-     read from, although a default provision of a way to read the \
-     specification from a file is acceptable.
+* There should be no assumption of where the data specification is read from,
+  although a default provision of a way to read the specification from a file
+  is acceptable.
 
 Use Cases
 =========
 
 There are a number of use-cases of this library:
 
-  * :py:class:`DataSpecificationGenerator` \
-    is used to create a compressed memory image which can be expanded later, \
-    to reduce the amount of data that needs to be transferred over a slow \
-    connection.
+* :py:class:`DataSpecificationGenerator` is used to create a compressed memory
+  image which can be expanded later, to reduce the amount of data that needs
+  to be transferred over a slow connection.
 
-  * :py:class:`DataSpecificationExecutor` \
-    is used to execute a previously generated specification at the receiving \
-    end of a slow connection.
+* :py:class:`DataSpecificationExecutor` is used to execute a previously
+  generated specification at the receiving end of a slow connection.
+
+Main API
+========
 """
 from data_specification._version import (  # noqa
     __version__, __version_name__, __version_month__, __version_year__)
diff --git a/data_specification/data_specification_executor_functions.py b/data_specification/data_specification_executor_functions.py
index c87cc6d..eac33dc 100644
--- a/data_specification/data_specification_executor_functions.py
+++ b/data_specification/data_specification_executor_functions.py
@@ -37,6 +37,10 @@
 class DataSpecificationExecutorFunctions(AbstractExecutorFunctions):
     """ This class includes the function related to each of the commands\
         of the data specification file.
+
+    .. note::
+        DSG operations not mentioned in this class will cause an error during
+        DSE if used.
     """
 
     __slots__ = [
diff --git a/data_specification/data_specification_generator.py b/data_specification/data_specification_generator.py
index fa3a8fc..1fe8530 100644
--- a/data_specification/data_specification_generator.py
+++ b/data_specification/data_specification_generator.py
@@ -2379,10 +2379,11 @@ def _write_command_to_files(self, cmd_word_list, cmd_string, indent=False,
                                 outdent=False, no_instruction_number=False):
         """ Writes the binary command to the binary output file and, if the\
             user has requested a text output for debug purposes, also write\
-            the text version to the text file.\
-            Setting the optional parameter ``indent`` to True causes\
-            subsequent commands to be indented by two spaces relative to this\
-            one. Similarly, setting ``outdent`` to True, reverses this spacing.
+            the text version to the text file.
+
+        Setting the optional parameter ``indent`` to ``True`` causes subsequent
+        commands to be indented by two spaces relative to this one. Similarly,
+        setting ``outdent`` to ``True`` reverses this spacing.
 
         :param bytearray cmd_word_list: list of binary words to be added to
             the binary data specification file
@@ -2420,8 +2421,10 @@ def _write_command_to_files(self, cmd_word_list, cmd_string, indent=False,
 
     @property
     def region_sizes(self):
-        """ A list of sizes of each region that has been reserved. Note that\
-            the list will include 0s for each non-reserved region.
+        """ A list of sizes of each region that has been reserved.
+
+        .. note::
+            The list will include ``0`` for each non-reserved region.
 
         :rtype: list(int)
         """
@@ -2430,7 +2433,7 @@ def region_sizes(self):
     @property
     def current_region(self):
         """ The ID of the current DSG region we're writing to.\
-            If not yet writing to any region, None.
+            If not yet writing to any region, ``None``.
 
         :rtype: int or None
         """
diff --git a/data_specification/spi/abstract_executor_functions.py b/data_specification/spi/abstract_executor_functions.py
index 7128a92..7b79cd5 100644
--- a/data_specification/spi/abstract_executor_functions.py
+++ b/data_specification/spi/abstract_executor_functions.py
@@ -29,6 +29,8 @@ def execute_break(self, cmd):  # pragma: no cover
         """ This command raises an exception to stop the execution of the \
             data spec executor (DSE).
 
+        Implements :py:obj:`~.BREAK`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -41,6 +43,8 @@ def execute_break(self, cmd):  # pragma: no cover
     def execute_nop(self, cmd):
         """ This command executes no operation.
 
+        Implements :py:obj:`~.NOP`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :rtype: None
@@ -52,6 +56,8 @@ def execute_reserve(self, cmd):  # pragma: no cover
         """ This command reserves a region and assigns some memory space \
             to it.
 
+        Implements :py:obj:`~.RESERVE`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -64,6 +70,8 @@ def execute_reserve(self, cmd):  # pragma: no cover
     def execute_free(self, cmd):  # pragma: no cover
         """ This command frees some memory.
 
+        Implements :py:obj:`~.FREE`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -76,6 +84,8 @@ def execute_free(self, cmd):  # pragma: no cover
     def execute_declare_rng(self, cmd):  # pragma: no cover
         """ This command declares a random number generator.
 
+        Implements :py:obj:`~.DECLARE_RNG`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -88,6 +98,8 @@ def execute_declare_rng(self, cmd):  # pragma: no cover
     def execute_random_dist(self, cmd):  # pragma: no cover
         """ This command defines a random disribution.
 
+        Implements :py:obj:`~.DECLARE_RANDOM_DIST`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -100,6 +112,8 @@ def execute_random_dist(self, cmd):  # pragma: no cover
     def execute_get_random_rumber(self, cmd):  # pragma: no cover
         """ This command obtains a random number from a distribution.
 
+        Implements :py:obj:`~.GET_RANDOM_NUMBER`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -112,6 +126,8 @@ def execute_get_random_rumber(self, cmd):  # pragma: no cover
     def execute_start_struct(self, cmd):  # pragma: no cover
         """ This command starts to define a structure.
 
+        Implements :py:obj:`~.START_STRUCT`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -124,6 +140,8 @@ def execute_start_struct(self, cmd):  # pragma: no cover
     def execute_struct_elem(self, cmd):  # pragma: no cover
         """ This command adds an element to a structure.
 
+        Implements :py:obj:`~.STRUCT_ELEM`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -136,6 +154,8 @@ def execute_struct_elem(self, cmd):  # pragma: no cover
     def execute_end_struct(self, cmd):  # pragma: no cover
         """ This command completes the definition of a structure.
 
+        Implements :py:obj:`~.END_STRUCT`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -148,6 +168,8 @@ def execute_end_struct(self, cmd):  # pragma: no cover
     def execute_start_constructor(self, cmd):  # pragma: no cover
         """ This command starts the definition of a function.
 
+        Implements :py:obj:`~.START_CONSTRUCTOR`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -160,6 +182,8 @@ def execute_start_constructor(self, cmd):  # pragma: no cover
     def execute_end_constructor(self, cmd):  # pragma: no cover
         """ This command ends the definition of a function.
 
+        Implements :py:obj:`~.END_CONSTRUCTOR`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -172,6 +196,8 @@ def execute_end_constructor(self, cmd):  # pragma: no cover
     def execute_construct(self, cmd):  # pragma: no cover
         """ This command calls a function.
 
+        Implements :py:obj:`~.CONSTRUCT`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -184,6 +210,8 @@ def execute_construct(self, cmd):  # pragma: no cover
     def execute_read(self, cmd):  # pragma: no cover
         """ This command reads a word from memory.
 
+        Implements :py:obj:`~.READ`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -198,6 +226,8 @@ def execute_write(self, cmd):  # pragma: no cover
             number of times as identified by either a value in the command \
             or a register value.
 
+        Implements :py:obj:`~.WRITE`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -210,6 +240,8 @@ def execute_write(self, cmd):  # pragma: no cover
     def execute_write_array(self, cmd):  # pragma: no cover
         """ This command writes an array of values in the specified region.
 
+        Implements :py:obj:`~.WRITE_ARRAY`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -222,6 +254,8 @@ def execute_write_array(self, cmd):  # pragma: no cover
     def execute_write_struct(self, cmd):  # pragma: no cover
         """ This command writes a structure to memory.
 
+        Implements :py:obj:`~.WRITE_STRUCT`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -235,6 +269,8 @@ def execute_block_copy(self, cmd):  # pragma: no cover
         """ This command copies a block of memory from one location to \
             another.
 
+        Implements :py:obj:`~.BLOCK_COPY`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -248,6 +284,8 @@ def execute_switch_focus(self, cmd):  # pragma: no cover
         """ This command switches the focus to the desired, already allocated,\
             memory region.
 
+        Implements :py:obj:`~.SWITCH_FOCUS`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -260,6 +298,8 @@ def execute_switch_focus(self, cmd):  # pragma: no cover
     def execute_loop(self, cmd):  # pragma: no cover
         """ This command starts a loop.
 
+        Implements :py:obj:`~.LOOP`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -272,6 +312,8 @@ def execute_loop(self, cmd):  # pragma: no cover
     def execute_break_loop(self, cmd):  # pragma: no cover
         """ This command stops a loop early.
 
+        Implements :py:obj:`~.BREAK_LOOP`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -284,6 +326,8 @@ def execute_break_loop(self, cmd):  # pragma: no cover
     def execute_end_loop(self, cmd):  # pragma: no cover
         """ This command finishes a loop.
 
+        Implements :py:obj:`~.END_LOOP`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -296,6 +340,8 @@ def execute_end_loop(self, cmd):  # pragma: no cover
     def execute_if(self, cmd):  # pragma: no cover
         """ This command does a conditional branch.
 
+        Implements :py:obj:`~.IF`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -308,6 +354,8 @@ def execute_if(self, cmd):  # pragma: no cover
     def execute_else(self, cmd):  # pragma: no cover
         """ This command handles the other branch of a conditional.
 
+        Implements :py:obj:`~.ELSE`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -320,6 +368,8 @@ def execute_else(self, cmd):  # pragma: no cover
     def execute_end_if(self, cmd):  # pragma: no cover
         """ This command ends a conditional.
 
+        Implements :py:obj:`~.END_IF`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -333,6 +383,8 @@ def execute_mv(self, cmd):  # pragma: no cover
         """ This command moves an immediate value to a register or copies the \
             value of a register to another register.
 
+        Implements :py:obj:`~.MV`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -345,6 +397,8 @@ def execute_mv(self, cmd):  # pragma: no cover
     def execute_get_wr_ptr(self, cmd):  # pragma: no cover
         """ This command gets the current write pointer.
 
+        Implements :py:obj:`~.GET_WR_PTR`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -357,6 +411,8 @@ def execute_get_wr_ptr(self, cmd):  # pragma: no cover
     def execute_set_wr_ptr(self, cmd):  # pragma: no cover
         """ This command sets the current write pointer.
 
+        Implements :py:obj:`~.SET_WR_PTR`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -383,6 +439,8 @@ def execute_align_wr_ptr(self, cmd):  # pragma: no cover
         """ This command moves the write pointer to be at the start of the \
             next word if it isn't already at the start of a word.
 
+        Implements :py:obj:`~.ALIGN_WR_PTR`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -395,6 +453,8 @@ def execute_align_wr_ptr(self, cmd):  # pragma: no cover
     def execute_arith_op(self, cmd):  # pragma: no cover
         """ This command performs an arithmetic operation.
 
+        Implements :py:obj:`~.ARITH_OP`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -407,6 +467,8 @@ def execute_arith_op(self, cmd):  # pragma: no cover
     def execute_logic_op(self, cmd):  # pragma: no cover
         """ This command performs a logical operation.
 
+        Implements :py:obj:`~.LOGIC_OP`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -419,6 +481,8 @@ def execute_logic_op(self, cmd):  # pragma: no cover
     def execute_reformat(self, cmd):  # pragma: no cover
         """ This command is never generated!
 
+        Implements :py:obj:`~.REFORMAT`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -431,6 +495,8 @@ def execute_reformat(self, cmd):  # pragma: no cover
     def execute_copy_struct(self, cmd):  # pragma: no cover
         """ This command copies a structure from one slot to another.
 
+        Implements :py:obj:`~.COPY_STRUCT`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -444,6 +510,8 @@ def execute_copy_param(self, cmd):  # pragma: no cover
         """ This command copies a field of a structure to another field of \
             a possibly-different structure.
 
+        Implements :py:obj:`~.COPY_PARAM`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -456,6 +524,8 @@ def execute_copy_param(self, cmd):  # pragma: no cover
     def execute_write_param(self, cmd):  # pragma: no cover
         """ This command handles a single element of a structure.
 
+        Implements :py:obj:`~.WRITE_PARAM`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -468,6 +538,8 @@ def execute_write_param(self, cmd):  # pragma: no cover
     def execute_write_param_component(self, cmd):  # pragma: no cover
         """ This command is never generated!
 
+        Implements :py:obj:`~.WRITE_PARAM_COMPONENT`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -480,6 +552,8 @@ def execute_write_param_component(self, cmd):  # pragma: no cover
     def execute_print_val(self, cmd):  # pragma: no cover
         """ This command prints a value to the log.
 
+        Implements :py:obj:`~.PRINT_VAL`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -492,6 +566,8 @@ def execute_print_val(self, cmd):  # pragma: no cover
     def execute_print_txt(self, cmd):  # pragma: no cover
         """ This command prints a short string to the log.
 
+        Implements :py:obj:`~.PRINT_TXT`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -504,6 +580,8 @@ def execute_print_txt(self, cmd):  # pragma: no cover
     def execute_print_struct(self, cmd):  # pragma: no cover
         """ This command prints a structure to the log.
 
+        Implements :py:obj:`~.PRINT_STRUCT`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -516,6 +594,8 @@ def execute_print_struct(self, cmd):  # pragma: no cover
     def execute_read_param(self, cmd):  # pragma: no cover
         """ This command extracts an element from a structure.
 
+        Implements :py:obj:`~.READ_PARAM`
+
         :param int cmd: the command which triggered the function call
         :return: No value returned
         :raise DataSpecificationSyntaxError:\
@@ -528,6 +608,8 @@ def execute_read_param(self, cmd):  # pragma: no cover
     def execute_end_spec(self, cmd):  # pragma: no cover
         """ This command marks the end of the specification program.
 
+        Implements :py:obj:`~.END_SPEC`
+
         :param int cmd: the command which triggered the function call
         :return: A special marker to signal the end.
         :raise DataSpecificationSyntaxError:\
diff --git a/doc/source/conf.py b/doc/source/conf.py
index ca2e934..7cae536 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -29,7 +29,6 @@
 
 # import sys
 import os
-from sphinx import apidoc
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -53,7 +52,7 @@
 
 intersphinx_mapping = {
     'python': ('https://docs.python.org/3.6', None),
-    'numpy': ("https://docs.scipy.org/doc/numpy/", None),
+    'numpy': ("https://numpy.org/doc/stable/", None),
     'spinn_machine': (
         'https://spinnmachine.readthedocs.io/en/latest/', None),
 }
@@ -363,8 +362,43 @@
     if (os.path.isfile(f) and f.endswith(
             ".rst") and f != "index.rst" and f != "modules.rst"):
         os.remove(f)
-apidoc.main([None, '-o', ".", "../../data_specification",
-             # Exclusions
-             "../../data_specification/[dm]*.py",
-             "../../data_specification/spi/a*.py",
-             "../../data_specification/enums/[a-z]*.py"])
+
+
+# We want to document __call__ when encountered
+autodoc_default_options = {
+    "members": True,
+    "special-members": "__call__"
+}
+
+
+def filtered_files(base, excludes=None):
+    if not excludes:
+        excludes = []
+    for root, _dirs, files in os.walk(base):
+        for filename in files:
+            if filename.endswith(".py") and not filename.startswith("_"):
+                full = root + "/" + filename
+                if full not in excludes:
+                    yield full
+
+
+# UGH!
+output_dir = os.path.abspath(".")
+os.chdir("../..")
+
+# We only document __init__.py files... except for these special cases.
+# Use the unix full pathname from the root of the checked out repo
+explicit_wanted_files = [
+    "data_specification/constants.py",
+    "data_specification/utility_calls.py",
+    "data_specification/exceptions.py"]
+options = ['-o', output_dir, "data_specification"]
+options.extend(filtered_files("data_specification", explicit_wanted_files))
+try:
+    # Old style API; Python 2.7
+    from sphinx import apidoc
+    options = [None] + options
+except ImportError:
+    # New style API; Python 3.6 onwards
+    from sphinx.ext import apidoc
+apidoc.main(options)
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 6b25e10..7382258 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -1,21 +1,20 @@
 These pages document the python code for the DataSpecification_ module
 which is part of the SpiNNaker_ Project.
 
-This code depends on SpiNNUtils_, SpiNNMachine_ and SpiNNStorageHandlers_  (Combined_documentation_).
+This code depends on SpiNNUtils_ and SpiNNMachine_ (Combined_documentation_).
 
 .. _SpiNNaker: http://apt.cs.manchester.ac.uk/projects/SpiNNaker/
 .. _DataSpecification: https://github.com/SpiNNakerManchester/DataSpecification
 .. _SpiNNUtils: http://spinnutils.readthedocs.io
 .. _SpiNNMachine: http://spinnmachine.readthedocs.io
-.. _SpiNNStorageHandlers: http://spinnstoragehandlers.readthedocs.io
 .. _Combined_documentation: http://spinnakermanchester.readthedocs.io
 
-
 Data Specification
 ==================
 
 .. automodule:: data_specification
    :special-members:
+   :noindex:
 
 Contents
 --------
@@ -25,11 +24,9 @@ Contents
 
    modules
 
-
 Indices and tables
 ------------------
 
 * :ref:`genindex`
 * :ref:`modindex`
 * :ref:`search`
-