diff --git a/.gitignore b/.gitignore
index c3957d2e0..c80e00ac7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,6 @@
 # python artifacts
 *.pyc
+docs/projectq.*.rst
+*.so
+build/
+var/
diff --git a/docs/conf.py b/docs/conf.py
index 971cefd8d..ef791d9ae 100755
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -21,6 +21,18 @@
 import sys
 sys.path.insert(0, os.path.abspath('..'))
 
+import projectq
+# Also import all the modules that are not automatically imported
+import projectq.libs.math
+import projectq.libs.revkit
+import projectq.setups.default
+import projectq.setups.grid
+import projectq.setups.ibm
+import projectq.setups.ibm16
+import projectq.setups.linear
+import projectq.setups.restrictedgateset
+import projectq.setups.decompositions
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -33,8 +45,11 @@
 import sphinx_rtd_theme
 
 extensions = [
-    'sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'sphinx.ext.mathjax',
-    'sphinx.ext.autosummary', 'sphinx.ext.linkcode',
+    'sphinx.ext.autodoc',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.linkcode',
 ]
 
 autosummary_generate = True
@@ -125,7 +140,6 @@
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
-
 # -- Options for HTML output ----------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -271,8 +285,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'projectq.tex', 'projectq Documentation',
-     'a', 'manual'),
+    (master_doc, 'projectq.tex', 'projectq Documentation', 'a', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -307,30 +320,24 @@
 #
 # latex_domain_indices = True
 
-
 # -- Options for manual page output ---------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'projectq', 'projectq Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, 'projectq', 'projectq Documentation', [author], 1)]
 
 # If true, show URL addresses after external links.
 #
 # man_show_urls = False
 
-
 # -- Options for Texinfo output -------------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'projectq', 'projectq Documentation',
-     author, 'projectq', 'One line description of project.',
-     'Miscellaneous'),
+    (master_doc, 'projectq', 'projectq Documentation', author, 'projectq',
+     'One line description of project.', 'Miscellaneous'),
 ]
 
 # Documents to append as an appendix to all manuals.
@@ -351,7 +358,6 @@
 
 # -- Options for sphinx.ext.linkcode --------------------------------------
 import inspect
-import projectq
 
 
 def linkcode_resolve(domain, info):
@@ -381,7 +387,11 @@ def linkcode_resolve(domain, info):
         return None
     else:
         try:
-            obj = eval(info['module'] + '.' + info['fullname'])
+            if ('module' in info and 'fullname' in info
+                and info['module'] and info['fullname']):
+                obj = eval(info['module'] + '.' + info['fullname'])
+            else:
+                return None
         except AttributeError:
             # Object might be a non-static attribute of a class, e.g.,
             # self.num_qubits, which would only exist after init was called.
@@ -400,8 +410,8 @@ def linkcode_resolve(domain, info):
                 if len(new_higher_name) <= 1:
                     obj = eval(info['module'])
                 else:
-                    obj = eval(info['module'] + '.' +
-                               '.'.join(new_higher_name[:-1]))
+                    obj = eval(info['module'] + '.'
+                               + '.'.join(new_higher_name[:-1]))
                 filepath = inspect.getsourcefile(obj)
                 line_number = inspect.getsourcelines(obj)[1]
             except:
@@ -409,6 +419,124 @@ def linkcode_resolve(domain, info):
         # Only require relative path projectq/relative_path
         projectq_path = inspect.getsourcefile(projectq)[:-11]
         relative_path = os.path.relpath(filepath, projectq_path)
-        url = (github_url + github_tag + "/projectq/" + relative_path + "#L" +
-               str(line_number))
+        url = (github_url + github_tag + "/projectq/" + relative_path + "#L"
+               + str(line_number))
         return url
+
+
+# ------------------------------------------------------------------------------
+
+import importlib
+sys.path.append(os.path.abspath('.'))
+desc = importlib.import_module('package_description')
+
+PackageDescription = desc.PackageDescription
+
+# ------------------------------------------------------------------------------
+# Define the description of ProjectQ packages and their submodules below.
+#
+# In order for the automatic package recognition to work properly, it is
+# important that PackageDescription of sub-packages appear earlier in the list
+# than their parent package (see for example libs.math and libs.revkit
+# compared to libs).
+#
+# It is also possible to customize the presentation of submodules (see for
+# example the setups and setups.decompositions) or even to have private
+# sub-modules listed in the documentation page of a parent packages (see for
+# example the cengines package)
+
+descriptions = [
+    PackageDescription('backends'),
+    PackageDescription('cengines',
+                       desc='''
+The ProjectQ compiler engines package.
+'''),
+    PackageDescription('libs.math',
+                       desc='''
+A tiny math library which will be extended thoughout the next weeks. Right now, it only contains the math functions necessary to run Beauregard's implementation of Shor's algorithm.
+'''),
+    PackageDescription('libs.revkit',
+                       desc='''
+This library integrates `RevKit <https://msoeken.github.io/revkit.html>`_ into
+ProjectQ to allow some automatic synthesis routines for reversible logic.  The
+library adds the following operations that can be used to construct quantum
+circuits:
+
+- :class:`~projectq.libs.revkit.ControlFunctionOracle`: Synthesizes a reversible circuit from Boolean control function
+- :class:`~projectq.libs.revkit.PermutationOracle`: Synthesizes a reversible circuit for a permutation
+- :class:`~projectq.libs.revkit.PhaseOracle`: Synthesizes phase circuit from an arbitrary Boolean function
+
+RevKit can be installed from PyPi with `pip install revkit`.
+
+.. note::
+
+    The RevKit Python module must be installed in order to use this ProjectQ library.
+
+    There exist precompiled binaries in PyPi, as well as a source distribution.
+    Note that a C++ compiler with C++17 support is required to build the RevKit
+    python module from source.  Examples for compatible compilers are Clang
+    6.0, GCC 7.3, and GCC 8.1.
+
+The integration of RevKit into ProjectQ and other quantum programming languages is described in the paper
+
+    * Mathias Soeken, Thomas Haener, and Martin Roetteler "Programming Quantum Computers Using Design Automation," in: Design Automation and Test in Europe (2018) [`arXiv:1803.01022 <https://arxiv.org/abs/1803.01022>`_]
+''',
+                       module_special_members='__init__,__or__'),
+    PackageDescription('libs',
+                       desc='''
+The library collection of ProjectQ which, for now, consists of a tiny math library and an interface library to RevKit. Soon, more libraries will be added.
+'''),
+    PackageDescription('meta',
+                       desc='''
+Contains meta statements which allow more optimal code while making it easier for users to write their code.
+Examples are `with Compute`, followed by an automatic uncompute or `with Control`, which allows the user to condition an entire code block upon the state of a qubit.
+'''),
+    PackageDescription('ops',
+                       desc='''
+The operations collection consists of various default gates and is a work-in-progress, as users start to work with ProjectQ.
+''',
+                       module_special_members='__init__,__or__'),
+    PackageDescription('setups.decompositions',
+                       desc='''
+The decomposition package is a collection of gate decomposition / replacement rules which can be used by, e.g., the AutoReplacer engine.
+'''),
+    PackageDescription('setups',
+                       desc='''
+The setups package contains a collection of setups which can be loaded by the `MainEngine`. Each setup contains a `get_engine_list` function which returns a list of compiler engines:
+
+Example:
+    .. code-block:: python
+
+        import projectq.setups.ibm as ibm_setup
+        from projectq import MainEngine
+        eng = MainEngine(engine_list=ibm_setup.get_engine_list())
+        # eng uses the default Simulator backend
+
+The subpackage decompositions contains all the individual decomposition rules
+which can be given to, e.g., an `AutoReplacer`.
+''',
+                       submodules_desc='''
+Each of the submodules contains a setup which can be used to specify the
+`engine_list` used by the `MainEngine` :''',
+                       submodule_special_members='__init__'),
+    PackageDescription(
+        'types', '''
+The types package contains quantum types such as Qubit, Qureg, and WeakQubitRef. With further development of the math library, also quantum integers, quantum fixed point numbers etc. will be added.
+'''),
+]
+# ------------------------------------------------------------------------------
+# Automatically generate ReST files for each package of ProjectQ
+
+for desc in descriptions:
+    fname = os.path.join(os.path.dirname(os.path.abspath('__file__')),
+                         'projectq.{}.rst'.format(desc.name))
+    lines = None
+    if os.path.exists(fname):
+        with open(fname, 'r') as fd:
+            lines = [line[:-1] for line in fd.readlines()]
+
+    new_lines = desc.get_ReST()
+
+    if new_lines != lines:
+        with open(fname, 'w') as fd:
+            fd.write('\n'.join(desc.get_ReST()))
diff --git a/docs/package_description.py b/docs/package_description.py
new file mode 100644
index 000000000..afb18ba18
--- /dev/null
+++ b/docs/package_description.py
@@ -0,0 +1,167 @@
+import inspect
+import sys
+import os
+
+
+class PackageDescription(object):
+    package_list = []
+
+    def __init__(self, name, desc='', module_special_members='__init__',
+                 submodule_special_members='', submodules_desc='',
+                 helper_submodules=None):
+        """
+        Args:
+            name (str): Name of ProjectQ module
+            desc (str): (optional) Description of module
+            module_special_members (str): (optional) Special members to include
+                in the documentation of the module
+            submodule_special_members (str): (optional) Special members to
+                include in the documentation of submodules
+            submodules_desc (str): (optional) Description to print out before
+                the list of submodules
+            helper_submodules (list): (optional) List of tuples for helper
+                sub-modules to include in the documentation.
+                Tuples are (section_title, submodukle_name,
+                            automodule_properties)
+        """
+
+        self.name = name
+        self.desc = desc
+        if name not in PackageDescription.package_list:
+            PackageDescription.package_list.append(name)
+
+        self.module = sys.modules['projectq.{}'.format(self.name)]
+        self.module_special_members = module_special_members
+
+        self.submodule_special_members = module_special_members
+        self.submodules_desc = submodules_desc
+
+        self.helper_submodules = helper_submodules
+
+        module_root = os.path.dirname(self.module.__file__)
+        sub = [(name, obj) for name, obj in inspect.getmembers(
+            self.module,
+            lambda obj: inspect.ismodule(obj) and module_root in obj.__file__)
+               if name[0] != '_']
+
+        self.subpackages = []
+        self.submodules = []
+        for name, obj in sub:
+            if '{}.{}'.format(self.name,
+                              name) in PackageDescription.package_list:
+                self.subpackages.append((name, obj))
+            else:
+                self.submodules.append((name, obj))
+
+        self.subpackages.sort(key=lambda x: x[0].lower())
+        self.submodules.sort(key=lambda x: x[0].lower())
+
+        self.members = [(name, obj)
+                        for name, obj in inspect.getmembers(
+                                self.module,
+                                lambda obj: (inspect.isclass(obj)
+                                             or inspect.isfunction(obj)
+                                             or isinstance(obj, (int,
+                                                                 float,
+                                                                 tuple,
+                                                                 list,
+                                                                 dict,
+                                                                 set,
+                                                                 frozenset,
+                                                                 str))))
+                        if name[0] != '_']
+        self.members.sort(key=lambda x: x[0].lower())
+
+    def get_ReST(self):
+        new_lines = []
+        new_lines.append(self.name)
+        new_lines.append('=' * len(self.name))
+        new_lines.append('')
+
+        if self.desc:
+            new_lines.append(self.desc.strip())
+            new_lines.append('')
+
+        submodule_has_index = False
+
+        if self.subpackages:
+            new_lines.append('Subpackages')
+            new_lines.append('-' * len(new_lines[-1]))
+            new_lines.append('')
+            new_lines.append('.. toctree::')
+            new_lines.append('    :maxdepth: 1')
+            new_lines.append('')
+            for name, _ in self.subpackages:
+                new_lines.append('    projectq.{}.{}'.format(self.name, name))
+            new_lines.append('')
+        else:
+            submodule_has_index = True
+            new_lines.append('.. autosummary::')
+            new_lines.append('')
+            if self.submodules:
+                for name, _ in self.submodules:
+                    new_lines.append('\tprojectq.{}.{}'.format(self.name,
+                                                               name))
+                new_lines.append('')
+            if self.members:
+                for name, _ in self.members:
+                    new_lines.append('\tprojectq.{}.{}'.format(self.name,
+                                                               name))
+                new_lines.append('')
+
+        if self.submodules:
+            new_lines.append('Submodules')
+            new_lines.append('-' * len(new_lines[-1]))
+            new_lines.append('')
+            if self.submodules_desc:
+                new_lines.append(self.submodules_desc.strip())
+                new_lines.append('')
+
+            if not submodule_has_index:
+                new_lines.append('.. autosummary::')
+                new_lines.append('')
+                for name, _ in self.submodules:
+                    new_lines.append('    projectq.{}.{}'.format(self.name,
+                                                                 name))
+                new_lines.append('')
+
+            for name, _ in self.submodules:
+                new_lines.append(name)
+                new_lines.append('^' * len(new_lines[-1]))
+                new_lines.append('')
+                new_lines.append('.. automodule:: projectq.{}.{}'.format(
+                    self.name, name))
+                new_lines.append('    :members:')
+                if self.submodule_special_members:
+                    new_lines.append('    :special-members: {}'.format(
+                        self.submodule_special_members))
+                new_lines.append('    :undoc-members:')
+                new_lines.append('')
+
+        new_lines.append('Module contents')
+        new_lines.append('-' * len(new_lines[-1]))
+        new_lines.append('')
+        new_lines.append('.. automodule:: projectq.{}'.format(self.name))
+        new_lines.append('    :members:')
+        new_lines.append('    :undoc-members:')
+        new_lines.append('    :special-members: {}'.format(
+            self.module_special_members))
+        new_lines.append('    :imported-members:')
+        new_lines.append('')
+
+        if self.helper_submodules:
+            new_lines.append('Helper sub-modules')
+            new_lines.append('-' * len(new_lines[-1]))
+            new_lines.append('')
+            for title, name, params in self.helper_submodules:
+                new_lines.append(title)
+                new_lines.append('^' * len(title))
+                new_lines.append('')
+                new_lines.append('.. automodule:: projectq.{}.{}'.format(
+                    self.name, name))
+                for param in params:
+                    new_lines.append('    {}'.format(param))
+                new_lines.append('')
+
+        assert not new_lines[-1]
+        return new_lines[:-1]
diff --git a/docs/projectq.backends.rst b/docs/projectq.backends.rst
deleted file mode 100755
index cc6531df4..000000000
--- a/docs/projectq.backends.rst
+++ /dev/null
@@ -1,21 +0,0 @@
-backends
-========
-
-.. autosummary::
-	
-	projectq.backends.CommandPrinter
-	projectq.backends.CircuitDrawer
-	projectq.backends.CircuitDrawerMatplotlib
-	projectq.backends.Simulator
-	projectq.backends.ClassicalSimulator
-	projectq.backends.ResourceCounter
-	projectq.backends.IBMBackend
-
-
-Module contents
----------------
-
-.. automodule:: projectq.backends
-    :members:
-    :special-members: __init__
-    :imported-members:
diff --git a/docs/projectq.cengines.rst b/docs/projectq.cengines.rst
deleted file mode 100755
index 5a3c963a6..000000000
--- a/docs/projectq.cengines.rst
+++ /dev/null
@@ -1,33 +0,0 @@
-cengines
-========
-
-The ProjectQ compiler engines package.
-
-.. autosummary::
-	projectq.cengines.AutoReplacer
-	projectq.cengines.BasicEngine
-	projectq.cengines.BasicMapper
-	projectq.cengines.CommandModifier
-	projectq.cengines.CompareEngine
-	projectq.cengines.DecompositionRule
-	projectq.cengines.DecompositionRuleSet
-	projectq.cengines.DummyEngine
-	projectq.cengines.ForwarderEngine
-	projectq.cengines.GridMapper
-	projectq.cengines.InstructionFilter
-	projectq.cengines.IBM5QubitMapper
-	projectq.cengines.LinearMapper
-	projectq.cengines.LocalOptimizer
-	projectq.cengines.ManualMapper
-	projectq.cengines.MainEngine
-  projectq.cengines.SwapAndCNOTFlipper
-	projectq.cengines.TagRemover
-
-
-Module contents
----------------
-
-.. automodule:: projectq.cengines
-    :members:
-    :special-members: __init__
-    :imported-members:
diff --git a/docs/projectq.libs.math.rst b/docs/projectq.libs.math.rst
deleted file mode 100755
index 1567978b5..000000000
--- a/docs/projectq.libs.math.rst
+++ /dev/null
@@ -1,21 +0,0 @@
-math
-====
-
-A tiny math library which will be extended thoughout the next weeks. Right now, it only contains the math functions necessary to run Beauregard's implementation of Shor's algorithm.
-
-.. autosummary::
-
-	projectq.libs.math.all_defined_decomposition_rules
-	projectq.libs.math.AddConstant
-	projectq.libs.math.SubConstant
-	projectq.libs.math.AddConstantModN
-	projectq.libs.math.SubConstantModN
-	projectq.libs.math.MultiplyByConstantModN
-
-Module contents
----------------
-
-.. automodule:: projectq.libs.math
-    :members:
-    :special-members: __init__
-    :imported-members:
diff --git a/docs/projectq.libs.revkit.rst b/docs/projectq.libs.revkit.rst
deleted file mode 100644
index 90a2dbb18..000000000
--- a/docs/projectq.libs.revkit.rst
+++ /dev/null
@@ -1,34 +0,0 @@
-revkit
-======
-
-This library integrates `RevKit <https://msoeken.github.io/revkit.html>`_ into
-ProjectQ to allow some automatic synthesis routines for reversible logic.  The
-library adds the following operations that can be used to construct quantum
-circuits:
-
-- :class:`~projectq.libs.revkit.ControlFunctionOracle`: Synthesizes a reversible circuit from Boolean control function
-- :class:`~projectq.libs.revkit.PermutationOracle`: Synthesizes a reversible circuit for a permutation
-- :class:`~projectq.libs.revkit.PhaseOracle`: Synthesizes phase circuit from an arbitrary Boolean function
-
-RevKit can be installed from PyPi with `pip install revkit`.
-
-.. note::
-
-    The RevKit Python module must be installed in order to use this ProjectQ library.
-
-    There exist precompiled binaries in PyPi, as well as a source distribution.
-    Note that a C++ compiler with C++17 support is required to build the RevKit
-    python module from source.  Examples for compatible compilers are Clang
-    6.0, GCC 7.3, and GCC 8.1.
-
-The integration of RevKit into ProjectQ and other quantum programming languages is described in the paper
-
-    * Mathias Soeken, Thomas Haener, and Martin Roetteler "Programming Quantum Computers Using Design Automation," in: Design Automation and Test in Europe (2018) [`arXiv:1803.01022 <https://arxiv.org/abs/1803.01022>`_]
-
-Module contents
----------------
-
-.. automodule:: projectq.libs.revkit
-    :members:
-    :special-members: __init__,__or__
-    :imported-members:
diff --git a/docs/projectq.libs.rst b/docs/projectq.libs.rst
deleted file mode 100755
index 9f2c8cd4b..000000000
--- a/docs/projectq.libs.rst
+++ /dev/null
@@ -1,20 +0,0 @@
-libs
-====
-
-The library collection of ProjectQ which, for now, consists of a tiny math library and an interface library to RevKit. Soon, more libraries will be added.
-
-Subpackages
------------
-
-.. toctree::
-
-    projectq.libs.math
-    projectq.libs.revkit
-
-Module contents
----------------
-
-.. automodule:: projectq.libs
-    :members:
-    :special-members: __init__
-    :imported-members:
diff --git a/docs/projectq.meta.rst b/docs/projectq.meta.rst
deleted file mode 100755
index 14c3d9eea..000000000
--- a/docs/projectq.meta.rst
+++ /dev/null
@@ -1,32 +0,0 @@
-meta
-====
-
-Contains meta statements which allow more optimal code while making it easier for users to write their code.
-Examples are `with Compute`, followed by an automatic uncompute or `with Control`, which allows the user to condition an entire code block upon the state of a qubit.
-
-
-.. autosummary::
-
-	projectq.meta.DirtyQubitTag
-	projectq.meta.LogicalQubitIDTag
-	projectq.meta.LoopTag
-	projectq.meta.Loop
-	projectq.meta.Compute
-	projectq.meta.Uncompute
-	projectq.meta.CustomUncompute
-	projectq.meta.ComputeTag
-	projectq.meta.UncomputeTag
-	projectq.meta.Control
-	projectq.meta.get_control_count
-	projectq.meta.Dagger
-	projectq.meta.insert_engine
-	projectq.meta.drop_engine_after
-
-Module contents
----------------
-
-.. automodule:: projectq.meta
-    :members:
-    :undoc-members:
-    :special-members: __init__
-    :imported-members:
diff --git a/docs/projectq.ops.rst b/docs/projectq.ops.rst
deleted file mode 100755
index 6b9ec5936..000000000
--- a/docs/projectq.ops.rst
+++ /dev/null
@@ -1,67 +0,0 @@
-ops
-===
-
-The operations collection consists of various default gates and is a work-in-progress, as users start to work with ProjectQ.
-
-.. autosummary::
-
-	projectq.ops.BasicGate
-	projectq.ops.MatrixGate
-	projectq.ops.SelfInverseGate
-	projectq.ops.BasicRotationGate
-	projectq.ops.BasicPhaseGate
-	projectq.ops.ClassicalInstructionGate
-	projectq.ops.FastForwardingGate
-	projectq.ops.BasicMathGate
-	projectq.ops.apply_command
-	projectq.ops.Command
-	projectq.ops.H
-	projectq.ops.X
-	projectq.ops.Y
-	projectq.ops.Z
-	projectq.ops.S
-	projectq.ops.Sdag
-	projectq.ops.T
-	projectq.ops.Tdag
-	projectq.ops.SqrtX
-	projectq.ops.Swap
-	projectq.ops.SqrtSwap
-	projectq.ops.Entangle
-	projectq.ops.Ph
-	projectq.ops.Rx
-	projectq.ops.Ry
-	projectq.ops.Rz
-	projectq.ops.R
-	projectq.ops.FlushGate
-	projectq.ops.MeasureGate
-	projectq.ops.Allocate
-	projectq.ops.Deallocate
-	projectq.ops.AllocateDirty
-	projectq.ops.Barrier
-	projectq.ops.DaggeredGate
-	projectq.ops.ControlledGate
-	projectq.ops.C
-	projectq.ops.All
-	projectq.ops.Tensor
-	projectq.ops.QFT
-	projectq.ops.QubitOperator
-	projectq.ops.CRz
-	projectq.ops.CNOT
-	projectq.ops.CZ
-	projectq.ops.Toffoli
-	projectq.ops.TimeEvolution
-	projectq.ops.UniformlyControlledRy
-	projectq.ops.UniformlyControlledRz
-	projectq.ops.StatePreparation
-	projectq.ops.QPE
-	projectq.ops.FlipBits
-	projectq.ops.QAA
-
-
-Module contents
----------------
-
-.. automodule:: projectq.ops
-    :members:
-    :special-members: __init__,__or__
-    :imported-members:
diff --git a/docs/projectq.setups.decompositions.rst b/docs/projectq.setups.decompositions.rst
deleted file mode 100755
index 6206c4a95..000000000
--- a/docs/projectq.setups.decompositions.rst
+++ /dev/null
@@ -1,216 +0,0 @@
-decompositions
-==============
-
-The decomposition package is a collection of gate decomposition / replacement rules which can be used by, e.g., the AutoReplacer engine.
-
-
-.. autosummary::
-
-    projectq.setups.decompositions.arb1qubit2rzandry
-    projectq.setups.decompositions.barrier
-    projectq.setups.decompositions.carb1qubit2cnotrzandry
-    projectq.setups.decompositions.cnot2cz
-    projectq.setups.decompositions.cnot2rxx
-    projectq.setups.decompositions.cnu2toffoliandcu
-    projectq.setups.decompositions.crz2cxandrz
-    projectq.setups.decompositions.entangle
-    projectq.setups.decompositions.globalphase
-    projectq.setups.decompositions.h2rx
-    projectq.setups.decompositions.ph2r
-    projectq.setups.decompositions.qft2crandhadamard
-    projectq.setups.decompositions.qubitop2onequbit
-    projectq.setups.decompositions.r2rzandph
-    projectq.setups.decompositions.rx2rz
-    projectq.setups.decompositions.ry2rz
-    projectq.setups.decompositions.rz2rx
-    projectq.setups.decompositions.sqrtswap2cnot
-    projectq.setups.decompositions.stateprep2cnot
-    projectq.setups.decompositions.swap2cnot
-    projectq.setups.decompositions.time_evolution
-    projectq.setups.decompositions.toffoli2cnotandtgate
-    projectq.setups.decompositions.uniformlycontrolledr2cnot
-    projectq.setups.decompositions.phaseestimation
-    projectq.setups.decompositions.amplitudeamplification
-
-
-Submodules
-----------
-
-projectq.setups.decompositions.arb1qubit2rzandry module
--------------------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.arb1qubit2rzandry
-    :members:
-    :undoc-members:
-
-
-projectq.setups.decompositions.barrier module
----------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.barrier
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.carb1qubit2cnotrzandry module
-------------------------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.carb1qubit2cnotrzandry
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.cnot2cz module
----------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.cnot2cz
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.cnot2rxx module
----------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.cnot2rxx
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.cnu2toffoliandcu module
-------------------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.cnu2toffoliandcu
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.crz2cxandrz module
--------------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.crz2cxandrz
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.entangle module
-----------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.entangle
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.globalphase module
--------------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.globalphase
-    :members:
-    :undoc-members:
-
-
-projectq.setups.decompositions.h2rx module
-------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.ph2r
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.qft2crandhadamard module
--------------------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.qft2crandhadamard
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.qubitop2onequbit module
--------------------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.qubitop2onequbit
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.r2rzandph module
------------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.r2rzandph
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.rx2rz module
--------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.rx2rz
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.ry2rz module
--------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.ry2rz
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.rz2rx module
--------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.rz2rx
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.sqrtswap2cnot module
----------------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.sqrtswap2cnot
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.stateprep2cnot module
-----------------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.stateprep2cnot
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.swap2cnot module
------------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.swap2cnot
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.time_evolution module
-----------------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.time_evolution
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.toffoli2cnotandtgate module
-----------------------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.toffoli2cnotandtgate
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.uniformlycontrolledr2cnot module
----------------------------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.uniformlycontrolledr2cnot
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.phaseestimation module
----------------------------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.phaseestimation
-    :members:
-    :undoc-members:
-
-projectq.setups.decompositions.amplitudeamplification module
----------------------------------------------------------------
-
-.. automodule:: projectq.setups.decompositions.amplitudeamplification
-    :members:
-    :undoc-members:
-
-
-Module contents
----------------
-
-.. automodule:: projectq.setups.decompositions
-    :members:
-    :undoc-members:
-        :imported-members:
diff --git a/docs/projectq.setups.rst b/docs/projectq.setups.rst
deleted file mode 100755
index 98e7e611a..000000000
--- a/docs/projectq.setups.rst
+++ /dev/null
@@ -1,101 +0,0 @@
-setups
-======
-
-The setups package contains a collection of setups which can be loaded by the `MainEngine`. Each setup contains a `get_engine_list` function which returns a list of compiler engines:
-
-Example:
-    .. code-block:: python
-
-        import projectq.setups.ibm as ibm_setup
-        from projectq import MainEngine
-        eng = MainEngine(engine_list=ibm_setup.get_engine_list())
-        # eng uses the default Simulator backend
-
-The subpackage decompositions contains all the individual decomposition rules
-which can be given to, e.g., an `AutoReplacer`.
-
-
-Subpackages
------------
-
-.. toctree::
-    :maxdepth: 1
-
-    projectq.setups.decompositions
-
-Submodules
-----------
-
-Each of the submodules contains a setup which can be used to specify the
-`engine_list` used by the `MainEngine` :
-
-.. autosummary::
-
-    projectq.setups.default
-    projectq.setups.grid
-    projectq.setups.ibm
-    projectq.setups.ibm16
-    projectq.setups.linear
-    projectq.setups.restrictedgateset
-
-default
--------
-
-.. automodule:: projectq.setups.default
-    :members:
-    :special-members: __init__
-    :undoc-members:
-
-grid
-----
-
-.. automodule:: projectq.setups.grid
-    :members:
-    :special-members: __init__
-    :undoc-members:
-
-ibm
----
-
-.. automodule:: projectq.setups.ibm
-    :members:
-    :special-members: __init__
-    :undoc-members:
-
-ibm16
------
-
-.. automodule:: projectq.setups.ibm16
-    :members:
-    :special-members: __init__
-    :undoc-members:
-
-linear
-------
-
-.. automodule:: projectq.setups.linear
-    :members:
-    :special-members: __init__
-    :undoc-members:
-
-restrictedgateset
------------------
-
-.. automodule:: projectq.setups.restrictedgateset
-    :members:
-    :special-members: __init__
-    :undoc-members:
-
-trapped_ion_decomposer
-----------------------
-.. automodule:: projectq.setups.trapped_ion_decomposer
-    :members:
-    :special-members: __init__
-    :undoc-members:
-
-Module contents
----------------
-
-.. automodule:: projectq.setups
-    :members:
-    :special-members: __init__
diff --git a/docs/projectq.types.rst b/docs/projectq.types.rst
deleted file mode 100755
index 4f26edc9d..000000000
--- a/docs/projectq.types.rst
+++ /dev/null
@@ -1,18 +0,0 @@
-types
-=====
-
-The types package contains quantum types such as Qubit, Qureg, and WeakQubitRef. With further development of the math library, also quantum integers, quantum fixed point numbers etc. will be added.
-
-.. autosummary::
-	projectq.types.BasicQubit
-	projectq.types.Qubit
-	projectq.types.Qureg
-	projectq.types.WeakQubitRef
-
-Module contents
----------------
-
-.. automodule:: projectq.types
-    :members:
-    :special-members:
-    :imported-members: