From d89dd45cae8cb4883e305acccc54f91a659ad3d4 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Mon, 2 May 2022 11:40:24 +0200
Subject: [PATCH 01/33] Added structure for group entity

Adding global group entity:
- Added necessary group.py files
- Changed all necessary files (e.g. __init__)
- Study scripts run smoothly (more testing)
- So far no functionality to group (is mostly copy of social system)
---
 .../data_model/master_data_model/__init__.py  |   3 +
 .../data_model/master_data_model/group.py     |  27 +++
 .../model_components/abstract/__init__.py     |   1 +
 .../model_components/abstract/group.py        |  25 ++
 .../base/implementation/__init__.py           |   1 +
 .../base/implementation/group.py              | 226 ++++++++++++++++++
 .../model_components/base/interface.py        |  54 +++++
 pycopancore/model_components/base/model.py    |   4 +-
 8 files changed, 339 insertions(+), 2 deletions(-)
 create mode 100644 pycopancore/data_model/master_data_model/group.py
 create mode 100644 pycopancore/model_components/abstract/group.py
 create mode 100644 pycopancore/model_components/base/implementation/group.py

diff --git a/pycopancore/data_model/master_data_model/__init__.py b/pycopancore/data_model/master_data_model/__init__.py
index 4deb317a..f962b122 100644
--- a/pycopancore/data_model/master_data_model/__init__.py
+++ b/pycopancore/data_model/master_data_model/__init__.py
@@ -37,5 +37,8 @@
 from .individual import Individual as I
 from .individual import Individual as individual
 from .individual import Individual
+from .group import Group as G
+from .group import Group as group
+from .group import Group
 
 from .. import unity
diff --git a/pycopancore/data_model/master_data_model/group.py b/pycopancore/data_model/master_data_model/group.py
new file mode 100644
index 00000000..c636fff6
--- /dev/null
+++ b/pycopancore/data_model/master_data_model/group.py
@@ -0,0 +1,27 @@
+"""Master data model for group."""
+
+"""https://github.com/pik-copan/pycopancore/blob/master/docs/framework_documentation/abstract_level/entity_types/group.rst"""
+
+#from . import MET
+from .. import Variable
+
+
+class Group:
+
+    #TODO: add a group network possibility (in culture.py (?))
+
+    
+    has_leader = \
+        Variable("has a leader",
+                 "whether the group has a leader",
+                 scale="ordinal", levels=[False, True], default=False)
+
+    has_headquarter = \
+        Variable("has a headquarter",
+                 "whether the group has a headquarter located in a cell",
+                 scale="ordinal", levels=[False, True], default=False)
+        
+        
+        
+        
+
diff --git a/pycopancore/model_components/abstract/__init__.py b/pycopancore/model_components/abstract/__init__.py
index 6ee0e07a..e383543b 100644
--- a/pycopancore/model_components/abstract/__init__.py
+++ b/pycopancore/model_components/abstract/__init__.py
@@ -16,6 +16,7 @@
 from .social_system import SocialSystem
 from .cell import Cell
 from .individual import Individual
+from .group import Group
 
 from .environment import Environment
 from .metabolism import Metabolism
diff --git a/pycopancore/model_components/abstract/group.py b/pycopancore/model_components/abstract/group.py
new file mode 100644
index 00000000..f919b38e
--- /dev/null
+++ b/pycopancore/model_components/abstract/group.py
@@ -0,0 +1,25 @@
+"""Abstract Group entity type class, inherited by base model component."""
+
+# This file is part of pycopancore.
+#
+# Copyright (C) 2016-2017 by COPAN team at Potsdam Institute for Climate
+# Impact Research
+#
+# URL: <http://www.pik-potsdam.de/copan/software>
+# Contact: core@pik-potsdam.de
+# License: BSD 2-clause license
+
+from ...private import _AbstractEntityMixin
+from ...data_model import OrderedSet
+
+
+class Group (_AbstractEntityMixin):
+    """Abstract Group entity type class.
+
+    Inherited by base model component.
+    """
+
+    variables = OrderedSet()
+    """All variables occurring in this entity type"""
+
+
diff --git a/pycopancore/model_components/base/implementation/__init__.py b/pycopancore/model_components/base/implementation/__init__.py
index f782a260..a14081c7 100644
--- a/pycopancore/model_components/base/implementation/__init__.py
+++ b/pycopancore/model_components/base/implementation/__init__.py
@@ -17,6 +17,7 @@
 from .social_system import SocialSystem
 from .cell import Cell
 from .individual import Individual
+from .group import Group
 
 from .environment import Environment
 from .metabolism import Metabolism
diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
new file mode 100644
index 00000000..78c71a41
--- /dev/null
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -0,0 +1,226 @@
+""" """
+
+# This file is part of pycopancore.
+#
+# Copyright (C) 2016-2017 by COPAN team at Potsdam Institute for Climate
+# Impact Research
+#
+# URL: <http://www.pik-potsdam.de/copan/software>
+# Contact: core@pik-potsdam.de
+# License: BSD 2-clause license
+
+# only used in this component, not in others:
+from ... import abstract
+from .... import master_data_model as D
+from ....private import unknown
+
+from .. import interface as I
+
+
+class Group (I.Group, abstract.Group):
+    """Gropp entity type mixin implementation class.
+
+    Base component's Group mixin that every model must use in composing
+    their Group class. Inherits from I.Group as the interface with all
+    necessary variables and parameters.
+    """
+
+    # standard methods:
+
+    def __init__(self,
+                 *,
+                 socialsystem,
+                 next_higher_group=None,
+                 **kwargs
+                 ):
+        """Initialize an instance of Group.
+
+        Parameters
+        ----------
+        socialsystem: obj
+            SocialSystem the Group belongs to (default is None)
+        next_higher_group: obj
+            Optional Group the Group belongs to (default is None)
+        **kwargs
+            keyword arguments passed to super()
+
+        """
+        super().__init__(**kwargs)  # must be the first line
+
+        # init caches:
+        self._next_lower_group = set()
+        self._direct_cells = set()
+
+        # init and set variables implemented via properties:
+        self._socialsystem = None
+        self.socialsystem = socialsystem
+        self._next_higher_group = None
+        self.next_higher_group = next_higher_group
+
+    # getters and setters for references:
+
+    @property
+    def socialsystem(self):
+        """Get the World the SocialSystem is part of."""
+        return self._socialsystem
+
+    @socialsystem.setter
+    def socialsystem(self, w):
+        """Set the World the SocialSystem is part of."""
+        if self._socialsystem is not None:
+            self._socialsystem._groups.remove(self)
+        assert isinstance(w, I.SocialSystem), "socialsystem must be of entity type SocialSystem"
+        w._groups.add(self)
+        self._socialsystem = w
+
+    @property
+    def next_higher_group(self):
+        """Get next higher group."""
+        return self._next_higher_group
+
+    @next_higher_group.setter
+    def next_higher_group(self, s):
+        """Set next higher group."""
+        if self._next_higher_group is not None:
+            self._next_higher_group._next_lower_groups.remove(self)
+            # reset dependent cache:
+            self._next_higher_group.cells = unknown
+        if s is not None:
+            assert isinstance(s, I.Group), \
+                "next_higher_group must be of entity type group"
+            s._next_lower_groups.add(self)
+            # reset dependent cache:
+            s.cells = unknown
+        self._next_higher_group = s
+        # reset dependent caches:
+        self.higher_groups = unknown
+
+    # getters for backwards references and convenience variables:
+
+    @property  # read-only
+    def environment(self):
+        """Get the Environment of which the Group is a part."""
+        return self._world.environment
+
+    @property  # read-only
+    def metabolism(self):
+        """Get the Metabolism of which the Group is a part."""
+        return self._world.metabolism
+
+    @property  # read-only
+    def culture(self):
+        """Get the Culture of which the Group is a part."""
+        return self._world.culture
+
+    _higher_groups = unknown
+    """cache, depends on self.next_higher_group
+    and self.next_higher_group.higher_groups"""
+    @property  # read-only
+    def higher_groups(self):
+        """Get higher groups."""
+        if self._higher_groups is unknown:
+            # find recursively:
+            self._higher_groups = [] if self.next_higher_group is None \
+                else ([self.next_higher_group]
+                      + self.next_higher_group.groups)
+        return self._higher_groups
+
+    @higher_groups.setter
+    def higher_groups(self, u):
+        """Set higher groups."""
+        assert u == unknown, "setter can only be used to reset cache"
+        self._higher_groups = unknown
+        # reset dependent caches:
+        for s in self._next_lower_groups:
+            s.higher_groups = unknown
+        for c in self._direct_cells:
+            c.groups = unknown
+
+    @property  # read-only
+    def next_lower_groups(self):
+        """Get next lower groups."""
+        return self._next_lower_groups
+
+    @property  # read-only
+    def lower_groups(self):
+        """Get lower groups."""
+        # aggregate recursively:
+        l = self._next_lower_groups
+        for s in self._next_lower_groups:
+            l.update(s.lower_groups)
+        return l
+
+    @property  # read-only
+    def direct_cells(self):
+        """Get cells that directly belong to the SocialSystem."""
+        return self._direct_cells
+
+    _cells = unknown
+    """cache, depends on self.direct_cells, self._next_lower_social_systems,
+    and lowersocial_system.cells"""
+    @property  # read-only
+    def cells(self):
+        """Get cells that directly abd indirectly belong to the SocialSystem."""
+        if self._cells is unknown:
+            # aggregate recursively:
+            self._cells = self.direct_cells
+            for s in self._next_lower_social_systems:
+                self._cells.update(s.cells)
+        return self._cells
+
+    @cells.setter
+    def cells(self, u):
+        """Set cells that directly and indirectly belong to the SocialSystem."""
+        assert u == unknown, "setter can only be used to reset cache"
+        self._cells = unknown
+        # reset dependent caches:
+        if self.next_higher_social_system is not None:
+            self.next_higher_social_system.cells = unknown
+
+    _direct_individuals = unknown
+    """cache, depends on _direct_cells, directcell.individuals"""
+    @property  # read-only
+    def direct_individuals(self):
+        """Get resident Individuals not in subsocial_systems."""
+        if self._direct_individuals is unknown:
+            # aggregate from direct_cells:
+            self._direct_individuals = set()
+            for c in self._direct_cells:
+                self._direct_individuals.update(c.individuals)
+        return self._direct_individuals
+
+    @direct_individuals.setter
+    def direct_individuals(self, u):
+        """Set resident Individuals not in subsocial_systems."""
+        assert u == unknown, "setter can only be used to reset cache"
+        self._direct_individuals = unknown
+        # reset dependent caches:
+        pass
+
+    _individuals = unknown
+    """cache, depends on self.cells, cell.individuals"""
+    @property  # read-only
+    def individuals(self):
+        """Get direct and indirect resident Individuals."""
+        if self._individuals is unknown:
+            # aggregate from cells:
+            self._individuals = set()
+            for c in self.cells:
+                self._individuals.update(c.individuals)
+        return self._individuals
+
+    @individuals.setter
+    def individuals(self, u):
+        """Set direct and indirect resident Individuals."""
+        assert u == unknown, "setter can only be used to reset cache"
+        self._individuals = unknown
+        # reset dependent caches:
+        pass
+
+    # TODO: helper methods for mergers, splits, etc.
+
+    # no process-related methods
+
+    processes = []  # no processes in base
+
+
diff --git a/pycopancore/model_components/base/interface.py b/pycopancore/model_components/base/interface.py
index b3424218..15f491fd 100644
--- a/pycopancore/model_components/base/interface.py
+++ b/pycopancore/model_components/base/interface.py
@@ -288,3 +288,57 @@ class Individual (object, metaclass=_MixinType):
 SocialSystem.individuals.type = Individual
 Cell.individuals.type = Individual
 Individual.acquaintances.type = Individual
+
+
+
+class Group (object, metaclass=_MixinType):
+    """Basic Group interface.
+
+    It contains all variables specified as mandatory ("base variables").
+    """
+
+    # references:
+    socialsystem = ReferenceVariable("socialsystem", "", type=SocialSystem)
+    next_higher_group = ReferenceVariable("next higher group", "optional",
+                                            allow_none=True)  # type is Group, hence it can only be specified after class Group is defined, see below
+
+
+    # read-only attributes storing redundant information:
+    environment = ReferenceVariable("environment", "", type=Environment,
+                               readonly=True)
+    metabolism = ReferenceVariable("metabolism", "", type=Metabolism,
+                                   readonly=True)
+    culture = ReferenceVariable("culture", "", type=Culture,
+                                readonly=True)
+    higher_groups = SetVariable(
+        "higher groups",
+        "upward list of (in)direct super-Groups",
+        readonly=True)
+    next_lower_groups = SetVariable(
+        "next lower groups",
+        "set of sub-Groups of next lower level",
+        readonly=True)
+    lower_groups = SetVariable(
+        "lower groups",
+        "set of all direct and indirect sub-Groups",
+        readonly=True)
+    direct_cells = SetVariable("direct cells", "set of direct territory Cells",
+                               readonly=True)
+    cells = SetVariable("cells", "set of direct and indirect territory Cells",
+                        readonly=True)
+    direct_individuals = SetVariable(
+        "direct individuals",
+        "set of resident Individuals not in subgroups",
+        readonly=True)
+    individuals = SetVariable("individuals",
+                              "set of direct or indirect resident Individuals",
+                              readonly=True)
+
+
+# specified only now to avoid recursion errors:
+Group.next_higher_group.type = Group
+Group.higher_groups.type = Group
+Group.next_lower_groups.type = Group
+Group.lower_groups.type = Group
+#Group.groups.type = Group
+#SocialSystem.top_level_groups.type = Group
diff --git a/pycopancore/model_components/base/model.py b/pycopancore/model_components/base/model.py
index 0a417c29..b354528d 100644
--- a/pycopancore/model_components/base/model.py
+++ b/pycopancore/model_components/base/model.py
@@ -20,7 +20,7 @@
 from .. import abstract
 from . import interface as I
 from . import World, Cell, Environment, Individual, Culture, SocialSystem, \
-    Metabolism
+    Metabolism, Group
 
 
 class Model (I.Model, abstract.Model, ModelLogics):
@@ -34,5 +34,5 @@ class Model (I.Model, abstract.Model, ModelLogics):
 
     # specify entity types and process taxon classes 
     # defined in the base component:
-    entity_types = [World, Cell, Individual, SocialSystem]
+    entity_types = [World, Cell, Individual, SocialSystem, Group]
     process_taxa = [Environment, Culture, Metabolism]

From ffc4927e2a85b7f0046c41b67a96be866dd28c16 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Mon, 2 May 2022 12:15:20 +0200
Subject: [PATCH 02/33] Update group.py

Added a possible group_network logic
---
 pycopancore/data_model/master_data_model/group.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/pycopancore/data_model/master_data_model/group.py b/pycopancore/data_model/master_data_model/group.py
index c636fff6..5bb23744 100644
--- a/pycopancore/data_model/master_data_model/group.py
+++ b/pycopancore/data_model/master_data_model/group.py
@@ -2,15 +2,22 @@
 
 """https://github.com/pik-copan/pycopancore/blob/master/docs/framework_documentation/abstract_level/entity_types/group.rst"""
 
-#from . import MET
 from .. import Variable
 
+from networkx import Graph
 
 class Group:
 
     #TODO: add a group network possibility (in culture.py (?))
 
-    
+    group_network = \
+        Variable("group network",
+                 """Basic undirected social network between
+                 Groups.""",
+                 ref="https://en.wikipedia.org/wiki/Social_network#Meso_level",
+                 scale='nominal',
+                 datatype=Graph)    
+
     has_leader = \
         Variable("has a leader",
                  "whether the group has a leader",

From 7aebe13745f6e5e8ff274d8b91a7f07749189f8a Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Fri, 13 May 2022 11:20:52 +0200
Subject: [PATCH 03/33] social_system

---
 .../base/implementation/group.py              |  32 +--
 .../base/implementation/social_system.py      |  12 ++
 pycopancore/models/groups_seven_dwarfs.py     |  89 ++++++++
 studies/run_groups_test_seven_dwarfs.py       | 193 ++++++++++++++++++
 4 files changed, 311 insertions(+), 15 deletions(-)
 create mode 100644 pycopancore/models/groups_seven_dwarfs.py
 create mode 100644 studies/run_groups_test_seven_dwarfs.py

diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index 78c71a41..f3aeacd1 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -29,7 +29,7 @@ class Group (I.Group, abstract.Group):
 
     def __init__(self,
                  *,
-                 socialsystem,
+                 social_system,
                  next_higher_group=None,
                  **kwargs
                  ):
@@ -47,31 +47,33 @@ def __init__(self,
         """
         super().__init__(**kwargs)  # must be the first line
 
+        # init and set variables implemented via properties:
+        self._social_system = None
+        self.social_system = social_system
+        self._next_higher_group = None
+        self.next_higher_group = next_higher_group
+
         # init caches:
         self._next_lower_group = set()
         self._direct_cells = set()
 
-        # init and set variables implemented via properties:
-        self._socialsystem = None
-        self.socialsystem = socialsystem
-        self._next_higher_group = None
-        self.next_higher_group = next_higher_group
+
 
     # getters and setters for references:
 
     @property
-    def socialsystem(self):
+    def social_system(self):
         """Get the World the SocialSystem is part of."""
-        return self._socialsystem
+        return self._social_system
 
-    @socialsystem.setter
-    def socialsystem(self, w):
+    @social_system.setter
+    def social_system(self, s):
         """Set the World the SocialSystem is part of."""
-        if self._socialsystem is not None:
-            self._socialsystem._groups.remove(self)
-        assert isinstance(w, I.SocialSystem), "socialsystem must be of entity type SocialSystem"
-        w._groups.add(self)
-        self._socialsystem = w
+        if self._social_system is not None:
+            self._social_system._groups.remove(self)
+        assert isinstance(s, I.SocialSystem), "socialsystem must be of entity type SocialSystem"
+        s._groups.add(self)
+        self._social_system = s
 
     @property
     def next_higher_group(self):
diff --git a/pycopancore/model_components/base/implementation/social_system.py b/pycopancore/model_components/base/implementation/social_system.py
index 33b5ce68..b8dac8e3 100644
--- a/pycopancore/model_components/base/implementation/social_system.py
+++ b/pycopancore/model_components/base/implementation/social_system.py
@@ -219,6 +219,18 @@ def individuals(self, u):
         # reset dependent caches:
         pass
 
+    @property  # read-only
+    def groups(self):
+        """Get the set of all Groups in this SocialSystem."""
+        return self._groups
+    @groups.setter
+    def groups(self, g):
+        """Set the World the SocialSystem is part of."""
+        if self._groups is not None:
+            self._groups._social_system.remove(self)
+        assert isinstance(g, I.Culture), "groups must be of taxon type Group"
+        g._worlds.add(self)
+        self._culture = g
     # TODO: helper methods for mergers, splits, etc.
 
     # no process-related methods
diff --git a/pycopancore/models/groups_seven_dwarfs.py b/pycopancore/models/groups_seven_dwarfs.py
new file mode 100644
index 00000000..31be4f35
--- /dev/null
+++ b/pycopancore/models/groups_seven_dwarfs.py
@@ -0,0 +1,89 @@
+"""Model class seven_dwarfs."""
+
+# This file is part of pycopancore.
+#
+# Copyright (C) 2016-2017 by COPAN team at Potsdam Institute for Climate
+# Impact Research
+#
+# URL: <http://www.pik-potsdam.de/copan/software>
+# Contact: core@pik-potsdam.de
+# License: BSD 2-clause license
+
+#
+#  Imports
+#
+
+from .. import base  # all models must use the base component
+
+from ..model_components import seven_dwarfs as sd
+from ..model_components import snowwhite as sw
+
+# entity types:
+
+# by mixing the above model components' mixin classes of the same name.
+# Only compose those entity types and process taxons that the model needs,
+# delete the templates for the unneeded ones, and add those for missing ones:
+
+
+class World(sd.World,
+            base.World):
+    """World entity type."""
+
+    pass
+
+
+class SocialSystem(base.SocialSystem):
+    """SocialSystem entity type."""
+
+    pass
+
+
+class Cell(sd.Cell,
+           sw.Cell,
+           base.Cell):
+    """Cell entity type."""
+
+    pass
+
+
+class Individual(sd.Individual,
+                 base.Individual):
+    """Individual entity type."""
+
+    pass
+
+
+class SocialSystem(sd.SocialSystem,
+              base.SocialSystem):
+    """SocialSystem entity type."""
+
+    pass
+
+class Group(base.Group):
+    """Groups entity type"""
+
+# process taxa:
+
+class Culture(sd.Culture,
+              base.Culture):
+    """Culture process taxon."""
+
+    pass
+
+
+# Model class:
+
+class Model(sd.Model,
+            sw.Model,
+            base.Model):
+    """Class representing the whole model."""
+
+    name = "Seven dwarfs"
+    """Name of the model"""
+    description = "Tutorial model"
+    """Longer description"""
+
+    entity_types = [World, SocialSystem, Cell, Individual]
+    """List of entity types used in the model"""
+    process_taxa = [Culture]
+    """List of process taxa used in the model"""
diff --git a/studies/run_groups_test_seven_dwarfs.py b/studies/run_groups_test_seven_dwarfs.py
new file mode 100644
index 00000000..1c241a9b
--- /dev/null
+++ b/studies/run_groups_test_seven_dwarfs.py
@@ -0,0 +1,193 @@
+"""This is the test script for the seven dwarfs step by step tutorial.
+
+In this version only the Step-process 'aging' of entitytype 'Individual' is
+implemented, such that the only relevant attributes of 'Individual' are 'age'
+and 'cell'.
+"""
+
+# This file is part of pycopancore.
+#
+# Copyright (C) 2016-2017 by COPAN team at Potsdam Institute for Climate
+# Impact Research
+#
+# URL: <http://www.pik-potsdam.de/copan/software>
+# Contact: core@pik-potsdam.de
+# License: BSD 2-clause license
+
+import numpy as np
+from time import time
+import datetime as dt
+
+import networkx as nx
+import matplotlib.pyplot as plt
+
+import plotly.offline as py
+import plotly.graph_objs as go
+
+import pycopancore.models.groups_seven_dwarfs as M
+from pycopancore.runners.runner import Runner
+
+
+# setting timeinterval for run method 'Runner.run()'
+timeinterval = 10
+# setting time step to hand to 'Runner.run()'
+timestep = .1
+nc = 1  # number of caves
+dwarfs = 7  # number of dwarfs
+
+# instantiate model M (needs to be done in the beginning of each script).
+# This configures the model M through 'ModelLogics' in module
+# 'base.model_logics' such that initialisation of attributes and entities gets
+# possible
+model = M.Model()
+
+# instantiate process taxa culture:
+# In this certain case we need 'M.Culture()' for the acquaintance network.
+culture = M.Culture()
+
+# instantiate world:
+world = M.World(culture=culture)
+
+# instantiate one social system:
+social_system = M.SocialSystem(world=world)
+
+# instantiate cells (the caves):
+cells = [M.Cell(social_system=social_system,
+                eating_stock=100
+                )
+        for c in range(nc)
+        ]
+
+# instantiate dwarfs and assigning initial conditions
+individuals = [M.Individual(cell=cells[0],
+                            age=0,
+                            beard_length=0,
+                            beard_growth_parameter=0.5,
+                            eating_parameter=.1
+                            ) for i in range(dwarfs)
+               ]
+
+# assigning individuals to cell is not necessary since it is done by
+# initializing the individuals in 'base.Individuals' with the 'cell' method
+
+#instantiate groups
+ng = 2 #number of groups (group 1 hates snowwhite, group 2 loves her)
+groups = [M.Group(social_system=social_system)
+          for i in range (ng)
+          ]
+
+
+
+start = time()
+
+print("done ({})".format(dt.timedelta(seconds=(time() - start))))
+
+print('\n runner starting')
+
+# Define termination signals as list [ signal_method, object_method_works_on ]
+# the termination method 'check_for_extinction' must return a boolean
+termination_signal = [M.Culture.check_for_extinction,
+                      culture]
+
+# Define termination_callables as list of all signals
+termination_callables = [termination_signal]
+
+nx.draw(culture.acquaintance_network)
+plt.show()
+
+# Runner is instantiated
+r = Runner(model=model,
+           termination_calls=termination_callables
+           )
+
+start = time()
+# run the Runner and saving the return dict in traj
+traj = r.run(t_1=timeinterval, dt=timestep, add_to_output=[M.Culture.acquaintance_network])
+runtime = dt.timedelta(seconds=(time() - start))
+print('runtime: {runtime}'.format(**locals()))
+
+# saving time values to t
+t = np.array(traj['t'])
+print("max. time step", (t[1:]-t[:-1]).max())
+
+
+# proceeding for plotting
+
+# Create List of all dwarfes, not only the ones instantiated before the run,
+# but also the one created during the run.
+
+if M.Individual.idle_entities:
+    all_dwarfs = M.Individual.instances + M.Individual.idle_entities
+else:
+    all_dwarfs = M.Individual.instances
+
+individuals_age = np.array([traj[M.Individual.age][dwarf]
+                                 for dwarf in all_dwarfs])
+
+
+individuals_beard_length = np.array([traj[M.Individual.beard_length][dwarf]
+                                 for dwarf in all_dwarfs])
+
+cell_stock = np.array(traj[M.Cell.eating_stock][cells[0]])
+
+t = np.array(traj['t'])
+
+data_age = []
+print('data age', data_age)
+for i, dwarf in enumerate(all_dwarfs):
+    data_age.append(go.Scatter(
+        x=t,
+        y=individuals_age[i],
+        mode="lines",
+        name="age of dwarf no. {}".format(i),
+        line=dict(
+            color="green",
+            width=4
+        )
+    ))
+
+data_beard_length = []
+print('data beard', data_beard_length)
+for i, dwarf in enumerate(all_dwarfs):
+    data_beard_length.append(go.Scatter(
+        x=t,
+        y=individuals_beard_length[i],
+        mode="lines",
+        name="beard length of dwarf no. {}".format(i),
+        line=dict(
+            color="red",
+            width=4
+        )
+    ))
+
+data_stock = []
+data_stock.append(go.Scatter(
+    x=t,
+    y=cell_stock,
+    mode="lines",
+    name="stock of cell",
+    line=dict(color="blue",
+              width=4
+              )
+      ))
+
+
+layout = dict(title='seven dwarfs',
+              xaxis=dict(title='time [yr]'),
+              yaxis=dict(title='value'),
+              )
+
+
+# getting plots of two dwarfs:
+fig = dict(data=[data_age[0], data_beard_length[0], data_stock[0]],
+           layout=layout)
+py.plot(fig, filename="our-model-result{}.html".format(0))
+
+fig = dict(data=[data_age[5], data_beard_length[5], data_stock[0]],
+           layout=layout)
+py.plot(fig, filename="our-model-result{}.html".format(5))
+
+#nx.draw(traj[M.Culture.acquaintance_network][culture][1])
+#plt.show()
+for i in range(len(traj['t'])):
+    print(list(traj[M.Culture.acquaintance_network][culture][i].nodes()))

From 710242abdead92887ada253299b5c26f90d398eb Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Tue, 31 May 2022 18:20:55 +0200
Subject: [PATCH 04/33] typo cleanup

minor typo and some todos
---
 pycopancore/data_model/master_data_model/group.py             | 4 +++-
 pycopancore/model_components/base/implementation/group.py     | 4 +++-
 .../model_components/base/implementation/individual.py        | 1 +
 pycopancore/model_components/base/interface.py                | 2 +-
 4 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/pycopancore/data_model/master_data_model/group.py b/pycopancore/data_model/master_data_model/group.py
index 5bb23744..26cf6ce5 100644
--- a/pycopancore/data_model/master_data_model/group.py
+++ b/pycopancore/data_model/master_data_model/group.py
@@ -8,7 +8,9 @@
 
 class Group:
 
-    #TODO: add a group network possibility (in culture.py (?))
+    #TODO: add a group network possibility (in culture.py (!))
+    #TODO: inter/intra group network
+    #TODO: specify edges
 
     group_network = \
         Variable("group network",
diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index f3aeacd1..0aa1d663 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -29,7 +29,7 @@ class Group (I.Group, abstract.Group):
 
     def __init__(self,
                  *,
-                 social_system,
+                 social_system=None,
                  next_higher_group=None,
                  **kwargs
                  ):
@@ -179,6 +179,8 @@ def cells(self, u):
         if self.next_higher_social_system is not None:
             self.next_higher_social_system.cells = unknown
 
+    #TODO: direct_inds to members
+    
     _direct_individuals = unknown
     """cache, depends on _direct_cells, directcell.individuals"""
     @property  # read-only
diff --git a/pycopancore/model_components/base/implementation/individual.py b/pycopancore/model_components/base/implementation/individual.py
index 7f9eb2a3..e82c5fc5 100644
--- a/pycopancore/model_components/base/implementation/individual.py
+++ b/pycopancore/model_components/base/implementation/individual.py
@@ -16,6 +16,7 @@
 
 from .. import interface as I
 
+#TODO: set variable membership
 
 class Individual (I.Individual, abstract.Individual):
     """Individual entity type mixin implementation class.
diff --git a/pycopancore/model_components/base/interface.py b/pycopancore/model_components/base/interface.py
index 15f491fd..deb77458 100644
--- a/pycopancore/model_components/base/interface.py
+++ b/pycopancore/model_components/base/interface.py
@@ -298,7 +298,7 @@ class Group (object, metaclass=_MixinType):
     """
 
     # references:
-    socialsystem = ReferenceVariable("socialsystem", "", type=SocialSystem)
+    #social_system = ReferenceVariable("socialsystem", "", type=SocialSystem)
     next_higher_group = ReferenceVariable("next higher group", "optional",
                                             allow_none=True)  # type is Group, hence it can only be specified after class Group is defined, see below
 

From 1ffd331b144fb15de98a5429f2c84d022f9e4932 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Wed, 1 Jun 2022 14:22:50 +0200
Subject: [PATCH 05/33] Fix Social Update

had error in runner:
TypeError: 'dict_keyiterator' object cannot be interpreted as an integer
[...]
in numpy.random.mtrand.RandomState.choice ValueError: a must be 1-dimensional or an integer
File "C:\Users\bigma\PycharmProjects\pycopancore\pycopancore\model_components\exploit_social_learning\implementation\culture.py", line 42, in social_update
    agent_j = np.random.choice(self.acquaintance_network.neighbors(agent_i))
with (self.acquaintance_network.neighbors(agent_i)) being
<dict_keyiterator object at 0x00000226F0049F90>

FIX:
extracting list from key with list()

agent_j = np.random.choice(list(self.acquaintance_network.neighbors(agent_i)))
---
 .../exploit_social_learning/implementation/culture.py           | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pycopancore/model_components/exploit_social_learning/implementation/culture.py b/pycopancore/model_components/exploit_social_learning/implementation/culture.py
index 4cf957c5..734b0ccf 100644
--- a/pycopancore/model_components/exploit_social_learning/implementation/culture.py
+++ b/pycopancore/model_components/exploit_social_learning/implementation/culture.py
@@ -40,7 +40,7 @@ def social_update(self, t):
         # Step (1)
         if self.acquaintance_network.neighbors(agent_i):
             agent_j = np.random.choice(
-                self.acquaintance_network.neighbors(agent_i))
+                list(self.acquaintance_network.neighbors(agent_i)))
             # Step (2): Compare strategies of i and j:
             # If they are the same, do nothing. Else change i's strategy.
             if agent_i.strategy != agent_j.strategy:

From c0994c4009820713550cb13135e2a7fafb42c5c8 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Wed, 8 Jun 2022 15:52:00 +0200
Subject: [PATCH 06/33] Implementing Individual to Group relationships via a
 group_membership_network. Error while adding group to a culture (group needs
 to "live" somewhere, similar to cells for individuals that then give
 memberships to worlds and so on.

---
 .../data_model/master_data_model/culture.py   |  19 ++-
 .../data_model/master_data_model/group.py     |   9 +-
 .../base/implementation/culture.py            |  13 +-
 .../base/implementation/group.py              | 148 ++++++++----------
 .../base/implementation/individual.py         |  10 +-
 .../model_components/base/interface.py        |  27 ++--
 studies/run_groups_test_seven_dwarfs.py       |  99 ++----------
 7 files changed, 132 insertions(+), 193 deletions(-)

diff --git a/pycopancore/data_model/master_data_model/culture.py b/pycopancore/data_model/master_data_model/culture.py
index 755b8047..d89d2c82 100644
--- a/pycopancore/data_model/master_data_model/culture.py
+++ b/pycopancore/data_model/master_data_model/culture.py
@@ -94,7 +94,24 @@ class Culture:
                  scale='nominal',
                  datatype=set)
         
-        
+
+    # group entity related networks
+
+    inter_group_network = \
+        Variable("inter group network",
+                 """Basic undirected social network between
+                 Groups.""",
+                 ref="https://en.wikipedia.org/wiki/Social_network#Meso_level",
+                 scale='nominal',
+                 datatype=Graph)
+
+    group_membership_network = \
+        Variable("group membership network",
+                 """Directed network from individual to group that
+                 signifies membership (to avoid problems due to n to n relation)""",
+                 scale='nominal',
+                 datatype=DiGraph)
+
     # socio-cultural traits that may occur on different levels:
     
     is_environmentally_friendly = \
diff --git a/pycopancore/data_model/master_data_model/group.py b/pycopancore/data_model/master_data_model/group.py
index 26cf6ce5..cd7354cb 100644
--- a/pycopancore/data_model/master_data_model/group.py
+++ b/pycopancore/data_model/master_data_model/group.py
@@ -8,15 +8,12 @@
 
 class Group:
 
-    #TODO: add a group network possibility (in culture.py (!))
-    #TODO: inter/intra group network
     #TODO: specify edges
 
-    group_network = \
-        Variable("group network",
+    intra_group_network = \
+        Variable("intra group network",
                  """Basic undirected social network between
-                 Groups.""",
-                 ref="https://en.wikipedia.org/wiki/Social_network#Meso_level",
+                 Group members.""",
                  scale='nominal',
                  datatype=Graph)    
 
diff --git a/pycopancore/model_components/base/implementation/culture.py b/pycopancore/model_components/base/implementation/culture.py
index 6f342fcc..79cf5799 100644
--- a/pycopancore/model_components/base/implementation/culture.py
+++ b/pycopancore/model_components/base/implementation/culture.py
@@ -14,8 +14,7 @@
 
 from .. import interface as I
 
-from networkx import Graph
-
+from networkx import Graph, DiGraph
 
 class Culture (I.Culture, abstract.Culture):
     """Culture process taxon mixin implementation class."""
@@ -25,6 +24,7 @@ class Culture (I.Culture, abstract.Culture):
     def __init__(self,
                  *,
                  acquaintance_network=None,
+                 group_membership_network=None,
                  **kwargs):
         """Initialize the unique instance of Culture.
 
@@ -33,6 +33,9 @@ def __init__(self,
         acquaintance_network: Graph
             The Network of acquaintances which is managed by Culture
             (default is None)
+        group_membership_network: DiGraph
+            The Network between Individiuals and groups, which is managed
+            by Culture (default is None)
         **kwargs
             keyword arguments passed to super()
 
@@ -43,6 +46,12 @@ def __init__(self,
             acquaintance_network = Graph()
         assert isinstance(acquaintance_network, Graph)
         self.acquaintance_network = acquaintance_network
+
+        if group_membership_network is None:
+            group_membership_network = DiGraph()
+        assert isinstance(group_membership_network, DiGraph)
+        self.group_membership_network = group_membership_network
+
         self._worlds = set()
 
         # make sure all variable values are valid:
diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index 0aa1d663..22ce9ebd 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -29,7 +29,7 @@ class Group (I.Group, abstract.Group):
 
     def __init__(self,
                  *,
-                 social_system=None,
+                 culture=None,
                  next_higher_group=None,
                  **kwargs
                  ):
@@ -48,8 +48,10 @@ def __init__(self,
         super().__init__(**kwargs)  # must be the first line
 
         # init and set variables implemented via properties:
-        self._social_system = None
-        self.social_system = social_system
+        self._culture = None
+        self.culture = culture
+        # self._social_system = None
+        # self.social_system = social_system
         self._next_higher_group = None
         self.next_higher_group = next_higher_group
 
@@ -57,23 +59,48 @@ def __init__(self,
         self._next_lower_group = set()
         self._direct_cells = set()
 
+        if self.culture:
+            self.culture.group_membership_network.add_node(self)
+
+    def deactivate(self):
+        """Deactivate an individual.
+
+        In particular, deregister from all networks.
+
+        """
+        # deregister from all networks:
+        if self.culture:
+            self.culture.group_membership_network.remove_node(self)
+        super().deactivate()  # must be the last line
+
+    def reactivate(self):
+        """Reactivate an individual.
+
+        In particular, deregister with all mandatory networks.
+
+        """
+        super().reactivate()  # must be the first line
+        # reregister with all mandatory networks:
+        if self.culture:
+            self.culture.group_membership_network.add_node(self)
 
 
     # getters and setters for references:
 
-    @property
-    def social_system(self):
-        """Get the World the SocialSystem is part of."""
-        return self._social_system
-
-    @social_system.setter
-    def social_system(self, s):
-        """Set the World the SocialSystem is part of."""
-        if self._social_system is not None:
-            self._social_system._groups.remove(self)
-        assert isinstance(s, I.SocialSystem), "socialsystem must be of entity type SocialSystem"
-        s._groups.add(self)
-        self._social_system = s
+
+    # @property
+    # def social_system(self):
+    #     """Get the SocialSystem the Group is part of."""
+    #     return self._social_system
+
+    # @social_system.setter
+    # def social_system(self, s):
+    #     """Set the SocialSystem the Group is part of."""
+    #     if self._social_system is not None:
+    #         self._social_system._groups.remove(self)
+    #     assert isinstance(s, I.SocialSystem), "socialsystem must be of entity type SocialSystem"
+    #     s._groups.add(self)
+    #     self._social_system = s
 
     @property
     def next_higher_group(self):
@@ -109,10 +136,22 @@ def metabolism(self):
         """Get the Metabolism of which the Group is a part."""
         return self._world.metabolism
 
-    @property  # read-only
+    @property
     def culture(self):
-        """Get the Culture of which the Group is a part."""
-        return self._world.culture
+        """Get groups's culture."""
+        return self._culture
+
+    @culture.setter
+    def culture(self, c):
+        """Set groups's culture."""
+        if self._culture is not None:
+            # first deregister from previous culture's list of worlds:
+            self._culture.groups.remove(self)
+        if c is not None:
+            assert isinstance(c, I.Culture), \
+                "Culture must be taxon type Culture"
+            c._groups.add(self)
+        self._culture = c
 
     _higher_groups = unknown
     """cache, depends on self.next_higher_group
@@ -152,74 +191,11 @@ def lower_groups(self):
             l.update(s.lower_groups)
         return l
 
-    @property  # read-only
-    def direct_cells(self):
-        """Get cells that directly belong to the SocialSystem."""
-        return self._direct_cells
-
-    _cells = unknown
-    """cache, depends on self.direct_cells, self._next_lower_social_systems,
-    and lowersocial_system.cells"""
-    @property  # read-only
-    def cells(self):
-        """Get cells that directly abd indirectly belong to the SocialSystem."""
-        if self._cells is unknown:
-            # aggregate recursively:
-            self._cells = self.direct_cells
-            for s in self._next_lower_social_systems:
-                self._cells.update(s.cells)
-        return self._cells
-
-    @cells.setter
-    def cells(self, u):
-        """Set cells that directly and indirectly belong to the SocialSystem."""
-        assert u == unknown, "setter can only be used to reset cache"
-        self._cells = unknown
-        # reset dependent caches:
-        if self.next_higher_social_system is not None:
-            self.next_higher_social_system.cells = unknown
-
-    #TODO: direct_inds to members
-    
-    _direct_individuals = unknown
-    """cache, depends on _direct_cells, directcell.individuals"""
-    @property  # read-only
-    def direct_individuals(self):
-        """Get resident Individuals not in subsocial_systems."""
-        if self._direct_individuals is unknown:
-            # aggregate from direct_cells:
-            self._direct_individuals = set()
-            for c in self._direct_cells:
-                self._direct_individuals.update(c.individuals)
-        return self._direct_individuals
-
-    @direct_individuals.setter
-    def direct_individuals(self, u):
-        """Set resident Individuals not in subsocial_systems."""
-        assert u == unknown, "setter can only be used to reset cache"
-        self._direct_individuals = unknown
-        # reset dependent caches:
-        pass
+    @property
+    def group_members(self):
+        """Get the set of Individuals associated with this Group."""
+        return self.culture.group_membership_network.predecessors(self) # .predeccessors as network is directed from inds to groups
 
-    _individuals = unknown
-    """cache, depends on self.cells, cell.individuals"""
-    @property  # read-only
-    def individuals(self):
-        """Get direct and indirect resident Individuals."""
-        if self._individuals is unknown:
-            # aggregate from cells:
-            self._individuals = set()
-            for c in self.cells:
-                self._individuals.update(c.individuals)
-        return self._individuals
-
-    @individuals.setter
-    def individuals(self, u):
-        """Set direct and indirect resident Individuals."""
-        assert u == unknown, "setter can only be used to reset cache"
-        self._individuals = unknown
-        # reset dependent caches:
-        pass
 
     # TODO: helper methods for mergers, splits, etc.
 
diff --git a/pycopancore/model_components/base/implementation/individual.py b/pycopancore/model_components/base/implementation/individual.py
index e82c5fc5..5eb11073 100644
--- a/pycopancore/model_components/base/implementation/individual.py
+++ b/pycopancore/model_components/base/implementation/individual.py
@@ -16,8 +16,6 @@
 
 from .. import interface as I
 
-#TODO: set variable membership
-
 class Individual (I.Individual, abstract.Individual):
     """Individual entity type mixin implementation class.
 
@@ -56,6 +54,7 @@ def __init__(self,
         # register with all mandatory networks:
         if self.culture:
             self.culture.acquaintance_network.add_node(self)
+            self.culture.group_membership_network.add_node(self) # TODO: does this work with DiGraph?
 
     def deactivate(self):
         """Deactivate an individual.
@@ -66,6 +65,7 @@ def deactivate(self):
         # deregister from all networks:
         if self.culture:
             self.culture.acquaintance_network.remove_node(self)
+            self.culture.group_membership_network.remove_node(self)
         super().deactivate()  # must be the last line
 
     def reactivate(self):
@@ -78,6 +78,7 @@ def reactivate(self):
         # reregister with all mandatory networks:
         if self.culture:
             self.culture.acquaintance_network.add_node(self)
+            self.culture.group_membership_network.add_node(self)
 
     # getters and setters for references:
 
@@ -157,6 +158,11 @@ def acquaintances(self):
         """Get the set of Individuals the Individual is acquainted with."""
         return self.culture.acquaintance_network.neighbors(self)
 
+    @property
+    def group_memberships(self):
+        """Get the set of Groups the Individual is associated with."""
+        return self.culture.group_membership_network.successors(self) # .successors as network is directed from inds to groups
+
     # no process-related methods
 
     processes = []  # no processes in base
diff --git a/pycopancore/model_components/base/interface.py b/pycopancore/model_components/base/interface.py
index deb77458..5d1676be 100644
--- a/pycopancore/model_components/base/interface.py
+++ b/pycopancore/model_components/base/interface.py
@@ -69,6 +69,8 @@ class Culture (object):
 
     acquaintance_network = CUL.acquaintance_network
 
+    group_membership_network = CUL.group_membership_network
+
     # read-only attributes storing redundant information:
     worlds = SetVariable("worlds",
                          "Set of Worlds governed by this Culture",
@@ -271,6 +273,10 @@ class Individual (object, metaclass=_MixinType):
                     "set of Individuals this one is acquainted with",
                     readonly=True)
 
+    group_memberships = SetVariable("group memberships",
+                                    "set of Groups this one is associated with",
+                                    readonly=True)
+
     # TODO: specify Variable objects for the following:
     population_share = None
     """share of social_system's direct population represented by this individual"""
@@ -291,6 +297,7 @@ class Individual (object, metaclass=_MixinType):
 
 
 
+
 class Group (object, metaclass=_MixinType):
     """Basic Group interface.
 
@@ -322,17 +329,13 @@ class Group (object, metaclass=_MixinType):
         "lower groups",
         "set of all direct and indirect sub-Groups",
         readonly=True)
-    direct_cells = SetVariable("direct cells", "set of direct territory Cells",
-                               readonly=True)
-    cells = SetVariable("cells", "set of direct and indirect territory Cells",
-                        readonly=True)
-    direct_individuals = SetVariable(
-        "direct individuals",
-        "set of resident Individuals not in subgroups",
-        readonly=True)
-    individuals = SetVariable("individuals",
-                              "set of direct or indirect resident Individuals",
-                              readonly=True)
+
+    group_members = SetVariable(
+        "group members",
+        "set of all individuals associated with the group",
+        readonly=True
+    )
+
 
 
 # specified only now to avoid recursion errors:
@@ -340,5 +343,7 @@ class Group (object, metaclass=_MixinType):
 Group.higher_groups.type = Group
 Group.next_lower_groups.type = Group
 Group.lower_groups.type = Group
+# Individual.group_memberships.type = Group # TODO: assert this is at the right place
+# Group.group_members.type = Individual
 #Group.groups.type = Group
 #SocialSystem.top_level_groups.type = Group
diff --git a/studies/run_groups_test_seven_dwarfs.py b/studies/run_groups_test_seven_dwarfs.py
index 1c241a9b..933a0aba 100644
--- a/studies/run_groups_test_seven_dwarfs.py
+++ b/studies/run_groups_test_seven_dwarfs.py
@@ -67,16 +67,20 @@
                             ) for i in range(dwarfs)
                ]
 
+print("\n The individuals: \n")
+print(individuals)
+print("\n \n")
+
 # assigning individuals to cell is not necessary since it is done by
 # initializing the individuals in 'base.Individuals' with the 'cell' method
 
 #instantiate groups
-ng = 2 #number of groups (group 1 hates snowwhite, group 2 loves her)
-groups = [M.Group(social_system=social_system)
-          for i in range (ng)
-          ]
-
+ng = 5 #number of groups
+groups = [M.Group(culture=culture) for i in range (ng)]
 
+print("\n The groups: \n")
+print(groups)
+print("\n \n")
 
 start = time()
 
@@ -84,6 +88,11 @@
 
 print('\n runner starting')
 
+# first test for group network
+nx.draw(culture.group_membership_network)
+
+plt.show()
+
 # Define termination signals as list [ signal_method, object_method_works_on ]
 # the termination method 'check_for_extinction' must return a boolean
 termination_signal = [M.Culture.check_for_extinction,
@@ -111,83 +120,3 @@
 print("max. time step", (t[1:]-t[:-1]).max())
 
 
-# proceeding for plotting
-
-# Create List of all dwarfes, not only the ones instantiated before the run,
-# but also the one created during the run.
-
-if M.Individual.idle_entities:
-    all_dwarfs = M.Individual.instances + M.Individual.idle_entities
-else:
-    all_dwarfs = M.Individual.instances
-
-individuals_age = np.array([traj[M.Individual.age][dwarf]
-                                 for dwarf in all_dwarfs])
-
-
-individuals_beard_length = np.array([traj[M.Individual.beard_length][dwarf]
-                                 for dwarf in all_dwarfs])
-
-cell_stock = np.array(traj[M.Cell.eating_stock][cells[0]])
-
-t = np.array(traj['t'])
-
-data_age = []
-print('data age', data_age)
-for i, dwarf in enumerate(all_dwarfs):
-    data_age.append(go.Scatter(
-        x=t,
-        y=individuals_age[i],
-        mode="lines",
-        name="age of dwarf no. {}".format(i),
-        line=dict(
-            color="green",
-            width=4
-        )
-    ))
-
-data_beard_length = []
-print('data beard', data_beard_length)
-for i, dwarf in enumerate(all_dwarfs):
-    data_beard_length.append(go.Scatter(
-        x=t,
-        y=individuals_beard_length[i],
-        mode="lines",
-        name="beard length of dwarf no. {}".format(i),
-        line=dict(
-            color="red",
-            width=4
-        )
-    ))
-
-data_stock = []
-data_stock.append(go.Scatter(
-    x=t,
-    y=cell_stock,
-    mode="lines",
-    name="stock of cell",
-    line=dict(color="blue",
-              width=4
-              )
-      ))
-
-
-layout = dict(title='seven dwarfs',
-              xaxis=dict(title='time [yr]'),
-              yaxis=dict(title='value'),
-              )
-
-
-# getting plots of two dwarfs:
-fig = dict(data=[data_age[0], data_beard_length[0], data_stock[0]],
-           layout=layout)
-py.plot(fig, filename="our-model-result{}.html".format(0))
-
-fig = dict(data=[data_age[5], data_beard_length[5], data_stock[0]],
-           layout=layout)
-py.plot(fig, filename="our-model-result{}.html".format(5))
-
-#nx.draw(traj[M.Culture.acquaintance_network][culture][1])
-#plt.show()
-for i in range(len(traj['t'])):
-    print(list(traj[M.Culture.acquaintance_network][culture][i].nodes()))

From 28952090465e016a27acb4988eb3c3e5cc7ab4a3 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Wed, 8 Jun 2022 16:06:00 +0200
Subject: [PATCH 07/33] Implement Network Solution for Group Memberships

Using an directed from Individual to Group Network to handle n to n group memberships.
---
 .../data_model/master_data_model/culture.py   |  19 ++-
 .../data_model/master_data_model/group.py     |   9 +-
 .../base/implementation/culture.py            |  13 +-
 .../base/implementation/group.py              | 148 ++++++++----------
 .../base/implementation/individual.py         |  10 +-
 .../model_components/base/interface.py        |  27 ++--
 6 files changed, 118 insertions(+), 108 deletions(-)

diff --git a/pycopancore/data_model/master_data_model/culture.py b/pycopancore/data_model/master_data_model/culture.py
index 755b8047..d89d2c82 100644
--- a/pycopancore/data_model/master_data_model/culture.py
+++ b/pycopancore/data_model/master_data_model/culture.py
@@ -94,7 +94,24 @@ class Culture:
                  scale='nominal',
                  datatype=set)
         
-        
+
+    # group entity related networks
+
+    inter_group_network = \
+        Variable("inter group network",
+                 """Basic undirected social network between
+                 Groups.""",
+                 ref="https://en.wikipedia.org/wiki/Social_network#Meso_level",
+                 scale='nominal',
+                 datatype=Graph)
+
+    group_membership_network = \
+        Variable("group membership network",
+                 """Directed network from individual to group that
+                 signifies membership (to avoid problems due to n to n relation)""",
+                 scale='nominal',
+                 datatype=DiGraph)
+
     # socio-cultural traits that may occur on different levels:
     
     is_environmentally_friendly = \
diff --git a/pycopancore/data_model/master_data_model/group.py b/pycopancore/data_model/master_data_model/group.py
index 26cf6ce5..cd7354cb 100644
--- a/pycopancore/data_model/master_data_model/group.py
+++ b/pycopancore/data_model/master_data_model/group.py
@@ -8,15 +8,12 @@
 
 class Group:
 
-    #TODO: add a group network possibility (in culture.py (!))
-    #TODO: inter/intra group network
     #TODO: specify edges
 
-    group_network = \
-        Variable("group network",
+    intra_group_network = \
+        Variable("intra group network",
                  """Basic undirected social network between
-                 Groups.""",
-                 ref="https://en.wikipedia.org/wiki/Social_network#Meso_level",
+                 Group members.""",
                  scale='nominal',
                  datatype=Graph)    
 
diff --git a/pycopancore/model_components/base/implementation/culture.py b/pycopancore/model_components/base/implementation/culture.py
index 6f342fcc..79cf5799 100644
--- a/pycopancore/model_components/base/implementation/culture.py
+++ b/pycopancore/model_components/base/implementation/culture.py
@@ -14,8 +14,7 @@
 
 from .. import interface as I
 
-from networkx import Graph
-
+from networkx import Graph, DiGraph
 
 class Culture (I.Culture, abstract.Culture):
     """Culture process taxon mixin implementation class."""
@@ -25,6 +24,7 @@ class Culture (I.Culture, abstract.Culture):
     def __init__(self,
                  *,
                  acquaintance_network=None,
+                 group_membership_network=None,
                  **kwargs):
         """Initialize the unique instance of Culture.
 
@@ -33,6 +33,9 @@ def __init__(self,
         acquaintance_network: Graph
             The Network of acquaintances which is managed by Culture
             (default is None)
+        group_membership_network: DiGraph
+            The Network between Individiuals and groups, which is managed
+            by Culture (default is None)
         **kwargs
             keyword arguments passed to super()
 
@@ -43,6 +46,12 @@ def __init__(self,
             acquaintance_network = Graph()
         assert isinstance(acquaintance_network, Graph)
         self.acquaintance_network = acquaintance_network
+
+        if group_membership_network is None:
+            group_membership_network = DiGraph()
+        assert isinstance(group_membership_network, DiGraph)
+        self.group_membership_network = group_membership_network
+
         self._worlds = set()
 
         # make sure all variable values are valid:
diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index 0aa1d663..22ce9ebd 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -29,7 +29,7 @@ class Group (I.Group, abstract.Group):
 
     def __init__(self,
                  *,
-                 social_system=None,
+                 culture=None,
                  next_higher_group=None,
                  **kwargs
                  ):
@@ -48,8 +48,10 @@ def __init__(self,
         super().__init__(**kwargs)  # must be the first line
 
         # init and set variables implemented via properties:
-        self._social_system = None
-        self.social_system = social_system
+        self._culture = None
+        self.culture = culture
+        # self._social_system = None
+        # self.social_system = social_system
         self._next_higher_group = None
         self.next_higher_group = next_higher_group
 
@@ -57,23 +59,48 @@ def __init__(self,
         self._next_lower_group = set()
         self._direct_cells = set()
 
+        if self.culture:
+            self.culture.group_membership_network.add_node(self)
+
+    def deactivate(self):
+        """Deactivate an individual.
+
+        In particular, deregister from all networks.
+
+        """
+        # deregister from all networks:
+        if self.culture:
+            self.culture.group_membership_network.remove_node(self)
+        super().deactivate()  # must be the last line
+
+    def reactivate(self):
+        """Reactivate an individual.
+
+        In particular, deregister with all mandatory networks.
+
+        """
+        super().reactivate()  # must be the first line
+        # reregister with all mandatory networks:
+        if self.culture:
+            self.culture.group_membership_network.add_node(self)
 
 
     # getters and setters for references:
 
-    @property
-    def social_system(self):
-        """Get the World the SocialSystem is part of."""
-        return self._social_system
-
-    @social_system.setter
-    def social_system(self, s):
-        """Set the World the SocialSystem is part of."""
-        if self._social_system is not None:
-            self._social_system._groups.remove(self)
-        assert isinstance(s, I.SocialSystem), "socialsystem must be of entity type SocialSystem"
-        s._groups.add(self)
-        self._social_system = s
+
+    # @property
+    # def social_system(self):
+    #     """Get the SocialSystem the Group is part of."""
+    #     return self._social_system
+
+    # @social_system.setter
+    # def social_system(self, s):
+    #     """Set the SocialSystem the Group is part of."""
+    #     if self._social_system is not None:
+    #         self._social_system._groups.remove(self)
+    #     assert isinstance(s, I.SocialSystem), "socialsystem must be of entity type SocialSystem"
+    #     s._groups.add(self)
+    #     self._social_system = s
 
     @property
     def next_higher_group(self):
@@ -109,10 +136,22 @@ def metabolism(self):
         """Get the Metabolism of which the Group is a part."""
         return self._world.metabolism
 
-    @property  # read-only
+    @property
     def culture(self):
-        """Get the Culture of which the Group is a part."""
-        return self._world.culture
+        """Get groups's culture."""
+        return self._culture
+
+    @culture.setter
+    def culture(self, c):
+        """Set groups's culture."""
+        if self._culture is not None:
+            # first deregister from previous culture's list of worlds:
+            self._culture.groups.remove(self)
+        if c is not None:
+            assert isinstance(c, I.Culture), \
+                "Culture must be taxon type Culture"
+            c._groups.add(self)
+        self._culture = c
 
     _higher_groups = unknown
     """cache, depends on self.next_higher_group
@@ -152,74 +191,11 @@ def lower_groups(self):
             l.update(s.lower_groups)
         return l
 
-    @property  # read-only
-    def direct_cells(self):
-        """Get cells that directly belong to the SocialSystem."""
-        return self._direct_cells
-
-    _cells = unknown
-    """cache, depends on self.direct_cells, self._next_lower_social_systems,
-    and lowersocial_system.cells"""
-    @property  # read-only
-    def cells(self):
-        """Get cells that directly abd indirectly belong to the SocialSystem."""
-        if self._cells is unknown:
-            # aggregate recursively:
-            self._cells = self.direct_cells
-            for s in self._next_lower_social_systems:
-                self._cells.update(s.cells)
-        return self._cells
-
-    @cells.setter
-    def cells(self, u):
-        """Set cells that directly and indirectly belong to the SocialSystem."""
-        assert u == unknown, "setter can only be used to reset cache"
-        self._cells = unknown
-        # reset dependent caches:
-        if self.next_higher_social_system is not None:
-            self.next_higher_social_system.cells = unknown
-
-    #TODO: direct_inds to members
-    
-    _direct_individuals = unknown
-    """cache, depends on _direct_cells, directcell.individuals"""
-    @property  # read-only
-    def direct_individuals(self):
-        """Get resident Individuals not in subsocial_systems."""
-        if self._direct_individuals is unknown:
-            # aggregate from direct_cells:
-            self._direct_individuals = set()
-            for c in self._direct_cells:
-                self._direct_individuals.update(c.individuals)
-        return self._direct_individuals
-
-    @direct_individuals.setter
-    def direct_individuals(self, u):
-        """Set resident Individuals not in subsocial_systems."""
-        assert u == unknown, "setter can only be used to reset cache"
-        self._direct_individuals = unknown
-        # reset dependent caches:
-        pass
+    @property
+    def group_members(self):
+        """Get the set of Individuals associated with this Group."""
+        return self.culture.group_membership_network.predecessors(self) # .predeccessors as network is directed from inds to groups
 
-    _individuals = unknown
-    """cache, depends on self.cells, cell.individuals"""
-    @property  # read-only
-    def individuals(self):
-        """Get direct and indirect resident Individuals."""
-        if self._individuals is unknown:
-            # aggregate from cells:
-            self._individuals = set()
-            for c in self.cells:
-                self._individuals.update(c.individuals)
-        return self._individuals
-
-    @individuals.setter
-    def individuals(self, u):
-        """Set direct and indirect resident Individuals."""
-        assert u == unknown, "setter can only be used to reset cache"
-        self._individuals = unknown
-        # reset dependent caches:
-        pass
 
     # TODO: helper methods for mergers, splits, etc.
 
diff --git a/pycopancore/model_components/base/implementation/individual.py b/pycopancore/model_components/base/implementation/individual.py
index e82c5fc5..5eb11073 100644
--- a/pycopancore/model_components/base/implementation/individual.py
+++ b/pycopancore/model_components/base/implementation/individual.py
@@ -16,8 +16,6 @@
 
 from .. import interface as I
 
-#TODO: set variable membership
-
 class Individual (I.Individual, abstract.Individual):
     """Individual entity type mixin implementation class.
 
@@ -56,6 +54,7 @@ def __init__(self,
         # register with all mandatory networks:
         if self.culture:
             self.culture.acquaintance_network.add_node(self)
+            self.culture.group_membership_network.add_node(self) # TODO: does this work with DiGraph?
 
     def deactivate(self):
         """Deactivate an individual.
@@ -66,6 +65,7 @@ def deactivate(self):
         # deregister from all networks:
         if self.culture:
             self.culture.acquaintance_network.remove_node(self)
+            self.culture.group_membership_network.remove_node(self)
         super().deactivate()  # must be the last line
 
     def reactivate(self):
@@ -78,6 +78,7 @@ def reactivate(self):
         # reregister with all mandatory networks:
         if self.culture:
             self.culture.acquaintance_network.add_node(self)
+            self.culture.group_membership_network.add_node(self)
 
     # getters and setters for references:
 
@@ -157,6 +158,11 @@ def acquaintances(self):
         """Get the set of Individuals the Individual is acquainted with."""
         return self.culture.acquaintance_network.neighbors(self)
 
+    @property
+    def group_memberships(self):
+        """Get the set of Groups the Individual is associated with."""
+        return self.culture.group_membership_network.successors(self) # .successors as network is directed from inds to groups
+
     # no process-related methods
 
     processes = []  # no processes in base
diff --git a/pycopancore/model_components/base/interface.py b/pycopancore/model_components/base/interface.py
index deb77458..5d1676be 100644
--- a/pycopancore/model_components/base/interface.py
+++ b/pycopancore/model_components/base/interface.py
@@ -69,6 +69,8 @@ class Culture (object):
 
     acquaintance_network = CUL.acquaintance_network
 
+    group_membership_network = CUL.group_membership_network
+
     # read-only attributes storing redundant information:
     worlds = SetVariable("worlds",
                          "Set of Worlds governed by this Culture",
@@ -271,6 +273,10 @@ class Individual (object, metaclass=_MixinType):
                     "set of Individuals this one is acquainted with",
                     readonly=True)
 
+    group_memberships = SetVariable("group memberships",
+                                    "set of Groups this one is associated with",
+                                    readonly=True)
+
     # TODO: specify Variable objects for the following:
     population_share = None
     """share of social_system's direct population represented by this individual"""
@@ -291,6 +297,7 @@ class Individual (object, metaclass=_MixinType):
 
 
 
+
 class Group (object, metaclass=_MixinType):
     """Basic Group interface.
 
@@ -322,17 +329,13 @@ class Group (object, metaclass=_MixinType):
         "lower groups",
         "set of all direct and indirect sub-Groups",
         readonly=True)
-    direct_cells = SetVariable("direct cells", "set of direct territory Cells",
-                               readonly=True)
-    cells = SetVariable("cells", "set of direct and indirect territory Cells",
-                        readonly=True)
-    direct_individuals = SetVariable(
-        "direct individuals",
-        "set of resident Individuals not in subgroups",
-        readonly=True)
-    individuals = SetVariable("individuals",
-                              "set of direct or indirect resident Individuals",
-                              readonly=True)
+
+    group_members = SetVariable(
+        "group members",
+        "set of all individuals associated with the group",
+        readonly=True
+    )
+
 
 
 # specified only now to avoid recursion errors:
@@ -340,5 +343,7 @@ class Group (object, metaclass=_MixinType):
 Group.higher_groups.type = Group
 Group.next_lower_groups.type = Group
 Group.lower_groups.type = Group
+# Individual.group_memberships.type = Group # TODO: assert this is at the right place
+# Group.group_members.type = Individual
 #Group.groups.type = Group
 #SocialSystem.top_level_groups.type = Group

From 9c473e1ed26d3f23b5a254b6b93446e9fbf241a4 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Wed, 8 Jun 2022 16:08:15 +0200
Subject: [PATCH 08/33] Update run_groups_test_seven_dwarfs.py

---
 studies/run_groups_test_seven_dwarfs.py | 99 ++++---------------------
 1 file changed, 14 insertions(+), 85 deletions(-)

diff --git a/studies/run_groups_test_seven_dwarfs.py b/studies/run_groups_test_seven_dwarfs.py
index 1c241a9b..933a0aba 100644
--- a/studies/run_groups_test_seven_dwarfs.py
+++ b/studies/run_groups_test_seven_dwarfs.py
@@ -67,16 +67,20 @@
                             ) for i in range(dwarfs)
                ]
 
+print("\n The individuals: \n")
+print(individuals)
+print("\n \n")
+
 # assigning individuals to cell is not necessary since it is done by
 # initializing the individuals in 'base.Individuals' with the 'cell' method
 
 #instantiate groups
-ng = 2 #number of groups (group 1 hates snowwhite, group 2 loves her)
-groups = [M.Group(social_system=social_system)
-          for i in range (ng)
-          ]
-
+ng = 5 #number of groups
+groups = [M.Group(culture=culture) for i in range (ng)]
 
+print("\n The groups: \n")
+print(groups)
+print("\n \n")
 
 start = time()
 
@@ -84,6 +88,11 @@
 
 print('\n runner starting')
 
+# first test for group network
+nx.draw(culture.group_membership_network)
+
+plt.show()
+
 # Define termination signals as list [ signal_method, object_method_works_on ]
 # the termination method 'check_for_extinction' must return a boolean
 termination_signal = [M.Culture.check_for_extinction,
@@ -111,83 +120,3 @@
 print("max. time step", (t[1:]-t[:-1]).max())
 
 
-# proceeding for plotting
-
-# Create List of all dwarfes, not only the ones instantiated before the run,
-# but also the one created during the run.
-
-if M.Individual.idle_entities:
-    all_dwarfs = M.Individual.instances + M.Individual.idle_entities
-else:
-    all_dwarfs = M.Individual.instances
-
-individuals_age = np.array([traj[M.Individual.age][dwarf]
-                                 for dwarf in all_dwarfs])
-
-
-individuals_beard_length = np.array([traj[M.Individual.beard_length][dwarf]
-                                 for dwarf in all_dwarfs])
-
-cell_stock = np.array(traj[M.Cell.eating_stock][cells[0]])
-
-t = np.array(traj['t'])
-
-data_age = []
-print('data age', data_age)
-for i, dwarf in enumerate(all_dwarfs):
-    data_age.append(go.Scatter(
-        x=t,
-        y=individuals_age[i],
-        mode="lines",
-        name="age of dwarf no. {}".format(i),
-        line=dict(
-            color="green",
-            width=4
-        )
-    ))
-
-data_beard_length = []
-print('data beard', data_beard_length)
-for i, dwarf in enumerate(all_dwarfs):
-    data_beard_length.append(go.Scatter(
-        x=t,
-        y=individuals_beard_length[i],
-        mode="lines",
-        name="beard length of dwarf no. {}".format(i),
-        line=dict(
-            color="red",
-            width=4
-        )
-    ))
-
-data_stock = []
-data_stock.append(go.Scatter(
-    x=t,
-    y=cell_stock,
-    mode="lines",
-    name="stock of cell",
-    line=dict(color="blue",
-              width=4
-              )
-      ))
-
-
-layout = dict(title='seven dwarfs',
-              xaxis=dict(title='time [yr]'),
-              yaxis=dict(title='value'),
-              )
-
-
-# getting plots of two dwarfs:
-fig = dict(data=[data_age[0], data_beard_length[0], data_stock[0]],
-           layout=layout)
-py.plot(fig, filename="our-model-result{}.html".format(0))
-
-fig = dict(data=[data_age[5], data_beard_length[5], data_stock[0]],
-           layout=layout)
-py.plot(fig, filename="our-model-result{}.html".format(5))
-
-#nx.draw(traj[M.Culture.acquaintance_network][culture][1])
-#plt.show()
-for i in range(len(traj['t'])):
-    print(list(traj[M.Culture.acquaintance_network][culture][i].nodes()))

From fbb26f6e6a3295b578c62ab93174b0dcd689d3dc Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Wed, 8 Jun 2022 16:38:05 +0200
Subject: [PATCH 09/33] Group now gets culture and further things over being
 part of a world.

---
 .../base/implementation/group.py              | 161 ++++++++++--------
 .../model_components/base/interface.py        |  39 +++--
 studies/run_groups_test_seven_dwarfs.py       |  17 +-
 3 files changed, 123 insertions(+), 94 deletions(-)

diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index 22ce9ebd..37684ac7 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -29,7 +29,8 @@ class Group (I.Group, abstract.Group):
 
     def __init__(self,
                  *,
-                 culture=None,
+                 world,
+                 # culture=None,
                  next_higher_group=None,
                  **kwargs
                  ):
@@ -48,8 +49,11 @@ def __init__(self,
         super().__init__(**kwargs)  # must be the first line
 
         # init and set variables implemented via properties:
-        self._culture = None
-        self.culture = culture
+        # self._culture = None
+        # self.culture = culture
+        self._world = None
+        self.world = world
+
         # self._social_system = None
         # self.social_system = social_system
         self._next_higher_group = None
@@ -87,6 +91,19 @@ def reactivate(self):
 
     # getters and setters for references:
 
+    @property
+    def world(self):
+        """Get the World the Group is part of."""
+        return self._world
+
+    @world.setter
+    def world(self, w):
+        """Set the World the Group is part of."""
+        if self._world is not None:
+            self._world._social_systems.remove(self)
+        assert isinstance(w, I.World), "world must be of entity type World"
+        w._social_systems.add(self)
+        self._world = w
 
     # @property
     # def social_system(self):
@@ -102,27 +119,27 @@ def reactivate(self):
     #     s._groups.add(self)
     #     self._social_system = s
 
-    @property
-    def next_higher_group(self):
-        """Get next higher group."""
-        return self._next_higher_group
-
-    @next_higher_group.setter
-    def next_higher_group(self, s):
-        """Set next higher group."""
-        if self._next_higher_group is not None:
-            self._next_higher_group._next_lower_groups.remove(self)
-            # reset dependent cache:
-            self._next_higher_group.cells = unknown
-        if s is not None:
-            assert isinstance(s, I.Group), \
-                "next_higher_group must be of entity type group"
-            s._next_lower_groups.add(self)
-            # reset dependent cache:
-            s.cells = unknown
-        self._next_higher_group = s
+    # @property
+    # def next_higher_group(self):
+    #     """Get next higher group."""
+    #     return self._next_higher_group
+
+    # @next_higher_group.setter
+    # def next_higher_group(self, s):
+    #     """Set next higher group."""
+    #     if self._next_higher_group is not None:
+    #         self._next_higher_group._next_lower_groups.remove(self)
+    #         reset dependent cache:
+            # self._next_higher_group.cells = unknown
+        # if s is not None:
+        #     assert isinstance(s, I.Group), \
+        #         "next_higher_group must be of entity type group"
+        #     s._next_lower_groups.add(self)
+        #     reset dependent cache:
+        #     s.cells = unknown
+        # self._next_higher_group = s
         # reset dependent caches:
-        self.higher_groups = unknown
+        # self.higher_groups = unknown
 
     # getters for backwards references and convenience variables:
 
@@ -136,60 +153,60 @@ def metabolism(self):
         """Get the Metabolism of which the Group is a part."""
         return self._world.metabolism
 
-    @property
-    def culture(self):
-        """Get groups's culture."""
-        return self._culture
-
-    @culture.setter
-    def culture(self, c):
-        """Set groups's culture."""
-        if self._culture is not None:
-            # first deregister from previous culture's list of worlds:
-            self._culture.groups.remove(self)
-        if c is not None:
-            assert isinstance(c, I.Culture), \
-                "Culture must be taxon type Culture"
-            c._groups.add(self)
-        self._culture = c
-
-    _higher_groups = unknown
+    # @property
+    # def culture(self):
+    #     """Get groups's culture."""
+    #     return self._culture
+
+    # @culture.setter
+    # def culture(self, c):
+    #     """Set groups's culture."""
+    #     if self._culture is not None:
+    #         first deregister from previous culture's list of worlds:
+            # self._culture.groups.remove(self)
+        # if c is not None:
+        #     assert isinstance(c, I.Culture), \
+        #         "Culture must be taxon type Culture"
+        #     c._groups.add(self)
+        # self._culture = c
+
+    # _higher_groups = unknown
     """cache, depends on self.next_higher_group
     and self.next_higher_group.higher_groups"""
-    @property  # read-only
-    def higher_groups(self):
-        """Get higher groups."""
-        if self._higher_groups is unknown:
+    # @property  # read-only
+    # def higher_groups(self):
+    #     """Get higher groups."""
+    #     if self._higher_groups is unknown:
             # find recursively:
-            self._higher_groups = [] if self.next_higher_group is None \
-                else ([self.next_higher_group]
-                      + self.next_higher_group.groups)
-        return self._higher_groups
-
-    @higher_groups.setter
-    def higher_groups(self, u):
-        """Set higher groups."""
-        assert u == unknown, "setter can only be used to reset cache"
-        self._higher_groups = unknown
+            # self._higher_groups = [] if self.next_higher_group is None \
+            #     else ([self.next_higher_group]
+            #           + self.next_higher_group.groups)
+        # return self._higher_groups
+
+    # @higher_groups.setter
+    # def higher_groups(self, u):
+    #     """Set higher groups."""
+    #     assert u == unknown, "setter can only be used to reset cache"
+    #     self._higher_groups = unknown
         # reset dependent caches:
-        for s in self._next_lower_groups:
-            s.higher_groups = unknown
-        for c in self._direct_cells:
-            c.groups = unknown
-
-    @property  # read-only
-    def next_lower_groups(self):
-        """Get next lower groups."""
-        return self._next_lower_groups
-
-    @property  # read-only
-    def lower_groups(self):
-        """Get lower groups."""
+        # for s in self._next_lower_groups:
+        #     s.higher_groups = unknown
+        # for c in self._direct_cells:
+        #     c.groups = unknown
+
+    # @property  # read-only
+    # def next_lower_groups(self):
+    #     """Get next lower groups."""
+    #     return self._next_lower_groups
+
+    # @property  # read-only
+    # def lower_groups(self):
+    #     """Get lower groups."""
         # aggregate recursively:
-        l = self._next_lower_groups
-        for s in self._next_lower_groups:
-            l.update(s.lower_groups)
-        return l
+        # l = self._next_lower_groups
+        # for s in self._next_lower_groups:
+        #     l.update(s.lower_groups)
+        # return l
 
     @property
     def group_members(self):
diff --git a/pycopancore/model_components/base/interface.py b/pycopancore/model_components/base/interface.py
index 5d1676be..5d8d3975 100644
--- a/pycopancore/model_components/base/interface.py
+++ b/pycopancore/model_components/base/interface.py
@@ -122,6 +122,9 @@ class World (object, metaclass=_MixinType):
     individuals = SetVariable("individuals",
                               "Set of Individuals residing on this world",
                               readonly=True)
+    groups = SetVariable("groups",
+                         "Set of Groups existing on this world",
+                         readonly=True)
 
 
 # specified only now to avoid recursion errors:
@@ -306,8 +309,8 @@ class Group (object, metaclass=_MixinType):
 
     # references:
     #social_system = ReferenceVariable("socialsystem", "", type=SocialSystem)
-    next_higher_group = ReferenceVariable("next higher group", "optional",
-                                            allow_none=True)  # type is Group, hence it can only be specified after class Group is defined, see below
+    # next_higher_group = ReferenceVariable("next higher group", "optional",
+    #                                         allow_none=True)  # type is Group, hence it can only be specified after class Group is defined, see below
 
 
     # read-only attributes storing redundant information:
@@ -317,18 +320,18 @@ class Group (object, metaclass=_MixinType):
                                    readonly=True)
     culture = ReferenceVariable("culture", "", type=Culture,
                                 readonly=True)
-    higher_groups = SetVariable(
-        "higher groups",
-        "upward list of (in)direct super-Groups",
-        readonly=True)
-    next_lower_groups = SetVariable(
-        "next lower groups",
-        "set of sub-Groups of next lower level",
-        readonly=True)
-    lower_groups = SetVariable(
-        "lower groups",
-        "set of all direct and indirect sub-Groups",
-        readonly=True)
+    # higher_groups = SetVariable(
+    #     "higher groups",
+    #     "upward list of (in)direct super-Groups",
+    #     readonly=True)
+    # next_lower_groups = SetVariable(
+    #     "next lower groups",
+    #     "set of sub-Groups of next lower level",
+    #     readonly=True)
+    # lower_groups = SetVariable(
+    #     "lower groups",
+    #     "set of all direct and indirect sub-Groups",
+    #     readonly=True)
 
     group_members = SetVariable(
         "group members",
@@ -339,10 +342,10 @@ class Group (object, metaclass=_MixinType):
 
 
 # specified only now to avoid recursion errors:
-Group.next_higher_group.type = Group
-Group.higher_groups.type = Group
-Group.next_lower_groups.type = Group
-Group.lower_groups.type = Group
+# Group.next_higher_group.type = Group
+# Group.higher_groups.type = Group
+# Group.next_lower_groups.type = Group
+# Group.lower_groups.type = Group
 # Individual.group_memberships.type = Group # TODO: assert this is at the right place
 # Group.group_members.type = Individual
 #Group.groups.type = Group
diff --git a/studies/run_groups_test_seven_dwarfs.py b/studies/run_groups_test_seven_dwarfs.py
index 933a0aba..f2ce6424 100644
--- a/studies/run_groups_test_seven_dwarfs.py
+++ b/studies/run_groups_test_seven_dwarfs.py
@@ -15,6 +15,7 @@
 # License: BSD 2-clause license
 
 import numpy as np
+from numpy.random import uniform
 from time import time
 import datetime as dt
 
@@ -33,7 +34,7 @@
 # setting time step to hand to 'Runner.run()'
 timestep = .1
 nc = 1  # number of caves
-dwarfs = 7  # number of dwarfs
+dwarfs = 10  # number of dwarfs
 
 # instantiate model M (needs to be done in the beginning of each script).
 # This configures the model M through 'ModelLogics' in module
@@ -75,8 +76,8 @@
 # initializing the individuals in 'base.Individuals' with the 'cell' method
 
 #instantiate groups
-ng = 5 #number of groups
-groups = [M.Group(culture=culture) for i in range (ng)]
+ng = 10 #number of groups
+groups = [M.Group(world=world) for i in range (ng)]
 
 print("\n The groups: \n")
 print(groups)
@@ -89,8 +90,16 @@
 print('\n runner starting')
 
 # first test for group network
-nx.draw(culture.group_membership_network)
+#nx.draw(culture.group_membership_network)
+#plt.show()
+
 
+# initialize some network:
+for i in enumerate(individuals):
+    for j in enumerate(groups):
+        culture.group_membership_network.add_edge(i, j)
+
+nx.draw(culture.group_membership_network)
 plt.show()
 
 # Define termination signals as list [ signal_method, object_method_works_on ]

From bdeb1282ddfb15fa112b2a18ecc668dfb60eddfc Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Wed, 8 Jun 2022 16:44:25 +0200
Subject: [PATCH 10/33] little fix

---
 pycopancore/model_components/base/implementation/group.py | 4 ++--
 pycopancore/model_components/base/implementation/world.py | 6 ++++++
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index 37684ac7..b8b6b3d1 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -100,9 +100,9 @@ def world(self):
     def world(self, w):
         """Set the World the Group is part of."""
         if self._world is not None:
-            self._world._social_systems.remove(self)
+            self._world._groups.remove(self)
         assert isinstance(w, I.World), "world must be of entity type World"
-        w._social_systems.add(self)
+        w._groups.add(self)
         self._world = w
 
     # @property
diff --git a/pycopancore/model_components/base/implementation/world.py b/pycopancore/model_components/base/implementation/world.py
index 05dea718..9457f44e 100644
--- a/pycopancore/model_components/base/implementation/world.py
+++ b/pycopancore/model_components/base/implementation/world.py
@@ -59,6 +59,7 @@ def __init__(self,
         self.culture = culture
         self._social_systems = set()
         self._cells = set()
+        self._groups = set()
 
         # make sure all variable values are valid:
         self.assert_valid()
@@ -164,6 +165,11 @@ def individuals(self, u):
         # reset dependent caches:
         pass
 
+    @property  # read-only
+    def groups(self):
+        """Get the set of all Groups on this World."""
+        return self._groups
+
 
     processes = [
         # TODO: convert this into an Implicit equation once supported:

From 9747ce5c9707551b03598983972fa19dae3da63f Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Thu, 9 Jun 2022 14:30:59 +0200
Subject: [PATCH 11/33] run_group_test_seven_dwarfs.py now demonstrates minimum
 features of the new group entity

---
 studies/run_groups_test_seven_dwarfs.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/studies/run_groups_test_seven_dwarfs.py b/studies/run_groups_test_seven_dwarfs.py
index f2ce6424..f03ec4a6 100644
--- a/studies/run_groups_test_seven_dwarfs.py
+++ b/studies/run_groups_test_seven_dwarfs.py
@@ -95,13 +95,21 @@
 
 
 # initialize some network:
-for i in enumerate(individuals):
+for i in individuals:
     for j in enumerate(groups):
         culture.group_membership_network.add_edge(i, j)
 
 nx.draw(culture.group_membership_network)
 plt.show()
 
+# print("Group Members: \n")
+# for i in groups:
+#     print(i.group_members)
+print("Individual 1 Group Memberships: \n")
+print(list(individuals[0].group_memberships))
+# for i in individuals:
+#     print(i.group_memberships)
+
 # Define termination signals as list [ signal_method, object_method_works_on ]
 # the termination method 'check_for_extinction' must return a boolean
 termination_signal = [M.Culture.check_for_extinction,

From 032528caa54d4a13d87779c573afce7112c09122 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Mon, 13 Jun 2022 16:51:31 +0200
Subject: [PATCH 12/33] run_group_test_seven_dwarfs.py now demonstrates minimum
 features of the new group entity

---
 .../base/implementation/group.py              | 19 +++++++++++------
 .../base/implementation/individual.py         |  2 +-
 studies/run_groups_test_seven_dwarfs.py       | 21 ++++++++++++-------
 3 files changed, 28 insertions(+), 14 deletions(-)

diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index b8b6b3d1..012b15a0 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -38,8 +38,8 @@ def __init__(self,
 
         Parameters
         ----------
-        socialsystem: obj
-            SocialSystem the Group belongs to (default is None)
+        world: obj
+            World the Group belongs to
         next_higher_group: obj
             Optional Group the Group belongs to (default is None)
         **kwargs
@@ -67,7 +67,7 @@ def __init__(self,
             self.culture.group_membership_network.add_node(self)
 
     def deactivate(self):
-        """Deactivate an individual.
+        """Deactivate a group.
 
         In particular, deregister from all networks.
 
@@ -78,7 +78,7 @@ def deactivate(self):
         super().deactivate()  # must be the last line
 
     def reactivate(self):
-        """Reactivate an individual.
+        """Reactivate a group.
 
         In particular, deregister with all mandatory networks.
 
@@ -88,6 +88,12 @@ def reactivate(self):
         if self.culture:
             self.culture.group_membership_network.add_node(self)
 
+    def member_mean(self, state):
+        """
+        Calculate the arithmetic mean of a state of all members of a groups.
+        """
+
+
 
     # getters and setters for references:
 
@@ -211,10 +217,11 @@ def metabolism(self):
     @property
     def group_members(self):
         """Get the set of Individuals associated with this Group."""
-        return self.culture.group_membership_network.predecessors(self) # .predeccessors as network is directed from inds to groups
+        return self.culture.group_membership_network.neighbors(self) # .predeccessors as network is directed from inds to groups
+
+
 
 
-    # TODO: helper methods for mergers, splits, etc.
 
     # no process-related methods
 
diff --git a/pycopancore/model_components/base/implementation/individual.py b/pycopancore/model_components/base/implementation/individual.py
index 5eb11073..8ae255f4 100644
--- a/pycopancore/model_components/base/implementation/individual.py
+++ b/pycopancore/model_components/base/implementation/individual.py
@@ -161,7 +161,7 @@ def acquaintances(self):
     @property
     def group_memberships(self):
         """Get the set of Groups the Individual is associated with."""
-        return self.culture.group_membership_network.successors(self) # .successors as network is directed from inds to groups
+        return self.culture.group_membership_network.neighbors(self) # .successors as network is directed from inds to groups
 
     # no process-related methods
 
diff --git a/studies/run_groups_test_seven_dwarfs.py b/studies/run_groups_test_seven_dwarfs.py
index f03ec4a6..f200cd1e 100644
--- a/studies/run_groups_test_seven_dwarfs.py
+++ b/studies/run_groups_test_seven_dwarfs.py
@@ -99,16 +99,23 @@
     for j in enumerate(groups):
         culture.group_membership_network.add_edge(i, j)
 
+
+print("Individual 1 Group Memberships:")
+print(list(individuals[0].group_memberships))
+print("\n")
+
+print("Group Members:")
+print(groups[0])
+# print(groups[0].group_members)
+print("\n")
+
+#draw network of one group
+nx.draw(individuals[0].culture.group_membership_network)
+
 nx.draw(culture.group_membership_network)
 plt.show()
 
-# print("Group Members: \n")
-# for i in groups:
-#     print(i.group_members)
-print("Individual 1 Group Memberships: \n")
-print(list(individuals[0].group_memberships))
-# for i in individuals:
-#     print(i.group_memberships)
+
 
 # Define termination signals as list [ signal_method, object_method_works_on ]
 # the termination method 'check_for_extinction' must return a boolean

From b3bc2c6b3c029a9c89d8c03116b12048515041c8 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Thu, 16 Jun 2022 11:09:18 +0200
Subject: [PATCH 13/33] - Change group from living in World to living in
 Culture - Add visualisation of layered group network in
 run_group_test_seven_dwarfs.py - Fix minor issues

---
 .../base/implementation/culture.py            |  6 +++
 .../base/implementation/group.py              | 54 +++++++++----------
 .../base/implementation/individual.py         |  4 +-
 .../base/implementation/world.py              |  7 ---
 .../model_components/base/interface.py        |  9 ++--
 studies/run_exploit.py                        |  1 +
 studies/run_groups_test_seven_dwarfs.py       | 42 ++++++++++++---
 7 files changed, 76 insertions(+), 47 deletions(-)

diff --git a/pycopancore/model_components/base/implementation/culture.py b/pycopancore/model_components/base/implementation/culture.py
index 79cf5799..1d2239af 100644
--- a/pycopancore/model_components/base/implementation/culture.py
+++ b/pycopancore/model_components/base/implementation/culture.py
@@ -53,6 +53,7 @@ def __init__(self,
         self.group_membership_network = group_membership_network
 
         self._worlds = set()
+        self._groups = set()
 
         # make sure all variable values are valid:
         self.assert_valid()
@@ -63,6 +64,11 @@ def worlds(self):
         """Get the set of all Worlds this Culture acts in."""
         return self._worlds
 
+    @property  # read-only
+    def groups(self):
+        """Get the set of all Groups in this Culture."""
+        return self._groups
+
     # no process-related methods
 
     processes = []  # no processes in base
diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index 012b15a0..063b7342 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -29,8 +29,7 @@ class Group (I.Group, abstract.Group):
 
     def __init__(self,
                  *,
-                 world,
-                 # culture=None,
+                 culture,
                  next_higher_group=None,
                  **kwargs
                  ):
@@ -38,8 +37,8 @@ def __init__(self,
 
         Parameters
         ----------
-        world: obj
-            World the Group belongs to
+        culture: obj
+            Culture the Group belongs to
         next_higher_group: obj
             Optional Group the Group belongs to (default is None)
         **kwargs
@@ -49,10 +48,10 @@ def __init__(self,
         super().__init__(**kwargs)  # must be the first line
 
         # init and set variables implemented via properties:
-        # self._culture = None
-        # self.culture = culture
-        self._world = None
-        self.world = world
+        self._culture = None
+        self.culture = culture
+        # self._world = None
+        # self.world = world
 
         # self._social_system = None
         # self.social_system = social_system
@@ -64,7 +63,7 @@ def __init__(self,
         self._direct_cells = set()
 
         if self.culture:
-            self.culture.group_membership_network.add_node(self)
+            self.culture.group_membership_network.add_node(self, type="Group", color="green")
 
     def deactivate(self):
         """Deactivate a group.
@@ -86,7 +85,7 @@ def reactivate(self):
         super().reactivate()  # must be the first line
         # reregister with all mandatory networks:
         if self.culture:
-            self.culture.group_membership_network.add_node(self)
+            self.culture.group_membership_network.add_node(self, type="Group", color="green")
 
     def member_mean(self, state):
         """
@@ -159,22 +158,22 @@ def metabolism(self):
         """Get the Metabolism of which the Group is a part."""
         return self._world.metabolism
 
-    # @property
-    # def culture(self):
-    #     """Get groups's culture."""
-    #     return self._culture
-
-    # @culture.setter
-    # def culture(self, c):
-    #     """Set groups's culture."""
-    #     if self._culture is not None:
-    #         first deregister from previous culture's list of worlds:
-            # self._culture.groups.remove(self)
-        # if c is not None:
-        #     assert isinstance(c, I.Culture), \
-        #         "Culture must be taxon type Culture"
-        #     c._groups.add(self)
-        # self._culture = c
+    @property
+    def culture(self):
+        """Get culture group is part of."""
+        return self._culture
+
+    @culture.setter
+    def culture(self, c):
+        """Set culture group is part of."""
+        if self._culture is not None:
+            # first deregister from previous culture's list of worlds:
+            self._culture.groups.remove(self)
+        if c is not None:
+            assert isinstance(c, I.Culture), \
+                "Culture must be taxon type Culture"
+            c._groups.add(self)
+        self._culture = c
 
     # _higher_groups = unknown
     """cache, depends on self.next_higher_group
@@ -217,7 +216,8 @@ def metabolism(self):
     @property
     def group_members(self):
         """Get the set of Individuals associated with this Group."""
-        return self.culture.group_membership_network.neighbors(self) # .predeccessors as network is directed from inds to groups
+        # return self.culture.group_membership_network.neighbors(self)
+        return self.culture.group_membership_network.predecessors(self) # .predecessors as network is directed from inds to groups
 
 
 
diff --git a/pycopancore/model_components/base/implementation/individual.py b/pycopancore/model_components/base/implementation/individual.py
index 8ae255f4..dcaa0ffb 100644
--- a/pycopancore/model_components/base/implementation/individual.py
+++ b/pycopancore/model_components/base/implementation/individual.py
@@ -54,7 +54,7 @@ def __init__(self,
         # register with all mandatory networks:
         if self.culture:
             self.culture.acquaintance_network.add_node(self)
-            self.culture.group_membership_network.add_node(self) # TODO: does this work with DiGraph?
+            self.culture.group_membership_network.add_node(self, type="Individual", color="yellow")
 
     def deactivate(self):
         """Deactivate an individual.
@@ -78,7 +78,7 @@ def reactivate(self):
         # reregister with all mandatory networks:
         if self.culture:
             self.culture.acquaintance_network.add_node(self)
-            self.culture.group_membership_network.add_node(self)
+            self.culture.group_membership_network.add_node(self, type="Individual", color="yellow")
 
     # getters and setters for references:
 
diff --git a/pycopancore/model_components/base/implementation/world.py b/pycopancore/model_components/base/implementation/world.py
index 9457f44e..3e12fe08 100644
--- a/pycopancore/model_components/base/implementation/world.py
+++ b/pycopancore/model_components/base/implementation/world.py
@@ -59,7 +59,6 @@ def __init__(self,
         self.culture = culture
         self._social_systems = set()
         self._cells = set()
-        self._groups = set()
 
         # make sure all variable values are valid:
         self.assert_valid()
@@ -165,12 +164,6 @@ def individuals(self, u):
         # reset dependent caches:
         pass
 
-    @property  # read-only
-    def groups(self):
-        """Get the set of all Groups on this World."""
-        return self._groups
-
-
     processes = [
         # TODO: convert this into an Implicit equation once supported:
         Explicit("aggregate cell carbon stocks",
diff --git a/pycopancore/model_components/base/interface.py b/pycopancore/model_components/base/interface.py
index 5d8d3975..6ac69ebb 100644
--- a/pycopancore/model_components/base/interface.py
+++ b/pycopancore/model_components/base/interface.py
@@ -78,6 +78,9 @@ class Culture (object):
 
 # entity types:
 
+    groups = SetVariable("groups",
+                         "Set of Groups existing on this world",
+                         readonly=True)
 
 # TODO: clarify whether it is necessary to specify the metaclass here!
 class World (object, metaclass=_MixinType):
@@ -122,9 +125,7 @@ class World (object, metaclass=_MixinType):
     individuals = SetVariable("individuals",
                               "Set of Individuals residing on this world",
                               readonly=True)
-    groups = SetVariable("groups",
-                         "Set of Groups existing on this world",
-                         readonly=True)
+
 
 
 # specified only now to avoid recursion errors:
@@ -339,7 +340,7 @@ class Group (object, metaclass=_MixinType):
         readonly=True
     )
 
-
+Culture.groups.type = Group
 
 # specified only now to avoid recursion errors:
 # Group.next_higher_group.type = Group
diff --git a/studies/run_exploit.py b/studies/run_exploit.py
index 3275f221..23ab8837 100755
--- a/studies/run_exploit.py
+++ b/studies/run_exploit.py
@@ -18,6 +18,7 @@
 from time import time
 import datetime as dt
 from numpy import random
+import argparse
 
 import plotly.offline as py
 import plotly.graph_objs as go
diff --git a/studies/run_groups_test_seven_dwarfs.py b/studies/run_groups_test_seven_dwarfs.py
index f200cd1e..e751ec4c 100644
--- a/studies/run_groups_test_seven_dwarfs.py
+++ b/studies/run_groups_test_seven_dwarfs.py
@@ -20,6 +20,7 @@
 import datetime as dt
 
 import networkx as nx
+from networkx.algorithms import bipartite
 import matplotlib.pyplot as plt
 
 import plotly.offline as py
@@ -77,7 +78,7 @@
 
 #instantiate groups
 ng = 10 #number of groups
-groups = [M.Group(world=world) for i in range (ng)]
+groups = [M.Group(culture=culture) for i in range (ng)]
 
 print("\n The groups: \n")
 print(groups)
@@ -96,9 +97,8 @@
 
 # initialize some network:
 for i in individuals:
-    for j in enumerate(groups):
-        culture.group_membership_network.add_edge(i, j)
-
+    for g in groups:
+        culture.group_membership_network.add_edge(i, g)
 
 print("Individual 1 Group Memberships:")
 print(list(individuals[0].group_memberships))
@@ -106,13 +106,41 @@
 
 print("Group Members:")
 print(groups[0])
-# print(groups[0].group_members)
+print(list(groups[0].group_members))
 print("\n")
 
 #draw network of one group
-nx.draw(individuals[0].culture.group_membership_network)
+# nx.draw(individuals[0].culture.group_membership_network)
+# plt.show()
+
+GM = culture.group_membership_network
+
+print(GM.nodes.data())
+
+
+color_map = []
+shape_map = []
+for node in list(GM.nodes):
+    print(node)
+    print(GM.nodes[node])
+    color_map.append(GM.nodes[node]["color"])
+
+    if GM.nodes[node]["type"] == "Group":
+        shape_map.append("o")
+    else:
+        shape_map.append("^")
+
+
+
+top_nodes = {n for n, d in GM.nodes(data=True) if d["type"] == "Group"}
+bottom_nodes = set(GM) - top_nodes
+
+print(list(top_nodes))
+
+nx.draw(GM, node_color=color_map, with_labels=True,
+        pos=nx.bipartite_layout(GM, bottom_nodes, align="horizontal", aspect_ratio=4/1))
 
-nx.draw(culture.group_membership_network)
+# nx.draw(culture.group_membership_network)
 plt.show()
 
 

From 4019e10024aa5432115f9af2a023abb44507c090 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Mon, 20 Jun 2022 15:33:54 +0200
Subject: [PATCH 14/33] add/adjust documentation

---
 .../abstract_level/entity_types/group.rst     | 21 ++++++++++++-------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/docs/framework_documentation/abstract_level/entity_types/group.rst b/docs/framework_documentation/abstract_level/entity_types/group.rst
index 7ef8158c..173ad33e 100644
--- a/docs/framework_documentation/abstract_level/entity_types/group.rst
+++ b/docs/framework_documentation/abstract_level/entity_types/group.rst
@@ -11,7 +11,7 @@ may not be sufficient and a distinction of social strata or other social groups
 "indigenous people", "social democrats", a certain NGO, ...)
 that is transverse to the former partitioning is helpful in addition.
 
-For this, we will in the future provide an entity-type "group" 
+For this, the entity-type "group" is provided
 which is meant to represent any grouping of individuals (that may come from one or several social systems) 
 by meaningful cultural or social-metabolic aspects.
 
@@ -33,19 +33,24 @@ Basic relationships to other entity-types
 
 A group will usually...
 
--  have several member :doc:`individuals<individual>`
+-  have several members :doc:`individuals<individual>`,
+   which is represented by a group membership directed network owned by the culture taxon
 
 In addition, a group may...
 
--  have one or several "leader" :doc:`individuals<individual>`, 
-   of which one may be the dominant leader
+-  have an "intra" group network between members :doc:`individuals<individual>`
+   (this feature is not completely implemented yet)
 
--  have a "headquarters" :doc:`cell<cell>`
+-  have one or several "leader" :doc:`individuals<individual>`,
+   of which one may be the dominant leader (this feature is not implemented yet)
 
--  be related to other groups via some network owned by the culture taxon 
+-  have a "headquarters" :doc:`cell<cell>` (this feature is not implemented yet)
+
+-  be related to other groups via an "inter" network owned by the culture taxon
    (which will typically interact with the network of personal acquaintance between member individuals)
+   - (this feature is not completely implemented yet)
 
--  act as the current "elite" in some :doc:`social system<social system>`
+-  act as the current "elite" in some :doc:`social system<social system>` (this feature is not implemented yet)
 
 All these relationships may be dynamic.
 
@@ -53,5 +58,5 @@ Finally, a group may...
 
 -  be a permanent subgroup of a larger group or :doc:`social system<social system>` *by definition* 
    (rather than by coincidence, e.g., "scientists" are by definition a subgroup of the group "academics",
-   and "German workers" may be by definition a subgroup of the social system "Germany")
+   and "German workers" may be by definition a subgroup of the social system "Germany") - (this feature is not implemented yet)
 

From 30409daf4f8bf858288989c94acd6e180dee8bf6 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Mon, 2 May 2022 11:40:24 +0200
Subject: [PATCH 15/33] Added structure for group entity

Adding global group entity:
- Added necessary group.py files
- Changed all necessary files (e.g. __init__)
- Study scripts run smoothly (more testing)
- So far no functionality to group (is mostly copy of social system)
---
 .../data_model/master_data_model/__init__.py  |   3 +
 .../data_model/master_data_model/group.py     |  27 +++
 .../model_components/abstract/__init__.py     |   1 +
 .../model_components/abstract/group.py        |  25 ++
 .../base/implementation/__init__.py           |   1 +
 .../base/implementation/group.py              | 226 ++++++++++++++++++
 .../model_components/base/interface.py        |  54 +++++
 pycopancore/model_components/base/model.py    |   4 +-
 8 files changed, 339 insertions(+), 2 deletions(-)
 create mode 100644 pycopancore/data_model/master_data_model/group.py
 create mode 100644 pycopancore/model_components/abstract/group.py
 create mode 100644 pycopancore/model_components/base/implementation/group.py

diff --git a/pycopancore/data_model/master_data_model/__init__.py b/pycopancore/data_model/master_data_model/__init__.py
index 4deb317a..f962b122 100644
--- a/pycopancore/data_model/master_data_model/__init__.py
+++ b/pycopancore/data_model/master_data_model/__init__.py
@@ -37,5 +37,8 @@
 from .individual import Individual as I
 from .individual import Individual as individual
 from .individual import Individual
+from .group import Group as G
+from .group import Group as group
+from .group import Group
 
 from .. import unity
diff --git a/pycopancore/data_model/master_data_model/group.py b/pycopancore/data_model/master_data_model/group.py
new file mode 100644
index 00000000..c636fff6
--- /dev/null
+++ b/pycopancore/data_model/master_data_model/group.py
@@ -0,0 +1,27 @@
+"""Master data model for group."""
+
+"""https://github.com/pik-copan/pycopancore/blob/master/docs/framework_documentation/abstract_level/entity_types/group.rst"""
+
+#from . import MET
+from .. import Variable
+
+
+class Group:
+
+    #TODO: add a group network possibility (in culture.py (?))
+
+    
+    has_leader = \
+        Variable("has a leader",
+                 "whether the group has a leader",
+                 scale="ordinal", levels=[False, True], default=False)
+
+    has_headquarter = \
+        Variable("has a headquarter",
+                 "whether the group has a headquarter located in a cell",
+                 scale="ordinal", levels=[False, True], default=False)
+        
+        
+        
+        
+
diff --git a/pycopancore/model_components/abstract/__init__.py b/pycopancore/model_components/abstract/__init__.py
index 6ee0e07a..e383543b 100644
--- a/pycopancore/model_components/abstract/__init__.py
+++ b/pycopancore/model_components/abstract/__init__.py
@@ -16,6 +16,7 @@
 from .social_system import SocialSystem
 from .cell import Cell
 from .individual import Individual
+from .group import Group
 
 from .environment import Environment
 from .metabolism import Metabolism
diff --git a/pycopancore/model_components/abstract/group.py b/pycopancore/model_components/abstract/group.py
new file mode 100644
index 00000000..f919b38e
--- /dev/null
+++ b/pycopancore/model_components/abstract/group.py
@@ -0,0 +1,25 @@
+"""Abstract Group entity type class, inherited by base model component."""
+
+# This file is part of pycopancore.
+#
+# Copyright (C) 2016-2017 by COPAN team at Potsdam Institute for Climate
+# Impact Research
+#
+# URL: <http://www.pik-potsdam.de/copan/software>
+# Contact: core@pik-potsdam.de
+# License: BSD 2-clause license
+
+from ...private import _AbstractEntityMixin
+from ...data_model import OrderedSet
+
+
+class Group (_AbstractEntityMixin):
+    """Abstract Group entity type class.
+
+    Inherited by base model component.
+    """
+
+    variables = OrderedSet()
+    """All variables occurring in this entity type"""
+
+
diff --git a/pycopancore/model_components/base/implementation/__init__.py b/pycopancore/model_components/base/implementation/__init__.py
index f782a260..a14081c7 100644
--- a/pycopancore/model_components/base/implementation/__init__.py
+++ b/pycopancore/model_components/base/implementation/__init__.py
@@ -17,6 +17,7 @@
 from .social_system import SocialSystem
 from .cell import Cell
 from .individual import Individual
+from .group import Group
 
 from .environment import Environment
 from .metabolism import Metabolism
diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
new file mode 100644
index 00000000..78c71a41
--- /dev/null
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -0,0 +1,226 @@
+""" """
+
+# This file is part of pycopancore.
+#
+# Copyright (C) 2016-2017 by COPAN team at Potsdam Institute for Climate
+# Impact Research
+#
+# URL: <http://www.pik-potsdam.de/copan/software>
+# Contact: core@pik-potsdam.de
+# License: BSD 2-clause license
+
+# only used in this component, not in others:
+from ... import abstract
+from .... import master_data_model as D
+from ....private import unknown
+
+from .. import interface as I
+
+
+class Group (I.Group, abstract.Group):
+    """Gropp entity type mixin implementation class.
+
+    Base component's Group mixin that every model must use in composing
+    their Group class. Inherits from I.Group as the interface with all
+    necessary variables and parameters.
+    """
+
+    # standard methods:
+
+    def __init__(self,
+                 *,
+                 socialsystem,
+                 next_higher_group=None,
+                 **kwargs
+                 ):
+        """Initialize an instance of Group.
+
+        Parameters
+        ----------
+        socialsystem: obj
+            SocialSystem the Group belongs to (default is None)
+        next_higher_group: obj
+            Optional Group the Group belongs to (default is None)
+        **kwargs
+            keyword arguments passed to super()
+
+        """
+        super().__init__(**kwargs)  # must be the first line
+
+        # init caches:
+        self._next_lower_group = set()
+        self._direct_cells = set()
+
+        # init and set variables implemented via properties:
+        self._socialsystem = None
+        self.socialsystem = socialsystem
+        self._next_higher_group = None
+        self.next_higher_group = next_higher_group
+
+    # getters and setters for references:
+
+    @property
+    def socialsystem(self):
+        """Get the World the SocialSystem is part of."""
+        return self._socialsystem
+
+    @socialsystem.setter
+    def socialsystem(self, w):
+        """Set the World the SocialSystem is part of."""
+        if self._socialsystem is not None:
+            self._socialsystem._groups.remove(self)
+        assert isinstance(w, I.SocialSystem), "socialsystem must be of entity type SocialSystem"
+        w._groups.add(self)
+        self._socialsystem = w
+
+    @property
+    def next_higher_group(self):
+        """Get next higher group."""
+        return self._next_higher_group
+
+    @next_higher_group.setter
+    def next_higher_group(self, s):
+        """Set next higher group."""
+        if self._next_higher_group is not None:
+            self._next_higher_group._next_lower_groups.remove(self)
+            # reset dependent cache:
+            self._next_higher_group.cells = unknown
+        if s is not None:
+            assert isinstance(s, I.Group), \
+                "next_higher_group must be of entity type group"
+            s._next_lower_groups.add(self)
+            # reset dependent cache:
+            s.cells = unknown
+        self._next_higher_group = s
+        # reset dependent caches:
+        self.higher_groups = unknown
+
+    # getters for backwards references and convenience variables:
+
+    @property  # read-only
+    def environment(self):
+        """Get the Environment of which the Group is a part."""
+        return self._world.environment
+
+    @property  # read-only
+    def metabolism(self):
+        """Get the Metabolism of which the Group is a part."""
+        return self._world.metabolism
+
+    @property  # read-only
+    def culture(self):
+        """Get the Culture of which the Group is a part."""
+        return self._world.culture
+
+    _higher_groups = unknown
+    """cache, depends on self.next_higher_group
+    and self.next_higher_group.higher_groups"""
+    @property  # read-only
+    def higher_groups(self):
+        """Get higher groups."""
+        if self._higher_groups is unknown:
+            # find recursively:
+            self._higher_groups = [] if self.next_higher_group is None \
+                else ([self.next_higher_group]
+                      + self.next_higher_group.groups)
+        return self._higher_groups
+
+    @higher_groups.setter
+    def higher_groups(self, u):
+        """Set higher groups."""
+        assert u == unknown, "setter can only be used to reset cache"
+        self._higher_groups = unknown
+        # reset dependent caches:
+        for s in self._next_lower_groups:
+            s.higher_groups = unknown
+        for c in self._direct_cells:
+            c.groups = unknown
+
+    @property  # read-only
+    def next_lower_groups(self):
+        """Get next lower groups."""
+        return self._next_lower_groups
+
+    @property  # read-only
+    def lower_groups(self):
+        """Get lower groups."""
+        # aggregate recursively:
+        l = self._next_lower_groups
+        for s in self._next_lower_groups:
+            l.update(s.lower_groups)
+        return l
+
+    @property  # read-only
+    def direct_cells(self):
+        """Get cells that directly belong to the SocialSystem."""
+        return self._direct_cells
+
+    _cells = unknown
+    """cache, depends on self.direct_cells, self._next_lower_social_systems,
+    and lowersocial_system.cells"""
+    @property  # read-only
+    def cells(self):
+        """Get cells that directly abd indirectly belong to the SocialSystem."""
+        if self._cells is unknown:
+            # aggregate recursively:
+            self._cells = self.direct_cells
+            for s in self._next_lower_social_systems:
+                self._cells.update(s.cells)
+        return self._cells
+
+    @cells.setter
+    def cells(self, u):
+        """Set cells that directly and indirectly belong to the SocialSystem."""
+        assert u == unknown, "setter can only be used to reset cache"
+        self._cells = unknown
+        # reset dependent caches:
+        if self.next_higher_social_system is not None:
+            self.next_higher_social_system.cells = unknown
+
+    _direct_individuals = unknown
+    """cache, depends on _direct_cells, directcell.individuals"""
+    @property  # read-only
+    def direct_individuals(self):
+        """Get resident Individuals not in subsocial_systems."""
+        if self._direct_individuals is unknown:
+            # aggregate from direct_cells:
+            self._direct_individuals = set()
+            for c in self._direct_cells:
+                self._direct_individuals.update(c.individuals)
+        return self._direct_individuals
+
+    @direct_individuals.setter
+    def direct_individuals(self, u):
+        """Set resident Individuals not in subsocial_systems."""
+        assert u == unknown, "setter can only be used to reset cache"
+        self._direct_individuals = unknown
+        # reset dependent caches:
+        pass
+
+    _individuals = unknown
+    """cache, depends on self.cells, cell.individuals"""
+    @property  # read-only
+    def individuals(self):
+        """Get direct and indirect resident Individuals."""
+        if self._individuals is unknown:
+            # aggregate from cells:
+            self._individuals = set()
+            for c in self.cells:
+                self._individuals.update(c.individuals)
+        return self._individuals
+
+    @individuals.setter
+    def individuals(self, u):
+        """Set direct and indirect resident Individuals."""
+        assert u == unknown, "setter can only be used to reset cache"
+        self._individuals = unknown
+        # reset dependent caches:
+        pass
+
+    # TODO: helper methods for mergers, splits, etc.
+
+    # no process-related methods
+
+    processes = []  # no processes in base
+
+
diff --git a/pycopancore/model_components/base/interface.py b/pycopancore/model_components/base/interface.py
index b3424218..15f491fd 100644
--- a/pycopancore/model_components/base/interface.py
+++ b/pycopancore/model_components/base/interface.py
@@ -288,3 +288,57 @@ class Individual (object, metaclass=_MixinType):
 SocialSystem.individuals.type = Individual
 Cell.individuals.type = Individual
 Individual.acquaintances.type = Individual
+
+
+
+class Group (object, metaclass=_MixinType):
+    """Basic Group interface.
+
+    It contains all variables specified as mandatory ("base variables").
+    """
+
+    # references:
+    socialsystem = ReferenceVariable("socialsystem", "", type=SocialSystem)
+    next_higher_group = ReferenceVariable("next higher group", "optional",
+                                            allow_none=True)  # type is Group, hence it can only be specified after class Group is defined, see below
+
+
+    # read-only attributes storing redundant information:
+    environment = ReferenceVariable("environment", "", type=Environment,
+                               readonly=True)
+    metabolism = ReferenceVariable("metabolism", "", type=Metabolism,
+                                   readonly=True)
+    culture = ReferenceVariable("culture", "", type=Culture,
+                                readonly=True)
+    higher_groups = SetVariable(
+        "higher groups",
+        "upward list of (in)direct super-Groups",
+        readonly=True)
+    next_lower_groups = SetVariable(
+        "next lower groups",
+        "set of sub-Groups of next lower level",
+        readonly=True)
+    lower_groups = SetVariable(
+        "lower groups",
+        "set of all direct and indirect sub-Groups",
+        readonly=True)
+    direct_cells = SetVariable("direct cells", "set of direct territory Cells",
+                               readonly=True)
+    cells = SetVariable("cells", "set of direct and indirect territory Cells",
+                        readonly=True)
+    direct_individuals = SetVariable(
+        "direct individuals",
+        "set of resident Individuals not in subgroups",
+        readonly=True)
+    individuals = SetVariable("individuals",
+                              "set of direct or indirect resident Individuals",
+                              readonly=True)
+
+
+# specified only now to avoid recursion errors:
+Group.next_higher_group.type = Group
+Group.higher_groups.type = Group
+Group.next_lower_groups.type = Group
+Group.lower_groups.type = Group
+#Group.groups.type = Group
+#SocialSystem.top_level_groups.type = Group
diff --git a/pycopancore/model_components/base/model.py b/pycopancore/model_components/base/model.py
index 0a417c29..b354528d 100644
--- a/pycopancore/model_components/base/model.py
+++ b/pycopancore/model_components/base/model.py
@@ -20,7 +20,7 @@
 from .. import abstract
 from . import interface as I
 from . import World, Cell, Environment, Individual, Culture, SocialSystem, \
-    Metabolism
+    Metabolism, Group
 
 
 class Model (I.Model, abstract.Model, ModelLogics):
@@ -34,5 +34,5 @@ class Model (I.Model, abstract.Model, ModelLogics):
 
     # specify entity types and process taxon classes 
     # defined in the base component:
-    entity_types = [World, Cell, Individual, SocialSystem]
+    entity_types = [World, Cell, Individual, SocialSystem, Group]
     process_taxa = [Environment, Culture, Metabolism]

From 03ff3a0814cf0392d76f35d2fee33df1f6401719 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Mon, 2 May 2022 12:15:20 +0200
Subject: [PATCH 16/33] Update group.py

Added a possible group_network logic
---
 pycopancore/data_model/master_data_model/group.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/pycopancore/data_model/master_data_model/group.py b/pycopancore/data_model/master_data_model/group.py
index c636fff6..5bb23744 100644
--- a/pycopancore/data_model/master_data_model/group.py
+++ b/pycopancore/data_model/master_data_model/group.py
@@ -2,15 +2,22 @@
 
 """https://github.com/pik-copan/pycopancore/blob/master/docs/framework_documentation/abstract_level/entity_types/group.rst"""
 
-#from . import MET
 from .. import Variable
 
+from networkx import Graph
 
 class Group:
 
     #TODO: add a group network possibility (in culture.py (?))
 
-    
+    group_network = \
+        Variable("group network",
+                 """Basic undirected social network between
+                 Groups.""",
+                 ref="https://en.wikipedia.org/wiki/Social_network#Meso_level",
+                 scale='nominal',
+                 datatype=Graph)    
+
     has_leader = \
         Variable("has a leader",
                  "whether the group has a leader",

From 9b4aaa9557d1ed8cd6b489dfbfd0e28094fd92cf Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Fri, 13 May 2022 11:20:52 +0200
Subject: [PATCH 17/33] social_system

---
 .../base/implementation/group.py              |  32 +--
 .../base/implementation/social_system.py      |  12 ++
 pycopancore/models/groups_seven_dwarfs.py     |  89 ++++++++
 studies/run_groups_test_seven_dwarfs.py       | 193 ++++++++++++++++++
 4 files changed, 311 insertions(+), 15 deletions(-)
 create mode 100644 pycopancore/models/groups_seven_dwarfs.py
 create mode 100644 studies/run_groups_test_seven_dwarfs.py

diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index 78c71a41..f3aeacd1 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -29,7 +29,7 @@ class Group (I.Group, abstract.Group):
 
     def __init__(self,
                  *,
-                 socialsystem,
+                 social_system,
                  next_higher_group=None,
                  **kwargs
                  ):
@@ -47,31 +47,33 @@ def __init__(self,
         """
         super().__init__(**kwargs)  # must be the first line
 
+        # init and set variables implemented via properties:
+        self._social_system = None
+        self.social_system = social_system
+        self._next_higher_group = None
+        self.next_higher_group = next_higher_group
+
         # init caches:
         self._next_lower_group = set()
         self._direct_cells = set()
 
-        # init and set variables implemented via properties:
-        self._socialsystem = None
-        self.socialsystem = socialsystem
-        self._next_higher_group = None
-        self.next_higher_group = next_higher_group
+
 
     # getters and setters for references:
 
     @property
-    def socialsystem(self):
+    def social_system(self):
         """Get the World the SocialSystem is part of."""
-        return self._socialsystem
+        return self._social_system
 
-    @socialsystem.setter
-    def socialsystem(self, w):
+    @social_system.setter
+    def social_system(self, s):
         """Set the World the SocialSystem is part of."""
-        if self._socialsystem is not None:
-            self._socialsystem._groups.remove(self)
-        assert isinstance(w, I.SocialSystem), "socialsystem must be of entity type SocialSystem"
-        w._groups.add(self)
-        self._socialsystem = w
+        if self._social_system is not None:
+            self._social_system._groups.remove(self)
+        assert isinstance(s, I.SocialSystem), "socialsystem must be of entity type SocialSystem"
+        s._groups.add(self)
+        self._social_system = s
 
     @property
     def next_higher_group(self):
diff --git a/pycopancore/model_components/base/implementation/social_system.py b/pycopancore/model_components/base/implementation/social_system.py
index 33b5ce68..b8dac8e3 100644
--- a/pycopancore/model_components/base/implementation/social_system.py
+++ b/pycopancore/model_components/base/implementation/social_system.py
@@ -219,6 +219,18 @@ def individuals(self, u):
         # reset dependent caches:
         pass
 
+    @property  # read-only
+    def groups(self):
+        """Get the set of all Groups in this SocialSystem."""
+        return self._groups
+    @groups.setter
+    def groups(self, g):
+        """Set the World the SocialSystem is part of."""
+        if self._groups is not None:
+            self._groups._social_system.remove(self)
+        assert isinstance(g, I.Culture), "groups must be of taxon type Group"
+        g._worlds.add(self)
+        self._culture = g
     # TODO: helper methods for mergers, splits, etc.
 
     # no process-related methods
diff --git a/pycopancore/models/groups_seven_dwarfs.py b/pycopancore/models/groups_seven_dwarfs.py
new file mode 100644
index 00000000..31be4f35
--- /dev/null
+++ b/pycopancore/models/groups_seven_dwarfs.py
@@ -0,0 +1,89 @@
+"""Model class seven_dwarfs."""
+
+# This file is part of pycopancore.
+#
+# Copyright (C) 2016-2017 by COPAN team at Potsdam Institute for Climate
+# Impact Research
+#
+# URL: <http://www.pik-potsdam.de/copan/software>
+# Contact: core@pik-potsdam.de
+# License: BSD 2-clause license
+
+#
+#  Imports
+#
+
+from .. import base  # all models must use the base component
+
+from ..model_components import seven_dwarfs as sd
+from ..model_components import snowwhite as sw
+
+# entity types:
+
+# by mixing the above model components' mixin classes of the same name.
+# Only compose those entity types and process taxons that the model needs,
+# delete the templates for the unneeded ones, and add those for missing ones:
+
+
+class World(sd.World,
+            base.World):
+    """World entity type."""
+
+    pass
+
+
+class SocialSystem(base.SocialSystem):
+    """SocialSystem entity type."""
+
+    pass
+
+
+class Cell(sd.Cell,
+           sw.Cell,
+           base.Cell):
+    """Cell entity type."""
+
+    pass
+
+
+class Individual(sd.Individual,
+                 base.Individual):
+    """Individual entity type."""
+
+    pass
+
+
+class SocialSystem(sd.SocialSystem,
+              base.SocialSystem):
+    """SocialSystem entity type."""
+
+    pass
+
+class Group(base.Group):
+    """Groups entity type"""
+
+# process taxa:
+
+class Culture(sd.Culture,
+              base.Culture):
+    """Culture process taxon."""
+
+    pass
+
+
+# Model class:
+
+class Model(sd.Model,
+            sw.Model,
+            base.Model):
+    """Class representing the whole model."""
+
+    name = "Seven dwarfs"
+    """Name of the model"""
+    description = "Tutorial model"
+    """Longer description"""
+
+    entity_types = [World, SocialSystem, Cell, Individual]
+    """List of entity types used in the model"""
+    process_taxa = [Culture]
+    """List of process taxa used in the model"""
diff --git a/studies/run_groups_test_seven_dwarfs.py b/studies/run_groups_test_seven_dwarfs.py
new file mode 100644
index 00000000..1c241a9b
--- /dev/null
+++ b/studies/run_groups_test_seven_dwarfs.py
@@ -0,0 +1,193 @@
+"""This is the test script for the seven dwarfs step by step tutorial.
+
+In this version only the Step-process 'aging' of entitytype 'Individual' is
+implemented, such that the only relevant attributes of 'Individual' are 'age'
+and 'cell'.
+"""
+
+# This file is part of pycopancore.
+#
+# Copyright (C) 2016-2017 by COPAN team at Potsdam Institute for Climate
+# Impact Research
+#
+# URL: <http://www.pik-potsdam.de/copan/software>
+# Contact: core@pik-potsdam.de
+# License: BSD 2-clause license
+
+import numpy as np
+from time import time
+import datetime as dt
+
+import networkx as nx
+import matplotlib.pyplot as plt
+
+import plotly.offline as py
+import plotly.graph_objs as go
+
+import pycopancore.models.groups_seven_dwarfs as M
+from pycopancore.runners.runner import Runner
+
+
+# setting timeinterval for run method 'Runner.run()'
+timeinterval = 10
+# setting time step to hand to 'Runner.run()'
+timestep = .1
+nc = 1  # number of caves
+dwarfs = 7  # number of dwarfs
+
+# instantiate model M (needs to be done in the beginning of each script).
+# This configures the model M through 'ModelLogics' in module
+# 'base.model_logics' such that initialisation of attributes and entities gets
+# possible
+model = M.Model()
+
+# instantiate process taxa culture:
+# In this certain case we need 'M.Culture()' for the acquaintance network.
+culture = M.Culture()
+
+# instantiate world:
+world = M.World(culture=culture)
+
+# instantiate one social system:
+social_system = M.SocialSystem(world=world)
+
+# instantiate cells (the caves):
+cells = [M.Cell(social_system=social_system,
+                eating_stock=100
+                )
+        for c in range(nc)
+        ]
+
+# instantiate dwarfs and assigning initial conditions
+individuals = [M.Individual(cell=cells[0],
+                            age=0,
+                            beard_length=0,
+                            beard_growth_parameter=0.5,
+                            eating_parameter=.1
+                            ) for i in range(dwarfs)
+               ]
+
+# assigning individuals to cell is not necessary since it is done by
+# initializing the individuals in 'base.Individuals' with the 'cell' method
+
+#instantiate groups
+ng = 2 #number of groups (group 1 hates snowwhite, group 2 loves her)
+groups = [M.Group(social_system=social_system)
+          for i in range (ng)
+          ]
+
+
+
+start = time()
+
+print("done ({})".format(dt.timedelta(seconds=(time() - start))))
+
+print('\n runner starting')
+
+# Define termination signals as list [ signal_method, object_method_works_on ]
+# the termination method 'check_for_extinction' must return a boolean
+termination_signal = [M.Culture.check_for_extinction,
+                      culture]
+
+# Define termination_callables as list of all signals
+termination_callables = [termination_signal]
+
+nx.draw(culture.acquaintance_network)
+plt.show()
+
+# Runner is instantiated
+r = Runner(model=model,
+           termination_calls=termination_callables
+           )
+
+start = time()
+# run the Runner and saving the return dict in traj
+traj = r.run(t_1=timeinterval, dt=timestep, add_to_output=[M.Culture.acquaintance_network])
+runtime = dt.timedelta(seconds=(time() - start))
+print('runtime: {runtime}'.format(**locals()))
+
+# saving time values to t
+t = np.array(traj['t'])
+print("max. time step", (t[1:]-t[:-1]).max())
+
+
+# proceeding for plotting
+
+# Create List of all dwarfes, not only the ones instantiated before the run,
+# but also the one created during the run.
+
+if M.Individual.idle_entities:
+    all_dwarfs = M.Individual.instances + M.Individual.idle_entities
+else:
+    all_dwarfs = M.Individual.instances
+
+individuals_age = np.array([traj[M.Individual.age][dwarf]
+                                 for dwarf in all_dwarfs])
+
+
+individuals_beard_length = np.array([traj[M.Individual.beard_length][dwarf]
+                                 for dwarf in all_dwarfs])
+
+cell_stock = np.array(traj[M.Cell.eating_stock][cells[0]])
+
+t = np.array(traj['t'])
+
+data_age = []
+print('data age', data_age)
+for i, dwarf in enumerate(all_dwarfs):
+    data_age.append(go.Scatter(
+        x=t,
+        y=individuals_age[i],
+        mode="lines",
+        name="age of dwarf no. {}".format(i),
+        line=dict(
+            color="green",
+            width=4
+        )
+    ))
+
+data_beard_length = []
+print('data beard', data_beard_length)
+for i, dwarf in enumerate(all_dwarfs):
+    data_beard_length.append(go.Scatter(
+        x=t,
+        y=individuals_beard_length[i],
+        mode="lines",
+        name="beard length of dwarf no. {}".format(i),
+        line=dict(
+            color="red",
+            width=4
+        )
+    ))
+
+data_stock = []
+data_stock.append(go.Scatter(
+    x=t,
+    y=cell_stock,
+    mode="lines",
+    name="stock of cell",
+    line=dict(color="blue",
+              width=4
+              )
+      ))
+
+
+layout = dict(title='seven dwarfs',
+              xaxis=dict(title='time [yr]'),
+              yaxis=dict(title='value'),
+              )
+
+
+# getting plots of two dwarfs:
+fig = dict(data=[data_age[0], data_beard_length[0], data_stock[0]],
+           layout=layout)
+py.plot(fig, filename="our-model-result{}.html".format(0))
+
+fig = dict(data=[data_age[5], data_beard_length[5], data_stock[0]],
+           layout=layout)
+py.plot(fig, filename="our-model-result{}.html".format(5))
+
+#nx.draw(traj[M.Culture.acquaintance_network][culture][1])
+#plt.show()
+for i in range(len(traj['t'])):
+    print(list(traj[M.Culture.acquaintance_network][culture][i].nodes()))

From f08842309d99eac62e49f6cb632d03a0e7fa3737 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Tue, 31 May 2022 18:20:55 +0200
Subject: [PATCH 18/33] typo cleanup

minor typo and some todos
---
 pycopancore/data_model/master_data_model/group.py             | 4 +++-
 pycopancore/model_components/base/implementation/group.py     | 4 +++-
 .../model_components/base/implementation/individual.py        | 1 +
 pycopancore/model_components/base/interface.py                | 2 +-
 4 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/pycopancore/data_model/master_data_model/group.py b/pycopancore/data_model/master_data_model/group.py
index 5bb23744..26cf6ce5 100644
--- a/pycopancore/data_model/master_data_model/group.py
+++ b/pycopancore/data_model/master_data_model/group.py
@@ -8,7 +8,9 @@
 
 class Group:
 
-    #TODO: add a group network possibility (in culture.py (?))
+    #TODO: add a group network possibility (in culture.py (!))
+    #TODO: inter/intra group network
+    #TODO: specify edges
 
     group_network = \
         Variable("group network",
diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index f3aeacd1..0aa1d663 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -29,7 +29,7 @@ class Group (I.Group, abstract.Group):
 
     def __init__(self,
                  *,
-                 social_system,
+                 social_system=None,
                  next_higher_group=None,
                  **kwargs
                  ):
@@ -179,6 +179,8 @@ def cells(self, u):
         if self.next_higher_social_system is not None:
             self.next_higher_social_system.cells = unknown
 
+    #TODO: direct_inds to members
+    
     _direct_individuals = unknown
     """cache, depends on _direct_cells, directcell.individuals"""
     @property  # read-only
diff --git a/pycopancore/model_components/base/implementation/individual.py b/pycopancore/model_components/base/implementation/individual.py
index 7f9eb2a3..e82c5fc5 100644
--- a/pycopancore/model_components/base/implementation/individual.py
+++ b/pycopancore/model_components/base/implementation/individual.py
@@ -16,6 +16,7 @@
 
 from .. import interface as I
 
+#TODO: set variable membership
 
 class Individual (I.Individual, abstract.Individual):
     """Individual entity type mixin implementation class.
diff --git a/pycopancore/model_components/base/interface.py b/pycopancore/model_components/base/interface.py
index 15f491fd..deb77458 100644
--- a/pycopancore/model_components/base/interface.py
+++ b/pycopancore/model_components/base/interface.py
@@ -298,7 +298,7 @@ class Group (object, metaclass=_MixinType):
     """
 
     # references:
-    socialsystem = ReferenceVariable("socialsystem", "", type=SocialSystem)
+    #social_system = ReferenceVariable("socialsystem", "", type=SocialSystem)
     next_higher_group = ReferenceVariable("next higher group", "optional",
                                             allow_none=True)  # type is Group, hence it can only be specified after class Group is defined, see below
 

From 329ab84304eafbd6b2341475ce71a0c03dffad4f Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Wed, 8 Jun 2022 15:52:00 +0200
Subject: [PATCH 19/33] Implementing Individual to Group relationships via a
 group_membership_network. Error while adding group to a culture (group needs
 to "live" somewhere, similar to cells for individuals that then give
 memberships to worlds and so on.

---
 .../data_model/master_data_model/culture.py   |  19 ++-
 .../data_model/master_data_model/group.py     |   9 +-
 .../base/implementation/culture.py            |  13 +-
 .../base/implementation/group.py              | 148 ++++++++----------
 .../base/implementation/individual.py         |  10 +-
 .../model_components/base/interface.py        |  27 ++--
 studies/run_groups_test_seven_dwarfs.py       |  99 ++----------
 7 files changed, 132 insertions(+), 193 deletions(-)

diff --git a/pycopancore/data_model/master_data_model/culture.py b/pycopancore/data_model/master_data_model/culture.py
index 755b8047..d89d2c82 100644
--- a/pycopancore/data_model/master_data_model/culture.py
+++ b/pycopancore/data_model/master_data_model/culture.py
@@ -94,7 +94,24 @@ class Culture:
                  scale='nominal',
                  datatype=set)
         
-        
+
+    # group entity related networks
+
+    inter_group_network = \
+        Variable("inter group network",
+                 """Basic undirected social network between
+                 Groups.""",
+                 ref="https://en.wikipedia.org/wiki/Social_network#Meso_level",
+                 scale='nominal',
+                 datatype=Graph)
+
+    group_membership_network = \
+        Variable("group membership network",
+                 """Directed network from individual to group that
+                 signifies membership (to avoid problems due to n to n relation)""",
+                 scale='nominal',
+                 datatype=DiGraph)
+
     # socio-cultural traits that may occur on different levels:
     
     is_environmentally_friendly = \
diff --git a/pycopancore/data_model/master_data_model/group.py b/pycopancore/data_model/master_data_model/group.py
index 26cf6ce5..cd7354cb 100644
--- a/pycopancore/data_model/master_data_model/group.py
+++ b/pycopancore/data_model/master_data_model/group.py
@@ -8,15 +8,12 @@
 
 class Group:
 
-    #TODO: add a group network possibility (in culture.py (!))
-    #TODO: inter/intra group network
     #TODO: specify edges
 
-    group_network = \
-        Variable("group network",
+    intra_group_network = \
+        Variable("intra group network",
                  """Basic undirected social network between
-                 Groups.""",
-                 ref="https://en.wikipedia.org/wiki/Social_network#Meso_level",
+                 Group members.""",
                  scale='nominal',
                  datatype=Graph)    
 
diff --git a/pycopancore/model_components/base/implementation/culture.py b/pycopancore/model_components/base/implementation/culture.py
index 6f342fcc..79cf5799 100644
--- a/pycopancore/model_components/base/implementation/culture.py
+++ b/pycopancore/model_components/base/implementation/culture.py
@@ -14,8 +14,7 @@
 
 from .. import interface as I
 
-from networkx import Graph
-
+from networkx import Graph, DiGraph
 
 class Culture (I.Culture, abstract.Culture):
     """Culture process taxon mixin implementation class."""
@@ -25,6 +24,7 @@ class Culture (I.Culture, abstract.Culture):
     def __init__(self,
                  *,
                  acquaintance_network=None,
+                 group_membership_network=None,
                  **kwargs):
         """Initialize the unique instance of Culture.
 
@@ -33,6 +33,9 @@ def __init__(self,
         acquaintance_network: Graph
             The Network of acquaintances which is managed by Culture
             (default is None)
+        group_membership_network: DiGraph
+            The Network between Individiuals and groups, which is managed
+            by Culture (default is None)
         **kwargs
             keyword arguments passed to super()
 
@@ -43,6 +46,12 @@ def __init__(self,
             acquaintance_network = Graph()
         assert isinstance(acquaintance_network, Graph)
         self.acquaintance_network = acquaintance_network
+
+        if group_membership_network is None:
+            group_membership_network = DiGraph()
+        assert isinstance(group_membership_network, DiGraph)
+        self.group_membership_network = group_membership_network
+
         self._worlds = set()
 
         # make sure all variable values are valid:
diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index 0aa1d663..22ce9ebd 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -29,7 +29,7 @@ class Group (I.Group, abstract.Group):
 
     def __init__(self,
                  *,
-                 social_system=None,
+                 culture=None,
                  next_higher_group=None,
                  **kwargs
                  ):
@@ -48,8 +48,10 @@ def __init__(self,
         super().__init__(**kwargs)  # must be the first line
 
         # init and set variables implemented via properties:
-        self._social_system = None
-        self.social_system = social_system
+        self._culture = None
+        self.culture = culture
+        # self._social_system = None
+        # self.social_system = social_system
         self._next_higher_group = None
         self.next_higher_group = next_higher_group
 
@@ -57,23 +59,48 @@ def __init__(self,
         self._next_lower_group = set()
         self._direct_cells = set()
 
+        if self.culture:
+            self.culture.group_membership_network.add_node(self)
+
+    def deactivate(self):
+        """Deactivate an individual.
+
+        In particular, deregister from all networks.
+
+        """
+        # deregister from all networks:
+        if self.culture:
+            self.culture.group_membership_network.remove_node(self)
+        super().deactivate()  # must be the last line
+
+    def reactivate(self):
+        """Reactivate an individual.
+
+        In particular, deregister with all mandatory networks.
+
+        """
+        super().reactivate()  # must be the first line
+        # reregister with all mandatory networks:
+        if self.culture:
+            self.culture.group_membership_network.add_node(self)
 
 
     # getters and setters for references:
 
-    @property
-    def social_system(self):
-        """Get the World the SocialSystem is part of."""
-        return self._social_system
-
-    @social_system.setter
-    def social_system(self, s):
-        """Set the World the SocialSystem is part of."""
-        if self._social_system is not None:
-            self._social_system._groups.remove(self)
-        assert isinstance(s, I.SocialSystem), "socialsystem must be of entity type SocialSystem"
-        s._groups.add(self)
-        self._social_system = s
+
+    # @property
+    # def social_system(self):
+    #     """Get the SocialSystem the Group is part of."""
+    #     return self._social_system
+
+    # @social_system.setter
+    # def social_system(self, s):
+    #     """Set the SocialSystem the Group is part of."""
+    #     if self._social_system is not None:
+    #         self._social_system._groups.remove(self)
+    #     assert isinstance(s, I.SocialSystem), "socialsystem must be of entity type SocialSystem"
+    #     s._groups.add(self)
+    #     self._social_system = s
 
     @property
     def next_higher_group(self):
@@ -109,10 +136,22 @@ def metabolism(self):
         """Get the Metabolism of which the Group is a part."""
         return self._world.metabolism
 
-    @property  # read-only
+    @property
     def culture(self):
-        """Get the Culture of which the Group is a part."""
-        return self._world.culture
+        """Get groups's culture."""
+        return self._culture
+
+    @culture.setter
+    def culture(self, c):
+        """Set groups's culture."""
+        if self._culture is not None:
+            # first deregister from previous culture's list of worlds:
+            self._culture.groups.remove(self)
+        if c is not None:
+            assert isinstance(c, I.Culture), \
+                "Culture must be taxon type Culture"
+            c._groups.add(self)
+        self._culture = c
 
     _higher_groups = unknown
     """cache, depends on self.next_higher_group
@@ -152,74 +191,11 @@ def lower_groups(self):
             l.update(s.lower_groups)
         return l
 
-    @property  # read-only
-    def direct_cells(self):
-        """Get cells that directly belong to the SocialSystem."""
-        return self._direct_cells
-
-    _cells = unknown
-    """cache, depends on self.direct_cells, self._next_lower_social_systems,
-    and lowersocial_system.cells"""
-    @property  # read-only
-    def cells(self):
-        """Get cells that directly abd indirectly belong to the SocialSystem."""
-        if self._cells is unknown:
-            # aggregate recursively:
-            self._cells = self.direct_cells
-            for s in self._next_lower_social_systems:
-                self._cells.update(s.cells)
-        return self._cells
-
-    @cells.setter
-    def cells(self, u):
-        """Set cells that directly and indirectly belong to the SocialSystem."""
-        assert u == unknown, "setter can only be used to reset cache"
-        self._cells = unknown
-        # reset dependent caches:
-        if self.next_higher_social_system is not None:
-            self.next_higher_social_system.cells = unknown
-
-    #TODO: direct_inds to members
-    
-    _direct_individuals = unknown
-    """cache, depends on _direct_cells, directcell.individuals"""
-    @property  # read-only
-    def direct_individuals(self):
-        """Get resident Individuals not in subsocial_systems."""
-        if self._direct_individuals is unknown:
-            # aggregate from direct_cells:
-            self._direct_individuals = set()
-            for c in self._direct_cells:
-                self._direct_individuals.update(c.individuals)
-        return self._direct_individuals
-
-    @direct_individuals.setter
-    def direct_individuals(self, u):
-        """Set resident Individuals not in subsocial_systems."""
-        assert u == unknown, "setter can only be used to reset cache"
-        self._direct_individuals = unknown
-        # reset dependent caches:
-        pass
+    @property
+    def group_members(self):
+        """Get the set of Individuals associated with this Group."""
+        return self.culture.group_membership_network.predecessors(self) # .predeccessors as network is directed from inds to groups
 
-    _individuals = unknown
-    """cache, depends on self.cells, cell.individuals"""
-    @property  # read-only
-    def individuals(self):
-        """Get direct and indirect resident Individuals."""
-        if self._individuals is unknown:
-            # aggregate from cells:
-            self._individuals = set()
-            for c in self.cells:
-                self._individuals.update(c.individuals)
-        return self._individuals
-
-    @individuals.setter
-    def individuals(self, u):
-        """Set direct and indirect resident Individuals."""
-        assert u == unknown, "setter can only be used to reset cache"
-        self._individuals = unknown
-        # reset dependent caches:
-        pass
 
     # TODO: helper methods for mergers, splits, etc.
 
diff --git a/pycopancore/model_components/base/implementation/individual.py b/pycopancore/model_components/base/implementation/individual.py
index e82c5fc5..5eb11073 100644
--- a/pycopancore/model_components/base/implementation/individual.py
+++ b/pycopancore/model_components/base/implementation/individual.py
@@ -16,8 +16,6 @@
 
 from .. import interface as I
 
-#TODO: set variable membership
-
 class Individual (I.Individual, abstract.Individual):
     """Individual entity type mixin implementation class.
 
@@ -56,6 +54,7 @@ def __init__(self,
         # register with all mandatory networks:
         if self.culture:
             self.culture.acquaintance_network.add_node(self)
+            self.culture.group_membership_network.add_node(self) # TODO: does this work with DiGraph?
 
     def deactivate(self):
         """Deactivate an individual.
@@ -66,6 +65,7 @@ def deactivate(self):
         # deregister from all networks:
         if self.culture:
             self.culture.acquaintance_network.remove_node(self)
+            self.culture.group_membership_network.remove_node(self)
         super().deactivate()  # must be the last line
 
     def reactivate(self):
@@ -78,6 +78,7 @@ def reactivate(self):
         # reregister with all mandatory networks:
         if self.culture:
             self.culture.acquaintance_network.add_node(self)
+            self.culture.group_membership_network.add_node(self)
 
     # getters and setters for references:
 
@@ -157,6 +158,11 @@ def acquaintances(self):
         """Get the set of Individuals the Individual is acquainted with."""
         return self.culture.acquaintance_network.neighbors(self)
 
+    @property
+    def group_memberships(self):
+        """Get the set of Groups the Individual is associated with."""
+        return self.culture.group_membership_network.successors(self) # .successors as network is directed from inds to groups
+
     # no process-related methods
 
     processes = []  # no processes in base
diff --git a/pycopancore/model_components/base/interface.py b/pycopancore/model_components/base/interface.py
index deb77458..5d1676be 100644
--- a/pycopancore/model_components/base/interface.py
+++ b/pycopancore/model_components/base/interface.py
@@ -69,6 +69,8 @@ class Culture (object):
 
     acquaintance_network = CUL.acquaintance_network
 
+    group_membership_network = CUL.group_membership_network
+
     # read-only attributes storing redundant information:
     worlds = SetVariable("worlds",
                          "Set of Worlds governed by this Culture",
@@ -271,6 +273,10 @@ class Individual (object, metaclass=_MixinType):
                     "set of Individuals this one is acquainted with",
                     readonly=True)
 
+    group_memberships = SetVariable("group memberships",
+                                    "set of Groups this one is associated with",
+                                    readonly=True)
+
     # TODO: specify Variable objects for the following:
     population_share = None
     """share of social_system's direct population represented by this individual"""
@@ -291,6 +297,7 @@ class Individual (object, metaclass=_MixinType):
 
 
 
+
 class Group (object, metaclass=_MixinType):
     """Basic Group interface.
 
@@ -322,17 +329,13 @@ class Group (object, metaclass=_MixinType):
         "lower groups",
         "set of all direct and indirect sub-Groups",
         readonly=True)
-    direct_cells = SetVariable("direct cells", "set of direct territory Cells",
-                               readonly=True)
-    cells = SetVariable("cells", "set of direct and indirect territory Cells",
-                        readonly=True)
-    direct_individuals = SetVariable(
-        "direct individuals",
-        "set of resident Individuals not in subgroups",
-        readonly=True)
-    individuals = SetVariable("individuals",
-                              "set of direct or indirect resident Individuals",
-                              readonly=True)
+
+    group_members = SetVariable(
+        "group members",
+        "set of all individuals associated with the group",
+        readonly=True
+    )
+
 
 
 # specified only now to avoid recursion errors:
@@ -340,5 +343,7 @@ class Group (object, metaclass=_MixinType):
 Group.higher_groups.type = Group
 Group.next_lower_groups.type = Group
 Group.lower_groups.type = Group
+# Individual.group_memberships.type = Group # TODO: assert this is at the right place
+# Group.group_members.type = Individual
 #Group.groups.type = Group
 #SocialSystem.top_level_groups.type = Group
diff --git a/studies/run_groups_test_seven_dwarfs.py b/studies/run_groups_test_seven_dwarfs.py
index 1c241a9b..933a0aba 100644
--- a/studies/run_groups_test_seven_dwarfs.py
+++ b/studies/run_groups_test_seven_dwarfs.py
@@ -67,16 +67,20 @@
                             ) for i in range(dwarfs)
                ]
 
+print("\n The individuals: \n")
+print(individuals)
+print("\n \n")
+
 # assigning individuals to cell is not necessary since it is done by
 # initializing the individuals in 'base.Individuals' with the 'cell' method
 
 #instantiate groups
-ng = 2 #number of groups (group 1 hates snowwhite, group 2 loves her)
-groups = [M.Group(social_system=social_system)
-          for i in range (ng)
-          ]
-
+ng = 5 #number of groups
+groups = [M.Group(culture=culture) for i in range (ng)]
 
+print("\n The groups: \n")
+print(groups)
+print("\n \n")
 
 start = time()
 
@@ -84,6 +88,11 @@
 
 print('\n runner starting')
 
+# first test for group network
+nx.draw(culture.group_membership_network)
+
+plt.show()
+
 # Define termination signals as list [ signal_method, object_method_works_on ]
 # the termination method 'check_for_extinction' must return a boolean
 termination_signal = [M.Culture.check_for_extinction,
@@ -111,83 +120,3 @@
 print("max. time step", (t[1:]-t[:-1]).max())
 
 
-# proceeding for plotting
-
-# Create List of all dwarfes, not only the ones instantiated before the run,
-# but also the one created during the run.
-
-if M.Individual.idle_entities:
-    all_dwarfs = M.Individual.instances + M.Individual.idle_entities
-else:
-    all_dwarfs = M.Individual.instances
-
-individuals_age = np.array([traj[M.Individual.age][dwarf]
-                                 for dwarf in all_dwarfs])
-
-
-individuals_beard_length = np.array([traj[M.Individual.beard_length][dwarf]
-                                 for dwarf in all_dwarfs])
-
-cell_stock = np.array(traj[M.Cell.eating_stock][cells[0]])
-
-t = np.array(traj['t'])
-
-data_age = []
-print('data age', data_age)
-for i, dwarf in enumerate(all_dwarfs):
-    data_age.append(go.Scatter(
-        x=t,
-        y=individuals_age[i],
-        mode="lines",
-        name="age of dwarf no. {}".format(i),
-        line=dict(
-            color="green",
-            width=4
-        )
-    ))
-
-data_beard_length = []
-print('data beard', data_beard_length)
-for i, dwarf in enumerate(all_dwarfs):
-    data_beard_length.append(go.Scatter(
-        x=t,
-        y=individuals_beard_length[i],
-        mode="lines",
-        name="beard length of dwarf no. {}".format(i),
-        line=dict(
-            color="red",
-            width=4
-        )
-    ))
-
-data_stock = []
-data_stock.append(go.Scatter(
-    x=t,
-    y=cell_stock,
-    mode="lines",
-    name="stock of cell",
-    line=dict(color="blue",
-              width=4
-              )
-      ))
-
-
-layout = dict(title='seven dwarfs',
-              xaxis=dict(title='time [yr]'),
-              yaxis=dict(title='value'),
-              )
-
-
-# getting plots of two dwarfs:
-fig = dict(data=[data_age[0], data_beard_length[0], data_stock[0]],
-           layout=layout)
-py.plot(fig, filename="our-model-result{}.html".format(0))
-
-fig = dict(data=[data_age[5], data_beard_length[5], data_stock[0]],
-           layout=layout)
-py.plot(fig, filename="our-model-result{}.html".format(5))
-
-#nx.draw(traj[M.Culture.acquaintance_network][culture][1])
-#plt.show()
-for i in range(len(traj['t'])):
-    print(list(traj[M.Culture.acquaintance_network][culture][i].nodes()))

From 696eb7447a63c434a8de27d8b8377401c2297ca1 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Wed, 8 Jun 2022 16:38:05 +0200
Subject: [PATCH 20/33] Group now gets culture and further things over being
 part of a world.

---
 .../base/implementation/group.py              | 161 ++++++++++--------
 .../model_components/base/interface.py        |  39 +++--
 studies/run_groups_test_seven_dwarfs.py       |  17 +-
 3 files changed, 123 insertions(+), 94 deletions(-)

diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index 22ce9ebd..37684ac7 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -29,7 +29,8 @@ class Group (I.Group, abstract.Group):
 
     def __init__(self,
                  *,
-                 culture=None,
+                 world,
+                 # culture=None,
                  next_higher_group=None,
                  **kwargs
                  ):
@@ -48,8 +49,11 @@ def __init__(self,
         super().__init__(**kwargs)  # must be the first line
 
         # init and set variables implemented via properties:
-        self._culture = None
-        self.culture = culture
+        # self._culture = None
+        # self.culture = culture
+        self._world = None
+        self.world = world
+
         # self._social_system = None
         # self.social_system = social_system
         self._next_higher_group = None
@@ -87,6 +91,19 @@ def reactivate(self):
 
     # getters and setters for references:
 
+    @property
+    def world(self):
+        """Get the World the Group is part of."""
+        return self._world
+
+    @world.setter
+    def world(self, w):
+        """Set the World the Group is part of."""
+        if self._world is not None:
+            self._world._social_systems.remove(self)
+        assert isinstance(w, I.World), "world must be of entity type World"
+        w._social_systems.add(self)
+        self._world = w
 
     # @property
     # def social_system(self):
@@ -102,27 +119,27 @@ def reactivate(self):
     #     s._groups.add(self)
     #     self._social_system = s
 
-    @property
-    def next_higher_group(self):
-        """Get next higher group."""
-        return self._next_higher_group
-
-    @next_higher_group.setter
-    def next_higher_group(self, s):
-        """Set next higher group."""
-        if self._next_higher_group is not None:
-            self._next_higher_group._next_lower_groups.remove(self)
-            # reset dependent cache:
-            self._next_higher_group.cells = unknown
-        if s is not None:
-            assert isinstance(s, I.Group), \
-                "next_higher_group must be of entity type group"
-            s._next_lower_groups.add(self)
-            # reset dependent cache:
-            s.cells = unknown
-        self._next_higher_group = s
+    # @property
+    # def next_higher_group(self):
+    #     """Get next higher group."""
+    #     return self._next_higher_group
+
+    # @next_higher_group.setter
+    # def next_higher_group(self, s):
+    #     """Set next higher group."""
+    #     if self._next_higher_group is not None:
+    #         self._next_higher_group._next_lower_groups.remove(self)
+    #         reset dependent cache:
+            # self._next_higher_group.cells = unknown
+        # if s is not None:
+        #     assert isinstance(s, I.Group), \
+        #         "next_higher_group must be of entity type group"
+        #     s._next_lower_groups.add(self)
+        #     reset dependent cache:
+        #     s.cells = unknown
+        # self._next_higher_group = s
         # reset dependent caches:
-        self.higher_groups = unknown
+        # self.higher_groups = unknown
 
     # getters for backwards references and convenience variables:
 
@@ -136,60 +153,60 @@ def metabolism(self):
         """Get the Metabolism of which the Group is a part."""
         return self._world.metabolism
 
-    @property
-    def culture(self):
-        """Get groups's culture."""
-        return self._culture
-
-    @culture.setter
-    def culture(self, c):
-        """Set groups's culture."""
-        if self._culture is not None:
-            # first deregister from previous culture's list of worlds:
-            self._culture.groups.remove(self)
-        if c is not None:
-            assert isinstance(c, I.Culture), \
-                "Culture must be taxon type Culture"
-            c._groups.add(self)
-        self._culture = c
-
-    _higher_groups = unknown
+    # @property
+    # def culture(self):
+    #     """Get groups's culture."""
+    #     return self._culture
+
+    # @culture.setter
+    # def culture(self, c):
+    #     """Set groups's culture."""
+    #     if self._culture is not None:
+    #         first deregister from previous culture's list of worlds:
+            # self._culture.groups.remove(self)
+        # if c is not None:
+        #     assert isinstance(c, I.Culture), \
+        #         "Culture must be taxon type Culture"
+        #     c._groups.add(self)
+        # self._culture = c
+
+    # _higher_groups = unknown
     """cache, depends on self.next_higher_group
     and self.next_higher_group.higher_groups"""
-    @property  # read-only
-    def higher_groups(self):
-        """Get higher groups."""
-        if self._higher_groups is unknown:
+    # @property  # read-only
+    # def higher_groups(self):
+    #     """Get higher groups."""
+    #     if self._higher_groups is unknown:
             # find recursively:
-            self._higher_groups = [] if self.next_higher_group is None \
-                else ([self.next_higher_group]
-                      + self.next_higher_group.groups)
-        return self._higher_groups
-
-    @higher_groups.setter
-    def higher_groups(self, u):
-        """Set higher groups."""
-        assert u == unknown, "setter can only be used to reset cache"
-        self._higher_groups = unknown
+            # self._higher_groups = [] if self.next_higher_group is None \
+            #     else ([self.next_higher_group]
+            #           + self.next_higher_group.groups)
+        # return self._higher_groups
+
+    # @higher_groups.setter
+    # def higher_groups(self, u):
+    #     """Set higher groups."""
+    #     assert u == unknown, "setter can only be used to reset cache"
+    #     self._higher_groups = unknown
         # reset dependent caches:
-        for s in self._next_lower_groups:
-            s.higher_groups = unknown
-        for c in self._direct_cells:
-            c.groups = unknown
-
-    @property  # read-only
-    def next_lower_groups(self):
-        """Get next lower groups."""
-        return self._next_lower_groups
-
-    @property  # read-only
-    def lower_groups(self):
-        """Get lower groups."""
+        # for s in self._next_lower_groups:
+        #     s.higher_groups = unknown
+        # for c in self._direct_cells:
+        #     c.groups = unknown
+
+    # @property  # read-only
+    # def next_lower_groups(self):
+    #     """Get next lower groups."""
+    #     return self._next_lower_groups
+
+    # @property  # read-only
+    # def lower_groups(self):
+    #     """Get lower groups."""
         # aggregate recursively:
-        l = self._next_lower_groups
-        for s in self._next_lower_groups:
-            l.update(s.lower_groups)
-        return l
+        # l = self._next_lower_groups
+        # for s in self._next_lower_groups:
+        #     l.update(s.lower_groups)
+        # return l
 
     @property
     def group_members(self):
diff --git a/pycopancore/model_components/base/interface.py b/pycopancore/model_components/base/interface.py
index 5d1676be..5d8d3975 100644
--- a/pycopancore/model_components/base/interface.py
+++ b/pycopancore/model_components/base/interface.py
@@ -122,6 +122,9 @@ class World (object, metaclass=_MixinType):
     individuals = SetVariable("individuals",
                               "Set of Individuals residing on this world",
                               readonly=True)
+    groups = SetVariable("groups",
+                         "Set of Groups existing on this world",
+                         readonly=True)
 
 
 # specified only now to avoid recursion errors:
@@ -306,8 +309,8 @@ class Group (object, metaclass=_MixinType):
 
     # references:
     #social_system = ReferenceVariable("socialsystem", "", type=SocialSystem)
-    next_higher_group = ReferenceVariable("next higher group", "optional",
-                                            allow_none=True)  # type is Group, hence it can only be specified after class Group is defined, see below
+    # next_higher_group = ReferenceVariable("next higher group", "optional",
+    #                                         allow_none=True)  # type is Group, hence it can only be specified after class Group is defined, see below
 
 
     # read-only attributes storing redundant information:
@@ -317,18 +320,18 @@ class Group (object, metaclass=_MixinType):
                                    readonly=True)
     culture = ReferenceVariable("culture", "", type=Culture,
                                 readonly=True)
-    higher_groups = SetVariable(
-        "higher groups",
-        "upward list of (in)direct super-Groups",
-        readonly=True)
-    next_lower_groups = SetVariable(
-        "next lower groups",
-        "set of sub-Groups of next lower level",
-        readonly=True)
-    lower_groups = SetVariable(
-        "lower groups",
-        "set of all direct and indirect sub-Groups",
-        readonly=True)
+    # higher_groups = SetVariable(
+    #     "higher groups",
+    #     "upward list of (in)direct super-Groups",
+    #     readonly=True)
+    # next_lower_groups = SetVariable(
+    #     "next lower groups",
+    #     "set of sub-Groups of next lower level",
+    #     readonly=True)
+    # lower_groups = SetVariable(
+    #     "lower groups",
+    #     "set of all direct and indirect sub-Groups",
+    #     readonly=True)
 
     group_members = SetVariable(
         "group members",
@@ -339,10 +342,10 @@ class Group (object, metaclass=_MixinType):
 
 
 # specified only now to avoid recursion errors:
-Group.next_higher_group.type = Group
-Group.higher_groups.type = Group
-Group.next_lower_groups.type = Group
-Group.lower_groups.type = Group
+# Group.next_higher_group.type = Group
+# Group.higher_groups.type = Group
+# Group.next_lower_groups.type = Group
+# Group.lower_groups.type = Group
 # Individual.group_memberships.type = Group # TODO: assert this is at the right place
 # Group.group_members.type = Individual
 #Group.groups.type = Group
diff --git a/studies/run_groups_test_seven_dwarfs.py b/studies/run_groups_test_seven_dwarfs.py
index 933a0aba..f2ce6424 100644
--- a/studies/run_groups_test_seven_dwarfs.py
+++ b/studies/run_groups_test_seven_dwarfs.py
@@ -15,6 +15,7 @@
 # License: BSD 2-clause license
 
 import numpy as np
+from numpy.random import uniform
 from time import time
 import datetime as dt
 
@@ -33,7 +34,7 @@
 # setting time step to hand to 'Runner.run()'
 timestep = .1
 nc = 1  # number of caves
-dwarfs = 7  # number of dwarfs
+dwarfs = 10  # number of dwarfs
 
 # instantiate model M (needs to be done in the beginning of each script).
 # This configures the model M through 'ModelLogics' in module
@@ -75,8 +76,8 @@
 # initializing the individuals in 'base.Individuals' with the 'cell' method
 
 #instantiate groups
-ng = 5 #number of groups
-groups = [M.Group(culture=culture) for i in range (ng)]
+ng = 10 #number of groups
+groups = [M.Group(world=world) for i in range (ng)]
 
 print("\n The groups: \n")
 print(groups)
@@ -89,8 +90,16 @@
 print('\n runner starting')
 
 # first test for group network
-nx.draw(culture.group_membership_network)
+#nx.draw(culture.group_membership_network)
+#plt.show()
+
 
+# initialize some network:
+for i in enumerate(individuals):
+    for j in enumerate(groups):
+        culture.group_membership_network.add_edge(i, j)
+
+nx.draw(culture.group_membership_network)
 plt.show()
 
 # Define termination signals as list [ signal_method, object_method_works_on ]

From 75580f453ce9a9a438d28cbe49ae63f2ed6ab31e Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Wed, 8 Jun 2022 16:44:25 +0200
Subject: [PATCH 21/33] little fix

---
 pycopancore/model_components/base/implementation/group.py | 4 ++--
 pycopancore/model_components/base/implementation/world.py | 6 ++++++
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index 37684ac7..b8b6b3d1 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -100,9 +100,9 @@ def world(self):
     def world(self, w):
         """Set the World the Group is part of."""
         if self._world is not None:
-            self._world._social_systems.remove(self)
+            self._world._groups.remove(self)
         assert isinstance(w, I.World), "world must be of entity type World"
-        w._social_systems.add(self)
+        w._groups.add(self)
         self._world = w
 
     # @property
diff --git a/pycopancore/model_components/base/implementation/world.py b/pycopancore/model_components/base/implementation/world.py
index 05dea718..9457f44e 100644
--- a/pycopancore/model_components/base/implementation/world.py
+++ b/pycopancore/model_components/base/implementation/world.py
@@ -59,6 +59,7 @@ def __init__(self,
         self.culture = culture
         self._social_systems = set()
         self._cells = set()
+        self._groups = set()
 
         # make sure all variable values are valid:
         self.assert_valid()
@@ -164,6 +165,11 @@ def individuals(self, u):
         # reset dependent caches:
         pass
 
+    @property  # read-only
+    def groups(self):
+        """Get the set of all Groups on this World."""
+        return self._groups
+
 
     processes = [
         # TODO: convert this into an Implicit equation once supported:

From 244a6018c68b872e4c517299fca448999d1ebe2d Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Thu, 9 Jun 2022 14:30:59 +0200
Subject: [PATCH 22/33] run_group_test_seven_dwarfs.py now demonstrates minimum
 features of the new group entity

---
 studies/run_groups_test_seven_dwarfs.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/studies/run_groups_test_seven_dwarfs.py b/studies/run_groups_test_seven_dwarfs.py
index f2ce6424..f03ec4a6 100644
--- a/studies/run_groups_test_seven_dwarfs.py
+++ b/studies/run_groups_test_seven_dwarfs.py
@@ -95,13 +95,21 @@
 
 
 # initialize some network:
-for i in enumerate(individuals):
+for i in individuals:
     for j in enumerate(groups):
         culture.group_membership_network.add_edge(i, j)
 
 nx.draw(culture.group_membership_network)
 plt.show()
 
+# print("Group Members: \n")
+# for i in groups:
+#     print(i.group_members)
+print("Individual 1 Group Memberships: \n")
+print(list(individuals[0].group_memberships))
+# for i in individuals:
+#     print(i.group_memberships)
+
 # Define termination signals as list [ signal_method, object_method_works_on ]
 # the termination method 'check_for_extinction' must return a boolean
 termination_signal = [M.Culture.check_for_extinction,

From 53f58d98e0cd6942d5deffe95308465f3d626a9f Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Mon, 13 Jun 2022 16:51:31 +0200
Subject: [PATCH 23/33] run_group_test_seven_dwarfs.py now demonstrates minimum
 features of the new group entity

---
 .../base/implementation/group.py              | 19 +++++++++++------
 .../base/implementation/individual.py         |  2 +-
 studies/run_groups_test_seven_dwarfs.py       | 21 ++++++++++++-------
 3 files changed, 28 insertions(+), 14 deletions(-)

diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index b8b6b3d1..012b15a0 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -38,8 +38,8 @@ def __init__(self,
 
         Parameters
         ----------
-        socialsystem: obj
-            SocialSystem the Group belongs to (default is None)
+        world: obj
+            World the Group belongs to
         next_higher_group: obj
             Optional Group the Group belongs to (default is None)
         **kwargs
@@ -67,7 +67,7 @@ def __init__(self,
             self.culture.group_membership_network.add_node(self)
 
     def deactivate(self):
-        """Deactivate an individual.
+        """Deactivate a group.
 
         In particular, deregister from all networks.
 
@@ -78,7 +78,7 @@ def deactivate(self):
         super().deactivate()  # must be the last line
 
     def reactivate(self):
-        """Reactivate an individual.
+        """Reactivate a group.
 
         In particular, deregister with all mandatory networks.
 
@@ -88,6 +88,12 @@ def reactivate(self):
         if self.culture:
             self.culture.group_membership_network.add_node(self)
 
+    def member_mean(self, state):
+        """
+        Calculate the arithmetic mean of a state of all members of a groups.
+        """
+
+
 
     # getters and setters for references:
 
@@ -211,10 +217,11 @@ def metabolism(self):
     @property
     def group_members(self):
         """Get the set of Individuals associated with this Group."""
-        return self.culture.group_membership_network.predecessors(self) # .predeccessors as network is directed from inds to groups
+        return self.culture.group_membership_network.neighbors(self) # .predeccessors as network is directed from inds to groups
+
+
 
 
-    # TODO: helper methods for mergers, splits, etc.
 
     # no process-related methods
 
diff --git a/pycopancore/model_components/base/implementation/individual.py b/pycopancore/model_components/base/implementation/individual.py
index 5eb11073..8ae255f4 100644
--- a/pycopancore/model_components/base/implementation/individual.py
+++ b/pycopancore/model_components/base/implementation/individual.py
@@ -161,7 +161,7 @@ def acquaintances(self):
     @property
     def group_memberships(self):
         """Get the set of Groups the Individual is associated with."""
-        return self.culture.group_membership_network.successors(self) # .successors as network is directed from inds to groups
+        return self.culture.group_membership_network.neighbors(self) # .successors as network is directed from inds to groups
 
     # no process-related methods
 
diff --git a/studies/run_groups_test_seven_dwarfs.py b/studies/run_groups_test_seven_dwarfs.py
index f03ec4a6..f200cd1e 100644
--- a/studies/run_groups_test_seven_dwarfs.py
+++ b/studies/run_groups_test_seven_dwarfs.py
@@ -99,16 +99,23 @@
     for j in enumerate(groups):
         culture.group_membership_network.add_edge(i, j)
 
+
+print("Individual 1 Group Memberships:")
+print(list(individuals[0].group_memberships))
+print("\n")
+
+print("Group Members:")
+print(groups[0])
+# print(groups[0].group_members)
+print("\n")
+
+#draw network of one group
+nx.draw(individuals[0].culture.group_membership_network)
+
 nx.draw(culture.group_membership_network)
 plt.show()
 
-# print("Group Members: \n")
-# for i in groups:
-#     print(i.group_members)
-print("Individual 1 Group Memberships: \n")
-print(list(individuals[0].group_memberships))
-# for i in individuals:
-#     print(i.group_memberships)
+
 
 # Define termination signals as list [ signal_method, object_method_works_on ]
 # the termination method 'check_for_extinction' must return a boolean

From b602e719e0f26bef8a66e9ab5c9e896a931eaae8 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Thu, 16 Jun 2022 11:09:18 +0200
Subject: [PATCH 24/33] - Change group from living in World to living in
 Culture - Add visualisation of layered group network in
 run_group_test_seven_dwarfs.py - Fix minor issues

---
 .../base/implementation/culture.py            |  6 +++
 .../base/implementation/group.py              | 54 +++++++++----------
 .../base/implementation/individual.py         |  4 +-
 .../base/implementation/world.py              |  7 ---
 .../model_components/base/interface.py        |  9 ++--
 studies/run_exploit.py                        |  1 +
 studies/run_groups_test_seven_dwarfs.py       | 42 ++++++++++++---
 7 files changed, 76 insertions(+), 47 deletions(-)

diff --git a/pycopancore/model_components/base/implementation/culture.py b/pycopancore/model_components/base/implementation/culture.py
index 79cf5799..1d2239af 100644
--- a/pycopancore/model_components/base/implementation/culture.py
+++ b/pycopancore/model_components/base/implementation/culture.py
@@ -53,6 +53,7 @@ def __init__(self,
         self.group_membership_network = group_membership_network
 
         self._worlds = set()
+        self._groups = set()
 
         # make sure all variable values are valid:
         self.assert_valid()
@@ -63,6 +64,11 @@ def worlds(self):
         """Get the set of all Worlds this Culture acts in."""
         return self._worlds
 
+    @property  # read-only
+    def groups(self):
+        """Get the set of all Groups in this Culture."""
+        return self._groups
+
     # no process-related methods
 
     processes = []  # no processes in base
diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index 012b15a0..063b7342 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -29,8 +29,7 @@ class Group (I.Group, abstract.Group):
 
     def __init__(self,
                  *,
-                 world,
-                 # culture=None,
+                 culture,
                  next_higher_group=None,
                  **kwargs
                  ):
@@ -38,8 +37,8 @@ def __init__(self,
 
         Parameters
         ----------
-        world: obj
-            World the Group belongs to
+        culture: obj
+            Culture the Group belongs to
         next_higher_group: obj
             Optional Group the Group belongs to (default is None)
         **kwargs
@@ -49,10 +48,10 @@ def __init__(self,
         super().__init__(**kwargs)  # must be the first line
 
         # init and set variables implemented via properties:
-        # self._culture = None
-        # self.culture = culture
-        self._world = None
-        self.world = world
+        self._culture = None
+        self.culture = culture
+        # self._world = None
+        # self.world = world
 
         # self._social_system = None
         # self.social_system = social_system
@@ -64,7 +63,7 @@ def __init__(self,
         self._direct_cells = set()
 
         if self.culture:
-            self.culture.group_membership_network.add_node(self)
+            self.culture.group_membership_network.add_node(self, type="Group", color="green")
 
     def deactivate(self):
         """Deactivate a group.
@@ -86,7 +85,7 @@ def reactivate(self):
         super().reactivate()  # must be the first line
         # reregister with all mandatory networks:
         if self.culture:
-            self.culture.group_membership_network.add_node(self)
+            self.culture.group_membership_network.add_node(self, type="Group", color="green")
 
     def member_mean(self, state):
         """
@@ -159,22 +158,22 @@ def metabolism(self):
         """Get the Metabolism of which the Group is a part."""
         return self._world.metabolism
 
-    # @property
-    # def culture(self):
-    #     """Get groups's culture."""
-    #     return self._culture
-
-    # @culture.setter
-    # def culture(self, c):
-    #     """Set groups's culture."""
-    #     if self._culture is not None:
-    #         first deregister from previous culture's list of worlds:
-            # self._culture.groups.remove(self)
-        # if c is not None:
-        #     assert isinstance(c, I.Culture), \
-        #         "Culture must be taxon type Culture"
-        #     c._groups.add(self)
-        # self._culture = c
+    @property
+    def culture(self):
+        """Get culture group is part of."""
+        return self._culture
+
+    @culture.setter
+    def culture(self, c):
+        """Set culture group is part of."""
+        if self._culture is not None:
+            # first deregister from previous culture's list of worlds:
+            self._culture.groups.remove(self)
+        if c is not None:
+            assert isinstance(c, I.Culture), \
+                "Culture must be taxon type Culture"
+            c._groups.add(self)
+        self._culture = c
 
     # _higher_groups = unknown
     """cache, depends on self.next_higher_group
@@ -217,7 +216,8 @@ def metabolism(self):
     @property
     def group_members(self):
         """Get the set of Individuals associated with this Group."""
-        return self.culture.group_membership_network.neighbors(self) # .predeccessors as network is directed from inds to groups
+        # return self.culture.group_membership_network.neighbors(self)
+        return self.culture.group_membership_network.predecessors(self) # .predecessors as network is directed from inds to groups
 
 
 
diff --git a/pycopancore/model_components/base/implementation/individual.py b/pycopancore/model_components/base/implementation/individual.py
index 8ae255f4..dcaa0ffb 100644
--- a/pycopancore/model_components/base/implementation/individual.py
+++ b/pycopancore/model_components/base/implementation/individual.py
@@ -54,7 +54,7 @@ def __init__(self,
         # register with all mandatory networks:
         if self.culture:
             self.culture.acquaintance_network.add_node(self)
-            self.culture.group_membership_network.add_node(self) # TODO: does this work with DiGraph?
+            self.culture.group_membership_network.add_node(self, type="Individual", color="yellow")
 
     def deactivate(self):
         """Deactivate an individual.
@@ -78,7 +78,7 @@ def reactivate(self):
         # reregister with all mandatory networks:
         if self.culture:
             self.culture.acquaintance_network.add_node(self)
-            self.culture.group_membership_network.add_node(self)
+            self.culture.group_membership_network.add_node(self, type="Individual", color="yellow")
 
     # getters and setters for references:
 
diff --git a/pycopancore/model_components/base/implementation/world.py b/pycopancore/model_components/base/implementation/world.py
index 9457f44e..3e12fe08 100644
--- a/pycopancore/model_components/base/implementation/world.py
+++ b/pycopancore/model_components/base/implementation/world.py
@@ -59,7 +59,6 @@ def __init__(self,
         self.culture = culture
         self._social_systems = set()
         self._cells = set()
-        self._groups = set()
 
         # make sure all variable values are valid:
         self.assert_valid()
@@ -165,12 +164,6 @@ def individuals(self, u):
         # reset dependent caches:
         pass
 
-    @property  # read-only
-    def groups(self):
-        """Get the set of all Groups on this World."""
-        return self._groups
-
-
     processes = [
         # TODO: convert this into an Implicit equation once supported:
         Explicit("aggregate cell carbon stocks",
diff --git a/pycopancore/model_components/base/interface.py b/pycopancore/model_components/base/interface.py
index 5d8d3975..6ac69ebb 100644
--- a/pycopancore/model_components/base/interface.py
+++ b/pycopancore/model_components/base/interface.py
@@ -78,6 +78,9 @@ class Culture (object):
 
 # entity types:
 
+    groups = SetVariable("groups",
+                         "Set of Groups existing on this world",
+                         readonly=True)
 
 # TODO: clarify whether it is necessary to specify the metaclass here!
 class World (object, metaclass=_MixinType):
@@ -122,9 +125,7 @@ class World (object, metaclass=_MixinType):
     individuals = SetVariable("individuals",
                               "Set of Individuals residing on this world",
                               readonly=True)
-    groups = SetVariable("groups",
-                         "Set of Groups existing on this world",
-                         readonly=True)
+
 
 
 # specified only now to avoid recursion errors:
@@ -339,7 +340,7 @@ class Group (object, metaclass=_MixinType):
         readonly=True
     )
 
-
+Culture.groups.type = Group
 
 # specified only now to avoid recursion errors:
 # Group.next_higher_group.type = Group
diff --git a/studies/run_exploit.py b/studies/run_exploit.py
index 3275f221..23ab8837 100755
--- a/studies/run_exploit.py
+++ b/studies/run_exploit.py
@@ -18,6 +18,7 @@
 from time import time
 import datetime as dt
 from numpy import random
+import argparse
 
 import plotly.offline as py
 import plotly.graph_objs as go
diff --git a/studies/run_groups_test_seven_dwarfs.py b/studies/run_groups_test_seven_dwarfs.py
index f200cd1e..e751ec4c 100644
--- a/studies/run_groups_test_seven_dwarfs.py
+++ b/studies/run_groups_test_seven_dwarfs.py
@@ -20,6 +20,7 @@
 import datetime as dt
 
 import networkx as nx
+from networkx.algorithms import bipartite
 import matplotlib.pyplot as plt
 
 import plotly.offline as py
@@ -77,7 +78,7 @@
 
 #instantiate groups
 ng = 10 #number of groups
-groups = [M.Group(world=world) for i in range (ng)]
+groups = [M.Group(culture=culture) for i in range (ng)]
 
 print("\n The groups: \n")
 print(groups)
@@ -96,9 +97,8 @@
 
 # initialize some network:
 for i in individuals:
-    for j in enumerate(groups):
-        culture.group_membership_network.add_edge(i, j)
-
+    for g in groups:
+        culture.group_membership_network.add_edge(i, g)
 
 print("Individual 1 Group Memberships:")
 print(list(individuals[0].group_memberships))
@@ -106,13 +106,41 @@
 
 print("Group Members:")
 print(groups[0])
-# print(groups[0].group_members)
+print(list(groups[0].group_members))
 print("\n")
 
 #draw network of one group
-nx.draw(individuals[0].culture.group_membership_network)
+# nx.draw(individuals[0].culture.group_membership_network)
+# plt.show()
+
+GM = culture.group_membership_network
+
+print(GM.nodes.data())
+
+
+color_map = []
+shape_map = []
+for node in list(GM.nodes):
+    print(node)
+    print(GM.nodes[node])
+    color_map.append(GM.nodes[node]["color"])
+
+    if GM.nodes[node]["type"] == "Group":
+        shape_map.append("o")
+    else:
+        shape_map.append("^")
+
+
+
+top_nodes = {n for n, d in GM.nodes(data=True) if d["type"] == "Group"}
+bottom_nodes = set(GM) - top_nodes
+
+print(list(top_nodes))
+
+nx.draw(GM, node_color=color_map, with_labels=True,
+        pos=nx.bipartite_layout(GM, bottom_nodes, align="horizontal", aspect_ratio=4/1))
 
-nx.draw(culture.group_membership_network)
+# nx.draw(culture.group_membership_network)
 plt.show()
 
 

From 07035ab3cd7a83eddcbd7ce044fae0f9a596f011 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Mon, 20 Jun 2022 15:33:54 +0200
Subject: [PATCH 25/33] add/adjust documentation

---
 .../abstract_level/entity_types/group.rst     | 21 ++++++++++++-------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/docs/framework_documentation/abstract_level/entity_types/group.rst b/docs/framework_documentation/abstract_level/entity_types/group.rst
index 7ef8158c..173ad33e 100644
--- a/docs/framework_documentation/abstract_level/entity_types/group.rst
+++ b/docs/framework_documentation/abstract_level/entity_types/group.rst
@@ -11,7 +11,7 @@ may not be sufficient and a distinction of social strata or other social groups
 "indigenous people", "social democrats", a certain NGO, ...)
 that is transverse to the former partitioning is helpful in addition.
 
-For this, we will in the future provide an entity-type "group" 
+For this, the entity-type "group" is provided
 which is meant to represent any grouping of individuals (that may come from one or several social systems) 
 by meaningful cultural or social-metabolic aspects.
 
@@ -33,19 +33,24 @@ Basic relationships to other entity-types
 
 A group will usually...
 
--  have several member :doc:`individuals<individual>`
+-  have several members :doc:`individuals<individual>`,
+   which is represented by a group membership directed network owned by the culture taxon
 
 In addition, a group may...
 
--  have one or several "leader" :doc:`individuals<individual>`, 
-   of which one may be the dominant leader
+-  have an "intra" group network between members :doc:`individuals<individual>`
+   (this feature is not completely implemented yet)
 
--  have a "headquarters" :doc:`cell<cell>`
+-  have one or several "leader" :doc:`individuals<individual>`,
+   of which one may be the dominant leader (this feature is not implemented yet)
 
--  be related to other groups via some network owned by the culture taxon 
+-  have a "headquarters" :doc:`cell<cell>` (this feature is not implemented yet)
+
+-  be related to other groups via an "inter" network owned by the culture taxon
    (which will typically interact with the network of personal acquaintance between member individuals)
+   - (this feature is not completely implemented yet)
 
--  act as the current "elite" in some :doc:`social system<social system>`
+-  act as the current "elite" in some :doc:`social system<social system>` (this feature is not implemented yet)
 
 All these relationships may be dynamic.
 
@@ -53,5 +58,5 @@ Finally, a group may...
 
 -  be a permanent subgroup of a larger group or :doc:`social system<social system>` *by definition* 
    (rather than by coincidence, e.g., "scientists" are by definition a subgroup of the group "academics",
-   and "German workers" may be by definition a subgroup of the social system "Germany")
+   and "German workers" may be by definition a subgroup of the social system "Germany") - (this feature is not implemented yet)
 

From 356df4be9580ede7c52c969e2cc8b6b10027164b Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Thu, 28 Jul 2022 16:28:30 +0200
Subject: [PATCH 26/33] - bypassed AttributeErrors in base implementation for
 group by getting world, environment and metabolism the group lives in via
 necessary object world that is passed in study script along with culture:
 M.Group(culture=culture, world=world)

---
 .../base/implementation/group.py              | 57 ++++++++--------
 .../base/implementation/world.py              |  6 ++
 .../maxploit_individual_layer/__init__.py     | 18 +++++
 .../implementation/__init__.py                | 22 +++++++
 .../maxploit_social_norms/__init__.py         | 18 +++++
 .../implementation/__init__.py                | 22 +++++++
 .../seven_dwarfs/implementation/__init__.py   |  1 +
 .../seven_dwarfs/implementation/group.py      | 66 +++++++++++++++++++
 .../seven_dwarfs/interface.py                 |  7 ++
 .../model_components/seven_dwarfs/model.py    |  4 +-
 pycopancore/models/groups_seven_dwarfs.py     |  2 +-
 studies/run_groups_test_seven_dwarfs.py       | 15 +++--
 12 files changed, 202 insertions(+), 36 deletions(-)
 create mode 100644 pycopancore/model_components/maxploit_individual_layer/__init__.py
 create mode 100644 pycopancore/model_components/maxploit_individual_layer/implementation/__init__.py
 create mode 100644 pycopancore/model_components/maxploit_social_norms/__init__.py
 create mode 100644 pycopancore/model_components/maxploit_social_norms/implementation/__init__.py
 create mode 100644 pycopancore/model_components/seven_dwarfs/implementation/group.py

diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index 063b7342..6e39c053 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -30,6 +30,7 @@ class Group (I.Group, abstract.Group):
     def __init__(self,
                  *,
                  culture,
+                 world,
                  next_higher_group=None,
                  **kwargs
                  ):
@@ -39,6 +40,8 @@ def __init__(self,
         ----------
         culture: obj
             Culture the Group belongs to
+        world: obj
+            World the Group belongs to (to bypass AttributeErrors for now)
         next_higher_group: obj
             Optional Group the Group belongs to (default is None)
         **kwargs
@@ -50,17 +53,17 @@ def __init__(self,
         # init and set variables implemented via properties:
         self._culture = None
         self.culture = culture
-        # self._world = None
-        # self.world = world
+        self._world = None
+        self.world = world
 
         # self._social_system = None
         # self.social_system = social_system
-        self._next_higher_group = None
-        self.next_higher_group = next_higher_group
+        # self._next_higher_group = None
+        # self.next_higher_group = next_higher_group
 
         # init caches:
-        self._next_lower_group = set()
-        self._direct_cells = set()
+        # self._next_lower_group = set()
+        # self._direct_cells = set()
 
         if self.culture:
             self.culture.group_membership_network.add_node(self, type="Group", color="green")
@@ -87,14 +90,26 @@ def reactivate(self):
         if self.culture:
             self.culture.group_membership_network.add_node(self, type="Group", color="green")
 
-    def member_mean(self, state):
-        """
-        Calculate the arithmetic mean of a state of all members of a groups.
-        """
 
+    # getters and setters for references:
 
+    #culture needs to be before world, as group gets its world etc. over its culture
+    @property
+    def culture(self):
+        """Get culture group is part of."""
+        return self._culture
 
-    # getters and setters for references:
+    @culture.setter
+    def culture(self, c):
+        """Set culture group is part of."""
+        if self._culture is not None:
+            # first deregister from previous culture's list of worlds:
+            self._culture.groups.remove(self)
+        if c is not None:
+            assert isinstance(c, I.Culture), \
+                "Culture must be taxon type Culture"
+            c._groups.add(self)
+        self._culture = c
 
     @property
     def world(self):
@@ -105,7 +120,8 @@ def world(self):
     def world(self, w):
         """Set the World the Group is part of."""
         if self._world is not None:
-            self._world._groups.remove(self)
+            # first deregister from previous world's list of cells:
+            self._world.groups.remove(self)
         assert isinstance(w, I.World), "world must be of entity type World"
         w._groups.add(self)
         self._world = w
@@ -158,23 +174,6 @@ def metabolism(self):
         """Get the Metabolism of which the Group is a part."""
         return self._world.metabolism
 
-    @property
-    def culture(self):
-        """Get culture group is part of."""
-        return self._culture
-
-    @culture.setter
-    def culture(self, c):
-        """Set culture group is part of."""
-        if self._culture is not None:
-            # first deregister from previous culture's list of worlds:
-            self._culture.groups.remove(self)
-        if c is not None:
-            assert isinstance(c, I.Culture), \
-                "Culture must be taxon type Culture"
-            c._groups.add(self)
-        self._culture = c
-
     # _higher_groups = unknown
     """cache, depends on self.next_higher_group
     and self.next_higher_group.higher_groups"""
diff --git a/pycopancore/model_components/base/implementation/world.py b/pycopancore/model_components/base/implementation/world.py
index 3e12fe08..fa6851bb 100644
--- a/pycopancore/model_components/base/implementation/world.py
+++ b/pycopancore/model_components/base/implementation/world.py
@@ -59,6 +59,7 @@ def __init__(self,
         self.culture = culture
         self._social_systems = set()
         self._cells = set()
+        self._groups = set()
 
         # make sure all variable values are valid:
         self.assert_valid()
@@ -145,6 +146,11 @@ def cells(self):
         """Get the set of Cells on this World."""
         return self._cells
 
+    @property  # read-only
+    def groups(self):
+        """Get the set of Groups on this World."""
+        return self._groups
+
     _individuals = unknown
     """cache, depends on self.cells, cell.individuals"""
     @property  # read-only
diff --git a/pycopancore/model_components/maxploit_individual_layer/__init__.py b/pycopancore/model_components/maxploit_individual_layer/__init__.py
new file mode 100644
index 00000000..1e1226a7
--- /dev/null
+++ b/pycopancore/model_components/maxploit_individual_layer/__init__.py
@@ -0,0 +1,18 @@
+"""Model component package simple_extraction."""
+
+# This file is part of pycopancore.
+#
+# Copyright (C) 2016-2017 by COPAN team at Potsdam Institute for Climate
+# Impact Research
+#
+# URL: <http://www.pik-potsdam.de/copan/software>
+# Contact: core@pik-potsdam.de
+# License: BSD 2-clause license
+
+from . import interface
+
+# export all implementation classes:
+from .implementation import *
+
+# export model component mixin class:
+from .model import Model
diff --git a/pycopancore/model_components/maxploit_individual_layer/implementation/__init__.py b/pycopancore/model_components/maxploit_individual_layer/implementation/__init__.py
new file mode 100644
index 00000000..f990b981
--- /dev/null
+++ b/pycopancore/model_components/maxploit_individual_layer/implementation/__init__.py
@@ -0,0 +1,22 @@
+"""
+Model component implementation subpackage exploit_social_learning.
+"""
+
+# This file is part of pycopancore.
+#
+# Copyright (C) 2016-2017 by COPAN team at Potsdam Institute for Climate
+# Impact Research
+#
+# URL: <http://www.pik-potsdam.de/copan/software>
+# Contact: core@pik-potsdam.de
+# License: BSD 2-clause license
+
+# TODO: adjust the following lists to your needs:
+
+# export all provided entity type implementation mixin classes:
+from .world import World
+from .individual import Individual
+
+# export all provided process taxon implementation mixin classes:
+
+from .culture import Culture
diff --git a/pycopancore/model_components/maxploit_social_norms/__init__.py b/pycopancore/model_components/maxploit_social_norms/__init__.py
new file mode 100644
index 00000000..1e1226a7
--- /dev/null
+++ b/pycopancore/model_components/maxploit_social_norms/__init__.py
@@ -0,0 +1,18 @@
+"""Model component package simple_extraction."""
+
+# This file is part of pycopancore.
+#
+# Copyright (C) 2016-2017 by COPAN team at Potsdam Institute for Climate
+# Impact Research
+#
+# URL: <http://www.pik-potsdam.de/copan/software>
+# Contact: core@pik-potsdam.de
+# License: BSD 2-clause license
+
+from . import interface
+
+# export all implementation classes:
+from .implementation import *
+
+# export model component mixin class:
+from .model import Model
diff --git a/pycopancore/model_components/maxploit_social_norms/implementation/__init__.py b/pycopancore/model_components/maxploit_social_norms/implementation/__init__.py
new file mode 100644
index 00000000..3c7f3304
--- /dev/null
+++ b/pycopancore/model_components/maxploit_social_norms/implementation/__init__.py
@@ -0,0 +1,22 @@
+"""
+Model component implementation subpackage exploit_social_learning.
+"""
+
+# This file is part of pycopancore.
+#
+# Copyright (C) 2016-2017 by COPAN team at Potsdam Institute for Climate
+# Impact Research
+#
+# URL: <http://www.pik-potsdam.de/copan/software>
+# Contact: core@pik-potsdam.de
+# License: BSD 2-clause license
+
+# TODO: adjust the following lists to your needs:
+
+# export all provided entity type implementation mixin classes:
+from .individual import Individual
+from .group import Group
+
+# export all provided process taxon implementation mixin classes:
+
+from .culture import Culture
diff --git a/pycopancore/model_components/seven_dwarfs/implementation/__init__.py b/pycopancore/model_components/seven_dwarfs/implementation/__init__.py
index e28f51f0..044ca48a 100644
--- a/pycopancore/model_components/seven_dwarfs/implementation/__init__.py
+++ b/pycopancore/model_components/seven_dwarfs/implementation/__init__.py
@@ -17,3 +17,4 @@
 from .individual import Individual
 from .culture import Culture
 from .social_system import SocialSystem
+from .group import Group
diff --git a/pycopancore/model_components/seven_dwarfs/implementation/group.py b/pycopancore/model_components/seven_dwarfs/implementation/group.py
new file mode 100644
index 00000000..2e9ab8fc
--- /dev/null
+++ b/pycopancore/model_components/seven_dwarfs/implementation/group.py
@@ -0,0 +1,66 @@
+"""Group entity type class template.
+
+TODO: adjust or fill in code and documentation wherever marked by "TODO:",
+then remove these instructions
+"""
+
+# This file is part of pycopancore.
+#
+# Copyright (C) 2016-2017 by COPAN team at Potsdam Institute for Climate
+# Impact Research
+#
+# URL: <http://www.pik-potsdam.de/copan/software>
+# Contact: core@pik-potsdam.de
+# License: BSD 2-clause license
+
+from .. import interface as I
+# from .... import master_data_model as D
+
+# TODO: uncomment this if you need ref. variables such as B.Individual.cell:
+#from ...base import interface as B
+
+# TODO: import those process types you need:
+from .... import Explicit
+
+class Group (I.Group):
+    """Group entity type mixin implementation class."""
+
+    # standard methods:
+    # TODO: only uncomment when adding custom code!
+
+#     def __init__(self,
+#                  # *,  # TODO: uncomment when adding named args behind here
+#                  **kwargs):
+#         """Initialize an instance of Individual."""
+#         super().__init__(**kwargs)  # must be the first line
+#         # TODO: add custom code here:
+#         pass
+#
+#     def deactivate(self):
+#         """Deactivate a Group."""
+#         # TODO: add custom code here:
+#         pass
+#         super().deactivate()  # must be the last line
+#
+#     def reactivate(self):
+#         """Reactivate a Group."""
+#         super().reactivate()  # must be the first line
+#         # TODO: add custom code here:
+#         pass
+
+    # process-related methods:
+
+    def check_if_member(self, unused_t):
+        """Check if dwarf 1 is member of any group."""
+        for w in self.worlds:
+            return w.individuals[0].group_memberships
+
+
+
+
+
+    # TODO: add some if needed...
+
+    processes = [
+        Explicit("simple test", [I.Group.having_members], check_if_member)
+    ]  # TODO: instantiate and list process objects here
\ No newline at end of file
diff --git a/pycopancore/model_components/seven_dwarfs/interface.py b/pycopancore/model_components/seven_dwarfs/interface.py
index 62198fb4..4a417398 100644
--- a/pycopancore/model_components/seven_dwarfs/interface.py
+++ b/pycopancore/model_components/seven_dwarfs/interface.py
@@ -98,3 +98,10 @@ class SocialSystem(object):
 class Culture (object):
     """Interface for Culture mixin"""
     pass
+
+class Group(object):
+    """Interface for Group mixin"""
+
+    having_members = ("test", """test""")
+
+    pass
diff --git a/pycopancore/model_components/seven_dwarfs/model.py b/pycopancore/model_components/seven_dwarfs/model.py
index 73f9cddd..a68be807 100644
--- a/pycopancore/model_components/seven_dwarfs/model.py
+++ b/pycopancore/model_components/seven_dwarfs/model.py
@@ -15,7 +15,7 @@
 
 from . import interface as I
 # import all needed entity type implementation classes:
-from .implementation import World, Cell, Individual, Culture, SocialSystem
+from .implementation import World, Cell, Individual, Culture, SocialSystem, Group
 # import all needed process taxon implementation classes:
 
 
@@ -24,7 +24,7 @@ class Model(I.Model):
 
     # mixins provided by this model component:
 
-    entity_types = [World, Cell, Individual, SocialSystem]
+    entity_types = [World, Cell, Individual, SocialSystem, Group]
     """list of entity types augmented by this component"""
     process_taxa = [Culture]
     """list of process taxa augmented by this component"""
diff --git a/pycopancore/models/groups_seven_dwarfs.py b/pycopancore/models/groups_seven_dwarfs.py
index 31be4f35..f0d124d0 100644
--- a/pycopancore/models/groups_seven_dwarfs.py
+++ b/pycopancore/models/groups_seven_dwarfs.py
@@ -83,7 +83,7 @@ class Model(sd.Model,
     description = "Tutorial model"
     """Longer description"""
 
-    entity_types = [World, SocialSystem, Cell, Individual]
+    entity_types = [World, SocialSystem, Cell, Individual, Group]
     """List of entity types used in the model"""
     process_taxa = [Culture]
     """List of process taxa used in the model"""
diff --git a/studies/run_groups_test_seven_dwarfs.py b/studies/run_groups_test_seven_dwarfs.py
index e751ec4c..1e7e3b66 100644
--- a/studies/run_groups_test_seven_dwarfs.py
+++ b/studies/run_groups_test_seven_dwarfs.py
@@ -29,6 +29,10 @@
 import pycopancore.models.groups_seven_dwarfs as M
 from pycopancore.runners.runner import Runner
 
+from studies import plot_multilayer as pm
+from mpl_toolkits.mplot3d import Axes3D
+from mpl_toolkits.mplot3d.art3d import Line3DCollection
+
 
 # setting timeinterval for run method 'Runner.run()'
 timeinterval = 10
@@ -78,7 +82,7 @@
 
 #instantiate groups
 ng = 10 #number of groups
-groups = [M.Group(culture=culture) for i in range (ng)]
+groups = [M.Group(culture=culture, world=world) for i in range (ng)]
 
 print("\n The groups: \n")
 print(groups)
@@ -137,11 +141,11 @@
 
 print(list(top_nodes))
 
-nx.draw(GM, node_color=color_map, with_labels=True,
+nx.draw(GM, node_color=color_map, with_labels=False,
         pos=nx.bipartite_layout(GM, bottom_nodes, align="horizontal", aspect_ratio=4/1))
 
 # nx.draw(culture.group_membership_network)
-plt.show()
+# plt.show()
 
 
 
@@ -154,7 +158,7 @@
 termination_callables = [termination_signal]
 
 nx.draw(culture.acquaintance_network)
-plt.show()
+# plt.show()
 
 # Runner is instantiated
 r = Runner(model=model,
@@ -171,4 +175,7 @@
 t = np.array(traj['t'])
 print("max. time step", (t[1:]-t[:-1]).max())
 
+#save and print membership
+membercheck = np.array(traj['check_if_member'])
+
 

From 76474cd15701b8f05abe5e524e5a0e09edd0d0e3 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Fri, 5 Aug 2022 12:23:25 +0200
Subject: [PATCH 27/33] Add simple test function and plot groupmembership for a
 single dwarf over time

---
 .../seven_dwarfs/implementation/group.py      | 10 +++++---
 .../seven_dwarfs/interface.py                 |  5 ++--
 pycopancore/models/groups_seven_dwarfs.py     |  3 ++-
 studies/run_groups_test_seven_dwarfs.py       | 24 ++++++++++---------
 4 files changed, 25 insertions(+), 17 deletions(-)

diff --git a/pycopancore/model_components/seven_dwarfs/implementation/group.py b/pycopancore/model_components/seven_dwarfs/implementation/group.py
index 2e9ab8fc..4da3f6b7 100644
--- a/pycopancore/model_components/seven_dwarfs/implementation/group.py
+++ b/pycopancore/model_components/seven_dwarfs/implementation/group.py
@@ -17,7 +17,7 @@
 # from .... import master_data_model as D
 
 # TODO: uncomment this if you need ref. variables such as B.Individual.cell:
-#from ...base import interface as B
+from ...base import interface as B
 
 # TODO: import those process types you need:
 from .... import Explicit
@@ -52,8 +52,12 @@ class Group (I.Group):
 
     def check_if_member(self, unused_t):
         """Check if dwarf 1 is member of any group."""
-        for w in self.worlds:
-            return w.individuals[0].group_memberships
+        group_members = list(self.group_members)
+        i_0 = list(self.world.individuals)[0]
+        if i_0 in group_members:
+            self.having_members = True
+        else:
+            self.having_members = False
 
 
 
diff --git a/pycopancore/model_components/seven_dwarfs/interface.py b/pycopancore/model_components/seven_dwarfs/interface.py
index 4a417398..7176b1a8 100644
--- a/pycopancore/model_components/seven_dwarfs/interface.py
+++ b/pycopancore/model_components/seven_dwarfs/interface.py
@@ -90,7 +90,6 @@ class Individual (object):
                                 "eating speed of dwarf",
                                 default=1)
 
-
 class SocialSystem(object):
     """Interface for SocialSystem mixin"""
     pass
@@ -102,6 +101,8 @@ class Culture (object):
 class Group(object):
     """Interface for Group mixin"""
 
-    having_members = ("test", """test""")
+    having_members = Variable("test",
+                      "test",
+                      default=True)
 
     pass
diff --git a/pycopancore/models/groups_seven_dwarfs.py b/pycopancore/models/groups_seven_dwarfs.py
index f0d124d0..6c823150 100644
--- a/pycopancore/models/groups_seven_dwarfs.py
+++ b/pycopancore/models/groups_seven_dwarfs.py
@@ -59,7 +59,8 @@ class SocialSystem(sd.SocialSystem,
 
     pass
 
-class Group(base.Group):
+class Group(sd.Group,
+            base.Group):
     """Groups entity type"""
 
 # process taxa:
diff --git a/studies/run_groups_test_seven_dwarfs.py b/studies/run_groups_test_seven_dwarfs.py
index 1e7e3b66..fabf7154 100644
--- a/studies/run_groups_test_seven_dwarfs.py
+++ b/studies/run_groups_test_seven_dwarfs.py
@@ -29,9 +29,9 @@
 import pycopancore.models.groups_seven_dwarfs as M
 from pycopancore.runners.runner import Runner
 
-from studies import plot_multilayer as pm
-from mpl_toolkits.mplot3d import Axes3D
-from mpl_toolkits.mplot3d.art3d import Line3DCollection
+# from studies import plot_multilayer as pm
+# from mpl_toolkits.mplot3d import Axes3D
+# from mpl_toolkits.mplot3d.art3d import Line3DCollection
 
 
 # setting timeinterval for run method 'Runner.run()'
@@ -114,8 +114,8 @@
 print("\n")
 
 #draw network of one group
-# nx.draw(individuals[0].culture.group_membership_network)
-# plt.show()
+nx.draw(individuals[0].culture.group_membership_network)
+plt.show()
 
 GM = culture.group_membership_network
 
@@ -143,9 +143,10 @@
 
 nx.draw(GM, node_color=color_map, with_labels=False,
         pos=nx.bipartite_layout(GM, bottom_nodes, align="horizontal", aspect_ratio=4/1))
+plt.show()
 
-# nx.draw(culture.group_membership_network)
-# plt.show()
+nx.draw(culture.group_membership_network)
+plt.show()
 
 
 
@@ -158,7 +159,7 @@
 termination_callables = [termination_signal]
 
 nx.draw(culture.acquaintance_network)
-# plt.show()
+plt.show()
 
 # Runner is instantiated
 r = Runner(model=model,
@@ -175,7 +176,8 @@
 t = np.array(traj['t'])
 print("max. time step", (t[1:]-t[:-1]).max())
 
-#save and print membership
-membercheck = np.array(traj['check_if_member'])
-
+# save and print membership
 
+membercheck = traj[M.Group.having_members]
+plt.plot(t, membercheck[groups[0]]) # plot if dwarf 0 was member of group 0
+plt.show()

From 447b6b8a81e3f2a2f03fc419e609cb30483630c0 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Wed, 10 Aug 2022 13:36:43 +0200
Subject: [PATCH 28/33] Make illustration study more clear

---
 ...n_dwarfs.py => run_groups_illustration.py} | 42 +++++++------------
 1 file changed, 16 insertions(+), 26 deletions(-)
 rename studies/{run_groups_test_seven_dwarfs.py => run_groups_illustration.py} (88%)

diff --git a/studies/run_groups_test_seven_dwarfs.py b/studies/run_groups_illustration.py
similarity index 88%
rename from studies/run_groups_test_seven_dwarfs.py
rename to studies/run_groups_illustration.py
index fabf7154..0fb64c54 100644
--- a/studies/run_groups_test_seven_dwarfs.py
+++ b/studies/run_groups_illustration.py
@@ -1,8 +1,4 @@
-"""This is the test script for the seven dwarfs step by step tutorial.
-
-In this version only the Step-process 'aging' of entitytype 'Individual' is
-implemented, such that the only relevant attributes of 'Individual' are 'age'
-and 'cell'.
+"""This is an illustration script for some of the features that come with the group entity based on the seven dwarfs model.
 """
 
 # This file is part of pycopancore.
@@ -73,7 +69,7 @@
                             ) for i in range(dwarfs)
                ]
 
-print("\n The individuals: \n")
+print("\n The individuals:")
 print(individuals)
 print("\n \n")
 
@@ -84,7 +80,7 @@
 ng = 10 #number of groups
 groups = [M.Group(culture=culture, world=world) for i in range (ng)]
 
-print("\n The groups: \n")
+print("\n The groups:")
 print(groups)
 print("\n \n")
 
@@ -99,29 +95,34 @@
 #plt.show()
 
 
-# initialize some network:
+# initialize the network:
 for i in individuals:
     for g in groups:
         culture.group_membership_network.add_edge(i, g)
 
-print("Individual 1 Group Memberships:")
+print("\n Individual 1 Group Memberships:")
 print(list(individuals[0].group_memberships))
 print("\n")
 
-print("Group Members:")
-print(groups[0])
+print("\n Group Members:")
 print(list(groups[0].group_members))
 print("\n")
 
 #draw network of one group
-nx.draw(individuals[0].culture.group_membership_network)
-plt.show()
+# nx.draw(individuals[0].culture.group_membership_network)
+# plt.show()
 
 GM = culture.group_membership_network
 
+print("\n The data structure in gm network:")
 print(GM.nodes.data())
+print("\n")
 
+# How networkx would classicaly plot the network
+nx.draw(culture.group_membership_network)
+plt.show()
 
+# How to plot more intuitively using the type and color information
 color_map = []
 shape_map = []
 for node in list(GM.nodes):
@@ -133,23 +134,12 @@
         shape_map.append("o")
     else:
         shape_map.append("^")
-
-
-
 top_nodes = {n for n, d in GM.nodes(data=True) if d["type"] == "Group"}
 bottom_nodes = set(GM) - top_nodes
-
-print(list(top_nodes))
-
 nx.draw(GM, node_color=color_map, with_labels=False,
         pos=nx.bipartite_layout(GM, bottom_nodes, align="horizontal", aspect_ratio=4/1))
 plt.show()
 
-nx.draw(culture.group_membership_network)
-plt.show()
-
-
-
 # Define termination signals as list [ signal_method, object_method_works_on ]
 # the termination method 'check_for_extinction' must return a boolean
 termination_signal = [M.Culture.check_for_extinction,
@@ -158,8 +148,8 @@
 # Define termination_callables as list of all signals
 termination_callables = [termination_signal]
 
-nx.draw(culture.acquaintance_network)
-plt.show()
+# nx.draw(culture.acquaintance_network)
+# plt.show()
 
 # Runner is instantiated
 r = Runner(model=model,

From 34904c641c9da2fe1638f8455deb13182cfbb6d4 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Thu, 11 Aug 2022 11:13:08 +0200
Subject: [PATCH 29/33] Make illustration study more clear

---
 studies/run_groups_illustration.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/studies/run_groups_illustration.py b/studies/run_groups_illustration.py
index 0fb64c54..c17fb1d6 100644
--- a/studies/run_groups_illustration.py
+++ b/studies/run_groups_illustration.py
@@ -76,7 +76,7 @@
 # assigning individuals to cell is not necessary since it is done by
 # initializing the individuals in 'base.Individuals' with the 'cell' method
 
-#instantiate groups
+# instantiate groups
 ng = 10 #number of groups
 groups = [M.Group(culture=culture, world=world) for i in range (ng)]
 

From bf446bf198685f1750433fc76a4990e64dfbc994 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Wed, 22 Nov 2023 12:43:15 +0100
Subject: [PATCH 30/33] resolve #175

---
 .../abstract_level/entity_types/group.rst     | 10 +--
 .../base/implementation/group.py              | 89 -------------------
 .../model_components/base/interface.py        | 23 -----
 3 files changed, 4 insertions(+), 118 deletions(-)

diff --git a/docs/framework_documentation/abstract_level/entity_types/group.rst b/docs/framework_documentation/abstract_level/entity_types/group.rst
index 173ad33e..44106df7 100644
--- a/docs/framework_documentation/abstract_level/entity_types/group.rst
+++ b/docs/framework_documentation/abstract_level/entity_types/group.rst
@@ -39,18 +39,16 @@ A group will usually...
 In addition, a group may...
 
 -  have an "intra" group network between members :doc:`individuals<individual>`
-   (this feature is not completely implemented yet)
 
 -  have one or several "leader" :doc:`individuals<individual>`,
-   of which one may be the dominant leader (this feature is not implemented yet)
+   of which one may be the dominant leader
 
--  have a "headquarters" :doc:`cell<cell>` (this feature is not implemented yet)
+-  have a "headquarters" :doc:`cell<cell>`
 
 -  be related to other groups via an "inter" network owned by the culture taxon
    (which will typically interact with the network of personal acquaintance between member individuals)
-   - (this feature is not completely implemented yet)
 
--  act as the current "elite" in some :doc:`social system<social system>` (this feature is not implemented yet)
+-  act as the current "elite" in some :doc:`social system<social system>`
 
 All these relationships may be dynamic.
 
@@ -58,5 +56,5 @@ Finally, a group may...
 
 -  be a permanent subgroup of a larger group or :doc:`social system<social system>` *by definition* 
    (rather than by coincidence, e.g., "scientists" are by definition a subgroup of the group "academics",
-   and "German workers" may be by definition a subgroup of the social system "Germany") - (this feature is not implemented yet)
+   and "German workers" may be by definition a subgroup of the social system "Germany")
 
diff --git a/pycopancore/model_components/base/implementation/group.py b/pycopancore/model_components/base/implementation/group.py
index 6e39c053..e28a71e0 100644
--- a/pycopancore/model_components/base/implementation/group.py
+++ b/pycopancore/model_components/base/implementation/group.py
@@ -31,7 +31,6 @@ def __init__(self,
                  *,
                  culture,
                  world,
-                 next_higher_group=None,
                  **kwargs
                  ):
         """Initialize an instance of Group.
@@ -42,8 +41,6 @@ def __init__(self,
             Culture the Group belongs to
         world: obj
             World the Group belongs to (to bypass AttributeErrors for now)
-        next_higher_group: obj
-            Optional Group the Group belongs to (default is None)
         **kwargs
             keyword arguments passed to super()
 
@@ -56,15 +53,6 @@ def __init__(self,
         self._world = None
         self.world = world
 
-        # self._social_system = None
-        # self.social_system = social_system
-        # self._next_higher_group = None
-        # self.next_higher_group = next_higher_group
-
-        # init caches:
-        # self._next_lower_group = set()
-        # self._direct_cells = set()
-
         if self.culture:
             self.culture.group_membership_network.add_node(self, type="Group", color="green")
 
@@ -126,42 +114,6 @@ def world(self, w):
         w._groups.add(self)
         self._world = w
 
-    # @property
-    # def social_system(self):
-    #     """Get the SocialSystem the Group is part of."""
-    #     return self._social_system
-
-    # @social_system.setter
-    # def social_system(self, s):
-    #     """Set the SocialSystem the Group is part of."""
-    #     if self._social_system is not None:
-    #         self._social_system._groups.remove(self)
-    #     assert isinstance(s, I.SocialSystem), "socialsystem must be of entity type SocialSystem"
-    #     s._groups.add(self)
-    #     self._social_system = s
-
-    # @property
-    # def next_higher_group(self):
-    #     """Get next higher group."""
-    #     return self._next_higher_group
-
-    # @next_higher_group.setter
-    # def next_higher_group(self, s):
-    #     """Set next higher group."""
-    #     if self._next_higher_group is not None:
-    #         self._next_higher_group._next_lower_groups.remove(self)
-    #         reset dependent cache:
-            # self._next_higher_group.cells = unknown
-        # if s is not None:
-        #     assert isinstance(s, I.Group), \
-        #         "next_higher_group must be of entity type group"
-        #     s._next_lower_groups.add(self)
-        #     reset dependent cache:
-        #     s.cells = unknown
-        # self._next_higher_group = s
-        # reset dependent caches:
-        # self.higher_groups = unknown
-
     # getters for backwards references and convenience variables:
 
     @property  # read-only
@@ -174,44 +126,6 @@ def metabolism(self):
         """Get the Metabolism of which the Group is a part."""
         return self._world.metabolism
 
-    # _higher_groups = unknown
-    """cache, depends on self.next_higher_group
-    and self.next_higher_group.higher_groups"""
-    # @property  # read-only
-    # def higher_groups(self):
-    #     """Get higher groups."""
-    #     if self._higher_groups is unknown:
-            # find recursively:
-            # self._higher_groups = [] if self.next_higher_group is None \
-            #     else ([self.next_higher_group]
-            #           + self.next_higher_group.groups)
-        # return self._higher_groups
-
-    # @higher_groups.setter
-    # def higher_groups(self, u):
-    #     """Set higher groups."""
-    #     assert u == unknown, "setter can only be used to reset cache"
-    #     self._higher_groups = unknown
-        # reset dependent caches:
-        # for s in self._next_lower_groups:
-        #     s.higher_groups = unknown
-        # for c in self._direct_cells:
-        #     c.groups = unknown
-
-    # @property  # read-only
-    # def next_lower_groups(self):
-    #     """Get next lower groups."""
-    #     return self._next_lower_groups
-
-    # @property  # read-only
-    # def lower_groups(self):
-    #     """Get lower groups."""
-        # aggregate recursively:
-        # l = self._next_lower_groups
-        # for s in self._next_lower_groups:
-        #     l.update(s.lower_groups)
-        # return l
-
     @property
     def group_members(self):
         """Get the set of Individuals associated with this Group."""
@@ -219,9 +133,6 @@ def group_members(self):
         return self.culture.group_membership_network.predecessors(self) # .predecessors as network is directed from inds to groups
 
 
-
-
-
     # no process-related methods
 
     processes = []  # no processes in base
diff --git a/pycopancore/model_components/base/interface.py b/pycopancore/model_components/base/interface.py
index 6ac69ebb..e2fb0de1 100644
--- a/pycopancore/model_components/base/interface.py
+++ b/pycopancore/model_components/base/interface.py
@@ -321,19 +321,6 @@ class Group (object, metaclass=_MixinType):
                                    readonly=True)
     culture = ReferenceVariable("culture", "", type=Culture,
                                 readonly=True)
-    # higher_groups = SetVariable(
-    #     "higher groups",
-    #     "upward list of (in)direct super-Groups",
-    #     readonly=True)
-    # next_lower_groups = SetVariable(
-    #     "next lower groups",
-    #     "set of sub-Groups of next lower level",
-    #     readonly=True)
-    # lower_groups = SetVariable(
-    #     "lower groups",
-    #     "set of all direct and indirect sub-Groups",
-    #     readonly=True)
-
     group_members = SetVariable(
         "group members",
         "set of all individuals associated with the group",
@@ -341,13 +328,3 @@ class Group (object, metaclass=_MixinType):
     )
 
 Culture.groups.type = Group
-
-# specified only now to avoid recursion errors:
-# Group.next_higher_group.type = Group
-# Group.higher_groups.type = Group
-# Group.next_lower_groups.type = Group
-# Group.lower_groups.type = Group
-# Individual.group_memberships.type = Group # TODO: assert this is at the right place
-# Group.group_members.type = Individual
-#Group.groups.type = Group
-#SocialSystem.top_level_groups.type = Group

From 519cac8408f8de7ca38b93d000323ccbff78c597 Mon Sep 17 00:00:00 2001
From: MaxBechthold <bechthold.wo@gmail.com>
Date: Tue, 18 Jun 2024 10:38:31 +0200
Subject: [PATCH 31/33] resolve #175

fully resolved comments (documentation only sporadically, since still coherent with rest of docs)
---
 pycopancore/data_model/master_data_model/group.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/pycopancore/data_model/master_data_model/group.py b/pycopancore/data_model/master_data_model/group.py
index cd7354cb..a114e4d9 100644
--- a/pycopancore/data_model/master_data_model/group.py
+++ b/pycopancore/data_model/master_data_model/group.py
@@ -1,7 +1,5 @@
 """Master data model for group."""
 
-"""https://github.com/pik-copan/pycopancore/blob/master/docs/framework_documentation/abstract_level/entity_types/group.rst"""
-
 from .. import Variable
 
 from networkx import Graph

From 098512cc4cabf49df22c15c777b045eacf2945ff Mon Sep 17 00:00:00 2001
From: Max Bechthold <64842372+zugnachpankow@users.noreply.github.com>
Date: Thu, 4 Jul 2024 11:41:30 +0200
Subject: [PATCH 32/33] Update setup.py

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 859db329..13679089 100644
--- a/setup.py
+++ b/setup.py
@@ -16,7 +16,7 @@
 # This creates a link insteaed of copying the files, so modifications in this directory are modifications in the installed package.
 
 setup(name="pycopancore",
-      version="0.6.1",
+      version="0.7.0",
       description="Reference implementation of the copan:CORE World-Earth modelling framework",
       url="https://github.com/pik-copan/pycopancore",
       author="COPAN team @ PIK",

From 7c31ec4eb48239873c8729c57af13788d072bd89 Mon Sep 17 00:00:00 2001
From: Max Bechthold <64842372+zugnachpankow@users.noreply.github.com>
Date: Thu, 4 Jul 2024 11:42:45 +0200
Subject: [PATCH 33/33] Update CITATION.cff

---
 CITATION.cff | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index 722a524a..2ea7e7af 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'pycopancore: Reference implementation of the copan:CORE World-Earth modelling framework'
-version: 0.6.0
-date-released: '2020-04-28'
+version: 0.7.0
+date-released: '2024-07-04'
 abstract: The pycopancore package is a python implementation of the copan:CORE
   modeling framework as described in this paper. The framework is designed to
   allow an easy implementation of World-Earth (i.e., global social-ecological)
@@ -14,6 +14,10 @@ abstract: The pycopancore package is a python implementation of the copan:CORE
   stochastic and deterministic events and therefore allows to compare different
   model and component types and implementations.
 authors:
+- family-names: Bechthold
+  given-names: Max
+  email: maxbecht@pik-potsdam.de
+  orcid: 0009-0007-7113-4814
 - family-names: Heitzig
   given-names: Jobst
   email: jobst.heitzig@pik-potsdam.de