Github issues fix

README.md

@@ -8,7 +8,7 @@ These instructions will get you a copy of the project up and running on your loc
 
 ### Prerequisites
 
-The code is run and tested with Python 3.6.3 on macOS 10.12.6.
+The code is run and tested with Python 3.6.3 and 3.7 on macOS 10.12.6., 10.13 and 10.14.
 Create a virtual environment for Python 3 with:
 
 ```
@@ -17,7 +17,14 @@ virtualenv -p python3 envname
 
 ### Installing packages
 
-The used Python libraries/packages can be installed with:
+Pip's install of pygraphviz is currently broken, thus run the following before using the makefile:
+
+```
+brew install graphviz
+pip3 install pygraphviz
+```
+
+Then the used Python libraries/packages can be installed with:
 
 ```
 make
@@ -54,4 +61,8 @@ In this file you can also change the configurations of the simulation.
 
 ## License
 
+See LICENSE.txt
+
 ## Acknowledgments
+
+Many thanks to Dominik Harz (nud3l) for his help and suggestions during development of this software.

config.ini

@@ -1,5 +1,5 @@
 [PARAMETERS]
-no_of_transactions = 22000
+no_of_transactions = 2000
 lambda = 50
 no_of_agents = 2
 alpha = 0.1
@@ -11,15 +11,10 @@ printing = True
 
 
 [EVENT1]
-step = 10000
+step = 1000
 agent_choice = [0.7,0.3]
 
 
 [EVENT2]
-step = 15000
+step = 1500
 distance = 1
-
-
-[EVENT3]
-step = 20000
-agent_choice = [0.5,0.5]

core.py

@@ -35,14 +35,9 @@
 start_time = timeit.default_timer()
 runs = 1
 
-number_of_agents = 10
-distances = create_random_graph_distances(number_of_agents)
-
-# distances = [[0.0, 80.0, 40.0, 60.0, 80.0, 40.0, 40.0, 20.0, 60.0, 40.0], [80.0, 0.0, 80.0, 60.0, 40.0, 80.0, 80.0, 60.0, 20.0, 40.0], [40.0, 80.0, 0.0, 60.0, 80.0, 40.0, 20.0, 20.0, 60.0, 40.0], [60.0, 60.0, 60.0, 0.0, 60.0, 60.0, 60.0, 40.0, 40.0, 20.0], [80.0, 40.0, 80.0, 60.0, 0.0, 80.0, 80.0, 60.0, 20.0, 40.0], [40.0, 80.0, 40.0, 60.0, 80.0, 0.0, 40.0, 20.0, 60.0, 40.0], [40.0, 80.0, 20.0, 60.0, 80.0, 40.0, 0.0, 20.0, 60.0, 40.0], [20.0, 60.0, 20.0, 40.0, 60.0, 20.0, 20.0, 0.0, 40.0, 20.0], [60.0, 20.0, 60.0, 40.0, 20.0, 60.0, 60.0, 40.0, 0.0, 20.0], [40.0, 40.0, 40.0, 20.0, 40.0, 40.0, 40.0, 20.0, 20.0, 0.0]]
-
 for i in range(runs):
 
- simu2 = Multi_Agent_Simulation(1000, 50, 2, 0.005, 1, "weighted", _agent_choice=[0.7,0.3], _printing=True)
+ simu2 = Multi_Agent_Simulation(800, 50, 2, 0.1, 1, "weighted", _printing=True)
  simu2.setup()
  simu2.run()
  # csv_export(simu2)
@@ -53,7 +48,8 @@
 # PLOTTING
 #############################################################################
 
-print_graph(simu2)
-print_tips_over_time(simu2)
-print_tips_over_time_multiple_agents(simu2, simu2.no_of_transactions)
+# print_graph(simu2)
+# print_tips_over_time(simu2)
+# print_tips_over_time_multiple_agents(simu2, simu2.no_of_transactions)
 print_tips_over_time_multiple_agents_with_tangle(simu2, simu2.no_of_transactions)
+# print_attachment_probabilities_all_agents(simu2)

requirements.txt

@@ -1,66 +1,78 @@
-appnope==0.1.0
-atomicwrites==1.1.5
-attrs==18.1.0
-bleach==2.1.3
-coverage==4.5.1
-cycler==0.10.0
-decorator==4.3.0
-entrypoints==0.2.3
-flake8==2.6.2
-hacking==1.1.0
-html5lib==1.0.1
-hypothesis==3.57.0
-ipykernel==4.8.2
-ipython==5.0.0
-ipython-genutils==0.2.0
-ipywidgets==7.2.1
-Jinja2==2.10
-jsonschema==2.6.0
-jupyter==1.0.0
-jupyter-client==5.2.3
-jupyter-console==5.2.0
-jupyter-core==4.4.0
-kiwisolver==1.0.1
-MarkupSafe==1.0
-matplotlib==2.2.2
-mccabe==0.5.3
-mistune==0.8.3
-more-itertools==4.2.0
-nbconvert==5.3.1
-nbformat==4.4.0
-networkx==2.1
-nose==1.3.7
-notebook==5.5.0
-numpy==1.14.3
-pandocfilters==1.4.2
-pbr==4.0.3
-pexpect==4.6.0
-pickleshare==0.7.4
-pluggy==0.6.0
-prompt-toolkit==1.0.15
-ptyprocess==0.5.2
-py==1.5.3
-pycodestyle==2.0.0
-pydot==1.2.4
-pyflakes==1.2.3
-Pygments==2.2.0
-pygraphviz==1.3.1
-pyparsing==2.2.0
-pyprof2calltree==1.4.3
-pysha3==1.0.2
-pytest==3.6.0
-python-dateutil==2.7.3
-pytz==2018.4
-pyzmq==17.0.0
-qtconsole==4.3.1
-Send2Trash==1.5.0
-simplegeneric==0.8.1
-six==1.11.0
-terminado==0.8.1
-testpath==0.3.1
-tornado==5.0.2
-traitlets==4.3.2
-utils==0.9.0
-wcwidth==0.1.7
-webencodings==0.5.1
-widgetsnbextension==3.2.1
+Package Version
+------------------ -------
+appnope 0.1.0 
+astroid 2.0.4 
+atomicwrites 1.1.5 
+attrs 18.1.0 
+bleach 2.1.3 
+coverage 4.5.1 
+cycler 0.10.0 
+decorator 4.3.0 
+entrypoints 0.2.3 
+flake8 2.6.2 
+hacking 1.1.0 
+html5lib 1.0.1 
+hypothesis 3.57.0 
+ipykernel 4.8.2 
+ipython 5.0.0 
+ipython-genutils 0.2.0 
+ipywidgets 7.2.1 
+isort 4.3.4 
+Jinja2 2.10 
+jsonschema 2.6.0 
+jupyter 1.0.0 
+jupyter-client 5.2.3 
+jupyter-console 5.2.0 
+jupyter-core 4.4.0 
+kiwisolver 1.0.1 
+lazy-object-proxy 1.3.1 
+MarkupSafe 1.0 
+matplotlib 2.2.2 
+mccabe 0.5.3 
+mistune 0.8.3 
+more-itertools 4.2.0 
+nbconvert 5.3.1 
+nbformat 4.4.0 
+networkx 2.1 
+nose 1.3.7 
+notebook 5.5.0 
+numpy 1.14.3 
+pandocfilters 1.4.2 
+pbr 4.0.3 
+pexpect 4.6.0 
+pickleshare 0.7.4 
+pip 10.0.1 
+pluggy 0.6.0 
+prompt-toolkit 1.0.15 
+ptyprocess 0.5.2 
+py 1.5.3 
+pycodestyle 2.0.0 
+pydot 1.2.4 
+pyflakes 1.2.3 
+Pygments 2.2.0 
+pygraphviz 2.2
+pylint 2.1.1 
+pyparsing 2.2.0 
+pyprof2calltree 1.4.3 
+pysha3 1.0.2 
+pytest 3.6.0 
+python-dateutil 2.7.3 
+pytz 2018.4 
+pyzmq 17.0.0 
+qtconsole 4.3.1 
+scipy 1.1.0 
+Send2Trash 1.5.0 
+setuptools 28.8.0 
+simplegeneric 0.8.1 
+six 1.11.0 
+terminado 0.8.1 
+testpath 0.3.1 
+tornado 5.0.2 
+traitlets 4.3.2 
+typed-ast 1.1.0 
+utils 0.9.0 
+virtualenv 16.0.0 
+wcwidth 0.1.7 
+webencodings 0.5.1 
+widgetsnbextension 3.2.1 
+wrapt 1.10.11

simulation/helpers.py

@@ -46,11 +46,10 @@ def create_random_graph_distances(no_of_agents):
 
  distances = (nx.floyd_warshall_numpy(G)).tolist()
 
- print(nx.closeness_centrality(G))
-
+ print("Closeness centrality per agent: " + str(nx.closeness_centrality(G)))
 
  # print the random graph
- # nx.draw(G, with_labels=True)
+ nx.draw(G, with_labels=True)
  # plt.savefig('agent_graph.png')
 
  return distances

simulation/plotting.py

@@ -49,7 +49,7 @@ def print_graph(self):
  col.append(self.DG.node[transaction]["node_color"])
 
  #Creating figure
- plt.figure(figsize=(14, 8))
+ plt.figure(figsize=(14, 7))
  nx.draw_networkx(self.DG, pos, with_labels=True, node_size = 100, font_size=5.5, node_color = col)
  # nx.draw_networkx_labels(self.DG, lower_pos, labels=labels, font_size=6)
 
@@ -68,7 +68,7 @@ def print_graph(self):
 
 def print_tips_over_time(self):
 
- plt.figure(figsize=(14, 8))
+ plt.figure(figsize=(14, 7))
 
  #Get no of tips per time
  no_tips = []
@@ -106,7 +106,7 @@ def print_tips_over_time(self):
 
 def print_tips_over_time_multiple_agents_with_tangle(self, no_current_transactions):
 
- plt.figure(figsize=(14, 8))
+ plt.figure(figsize=(14, 7))
  plt.subplot(2, 1, 1)
 
  #Get no of tips per time
@@ -187,7 +187,7 @@ def print_tips_over_time_multiple_agents_with_tangle(self, no_current_transactio
 
 def print_tips_over_time_multiple_agents(self, no_current_transactions):
 
- plt.figure(figsize=(14, 8))
+ plt.figure(figsize=(14, 7))
 
  #Get no of tips per time
  for agent in self.agents:
@@ -241,7 +241,7 @@ def print_attachment_probabilities_alone(self):
  with open('subtangle_attach_prob.pkl', 'wb') as handle:
  pickle.dump(self.record_attachment_probabilities, handle, protocol=pickle.HIGHEST_PROTOCOL)
 
- plt.figure(figsize=(14, 8))
+ plt.figure(figsize=(14, 7))
 
  x = np.squeeze([i[0] for i in self.record_attachment_probabilities])
  y = np.squeeze([i[1] for i in self.record_attachment_probabilities])
@@ -299,15 +299,15 @@ def print_attachment_probabilities_all_agents(self):
 
  data = []
 
- for agent in range(10):
+ for agent in range(self.no_of_agents):
  agent_data = [i[1][agent] for i in self.record_attachment_probabilities]
  data.append(agent_data)
 
  plt.boxplot(data, 0, '+')
  plt.xlabel("Agents")
- plt.xticks(np.arange(1, 11), np.arange(0, 10))
+ plt.xticks(np.arange(1, self.no_of_agents+1), np.arange(0, self.no_of_agents))
  plt.suptitle(title)
  plt.tight_layout()
  plt.subplots_adjust(top=0.94)
- # plt.show()
+ plt.show()
  # plt.savefig(str(no) + '.png')

simulation/simulation_multi_agent.py

@@ -140,7 +140,7 @@ def run(self):
 
  #Do something every 100th transition
  if (transaction.id >= 0 and
- transaction.id % 200 == 0):
+ transaction.id % 100 == 0):
  self.record_attachment_probabilities.append((transaction.id,self.calc_attachment_probabilities(transaction)))
  # self.record_attachment_probabilities.append(self.calc_attachment_probabilities(transaction))
 
@@ -517,7 +517,7 @@ def calc_attachment_probabilities(self, incoming_transaction):
 
  # print(attachment_probabilities_without_main)
  # print(attachment_probabilities_all)
- return attachment_probabilities_without_main
+ return attachment_probabilities_all
 
  #Performs 100 random walks per agent to caluclate attachment probabilities
  def attachment_probabilities_2(self, incoming_transaction):

tests/test_basic.py

@@ -14,7 +14,7 @@
 
 class SimulationSetupAndRunTestSuite(unittest.TestCase):
  def setUp(self):
- self.simu = Multi_Agent_Simulation(100, 10, 2, 0.005, 1, distances, "weighted")
+ self.simu = Multi_Agent_Simulation(100, 50, 2, 0.1, 1, "weighted", _printing=True)
 
  def tearDown(self):
  pass
@@ -32,7 +32,7 @@ def test_simulation_run(self):
 
 class AfterSimulationWeightedRandomWalkTestSuite(unittest.TestCase):
  def setUp(self):
- self.simu = Multi_Agent_Simulation(100, 10, 2, 0.005, 1, distances, "weighted")
+ self.simu = Multi_Agent_Simulation(100, 50, 2, 0.1, 1, "weighted", _printing=True)
  self.simu.setup()
  self.simu.run()