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Merge branch 'refactor-imports'

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* remove leftover import in example
* Update quickstart tutorial
* Add gitlab-ci
* Added missing gexf for tests
* Upgrade to python3.7 and pandas 0.3.4 because pandas has dropped support for
  python 3.4 -> There are some API changes in pandas, and I've updated the code
  accordingly.
* Set pytest as the default test runner
* Update dockerignore
* Skip testing long examples (>1000 steps)
This commit is contained in:
J. Fernando Sánchez 2018-12-09 12:42:25 +01:00
commit 01cc8e9128
37 changed files with 82126 additions and 405 deletions
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**/soil_output
.*

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image: python:3.7
steps:
- build
- test
build:
stage: build
image:
name: gcr.io/kaniko-project/executor:debug
entrypoint: [""]
script:
- echo "{\"auths\":{\"$CI_REGISTRY\":{\"username\":\"$CI_REGISTRY_USER\",\"password\":\"$CI_REGISTRY_PASSWORD\"}}}" > /kaniko/.docker/config.json
- /kaniko/executor --context $CI_PROJECT_DIR --dockerfile $CI_PROJECT_DIR/Dockerfile --destination $CI_REGISTRY_IMAGE:$CI_COMMIT_TAG
only:
- tags
test:
script:
python setup.py test

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FROM python:3.4-onbuild FROM python:3.7
WORKDIR /usr/src/app
COPY test-requirements.txt requirements.txt /usr/src/app/
RUN pip install --no-cache-dir -r test-requirements.txt -r requirements.txt
COPY ./ /usr/src/app
RUN pip install '.[web]' RUN pip install '.[web]'

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test:
docker-compose exec dev python -m pytest -s -v
.PHONY: test

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services: services:
dev: dev:
build: . build: .
environment:
PYTHONDONTWRITEBYTECODE: 1
volumes: volumes:
- .:/usr/src/app - .:/usr/src/app
tty: true tty: true

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Configuring a simulation
------------------------
There are two ways to configure a simulation: programmatically and with a configuration file.
In both cases, the parameters used are the same.
The advantage of a configuration file is that it is a clean declarative description, and it makes it easier to reproduce.
Simulation configuration files can be formatted in ``json`` or ``yaml`` and they define all the parameters of a simulation.
Here's an example (``example.yml``).
.. code:: yaml
---
name: MyExampleSimulation
max_time: 50
num_trials: 3
interval: 2
network_params:
generator: barabasi_albert_graph
n: 100
m: 2
network_agents:
- agent_type: SISaModel
weight: 1
state:
id: content
- agent_type: SISaModel
weight: 1
state:
id: discontent
- agent_type: SISaModel
weight: 8
state:
id: neutral
environment_params:
prob_infect: 0.075
This example configuration will run three trials (``num_trials``) of a simulation containing a randomly generated network (``network_params``).
The 100 nodes in the network will be SISaModel agents (``network_agents.agent_type``), which is an agent behavior that is included in Soil.
10% of the agents (``weight=1``) will start in the content state, 10% in the discontent state, and the remaining 80% (``weight=8``) in the neutral state.
All agents will have access to the environment (``environment_params``), which only contains one variable, ``prob_infected``.
The state of the agents will be updated every 2 seconds (``interval``).
Now run the simulation with the command line tool:
.. code:: bash
soil example.yml
Once the simulation finishes, its results will be stored in a folder named ``MyExampleSimulation``.
Three types of objects are saved by default: a pickle of the simulation; a ``YAML`` representation of the simulation (which can be used to re-launch it); and for every trial, a ``sqlite`` file with the content of the state of every network node and the environment parameters at every step of the simulation.
.. code::
soil_output
└── MyExampleSimulation
├── MyExampleSimulation.dumped.yml
├── MyExampleSimulation.simulation.pickle
├── MyExampleSimulation_trial_0.db.sqlite
├── MyExampleSimulation_trial_1.db.sqlite
└── MyExampleSimulation_trial_2.db.sqlite
You may also ask soil to export the states in a ``csv`` file, and the network in gephi format (``gexf``).
Network
=======
The network topology for the simulation can be loaded from an existing network file or generated with one of the random network generation methods from networkx.
Loading a network
#################
To load an existing network, specify its path in the configuration:
.. code:: yaml
---
network_params:
path: /tmp/mynetwork.gexf
Soil will try to guess what networkx method to use to read the file based on its extension.
However, we only test using ``gexf`` files.
For simple networks, you may also include them in the configuration itself using , using the ``topology`` parameter like so:
.. code:: yaml
---
topology:
nodes:
- id: First
- id: Second
links:
- source: First
target: Second
Generating a random network
###########################
To generate a random network using one of networkx's built-in methods, specify the `graph generation algorithm <https://networkx.github.io/documentation/development/reference/generators.html>`_ and other parameters.
For example, the following configuration is equivalent to :code:`nx.complete_graph(n=100)`:
.. code:: yaml
network_params:
generator: complete_graph
n: 100
Environment
============
The environment is the place where the shared state of the simulation is stored.
For instance, the probability of disease outbreak.
The configuration file may specify the initial value of the environment parameters:
.. code:: yaml
environment_params:
daily_probability_of_earthquake: 0.001
number_of_earthquakes: 0
All agents have access to the environment parameters.
In some scenarios, it is useful to have a custom environment, to provide additional methods or to control the way agents update environment state.
For example, if our agents play the lottery, the environment could provide a method to decide whether the agent wins, instead of leaving it to the agent.
Agents
======
Agents are a way of modelling behavior.
Agents can be characterized with two variables: agent type (``agent_type``) and state.
Only one agent is executed at a time (generally, every ``interval`` seconds), and it has access to its state and the environment parameters.
Through the environment, it can access the network topology and the state of other agents.
There are three three types of agents according to how they are added to the simulation: network agents and environment agent.
Network Agents
##############
Network agents are attached to a node in the topology.
The configuration file allows you to specify how agents will be mapped to topology nodes.
The simplest way is to specify a single type of agent.
Hence, every node in the network will be associated to an agent of that type.
.. code:: yaml
agent_type: SISaModel
It is also possible to add more than one type of agent to the simulation, and to control the ratio of each type (using the ``weight`` property).
For instance, with following configuration, it is five times more likely for a node to be assigned a CounterModel type than a SISaModel type.
.. code:: yaml
network_agents:
- agent_type: SISaModel
weight: 1
- agent_type: CounterModel
weight: 5
The third option is to specify the type of agent on the node itself, e.g.:
.. code:: yaml
topology:
nodes:
- id: first
agent_type: BaseAgent
states:
first:
agent_type: SISaModel
This would also work with a randomly generated network:
.. code:: yaml
network:
generator: complete
n: 5
agent_type: BaseAgent
states:
- agent_type: SISaModel
In addition to agent type, you may add a custom initial state to the distribution.
This is very useful to add the same agent type with different states.
e.g., to populate the network with SISaModel, roughly 10% of them with a discontent state:
.. code:: yaml
network_agents:
- agent_type: SISaModel
weight: 9
state:
id: neutral
- agent_type: SISaModel
weight: 1
state:
id: discontent
Lastly, the configuration may include initial state for one or more nodes.
For instance, to add a state for the two nodes in this configuration:
.. code:: yaml
agent_type: SISaModel
network:
generator: complete_graph
n: 2
states:
- id: content
- id: discontent
Or to add state only to specific nodes (by ``id``).
For example, to apply special skills to Linux Torvalds in a simulation:
.. literalinclude:: ../examples/torvalds.yml
:language: yaml
Environment Agents
##################
In addition to network agents, more agents can be added to the simulation.
These agents are programmed in much the same way as network agents, the only difference is that they will not be assigned to network nodes.
.. code::
environment_agents:
- agent_type: MyAgent
state:
mood: happy
- agent_type: DummyAgent
You may use environment agents to model events that a normal agent cannot control, such as natural disasters or chance.
They are also useful to add behavior that has little to do with the network and the interactions within that network.

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Welcome to Soil's documentation! Welcome to Soil's documentation!
================================ ================================
Soil is an Agent-based Social Simulator in Python for modelling and simulation of Social Networks. Soil is an Agent-based Social Simulator in Python focused on Social Networks.
If you use Soil in your research, do not forget to cite this paper: If you use Soil in your research, do not forget to cite this paper:
@ -39,6 +39,7 @@ If you use Soil in your research, do not forget to cite this paper:
installation installation
quickstart quickstart
configuration
Tutorial <soil_tutorial> Tutorial <soil_tutorial>
.. ..

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Quickstart Quickstart
---------- ----------
This section shows how to run simulations from simulation configuration files. This section shows how to run your first simulation with Soil.
First of all, you need to install the package (See :doc:`installation`) For installation instructions, see :doc:`installation`.
Simulation configuration files are ``json`` or ``yaml`` files that define all the parameters of a simulation. There are mainly two parts in a simulation: agent classes and simulation configuration.
Here's an example (``example.yml``). An agent class defines how the agent will behave throughout the simulation.
The configuration includes things such as number of agents to use and their type, network topology to use, etc.
.. code:: yaml
---
name: MyExampleSimulation
max_time: 50
num_trials: 3
interval: 2
network_params:
network_type: barabasi_albert_graph
n: 100
m: 2
agent_distribution:
- agent_type: SISaModel
weight: 1
state:
id: content
- agent_type: SISaModel
weight: 1
state:
id: discontent
- agent_type: SISaModel
weight: 8
state:
id: neutral
environment_params:
prob_infect: 0.075
This example configuration will run three trials of a simulation containing a randomly generated network. .. image:: soil.png
The 100 nodes in the network will be SISaModel agents, 10% of them will start in the content state, 10% in the discontent state, and the remaining 80% in the neutral state. :width: 80%
All agents will have access to the environment, which only contains one variable, ``prob_infected``. :align: center
The state of the agents will be updated every 2 seconds (``interval``).
Now run the simulation with the command line tool:
.. code:: bash
soil example.yml
Once the simulation finishes, its results will be stored in a folder named ``MyExampleSimulation``.
Four types of objects are saved by default: a pickle of the simulation; a ``YAML`` representation of the simulation (which can be used to re-launch it); and for every trial, a csv file with the content of the state of every network node and the environment parameters at every step of the simulation, as well as the network in gephi format (``gexf``).
.. code:: Soil includes several agent classes in the ``soil.agents`` module, and we will use them in this quickstart.
If you are interested in developing your own agents classes, see :doc:`soil_tutorial`.
The configuration is the following:
soil_output .. literalinclude:: quickstart.yml
├── Sim_prob_0
│   ├── Sim_prob_0.dumped.yml
│   ├── Sim_prob_0.simulation.pickle
│   ├── Sim_prob_0_trial_0.environment.csv
│   └── Sim_prob_0_trial_0.gexf
Network
=======
The network topology for the simulation can be loaded from an existing network file or generated with one of the random network generation methods from networkx.
Loading a network
#################
To load an existing network, specify its path in the configuration:
.. code:: yaml
---
network_params:
path: /tmp/mynetwork.gexf
Soil will try to guess what networkx method to use to read the file based on its extension.
However, we only test using ``gexf`` files.
Generating a random network
###########################
To generate a random network using one of networkx's built-in methods, specify the `graph generation algorithm <https://networkx.github.io/documentation/development/reference/generators.html>`_ and other parameters.
For example, the following configuration is equivalent to :code:`nx.complete_graph(100)`:
.. code:: yaml
network_params:
network_type: complete_graph
n: 100
Environment
============
The environment is the place where the shared state of the simulation is stored.
For instance, the probability of disease outbreak.
The configuration file may specify the initial value of the environment parameters:
.. code:: yaml
environment_params:
daily_probability_of_earthquake: 0.001
number_of_earthquakes: 0
Any agent has unrestricted access to the environment.
However, for the sake of simplicity, we recommend limiting environment updates to environment agents.
Agents
======
Agents are a way of modelling behavior.
Agents can be characterized with two variables: an agent type (``agent_type``) and its state.
Only one agent is executed at a time (generally, every ``interval`` seconds), and it has access to its state and the environment parameters.
Through the environment, it can access the network topology and the state of other agents.
There are three three types of agents according to how they are added to the simulation: network agents and environment agent.
Network Agents
##############
Network agents are attached to a node in the topology.
The configuration file allows you to specify how agents will be mapped to topology nodes.
The simplest way is to specify a single type of agent.
Hence, every node in the network will be associated to an agent of that type.
.. code:: yaml
agent_type: SISaModel
It is also possible to add more than one type of agent to the simulation, and to control the ratio of each type (using the ``weight`` property).
For instance, with following configuration, it is five times more likely for a node to be assigned a CounterModel type than a SISaModel type.
.. code:: yaml
agent_distribution:
- agent_type: SISaModel
weight: 1
- agent_type: CounterModel
weight: 5
In addition to agent type, you may also add a custom initial state to the distribution.
This is very useful to add the same agent type with different states.
e.g., to populate the network with SISaModel, roughly 10% of them with a discontent state:
.. code:: yaml
agent_distribution:
- agent_type: SISaModel
weight: 9
state:
id: neutral
- agent_type: SISaModel
weight: 1
state:
id: discontent
Lastly, the configuration may include initial state for one or more nodes.
For instance, to add a state for the two nodes in this configuration:
.. code:: yaml
agent_type: SISaModel
network:
network_type: complete_graph
n: 2
states:
- id: content
- id: discontent
Or to add state only to specific nodes (by ``id``).
For example, to apply special skills to Linux Torvalds in a simulation:
.. literalinclude:: ../examples/torvalds.yml
:language: yaml :language: yaml
Configuration
=============
Environment Agents You may :download:`download the file <quickstart.yml>` directly.
################## The agent type used, SISa, is a very simple model.
In addition to network agents, more agents can be added to the simulation. It only has three states (neutral, content and discontent),
These agens are programmed in much the same way as network agents, the only difference is that they will not be assigned to network nodes. Its parameters are the probabilities to change from one state to another, either spontaneously or because of contagion from neighboring agents.
Running the simulation
======================
To see the simulation in action, simply point soil to the configuration, and tell it to store the graph and the history of agent states and environment parameters at every point.
.. code:: .. code::
environment_agents: ❯ soil --graph --csv quickstart.yml [13:35:29]
- agent_type: MyAgent INFO:soil:Using config(s): quickstart
state: INFO:soil:Dumping results to soil_output/quickstart : ['csv', 'gexf']
mood: happy INFO:soil:Starting simulation quickstart at 13:35:30.
- agent_type: DummyAgent INFO:soil:Starting Simulation quickstart trial 0 at 13:35:30.
INFO:soil:Finished Simulation quickstart trial 0 at 13:35:49 in 19.43677067756653 seconds
INFO:soil:Starting Dumping simulation quickstart trial 0 at 13:35:49.
INFO:soil:Finished Dumping simulation quickstart trial 0 at 13:35:51 in 1.7733407020568848 seconds
INFO:soil:Dumping results to soil_output/quickstart
INFO:soil:Finished simulation quickstart at 13:35:51 in 21.29862952232361 seconds
Visualizing the results The ``CSV`` file should look like this:
=======================
The simulation will return a dynamic graph .gexf file which could be visualized with .. code::
agent_id,t_step,key,value
env,0,neutral_discontent_spon_prob,0.05
env,0,neutral_discontent_infected_prob,0.1
env,0,neutral_content_spon_prob,0.2
env,0,neutral_content_infected_prob,0.4
env,0,discontent_neutral,0.2
env,0,discontent_content,0.05
env,0,content_discontent,0.05
env,0,variance_d_c,0.05
env,0,variance_c_d,0.1
Results and visualization
=========================
The environment variables are marked as ``agent_id`` env.
Th exported values are only stored when they change.
To find out how to get every key and value at every point in the simulation, check out the :doc:`soil_tutorial`.
The dynamic graph is exported as a .gexf file which could be visualized with
`Gephi <https://gephi.org/users/download/>`__. `Gephi <https://gephi.org/users/download/>`__.
Now it is your turn to experiment with the simulation.
Change some of the parameters, such as the number of agents, the probability of becoming content, or the type of network, and see how the results change.
Soil also includes a web server that allows you to upload your simulations, change parameters, and visualize the results, including a timeline of the network.
To make it work, you have to install soil like this:
```
pip install soil[web]
```
Once installed, the soil web UI can be run in two ways:
```
soil-web
OR
python -m soil.web
```

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---
name: quickstart
num_trials: 1
max_time: 1000
network_agents:
- agent_type: SISaModel
state:
id: neutral
weight: 1
- agent_type: SISaModel
state:
id: content
weight: 2
network_params:
n: 100
k: 5
p: 0.2
generator: newman_watts_strogatz_graph
environment_params:
neutral_discontent_spon_prob: 0.05
neutral_discontent_infected_prob: 0.1
neutral_content_spon_prob: 0.2
neutral_content_infected_prob: 0.4
discontent_neutral: 0.2
discontent_content: 0.05
content_discontent: 0.05
variance_d_c: 0.05
variance_c_d: 0.1
content_neutral: 0.1
standard_variance: 0.1

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@ -214,7 +214,7 @@ nodes in that network. Notice how node 0 is the only one with a TV.
MAX_TIME = 100 MAX_TIME = 100
EVENT_TIME = 10 EVENT_TIME = 10
sim = soil.simulation.SoilSimulation(topology=G, sim = soil.Simulation(topology=G,
num_trials=1, num_trials=1,
max_time=MAX_TIME, max_time=MAX_TIME,
environment_agents=[{'agent_type': NewsEnvironmentAgent, environment_agents=[{'agent_type': NewsEnvironmentAgent,

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@ -2,14 +2,22 @@
"cells": [ "cells": [
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": 1,
"metadata": { "metadata": {
"ExecuteTime": { "ExecuteTime": {
"start_time": "2017-11-02T09:48:41.843Z" "start_time": "2017-11-02T09:48:41.843Z"
}, },
"scrolled": false "scrolled": false
}, },
"outputs": [], "outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Populating the interactive namespace from numpy and matplotlib\n"
]
}
],
"source": [ "source": [
"import soil\n", "import soil\n",
"import networkx as nx\n", "import networkx as nx\n",
@ -39,26 +47,216 @@
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"total 288K\r\n",
"drwxr-xr-x 7 j users 4.0K May 23 12:48 .\r\n",
"drwxr-xr-x 15 j users 20K May 7 18:59 ..\r\n",
"-rw-r--r-- 1 j users 451 Oct 17 2017 complete.yml\r\n",
"drwxr-xr-x 2 j users 4.0K Feb 18 11:22 .ipynb_checkpoints\r\n",
"drwxr-xr-x 2 j users 4.0K Oct 17 2017 long_running\r\n",
"-rw-r--r-- 1 j users 1.2K May 23 12:49 .nbgrader.log\r\n",
"drwxr-xr-x 4 j users 4.0K May 4 11:23 newsspread\r\n",
"-rw-r--r-- 1 j users 225K May 4 11:23 NewsSpread.ipynb\r\n",
"drwxr-xr-x 4 j users 4.0K May 4 11:21 rabbits\r\n",
"-rw-r--r-- 1 j users 42 Jul 3 2017 torvalds.edgelist\r\n",
"-rw-r--r-- 1 j users 245 Oct 13 2017 torvalds.yml\r\n",
"drwxr-xr-x 4 j users 4.0K May 4 11:23 tutorial\r\n"
]
}
],
"source": [
"!ls "
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": { "metadata": {
"ExecuteTime": { "ExecuteTime": {
"start_time": "2017-11-02T09:48:43.440Z" "start_time": "2017-11-02T09:48:43.440Z"
} }
}, },
"outputs": [], "outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"---\r\n",
"default_state: {}\r\n",
"load_module: newsspread\r\n",
"environment_agents: []\r\n",
"environment_params:\r\n",
" prob_neighbor_spread: 0.0\r\n",
" prob_tv_spread: 0.01\r\n",
"interval: 1\r\n",
"max_time: 30\r\n",
"name: Sim_all_dumb\r\n",
"network_agents:\r\n",
"- agent_type: DumbViewer\r\n",
" state:\r\n",
" has_tv: false\r\n",
" weight: 1\r\n",
"- agent_type: DumbViewer\r\n",
" state:\r\n",
" has_tv: true\r\n",
" weight: 1\r\n",
"network_params:\r\n",
" generator: barabasi_albert_graph\r\n",
" n: 500\r\n",
" m: 5\r\n",
"num_trials: 50\r\n",
"---\r\n",
"default_state: {}\r\n",
"load_module: newsspread\r\n",
"environment_agents: []\r\n",
"environment_params:\r\n",
" prob_neighbor_spread: 0.0\r\n",
" prob_tv_spread: 0.01\r\n",
"interval: 1\r\n",
"max_time: 30\r\n",
"name: Sim_half_herd\r\n",
"network_agents:\r\n",
"- agent_type: DumbViewer\r\n",
" state:\r\n",
" has_tv: false\r\n",
" weight: 1\r\n",
"- agent_type: DumbViewer\r\n",
" state:\r\n",
" has_tv: true\r\n",
" weight: 1\r\n",
"- agent_type: HerdViewer\r\n",
" state:\r\n",
" has_tv: false\r\n",
" weight: 1\r\n",
"- agent_type: HerdViewer\r\n",
" state:\r\n",
" has_tv: true\r\n",
" weight: 1\r\n",
"network_params:\r\n",
" generator: barabasi_albert_graph\r\n",
" n: 500\r\n",
" m: 5\r\n",
"num_trials: 50\r\n",
"---\r\n",
"default_state: {}\r\n",
"load_module: newsspread\r\n",
"environment_agents: []\r\n",
"environment_params:\r\n",
" prob_neighbor_spread: 0.0\r\n",
" prob_tv_spread: 0.01\r\n",
"interval: 1\r\n",
"max_time: 30\r\n",
"name: Sim_all_herd\r\n",
"network_agents:\r\n",
"- agent_type: HerdViewer\r\n",
" state:\r\n",
" has_tv: true\r\n",
" id: neutral\r\n",
" weight: 1\r\n",
"- agent_type: HerdViewer\r\n",
" state:\r\n",
" has_tv: true\r\n",
" id: neutral\r\n",
" weight: 1\r\n",
"network_params:\r\n",
" generator: barabasi_albert_graph\r\n",
" n: 500\r\n",
" m: 5\r\n",
"num_trials: 50\r\n",
"---\r\n",
"default_state: {}\r\n",
"load_module: newsspread\r\n",
"environment_agents: []\r\n",
"environment_params:\r\n",
" prob_neighbor_spread: 0.0\r\n",
" prob_tv_spread: 0.01\r\n",
" prob_neighbor_cure: 0.1\r\n",
"interval: 1\r\n",
"max_time: 30\r\n",
"name: Sim_wise_herd\r\n",
"network_agents:\r\n",
"- agent_type: HerdViewer\r\n",
" state:\r\n",
" has_tv: true\r\n",
" id: neutral\r\n",
" weight: 1\r\n",
"- agent_type: WiseViewer\r\n",
" state:\r\n",
" has_tv: true\r\n",
" weight: 1\r\n",
"network_params:\r\n",
" generator: barabasi_albert_graph\r\n",
" n: 500\r\n",
" m: 5\r\n",
"num_trials: 50\r\n",
"---\r\n",
"default_state: {}\r\n",
"load_module: newsspread\r\n",
"environment_agents: []\r\n",
"environment_params:\r\n",
" prob_neighbor_spread: 0.0\r\n",
" prob_tv_spread: 0.01\r\n",
" prob_neighbor_cure: 0.1\r\n",
"interval: 1\r\n",
"max_time: 30\r\n",
"name: Sim_all_wise\r\n",
"network_agents:\r\n",
"- agent_type: WiseViewer\r\n",
" state:\r\n",
" has_tv: true\r\n",
" id: neutral\r\n",
" weight: 1\r\n",
"- agent_type: WiseViewer\r\n",
" state:\r\n",
" has_tv: true\r\n",
" weight: 1\r\n",
"network_params:\r\n",
" generator: barabasi_albert_graph\r\n",
" n: 500\r\n",
" m: 5\r\n",
"network_params:\r\n",
" generator: barabasi_albert_graph\r\n",
" n: 500\r\n",
" m: 5\r\n",
"num_trials: 50\r\n"
]
}
],
"source": [ "source": [
"!cat NewsSpread.yml" "!cat newsspread/NewsSpread.yml"
] ]
}, },
{ {
"cell_type": "code", "cell_type": "code",
"execution_count": null, "execution_count": 10,
"metadata": { "metadata": {
"ExecuteTime": { "ExecuteTime": {
"start_time": "2017-11-02T09:48:43.879Z" "start_time": "2017-11-02T09:48:43.879Z"
} }
}, },
"outputs": [], "outputs": [
{
"ename": "ValueError",
"evalue": "No objects to concatenate",
"output_type": "error",
"traceback": [
"\u001b[0;31m----------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-10-bae848826594>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mevodumb\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0manalysis\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread_data\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'soil_output/Sim_all_dumb/'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mgroup\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mprocess\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0manalysis\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_count\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkeys\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'id'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m;\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/git/lab.gsi/soil/soil/soil/analysis.py\u001b[0m in \u001b[0;36mread_data\u001b[0;34m(group, *args, **kwargs)\u001b[0m\n\u001b[1;32m 11\u001b[0m \u001b[0miterable\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_read_data\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 12\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mgroup\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 13\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mgroup_trials\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0miterable\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 14\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 15\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0miterable\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/git/lab.gsi/soil/soil/soil/analysis.py\u001b[0m in \u001b[0;36mgroup_trials\u001b[0;34m(trials, aggfunc)\u001b[0m\n\u001b[1;32m 159\u001b[0m \u001b[0mtrials\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtrials\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 160\u001b[0m \u001b[0mtrials\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlist\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmap\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;32mlambda\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtuple\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32melse\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtrials\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 161\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mpd\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconcat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtrials\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgroupby\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlevel\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0magg\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0maggfunc\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mreorder_levels\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m2\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m,\u001b[0m\u001b[0maxis\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 162\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 163\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/.local/lib/python3.6/site-packages/pandas/core/reshape/concat.py\u001b[0m in \u001b[0;36mconcat\u001b[0;34m(objs, axis, join, join_axes, ignore_index, keys, levels, names, verify_integrity, copy)\u001b[0m\n\u001b[1;32m 210\u001b[0m \u001b[0mkeys\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mkeys\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mlevels\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mlevels\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnames\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mnames\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 211\u001b[0m \u001b[0mverify_integrity\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mverify_integrity\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 212\u001b[0;31m copy=copy)\n\u001b[0m\u001b[1;32m 213\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mop\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_result\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 214\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/.local/lib/python3.6/site-packages/pandas/core/reshape/concat.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, objs, axis, join, join_axes, keys, levels, names, ignore_index, verify_integrity, copy)\u001b[0m\n\u001b[1;32m 243\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 244\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mobjs\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 245\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mValueError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'No objects to concatenate'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 246\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 247\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mkeys\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mValueError\u001b[0m: No objects to concatenate"
]
}
],
"source": [ "source": [
"evodumb = analysis.read_data('soil_output/Sim_all_dumb/', group=True, process=analysis.get_count, keys=['id']);" "evodumb = analysis.read_data('soil_output/Sim_all_dumb/', group=True, process=analysis.get_count, keys=['id']);"
] ]
@ -302,7 +500,7 @@
"name": "python", "name": "python",
"nbconvert_exporter": "python", "nbconvert_exporter": "python",
"pygments_lexer": "ipython3", "pygments_lexer": "ipython3",
"version": "3.6.2" "version": "3.6.5"
}, },
"toc": { "toc": {
"colors": { "colors": {

80808
examples/Untitled.ipynb Normal file
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File diff suppressed because it is too large Load Diff

2
examples/complete.yml
View File

@ -2,6 +2,7 @@
name: simple name: simple
dir_path: "/tmp/" dir_path: "/tmp/"
num_trials: 3 num_trials: 3
dry_run: True
max_time: 100 max_time: 100
interval: 1 interval: 1
seed: "CompleteSeed!" seed: "CompleteSeed!"
@ -17,6 +18,7 @@ network_agents:
- agent_type: AggregatedCounter - agent_type: AggregatedCounter
weight: 0.2 weight: 0.2
environment_agents: [] environment_agents: []
environment_class: Environment
environment_params: environment_params:
am_i_complete: true am_i_complete: true
default_state: default_state:

10
examples/pubcrawl/README.md Normal file
View File

@ -0,0 +1,10 @@
Simulation of pubs and drinking pals that go from pub to pub.
Th custom environment includes a list of pubs and methods to allow agents to discover and enter pubs.
There are two types of agents:
* Patron. A patron will do three things, in this order:
* Look for other patrons to drink with
* Look for a pub where the agent and other agents in the same group can get in.
* While in the pub, patrons only drink, until they get drunk and taken home.
* Police. There is only one police agent that will take any drunk patrons home (kick them out of the pub).

174
examples/pubcrawl/pubcrawl.py Normal file
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@ -0,0 +1,174 @@
from soil.agents import FSM, state, default_state
from soil import Environment
from random import random, shuffle
from itertools import islice
import logging
class CityPubs(Environment):
'''Environment with Pubs'''
level = logging.INFO
def __init__(self, *args, number_of_pubs=3, pub_capacity=10, **kwargs):
super(CityPubs, self).__init__(*args, **kwargs)
pubs = {}
for i in range(number_of_pubs):
newpub = {
'name': 'The awesome pub #{}'.format(i),
'open': True,
'capacity': pub_capacity,
'occupancy': 0,
}
pubs[newpub['name']] = newpub
self['pubs'] = pubs
def enter(self, pub_id, *nodes):
'''Agents will try to enter. The pub checks if it is possible'''
try:
pub = self['pubs'][pub_id]
except KeyError:
raise ValueError('Pub {} is not available'.format(pub_id))
if not pub['open'] or (pub['capacity'] < (len(nodes) + pub['occupancy'])):
return False
pub['occupancy'] += len(nodes)
for node in nodes:
node['pub'] = pub_id
return True
def available_pubs(self):
for pub in self['pubs'].values():
if pub['open'] and (pub['occupancy'] < pub['capacity']):
yield pub['name']
def exit(self, pub_id, *node_ids):
'''Agents will notify the pub they want to leave'''
try:
pub = self['pubs'][pub_id]
except KeyError:
raise ValueError('Pub {} is not available'.format(pub_id))
for node_id in node_ids:
node = self.get_agent(node_id)
if pub_id == node['pub']:
del node['pub']
pub['occupancy'] -= 1
class Patron(FSM):
'''Agent that looks for friends to drink with. It will do three things:
1) Look for other patrons to drink with
2) Look for a bar where the agent and other agents in the same group can get in.
3) While in the bar, patrons only drink, until they get drunk and taken home.
'''
level = logging.INFO
defaults = {
'pub': None,
'drunk': False,
'pints': 0,
'max_pints': 3,
}
@default_state
@state
def looking_for_friends(self):
'''Look for friends to drink with'''
self.info('I am looking for friends')
available_friends = list(self.get_agents(drunk=False,
pub=None,
state_id=self.looking_for_friends.id))
if not available_friends:
self.info('Life sucks and I\'m alone!')
return self.at_home
befriended = self.try_friends(available_friends)
if befriended:
return self.looking_for_pub
@state
def looking_for_pub(self):
'''Look for a pub that accepts me and my friends'''
if self['pub'] != None:
return self.sober_in_pub
self.debug('I am looking for a pub')
group = list(self.get_neighboring_agents())
for pub in self.env.available_pubs():
self.debug('We\'re trying to get into {}: total: {}'.format(pub, len(group)))
if self.env.enter(pub, self, *group):
self.info('We\'re all {} getting in {}!'.format(len(group), pub))
return self.sober_in_pub
@state
def sober_in_pub(self):
'''Drink up.'''
self.drink()
if self['pints'] > self['max_pints']:
return self.drunk_in_pub
@state
def drunk_in_pub(self):
'''I'm out. Take me home!'''
self.info('I\'m so drunk. Take me home!')
self['drunk'] = True
pass # out drunk
@state
def at_home(self):
'''The end'''
self.debug('Life sucks. I\'m home!')
def drink(self):
self['pints'] += 1
self.debug('Cheers to that')
def kick_out(self):
self.set_state(self.at_home)
def befriend(self, other_agent, force=False):
'''
Try to become friends with another agent. The chances of
success depend on both agents' openness.
'''
if force or self['openness'] > random():
self.env.add_edge(self, other_agent)
self.info('Made some friend {}'.format(other_agent))
return True
return False
def try_friends(self, others):
''' Look for random agents around me and try to befriend them'''
befriended = False
k = int(10*self['openness'])
shuffle(others)
for friend in islice(others, k): # random.choice >= 3.7
if friend == self:
continue
if friend.befriend(self):
self.befriend(friend, force=True)
self.debug('Hooray! new friend: {}'.format(friend.id))
befriended = True
else:
self.debug('{} does not want to be friends'.format(friend.id))
return befriended
class Police(FSM):
'''Simple agent to take drunk people out of pubs.'''
level = logging.INFO
@default_state
@state
def patrol(self):
drunksters = list(self.get_agents(drunk=True,
state_id=Patron.drunk_in_pub.id))
for drunk in drunksters:
self.info('Kicking out the trash: {}'.format(drunk.id))
drunk.kick_out()
else:
self.info('No trash to take out. Too bad.')
if __name__ == '__main__':
from soil import simulation
simulation.run_from_config('pubcrawl.yml',
dry_run=True,
dump=None,
parallel=False)

26
examples/pubcrawl/pubcrawl.yml Normal file
View File

@ -0,0 +1,26 @@
---
name: pubcrawl
num_trials: 3
max_time: 10
dump: false
network_params:
# Generate 100 empty nodes. They will be assigned a network agent
generator: empty_graph
n: 30
network_agents:
- agent_type: pubcrawl.Patron
description: Extroverted patron
state:
openness: 1.0
weight: 9
- agent_type: pubcrawl.Patron
description: Introverted patron
state:
openness: 0.1
weight: 1
environment_agents:
- agent_type: pubcrawl.Police
environment_class: pubcrawl.CityPubs
environment_params:
altercations: 0
number_of_pubs: 3

2
examples/rabbits/rabbits.yml
View File

@ -1,7 +1,7 @@
--- ---
load_module: rabbit_agents load_module: rabbit_agents
name: rabbits_example name: rabbits_example
max_time: 1200 max_time: 500
interval: 1 interval: 1
seed: MySeed seed: MySeed
agent_type: RabbitModel agent_type: RabbitModel

2
examples/tutorial/soil_tutorial.html
View File

@ -12327,7 +12327,7 @@ Notice how node 0 is the only one with a TV.</p>
<span class="n">MAX_TIME</span> <span class="o">=</span> <span class="mi">100</span> <span class="n">MAX_TIME</span> <span class="o">=</span> <span class="mi">100</span>
<span class="n">EVENT_TIME</span> <span class="o">=</span> <span class="mi">10</span> <span class="n">EVENT_TIME</span> <span class="o">=</span> <span class="mi">10</span>
<span class="n">sim</span> <span class="o">=</span> <span class="n">soil</span><span class="o">.</span><span class="n">simulation</span><span class="o">.</span><span class="n">SoilSimulation</span><span class="p">(</span><span class="n">topology</span><span class="o">=</span><span class="n">G</span><span class="p">,</span> <span class="n">sim</span> <span class="o">=</span> <span class="n">soil</span><span class="o">.</span><span class="n">Simulation</span><span class="p">(</span><span class="n">topology</span><span class="o">=</span><span class="n">G</span><span class="p">,</span>
<span class="n">num_trials</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">num_trials</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span>
<span class="n">max_time</span><span class="o">=</span><span class="n">MAX_TIME</span><span class="p">,</span> <span class="n">max_time</span><span class="o">=</span><span class="n">MAX_TIME</span><span class="p">,</span>
<span class="n">environment_agents</span><span class="o">=</span><span class="p">[{</span><span class="s1">&#39;agent_type&#39;</span><span class="p">:</span> <span class="n">NewsEnvironmentAgent</span><span class="p">,</span> <span class="n">environment_agents</span><span class="o">=</span><span class="p">[{</span><span class="s1">&#39;agent_type&#39;</span><span class="p">:</span> <span class="n">NewsEnvironmentAgent</span><span class="p">,</span>

2
examples/tutorial/soil_tutorial.ipynb
View File

@ -426,7 +426,7 @@
"MAX_TIME = 100\n", "MAX_TIME = 100\n",
"EVENT_TIME = 10\n", "EVENT_TIME = 10\n",
"\n", "\n",
"sim = soil.simulation.SoilSimulation(topology=G,\n", "sim = soil.Simulation(topology=G,\n",
" num_trials=1,\n", " num_trials=1,\n",
" max_time=MAX_TIME,\n", " max_time=MAX_TIME,\n",
" environment_agents=[{'agent_type': NewsEnvironmentAgent,\n", " environment_agents=[{'agent_type': NewsEnvironmentAgent,\n",

4
setup.cfg Normal file
View File

@ -0,0 +1,4 @@
[aliases]
test=pytest
[tool:pytest]
addopts = --verbose

2
soil/VERSION
View File

@ -1 +1 @@
0.12.0 0.13.0

12
soil/__init__.py
View File

@ -14,12 +14,11 @@ except NameError:
logging.basicConfig() logging.basicConfig()
from . import agents from . import agents
from . import simulation from .simulation import *
from . import environment from .environment import Environment
from . import utils from . import utils
from . import analysis from . import analysis
def main(): def main():
import argparse import argparse
from . import simulation from . import simulation
@ -46,11 +45,12 @@ def main():
args = parser.parse_args() args = parser.parse_args()
if args.module: if os.getcwd() not in sys.path:
sys.path.append(os.getcwd()) sys.path.append(os.getcwd())
if args.module:
importlib.import_module(args.module) importlib.import_module(args.module)
logging.info('Loading config file: {}'.format(args.file, args.output)) logging.info('Loading config file: {}'.format(args.file))
try: try:
dump = [] dump = []
@ -64,7 +64,7 @@ def main():
dump=dump, dump=dump,
parallel=(not args.synchronous and not args.pdb), parallel=(not args.synchronous and not args.pdb),
results_dir=args.output) results_dir=args.output)
except Exception as ex: except Exception:
if args.pdb: if args.pdb:
pdb.post_mortem() pdb.post_mortem()
else: else:

36
soil/agents/SISaModel.py
View File

@ -10,7 +10,7 @@ class SISaModel(FSM):
neutral_discontent_infected_prob neutral_discontent_infected_prob
neutral_content_spong_prob neutral_content_spon_prob
neutral_content_infected_prob neutral_content_infected_prob
@ -29,27 +29,27 @@ class SISaModel(FSM):
standard_variance standard_variance
""" """
def __init__(self, environment=None, agent_id=0, state=()): def __init__(self, environment, agent_id=0, state=()):
super().__init__(environment=environment, agent_id=agent_id, state=state) super().__init__(environment=environment, agent_id=agent_id, state=state)
self.neutral_discontent_spon_prob = np.random.normal(environment.environment_params['neutral_discontent_spon_prob'], self.neutral_discontent_spon_prob = np.random.normal(self.env['neutral_discontent_spon_prob'],
environment.environment_params['standard_variance']) self.env['standard_variance'])
self.neutral_discontent_infected_prob = np.random.normal(environment.environment_params['neutral_discontent_infected_prob'], self.neutral_discontent_infected_prob = np.random.normal(self.env['neutral_discontent_infected_prob'],
environment.environment_params['standard_variance']) self.env['standard_variance'])
self.neutral_content_spon_prob = np.random.normal(environment.environment_params['neutral_content_spon_prob'], self.neutral_content_spon_prob = np.random.normal(self.env['neutral_content_spon_prob'],
environment.environment_params['standard_variance']) self.env['standard_variance'])
self.neutral_content_infected_prob = np.random.normal(environment.environment_params['neutral_content_infected_prob'], self.neutral_content_infected_prob = np.random.normal(self.env['neutral_content_infected_prob'],
environment.environment_params['standard_variance']) self.env['standard_variance'])
self.discontent_neutral = np.random.normal(environment.environment_params['discontent_neutral'], self.discontent_neutral = np.random.normal(self.env['discontent_neutral'],
environment.environment_params['standard_variance']) self.env['standard_variance'])
self.discontent_content = np.random.normal(environment.environment_params['discontent_content'], self.discontent_content = np.random.normal(self.env['discontent_content'],
environment.environment_params['variance_d_c']) self.env['variance_d_c'])
self.content_discontent = np.random.normal(environment.environment_params['content_discontent'], self.content_discontent = np.random.normal(self.env['content_discontent'],
environment.environment_params['variance_c_d']) self.env['variance_c_d'])
self.content_neutral = np.random.normal(environment.environment_params['content_neutral'], self.content_neutral = np.random.normal(self.env['content_neutral'],
environment.environment_params['standard_variance']) self.env['standard_variance'])
@state @state
def neutral(self): def neutral(self):

2
soil/agents/SentimentCorrelationModel.py
View File

@ -16,7 +16,7 @@ class SentimentCorrelationModel(BaseAgent):
disgust_prob disgust_prob
""" """
def __init__(self, environment=None, agent_id=0, state=()): def __init__(self, environment, agent_id=0, state=()):
super().__init__(environment=environment, agent_id=agent_id, state=state) super().__init__(environment=environment, agent_id=agent_id, state=state)
self.outside_effects_prob = environment.environment_params['outside_effects_prob'] self.outside_effects_prob = environment.environment_params['outside_effects_prob']
self.anger_prob = environment.environment_params['anger_prob'] self.anger_prob = environment.environment_params['anger_prob']

68
soil/agents/__init__.py
View File

@ -16,23 +16,15 @@ from functools import wraps
from .. import utils, history from .. import utils, history
agent_types = {}
class BaseAgent(nxsim.BaseAgent):
class MetaAgent(type):
def __init__(cls, name, bases, nmspc):
super(MetaAgent, cls).__init__(name, bases, nmspc)
agent_types[name] = cls
class BaseAgent(nxsim.BaseAgent, metaclass=MetaAgent):
""" """
A special simpy BaseAgent that keeps track of its state history. A special simpy BaseAgent that keeps track of its state history.
""" """
defaults = {} defaults = {}
def __init__(self, environment=None, agent_id=None, state=None, def __init__(self, environment, agent_id=None, state=None,
name='network_process', interval=None, **state_params): name='network_process', interval=None, **state_params):
# Check for REQUIRED arguments # Check for REQUIRED arguments
assert environment is not None, TypeError('__init__ missing 1 required keyword argument: \'environment\'. ' assert environment is not None, TypeError('__init__ missing 1 required keyword argument: \'environment\'. '
@ -152,14 +144,18 @@ class BaseAgent(nxsim.BaseAgent, metaclass=MetaAgent):
def count_neighboring_agents(self, state_id=None): def count_neighboring_agents(self, state_id=None):
return len(super().get_agents(state_id, limit_neighbors=True)) return len(super().get_agents(state_id, limit_neighbors=True))
def get_agents(self, state_id=None, limit_neighbors=False, iterator=False, **kwargs): def get_agents(self, state_id=None, agent_type=None, limit_neighbors=False, iterator=False, **kwargs):
agents = self.env.agents
if limit_neighbors: if limit_neighbors:
agents = super().get_agents(state_id, limit_neighbors) agents = super().get_agents(state_id, limit_neighbors)
else:
agents = filter(lambda x: state_id is None or x.state.get('id', None) == state_id,
self.env.agents)
def matches_all(agent): def matches_all(agent):
if state_id is not None:
if agent.state.get('id', None) != state_id:
return False
if agent_type is not None:
if type(agent) != agent_type:
return False
state = agent.state state = agent.state
for k, v in kwargs.items(): for k, v in kwargs.items():
if state.get(k, None) != v: if state.get(k, None) != v:
@ -219,7 +215,7 @@ def default_state(func):
return func return func
class MetaFSM(MetaAgent): class MetaFSM(type):
def __init__(cls, name, bases, nmspc): def __init__(cls, name, bases, nmspc):
super(MetaFSM, cls).__init__(name, bases, nmspc) super(MetaFSM, cls).__init__(name, bases, nmspc)
states = {} states = {}
@ -328,16 +324,39 @@ def calculate_distribution(network_agents=None,
return network_agents return network_agents
def _serialize_distribution(network_agents): def serialize_type(agent_type, known_modules=[], **kwargs):
d = _convert_agent_types(network_agents, if isinstance(agent_type, str):
to_string=True) return agent_type
known_modules += ['soil.agents']
return utils.serialize(agent_type, known_modules=known_modules, **kwargs)[1] # Get the name of the class
def serialize_distribution(network_agents, known_modules=[]):
''' '''
When serializing an agent distribution, remove the thresholds, in order When serializing an agent distribution, remove the thresholds, in order
to avoid cluttering the YAML definition file. to avoid cluttering the YAML definition file.
''' '''
d = deepcopy(network_agents)
for v in d: for v in d:
if 'threshold' in v: if 'threshold' in v:
del v['threshold'] del v['threshold']
v['agent_type'] = serialize_type(v['agent_type'],
known_modules=known_modules)
return d
def deserialize_type(agent_type, known_modules=[]):
if not isinstance(agent_type, str):
return agent_type
known = known_modules + ['soil.agents', 'soil.agents.custom' ]
agent_type = utils.deserializer(agent_type, known_modules=known)
return agent_type
def deserialize_distribution(ind, **kwargs):
d = deepcopy(ind)
for v in d:
v['agent_type'] = deserialize_type(v['agent_type'], **kwargs)
return d return d
@ -352,16 +371,11 @@ def _validate_states(states, topology):
return states return states
def _convert_agent_types(ind, to_string=False): def _convert_agent_types(ind, to_string=False, **kwargs):
'''Convenience method to allow specifying agents by class or class name.''' '''Convenience method to allow specifying agents by class or class name.'''
d = deepcopy(ind) if to_string:
for v in d: return serialize_distribution(ind, **kwargs)
agent_type = v['agent_type'] return deserialize_distribution(ind, **kwargs)
if to_string and not isinstance(agent_type, str):
v['agent_type'] = str(agent_type.__name__)
elif not to_string and isinstance(agent_type, str):
v['agent_type'] = agent_types[agent_type]
return d
def _agent_from_distribution(distribution, value=-1): def _agent_from_distribution(distribution, value=-1):

4
soil/analysis.py
View File

@ -56,7 +56,7 @@ def read_csv(filename, keys=None, convert_types=False, **kwargs):
def convert_row(row): def convert_row(row):
row['value'] = utils.convert(row['value'], row['value_type']) row['value'] = utils.deserialize(row['value_type'], row['value'])
return row return row
@ -123,7 +123,7 @@ def get_count(df, *keys):
df = df[list(keys)] df = df[list(keys)]
counts = pd.DataFrame() counts = pd.DataFrame()
for key in df.columns.levels[0]: for key in df.columns.levels[0]:
g = df[key].apply(pd.Series.value_counts, axis=1).fillna(0) g = df[[key]].apply(pd.Series.value_counts, axis=1).fillna(0)
for value, series in g.iteritems(): for value, series in g.iteritems():
counts[key, value] = series counts[key, value] = series
counts.columns = pd.MultiIndex.from_tuples(counts.columns) counts.columns = pd.MultiIndex.from_tuples(counts.columns)

41
soil/environment.py
View File

@ -15,7 +15,7 @@ import nxsim
from . import utils, agents, analysis, history from . import utils, agents, analysis, history
class SoilEnvironment(nxsim.NetworkEnvironment): class Environment(nxsim.NetworkEnvironment):
""" """
The environment is key in a simulation. It contains the network topology, The environment is key in a simulation. It contains the network topology,
a reference to network and environment agents, as well as the environment a reference to network and environment agents, as well as the environment
@ -23,7 +23,7 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
The environment parameters and the state of every agent can be accessed The environment parameters and the state of every agent can be accessed
both by using the environment as a dictionary or with the environment's both by using the environment as a dictionary or with the environment's
:meth:`soil.environment.SoilEnvironment.get` method. :meth:`soil.environment.Environment.get` method.
""" """
def __init__(self, name=None, def __init__(self, name=None,
@ -49,6 +49,7 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
self.dry_run = dry_run self.dry_run = dry_run
self.interval = interval self.interval = interval
self.dir_path = dir_path or tempfile.mkdtemp('soil-env') self.dir_path = dir_path or tempfile.mkdtemp('soil-env')
if not dry_run:
self.get_path() self.get_path()
self._history = history.History(name=self.name if not dry_run else None, self._history = history.History(name=self.name if not dry_run else None,
dir_path=self.dir_path) dir_path=self.dir_path)
@ -93,17 +94,35 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
if not network_agents: if not network_agents:
return return
for ix in self.G.nodes(): for ix in self.G.nodes():
agent, state = agents._agent_from_distribution(network_agents) self.init_agent(ix, agent_distribution=network_agents)
self.set_agent(ix, agent_type=agent, state=state)
def init_agent(self, agent_id, agent_distribution):
node = self.G.nodes[agent_id]
init = False
state = dict(node)
agent_type = None
if 'agent_type' in self.states.get(agent_id, {}):
agent_type = self.states[agent_id]
elif 'agent_type' in node:
agent_type = node['agent_type']
elif 'agent_type' in self.default_state:
agent_type = self.default_state['agent_type']
if agent_type:
agent_type = agents.deserialize_type(agent_type)
else:
agent_type, state = agents._agent_from_distribution(agent_distribution)
return self.set_agent(agent_id, agent_type, state)
def set_agent(self, agent_id, agent_type, state=None): def set_agent(self, agent_id, agent_type, state=None):
node = self.G.nodes[agent_id] node = self.G.nodes[agent_id]
defstate = deepcopy(self.default_state) defstate = deepcopy(self.default_state) or {}
defstate.update(self.states.get(agent_id, {})) defstate.update(self.states.get(agent_id, {}))
defstate.update(node.get('state', {}))
if state: if state:
defstate.update(state) defstate.update(state)
state = defstate state = defstate
state.update(node.get('state', {}))
a = agent_type(environment=self, a = agent_type(environment=self,
agent_id=agent_id, agent_id=agent_id,
state=state) state=state)
@ -118,6 +137,10 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
return a return a
def add_edge(self, agent1, agent2, attrs=None): def add_edge(self, agent1, agent2, attrs=None):
if hasattr(agent1, 'id'):
agent1 = agent1.id
if hasattr(agent2, 'id'):
agent2 = agent2.id
return self.G.add_edge(agent1, agent2) return self.G.add_edge(agent1, agent2)
def run(self, *args, **kwargs): def run(self, *args, **kwargs):
@ -202,7 +225,7 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
with open(csv_name, 'w') as f: with open(csv_name, 'w') as f:
cr = csv.writer(f) cr = csv.writer(f)
cr.writerow(('agent_id', 't_step', 'key', 'value', 'value_type')) cr.writerow(('agent_id', 't_step', 'key', 'value'))
for i in self.history_to_tuples(): for i in self.history_to_tuples():
cr.writerow(i) cr.writerow(i)
@ -302,7 +325,6 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
state['network_agents'] = agents._serialize_distribution(self.network_agents) state['network_agents'] = agents._serialize_distribution(self.network_agents)
state['environment_agents'] = agents._convert_agent_types(self.environment_agents, state['environment_agents'] = agents._convert_agent_types(self.environment_agents,
to_string=True) to_string=True)
del state['_queue']
return state return state
def __setstate__(self, state): def __setstate__(self, state):
@ -311,3 +333,6 @@ class SoilEnvironment(nxsim.NetworkEnvironment):
self.network_agents = self.calculate_distribution(self._convert_agent_types(self.network_agents)) self.network_agents = self.calculate_distribution(self._convert_agent_types(self.network_agents))
self.environment_agents = self._convert_agent_types(self.environment_agents) self.environment_agents = self._convert_agent_types(self.environment_agents)
return state return state
SoilEnvironment = Environment

81
soil/history.py
View File

@ -3,7 +3,7 @@ import os
import pandas as pd import pandas as pd
import sqlite3 import sqlite3
import copy import copy
from collections import UserDict, Iterable, namedtuple from collections import UserDict, namedtuple
from . import utils from . import utils
@ -17,12 +17,12 @@ class History:
if db_path is None and name: if db_path is None and name:
db_path = os.path.join(dir_path or os.getcwd(), db_path = os.path.join(dir_path or os.getcwd(),
'{}.db.sqlite'.format(name)) '{}.db.sqlite'.format(name))
if db_path is None: if db_path:
db_path = ":memory:"
else:
if backup and os.path.exists(db_path): if backup and os.path.exists(db_path):
newname = db_path + '.backup{}.sqlite'.format(time.time()) newname = db_path + '.backup{}.sqlite'.format(time.time())
os.rename(db_path, newname) os.rename(db_path, newname)
else:
db_path = ":memory:"
self.db_path = db_path self.db_path = db_path
self.db = db_path self.db = db_path
@ -34,12 +34,6 @@ class History:
self._dtypes = {} self._dtypes = {}
self._tups = [] self._tups = []
def conversors(self, key):
"""Get the serializer and deserializer for a given key."""
if key not in self._dtypes:
self.read_types()
return self._dtypes[key]
@property @property
def db(self): def db(self):
try: try:
@ -58,35 +52,67 @@ class History:
@property @property
def dtypes(self): def dtypes(self):
self.read_types()
return {k:v[0] for k, v in self._dtypes.items()} return {k:v[0] for k, v in self._dtypes.items()}
def save_tuples(self, tuples): def save_tuples(self, tuples):
'''
Save a series of tuples, converting them to records if necessary
'''
self.save_records(Record(*tup) for tup in tuples) self.save_records(Record(*tup) for tup in tuples)
def save_records(self, records): def save_records(self, records):
with self.db: '''
for rec in records: Save a collection of records
if not isinstance(rec, Record): '''
rec = Record(*rec) for record in records:
if rec.key not in self._dtypes: if not isinstance(record, Record):
name = utils.name(rec.value) record = Record(*record)
serializer = utils.serializer(name) self.save_record(*record)
deserializer = utils.deserializer(name)
self._dtypes[rec.key] = (name, serializer, deserializer)
self.db.execute("replace into value_types (key, value_type) values (?, ?)", (rec.key, name))
self.db.execute("replace into history(agent_id, t_step, key, value) values (?, ?, ?, ?)", (rec.agent_id, rec.t_step, rec.key, rec.value))
def save_record(self, *args, **kwargs): def save_record(self, agent_id, t_step, key, value):
self._tups.append(Record(*args, **kwargs)) '''
Save a collection of records to the database.
Database writes are cached.
'''
value = self.convert(key, value)
self._tups.append(Record(agent_id=agent_id,
t_step=t_step,
key=key,
value=value))
if len(self._tups) > 100: if len(self._tups) > 100:
self.flush_cache() self.flush_cache()
def convert(self, key, value):
"""Get the serialized value for a given key."""
if key not in self._dtypes:
self.read_types()
if key not in self._dtypes:
name = utils.name(value)
serializer = utils.serializer(name)
deserializer = utils.deserializer(name)
self._dtypes[key] = (name, serializer, deserializer)
with self.db:
self.db.execute("replace into value_types (key, value_type) values (?, ?)", (key, name))
return self._dtypes[key][1](value)
def recover(self, key, value):
"""Get the deserialized value for a given key, and the serialized version."""
if key not in self._dtypes:
self.read_types()
if key not in self._dtypes:
raise ValueError("Unknown datatype for {} and {}".format(key, value))
return self._dtypes[key][2](value)
def flush_cache(self): def flush_cache(self):
''' '''
Use a cache to save state changes to avoid opening a session for every change. Use a cache to save state changes to avoid opening a session for every change.
The cache will be flushed at the end of the simulation, and when history is accessed. The cache will be flushed at the end of the simulation, and when history is accessed.
''' '''
self.save_records(self._tups) with self.db:
for rec in self._tups:
self.db.execute("replace into history(agent_id, t_step, key, value) values (?, ?, ?, ?)", (rec.agent_id, rec.t_step, rec.key, rec.value))
self._tups = list() self._tups = list()
def to_tuples(self): def to_tuples(self):
@ -95,8 +121,8 @@ class History:
res = self.db.execute("select agent_id, t_step, key, value from history ").fetchall() res = self.db.execute("select agent_id, t_step, key, value from history ").fetchall()
for r in res: for r in res:
agent_id, t_step, key, value = r agent_id, t_step, key, value = r
_, _ , des = self.conversors(key) value = self.recover(key, value)
yield agent_id, t_step, key, des(value) yield agent_id, t_step, key, value
def read_types(self): def read_types(self):
with self.db: with self.db:
@ -107,6 +133,7 @@ class History:
self._dtypes[k] = (v, serializer, deserializer) self._dtypes[k] = (v, serializer, deserializer)
def __getitem__(self, key): def __getitem__(self, key):
self.flush_cache()
key = Key(*key) key = Key(*key)
agent_ids = [key.agent_id] if key.agent_id is not None else [] agent_ids = [key.agent_id] if key.agent_id is not None else []
t_steps = [key.t_step] if key.t_step is not None else [] t_steps = [key.t_step] if key.t_step is not None else []
@ -176,7 +203,7 @@ class History:
for k, v in self._dtypes.items(): for k, v in self._dtypes.items():
if k in df_p: if k in df_p:
dtype, _, deserial = v dtype, _, deserial = v
df_p[k] = df_p[k].fillna(method='ffill').fillna(deserial()).astype(dtype) df_p[k] = df_p[k].fillna(method='ffill').astype(dtype)
if t_steps: if t_steps:
df_p = df_p.reindex(t_steps, method='ffill') df_p = df_p.reindex(t_steps, method='ffill')
return df_p.ffill() return df_p.ffill()

146
soil/simulation.py
View File

@ -1,8 +1,9 @@
import os import os
import time import time
import imp import importlib
import sys import sys
import yaml import yaml
import traceback
import networkx as nx import networkx as nx
from networkx.readwrite import json_graph from networkx.readwrite import json_graph
from multiprocessing import Pool from multiprocessing import Pool
@ -12,11 +13,12 @@ import pickle
from nxsim import NetworkSimulation from nxsim import NetworkSimulation
from . import utils, environment, basestring, agents from . import utils, basestring, agents
from .environment import Environment
from .utils import logger from .utils import logger
class SoilSimulation(NetworkSimulation): class Simulation(NetworkSimulation):
""" """
Subclass of nsim.NetworkSimulation with three main differences: Subclass of nsim.NetworkSimulation with three main differences:
1) agent type can be specified by name or by class. 1) agent type can be specified by name or by class.
@ -43,13 +45,48 @@ class SoilSimulation(NetworkSimulation):
'agent_type_1'. 'agent_type_1'.
3) if no initial state is given, each node's state will be set 3) if no initial state is given, each node's state will be set
to `{'id': 0}`. to `{'id': 0}`.
Parameters
---------
name : str, optional
name of the Simulation
topology : networkx.Graph instance, optional
network_params : dict
parameters used to create a topology with networkx, if no topology is given
network_agents : dict
definition of agents to populate the topology with
agent_type : NetworkAgent subclass, optional
Default type of NetworkAgent to use for nodes not specified in network_agents
states : list, optional
List of initial states corresponding to the nodes in the topology. Basic form is a list of integers
whose value indicates the state
dir_path : str, optional
Directory path where to save pickled objects
seed : str, optional
Seed to use for the random generator
num_trials : int, optional
Number of independent simulation runs
max_time : int, optional
Time how long the simulation should run
environment_params : dict, optional
Dictionary of globally-shared environmental parameters
environment_agents: dict, optional
Similar to network_agents. Distribution of Agents that control the environment
environment_class: soil.environment.Environment subclass, optional
Class for the environment. It defailts to soil.environment.Environment
load_module : str, module name, deprecated
If specified, soil will load the content of this module under 'soil.agents.custom'
""" """
def __init__(self, name=None, topology=None, network_params=None, def __init__(self, name=None, topology=None, network_params=None,
network_agents=None, agent_type=None, states=None, network_agents=None, agent_type=None, states=None,
default_state=None, interval=1, dump=None, dry_run=False, default_state=None, interval=1, dump=None, dry_run=False,
dir_path=None, num_trials=1, max_time=100, dir_path=None, num_trials=1, max_time=100,
agent_module=None, load_module=None, seed=None, load_module=None, seed=None,
environment_agents=None, environment_params=None, **kwargs): environment_agents=None, environment_params=None,
environment_class=None, **kwargs):
if topology is None: if topology is None:
topology = utils.load_network(network_params, topology = utils.load_network(network_params,
@ -69,19 +106,21 @@ class SoilSimulation(NetworkSimulation):
self.seed = str(seed) or str(time.time()) self.seed = str(seed) or str(time.time())
self.dump = dump self.dump = dump
self.dry_run = dry_run self.dry_run = dry_run
self.environment_params = environment_params or {}
if load_module: sys.path += [self.dir_path, os.getcwd()]
path = sys.path + [self.dir_path, os.getcwd()]
f, fp, desc = imp.find_module(load_module, path) self.environment_params = environment_params or {}
imp.load_module('soil.agents.custom', f, fp, desc) self.environment_class = utils.deserialize(environment_class,
known_modules=['soil.environment', ]) or Environment
environment_agents = environment_agents or [] environment_agents = environment_agents or []
self.environment_agents = agents._convert_agent_types(environment_agents) self.environment_agents = agents._convert_agent_types(environment_agents,
known_modules=[self.load_module])
distro = agents.calculate_distribution(network_agents, distro = agents.calculate_distribution(network_agents,
agent_type) agent_type)
self.network_agents = agents._convert_agent_types(distro) self.network_agents = agents._convert_agent_types(distro,
known_modules=[self.load_module])
self.states = agents._validate_states(states, self.states = agents._validate_states(states,
self.topology) self.topology)
@ -97,13 +136,17 @@ class SoilSimulation(NetworkSimulation):
p = Pool() p = Pool()
with utils.timer('simulation {}'.format(self.name)): with utils.timer('simulation {}'.format(self.name)):
if parallel: if parallel:
func = partial(self.run_trial, dry_run=dry_run or self.dry_run, func = partial(self.run_trial_exceptions, dry_run=dry_run or self.dry_run,
return_env=not parallel, **kwargs) return_env=True,
**kwargs)
for i in p.imap_unordered(func, range(self.num_trials)): for i in p.imap_unordered(func, range(self.num_trials)):
if isinstance(i, Exception):
logger.error('Trial failed:\n\t{}'.format(i.message))
continue
yield i yield i
else: else:
for i in range(self.num_trials): for i in range(self.num_trials):
yield self.run_trial(i, dry_run=dry_run or self.dry_run, **kwargs) yield self.run_trial(i, dry_run = dry_run or self.dry_run, **kwargs)
if not (dry_run or self.dry_run): if not (dry_run or self.dry_run):
logger.info('Dumping results to {}'.format(self.dir_path)) logger.info('Dumping results to {}'.format(self.dir_path))
self.dump_pickle(self.dir_path) self.dump_pickle(self.dir_path)
@ -111,9 +154,9 @@ class SoilSimulation(NetworkSimulation):
else: else:
logger.info('NOT dumping results') logger.info('NOT dumping results')
def get_env(self, trial_id=0, **kwargs): def get_env(self, trial_id = 0, **kwargs):
opts = self.environment_params.copy() opts=self.environment_params.copy()
env_name = '{}_trial_{}'.format(self.name, trial_id) env_name='{}_trial_{}'.format(self.name, trial_id)
opts.update({ opts.update({
'name': env_name, 'name': env_name,
'topology': self.topology.copy(), 'topology': self.topology.copy(),
@ -128,10 +171,10 @@ class SoilSimulation(NetworkSimulation):
'dir_path': self.dir_path, 'dir_path': self.dir_path,
}) })
opts.update(kwargs) opts.update(kwargs)
env = environment.SoilEnvironment(**opts) env=self.environment_class(**opts)
return env return env
def run_trial(self, trial_id=0, until=None, return_env=True, **opts): def run_trial(self, trial_id = 0, until = None, return_env = True, **opts):
"""Run a single trial of the simulation """Run a single trial of the simulation
Parameters Parameters
@ -139,16 +182,27 @@ class SoilSimulation(NetworkSimulation):
trial_id : int trial_id : int
""" """
# Set-up trial environment and graph # Set-up trial environment and graph
until = until or self.max_time until=until or self.max_time
env = self.get_env(trial_id=trial_id, **opts) env=self.get_env(trial_id = trial_id, **opts)
# Set up agents on nodes # Set up agents on nodes
with utils.timer('Simulation {} trial {}'.format(self.name, trial_id)): with utils.timer('Simulation {} trial {}'.format(self.name, trial_id)):
env.run(until) env.run(until)
if self.dump and not self.dry_run: if self.dump and not self.dry_run:
with utils.timer('Dumping simulation {} trial {}'.format(self.name, trial_id)): with utils.timer('Dumping simulation {} trial {}'.format(self.name, trial_id)):
env.dump(formats=self.dump) env.dump(formats = self.dump)
if return_env: if return_env:
return env return env
def run_trial_exceptions(self, *args, **kwargs):
'''
A wrapper for run_trial that catches exceptions and returns them.
It is meant for async simulations
'''
try:
return self.run_trial(*args, **kwargs)
except Exception as ex:
c = ex.__cause__
c.message = ''.join(traceback.format_tb(c.__traceback__)[3:])
return c
def to_dict(self): def to_dict(self):
return self.__getstate__() return self.__getstate__()
@ -156,39 +210,53 @@ class SoilSimulation(NetworkSimulation):
def to_yaml(self): def to_yaml(self):
return yaml.dump(self.to_dict()) return yaml.dump(self.to_dict())
def dump_yaml(self, dir_path=None, file_name=None): def dump_yaml(self, dir_path = None, file_name = None):
dir_path = dir_path or self.dir_path dir_path=dir_path or self.dir_path
if not os.path.exists(dir_path): if not os.path.exists(dir_path):
os.makedirs(dir_path) os.makedirs(dir_path)
if not file_name: if not file_name:
file_name = os.path.join(dir_path, file_name=os.path.join(dir_path,
'{}.dumped.yml'.format(self.name)) '{}.dumped.yml'.format(self.name))
with open(file_name, 'w') as f: with open(file_name, 'w') as f:
f.write(self.to_yaml()) f.write(self.to_yaml())
def dump_pickle(self, dir_path=None, pickle_name=None): def dump_pickle(self, dir_path = None, pickle_name = None):
dir_path = dir_path or self.dir_path dir_path=dir_path or self.dir_path
if not os.path.exists(dir_path): if not os.path.exists(dir_path):
os.makedirs(dir_path) os.makedirs(dir_path)
if not pickle_name: if not pickle_name:
pickle_name = os.path.join(dir_path, pickle_name=os.path.join(dir_path,
'{}.simulation.pickle'.format(self.name)) '{}.simulation.pickle'.format(self.name))
with open(pickle_name, 'wb') as f: with open(pickle_name, 'wb') as f:
pickle.dump(self, f) pickle.dump(self, f)
def __getstate__(self): def __getstate__(self):
state = self.__dict__.copy() state={}
state['topology'] = json_graph.node_link_data(self.topology) for k, v in self.__dict__.items():
state['network_agents'] = agents._serialize_distribution(self.network_agents) if k[0] != '_':
state['environment_agents'] = agents._convert_agent_types(self.environment_agents, state[k]=v
to_string=True) state['topology']=json_graph.node_link_data(self.topology)
state['network_agents']=agents.serialize_distribution(self.network_agents,
known_modules = [])
state['environment_agents']=agents.serialize_distribution(self.environment_agents,
known_modules = [])
state['environment_class']=utils.serialize(self.environment_class,
known_modules=['soil.environment'])[1] # func, name
if state['load_module'] is None:
del state['load_module']
return state return state
def __setstate__(self, state): def __setstate__(self, state):
self.__dict__ = state self.__dict__ = state
self.load_module = getattr(self, 'load_module', None)
if self.dir_path not in sys.path:
sys.path += [self.dir_path, os.getcwd()]
self.topology = json_graph.node_link_graph(state['topology']) self.topology = json_graph.node_link_graph(state['topology'])
self.network_agents = agents.calculate_distribution(agents._convert_agent_types(self.network_agents)) self.network_agents = agents.calculate_distribution(agents._convert_agent_types(self.network_agents))
self.environment_agents = agents._convert_agent_types(self.environment_agents) self.environment_agents = agents._convert_agent_types(self.environment_agents,
known_modules=[self.load_module])
self.environment_class = utils.deserialize(self.environment_class,
known_modules=[self.load_module, 'soil.environment', ]) # func, name
return state return state
@ -197,11 +265,11 @@ def from_config(config):
if len(config) > 1: if len(config) > 1:
raise AttributeError('Provide only one configuration') raise AttributeError('Provide only one configuration')
config = config[0][0] config = config[0][0]
sim = SoilSimulation(**config) sim = Simulation(**config)
return sim return sim
def run_from_config(*configs, results_dir='soil_output', dry_run=False, dump=None, timestamp=False, **kwargs): def run_from_config(*configs, results_dir='soil_output', dump=None, timestamp=False, **kwargs):
for config_def in configs: for config_def in configs:
# logger.info("Found {} config(s)".format(len(ls))) # logger.info("Found {} config(s)".format(len(ls)))
for config, _ in utils.load_config(config_def): for config, _ in utils.load_config(config_def):
@ -214,6 +282,8 @@ def run_from_config(*configs, results_dir='soil_output', dry_run=False, dump=Non
else: else:
sim_folder = name sim_folder = name
dir_path = os.path.join(results_dir, sim_folder) dir_path = os.path.join(results_dir, sim_folder)
sim = SoilSimulation(dir_path=dir_path, dump=dump, **config) if dump is not None:
config['dump'] = dump
sim = Simulation(dir_path=dir_path, **config)
logger.info('Dumping results to {} : {}'.format(sim.dir_path, sim.dump)) logger.info('Dumping results to {} : {}'.format(sim.dir_path, sim.dump))
sim.run_simulation(**kwargs) sim.run_simulation(**kwargs)

101
soil/utils.py
View File

@ -1,8 +1,9 @@
import os import os
import ast
import yaml import yaml
import logging import logging
import importlib import importlib
from time import time import time
from glob import glob from glob import glob
from random import random from random import random
from copy import deepcopy from copy import deepcopy
@ -62,44 +63,92 @@ def load_config(config):
@contextmanager @contextmanager
def timer(name='task', pre="", function=logger.info, to_object=None): def timer(name='task', pre="", function=logger.info, to_object=None):
start = time() start = time.time()
function('{}Starting {} at {}.'.format(pre, name, start)) function('{}Starting {} at {}.'.format(pre, name,
time.strftime("%X", time.gmtime(start))))
yield start yield start
end = time() end = time.time()
function('{}Finished {} in {} seconds'.format(pre, name, str(end-start))) function('{}Finished {} at {} in {} seconds'.format(pre, name,
time.strftime("%X", time.gmtime(end)),
str(end-start)))
if to_object: if to_object:
to_object.start = start to_object.start = start
to_object.end = end to_object.end = end
def repr(v): builtins = importlib.import_module('builtins')
func = serializer(v)
tname = name(v)
return func(v), tname
def name(value, known_modules=[]):
def name(v): '''Return a name that can be imported, to serialize/deserialize an object'''
return type(v).__name__ if value is None:
return 'None'
if not isinstance(value, type): # Get the class name first
value = type(value)
tname = value.__name__
if hasattr(builtins, tname):
return tname
modname = value.__module__
if modname == '__main__':
return tname
if known_modules and modname in known_modules:
return tname
for kmod in known_modules:
if not kmod:
continue
module = importlib.import_module(kmod)
if hasattr(module, tname):
return tname
return '{}.{}'.format(modname, tname)
def serializer(type_): def serializer(type_):
if type_ == 'bool': if type_ != 'str' and hasattr(builtins, type_):
return lambda x: "true" if x else "" return repr
return lambda x: x return lambda x: x
def deserializer(type_): def serialize(v, known_modules=[]):
try: '''Get a text representation of an object.'''
# Check if it's a builtin type tname = name(v, known_modules=known_modules)
module = importlib.import_module('builtins') func = serializer(tname)
cls = getattr(module, type_) return func(v), tname
except AttributeError:
# if not, separate module and class def deserializer(type_, known_modules=[]):
if type_ == 'str':
return lambda x='': x
if type_ == 'None':
return lambda x=None: None
if hasattr(builtins, type_): # Check if it's a builtin type
cls = getattr(builtins, type_)
return lambda x=None: ast.literal_eval(x) if x is not None else cls()
# Otherwise, see if we can find the module and the class
modules = known_modules or []
options = []
for mod in modules:
if mod:
options.append((mod, type_))
if '.' in type_: # Fully qualified module
module, type_ = type_.rsplit(".", 1) module, type_ = type_.rsplit(".", 1)
module = importlib.import_module(module) options.append ((module, type_))
cls = getattr(module, type_)
return cls errors = []
for modname, tname in options:
try:
module = importlib.import_module(modname)
cls = getattr(module, tname)
return getattr(cls, 'deserialize', cls)
except (ImportError, AttributeError) as ex:
errors.append((modname, tname, ex))
raise Exception('Could not find type {}. Tried: {}'.format(type_, errors))
def convert(value, type_): def deserialize(type_, value=None, **kwargs):
return deserializer(type_)(value) '''Get an object from a text representation'''
if not isinstance(type_, str):
return type_
des = deserializer(type_, **kwargs)
if value is None:
return des
return des(value)

1
test-requirements.txt
View File

@ -0,0 +1 @@
pytest

12
tests/test.gexf Normal file
View File

@ -0,0 +1,12 @@
<?xml version='1.0' encoding='utf-8'?>
<gexf version="1.2" xmlns="http://www.gexf.net/1.2draft" xmlns:viz="http://www.gexf.net/1.2draft/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.w3.org/2001/XMLSchema-instance">
<graph defaultedgetype="undirected" mode="static">
<nodes>
<node id="0" label="0" />
<node id="1" label="1" />
</nodes>
<edges>
<edge id="0" source="0" target="1" />
</edges>
</graph>
</gexf>

48
tests/test_examples.py Normal file
View File

@ -0,0 +1,48 @@
from unittest import TestCase
import os
from os.path import join
from soil import utils, simulation
ROOT = os.path.abspath(os.path.dirname(__file__))
EXAMPLES = join(ROOT, '..', 'examples')
class TestExamples(TestCase):
pass
def make_example_test(path, config):
def wrapped(self):
root = os.getcwd()
os.chdir(os.path.dirname(path))
s = simulation.from_config(config)
iterations = s.max_time * s.num_trials
if iterations > 1000:
self.skipTest('This example would probably take too long')
envs = s.run_simulation(dry_run=True)
assert envs
for env in envs:
assert env
try:
n = config['network_params']['n']
assert len(list(env.network_agents)) == n
assert env.now > 2 # It has run
assert env.now <= config['max_time'] # But not further than allowed
except KeyError:
pass
os.chdir(root)
return wrapped
def add_example_tests():
for config, path in utils.load_config(join(EXAMPLES, '**', '*.yml')):
p = make_example_test(path=path, config=config)
fname = os.path.basename(path)
p.__name__ = 'test_example_file_%s' % fname
p.__doc__ = '%s should be a valid configuration' % fname
setattr(TestExamples, p.__name__, p)
del p
add_example_tests()

25
tests/test_history.py
View File

@ -116,6 +116,7 @@ class TestHistory(TestCase):
db_path = os.path.join(DBROOT, 'test') db_path = os.path.join(DBROOT, 'test')
h = history.History(db_path=db_path) h = history.History(db_path=db_path)
h.save_tuples(tuples) h.save_tuples(tuples)
h.flush_cache()
assert os.path.exists(db_path) assert os.path.exists(db_path)
# Recover the data # Recover the data
@ -128,6 +129,28 @@ class TestHistory(TestCase):
backuppaths = glob(db_path + '.backup*.sqlite') backuppaths = glob(db_path + '.backup*.sqlite')
assert len(backuppaths) == 1 assert len(backuppaths) == 1
backuppath = backuppaths[0] backuppath = backuppaths[0]
assert newhistory._db_path == h._db_path assert newhistory.db_path == h.db_path
assert os.path.exists(backuppath) assert os.path.exists(backuppath)
assert not len(newhistory[None, None, None]) assert not len(newhistory[None, None, None])
def test_history_tuples(self):
"""
The data recovered should be equal to the one recorded.
"""
tuples = (
('a_1', 0, 'id', 'v'),
('a_1', 1, 'id', 'a'),
('a_1', 2, 'id', 'l'),
('a_1', 3, 'id', 'u'),
('a_1', 4, 'id', 'e'),
('env', 1, 'prob', 1),
('env', 2, 'prob', 2),
('env', 3, 'prob', 3),
('a_2', 7, 'finished', True),
)
h = history.History()
h.save_tuples(tuples)
recovered = list(h.to_tuples())
assert recovered
for i in recovered:
assert i in tuples

110
tests/test_main.py
View File

@ -6,14 +6,18 @@ import networkx as nx
from functools import partial from functools import partial
from os.path import join from os.path import join
from soil import simulation, environment, agents, utils from soil import simulation, Environment, agents, utils, history
ROOT = os.path.abspath(os.path.dirname(__file__)) ROOT = os.path.abspath(os.path.dirname(__file__))
EXAMPLES = join(ROOT, '..', 'examples') EXAMPLES = join(ROOT, '..', 'examples')
class CustomAgent(agents.BaseAgent):
def step(self):
self.state['neighbors'] = self.count_agents(state_id=0,
limit_neighbors=True)
class TestMain(TestCase): class TestMain(TestCase):
def test_load_graph(self): def test_load_graph(self):
@ -127,10 +131,6 @@ class TestMain(TestCase):
def test_custom_agent(self): def test_custom_agent(self):
"""Allow for search of neighbors with a certain state_id""" """Allow for search of neighbors with a certain state_id"""
class CustomAgent(agents.BaseAgent):
def step(self):
self.state['neighbors'] = self.count_agents(state_id=0,
limit_neighbors=True)
config = { config = {
'dry_run': True, 'dry_run': True,
'network_params': { 'network_params': {
@ -188,8 +188,6 @@ class TestMain(TestCase):
recovered = yaml.load(serial) recovered = yaml.load(serial)
with utils.timer('deleting'): with utils.timer('deleting'):
del recovered['topology'] del recovered['topology']
del recovered['load_module']
del recovered['dry_run']
assert config == recovered assert config == recovered
def test_configuration_changes(self): def test_configuration_changes(self):
@ -197,25 +195,17 @@ class TestMain(TestCase):
The configuration should not change after running The configuration should not change after running
the simulation. the simulation.
""" """
config = utils.load_file('examples/complete.yml')[0] config = utils.load_file(join(EXAMPLES, 'complete.yml'))[0]
s = simulation.from_config(config) s = simulation.from_config(config)
s.dry_run = True s.dry_run = True
for i in range(5): for i in range(5):
s.run_simulation(dry_run=True) s.run_simulation(dry_run=True)
nconfig = s.to_dict() nconfig = s.to_dict()
del nconfig['topology'] del nconfig['topology']
del nconfig['dry_run']
del nconfig['load_module']
assert config == nconfig assert config == nconfig
def test_examples(self):
"""
Make sure all examples in the examples folder are correct
"""
pass
def test_row_conversion(self): def test_row_conversion(self):
env = environment.SoilEnvironment(dry_run=True) env = Environment(dry_run=True)
env['test'] = 'test_value' env['test'] = 'test_value'
res = list(env.history_to_tuples()) res = list(env.history_to_tuples())
@ -234,7 +224,7 @@ class TestMain(TestCase):
from geometric models. We should work around it. from geometric models. We should work around it.
""" """
G = nx.random_geometric_graph(20, 0.1) G = nx.random_geometric_graph(20, 0.1)
env = environment.SoilEnvironment(topology=G, dry_run=True) env = Environment(topology=G, dry_run=True)
env.dump_gexf('/tmp/dump-gexf') env.dump_gexf('/tmp/dump-gexf')
def test_save_graph(self): def test_save_graph(self):
@ -245,7 +235,7 @@ class TestMain(TestCase):
''' '''
G = nx.cycle_graph(5) G = nx.cycle_graph(5)
distribution = agents.calculate_distribution(None, agents.BaseAgent) distribution = agents.calculate_distribution(None, agents.BaseAgent)
env = environment.SoilEnvironment(topology=G, network_agents=distribution, dry_run=True) env = Environment(topology=G, network_agents=distribution, dry_run=True)
env[0, 0, 'testvalue'] = 'start' env[0, 0, 'testvalue'] = 'start'
env[0, 10, 'testvalue'] = 'finish' env[0, 10, 'testvalue'] = 'finish'
nG = env.history_to_graph() nG = env.history_to_graph()
@ -253,33 +243,65 @@ class TestMain(TestCase):
assert ('start', 0, 10) in values assert ('start', 0, 10) in values
assert ('finish', 10, None) in values assert ('finish', 10, None) in values
def test_serialize_class(self):
ser, name = utils.serialize(agents.BaseAgent)
assert name == 'soil.agents.BaseAgent'
assert ser == agents.BaseAgent
def make_example_test(path, config): class CustomAgent(agents.BaseAgent):
def wrapped(self):
root = os.getcwd()
os.chdir(os.path.dirname(path))
s = simulation.from_config(config)
envs = s.run_simulation(dry_run=True)
assert envs
for env in envs:
assert env
try:
n = config['network_params']['n']
assert len(env.get_agents()) == n
except KeyError:
pass pass
os.chdir(root)
return wrapped
ser, name = utils.serialize(CustomAgent)
assert name == 'test_main.CustomAgent'
assert ser == CustomAgent
def add_example_tests(): def test_serialize_builtin_types(self):
for config, path in utils.load_config(join(EXAMPLES, '*.yml')):
p = make_example_test(path=path, config=config)
fname = os.path.basename(path)
p.__name__ = 'test_example_file_%s' % fname
p.__doc__ = '%s should be a valid configuration' % fname
setattr(TestMain, p.__name__, p)
del p
for i in [1, None, True, False, {}, [], list(), dict()]:
ser, name = utils.serialize(i)
assert type(ser) == str
des = utils.deserialize(name, ser)
assert i == des
add_example_tests() def test_serialize_agent_type(self):
'''A class from soil.agents should be serialized without the module part'''
ser = agents.serialize_type(CustomAgent)
assert ser == 'test_main.CustomAgent'
ser = agents.serialize_type(agents.BaseAgent)
assert ser == 'BaseAgent'
def test_deserialize_agent_distribution(self):
agent_distro = [
{
'agent_type': 'CounterModel',
'weight': 1
},
{
'agent_type': 'test_main.CustomAgent',
'weight': 2
},
]
converted = agents.deserialize_distribution(agent_distro)
assert converted[0]['agent_type'] == agents.CounterModel
assert converted[1]['agent_type'] == CustomAgent
def test_serialize_agent_distribution(self):
agent_distro = [
{
'agent_type': agents.CounterModel,
'weight': 1
},
{
'agent_type': CustomAgent,
'weight': 2
},
]
converted = agents.serialize_distribution(agent_distro)
assert converted[0]['agent_type'] == 'CounterModel'
assert converted[1]['agent_type'] == 'test_main.CustomAgent'
def test_history(self):
'''Test storing in and retrieving from history (sqlite)'''
h = history.History()
h.save_record(agent_id=0, t_step=0, key="test", value="hello")
assert h[0, 0, "test"] == "hello"