v1.0.0rc11

* Improve text
* Move to docs
* Autogenerate with sphinx
* Fix naming issue `environment.run` (double name)
* Add to tests

.dockerignore

@@ -1,2 +1,7 @@
 **/soil_output
 .*
+**/.*
+**/__pycache__
+__pycache__
+*.pyc
+**/backup

.gitignore

@@ -8,3 +8,5 @@ soil_output
 docs/_build*
 build/*
 dist/*
+prof
+backup

.gitlab-ci.yml

@@ -1,9 +1,10 @@
 stages:
   - test
-  - build
+  - publish
+  - check_published
 
-build:
-  stage: build
+docker:
+  stage: publish
   image:
     name: gcr.io/kaniko-project/executor:debug
     entrypoint: [""]
@@ -16,13 +17,37 @@ build:
   only:
     - tags
 
-
 test:
-  except:
-    - tags  # Avoid running tests for tags, because they are already run for the branch
   tags:
     - docker
-  image: python:3.7
+  image: python:3.8
   stage: test
   script:
-    - python setup.py test
+    - pip install -r requirements.txt -r test-requirements.txt
+    - python setup.py test
+
+push_pypi:
+  only:
+    - tags
+  tags:
+    - docker
+  image: python:3.8
+  stage: publish
+  script:
+    - echo $CI_COMMIT_TAG > soil/VERSION
+    - pip install twine
+    - python setup.py sdist bdist_wheel
+    - TWINE_PASSWORD=$PYPI_PASSWORD TWINE_USERNAME=$PYPI_USERNAME python -m twine upload dist/*
+
+check_pypi:
+  only:
+    - tags
+  tags:
+    - docker
+  image: python:3.8
+  stage: check_published
+  script:
+    - pip install soil==$CI_COMMIT_TAG
+  # Allow PYPI to update its index before we try to install 
+  when: delayed
+  start_in: 2 minutes

CHANGELOG.md

@@ -3,6 +3,155 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [1.0.0 UNRELEASED]
+
+Version 1.0 will introduce multiple changes, especially on the `Simulation` class and anything related to how configuration is handled.
+For an explanation of the general changes in version 1.0, please refer to the file `docs/notes_v1.0.rst`.
+
+### Added
+* A modular set of classes for environments/models. Now the ability to configure the agents through an agent definition and a topology through a network configuration is split into two classes (`soil.agents.BaseEnvironment` for agents, `soil.agents.NetworkEnvironment` to add topology).
+* Environments now have a class method to make them easier to use without a simulation`.run`. Notice that this is different from `run_model`, which is an instance method.
+* Ability to run simulations using mesa models
+* The `soil.exporters` module to export the results of datacollectors (`model.datacollector`) into files at the end of trials/simulations
+* Agents can now have generators or async functions as their step or as states. They work similar to normal functions, with one caveat in the case of `FSM`: only time values (a float, int or None) can be awaited or yielded, not a state. This is because the state will not change, it will be resumed after the yield, at the appropriate time. To return to a different state, use the `delay` and `at` functions of the state.
+* Simulations can now specify a `matrix` with possible values for every simulation parameter. The final parameters will be calculated based on the `parameters` used and a cartesian product (i.e., all possible combinations) of each parameter.
+* Simple debugging capabilities in `soil.debugging`, with a custom `pdb.Debugger` subclass that exposes commands to list agents and their status and set breakpoints on states (for FSM agents). Try it with `soil --debug <simulation file>`
+* The `agent.after` and `agent.at` methods, to avoid having to return a time manually.
+### Changed
+* Configuration schema (`Simulation`) is very simplified. All simulations should be checked
+* Model / environment variables are expected (but not enforced) to be a single value. This is done to more closely align with mesa
+* `Exporter.iteration_end` now takes two parameters: `env` (same as before) and `params` (specific parameters for this environment). We considered including a `parameters` attribute in the environment, but this would not be compatible with mesa.
+* `num_trials` renamed to `iterations`
+* General renaming of `trial` to `iteration`, to work better with `mesa`
+* `model_parameters` renamed to `parameters` in simulation
+* Simulation results for every iteration of a simulation with the same name are stored in a single `sqlite` database
+
+### Removed
+* The `time.When` and `time.Cond` classes are removed
+* Any `tsih` and `History` integration in the main classes. To record the state of environments/agents, just use a datacollector. In some cases this may be slower or consume more memory than the previous system. However, few cases actually used the full potential of the history, and it came at the cost of unnecessary complexity and worse performance for the majority of cases.
+
+## [0.20.8]
+### Changed
+* Tsih bumped to version 0.1.8
+### Fixed
+* Mentions to `id` in docs. It should be `state_id` now.
+* Fixed bug: environment agents were not being added to the simulation
+
+## [0.20.7]
+### Changed
+* Creating a `time.When` from another `time.When` does not nest them anymore (it returns the argument)
+### Fixed
+* Bug with time.NEVER/time.INFINITY
+## [0.20.6]
+### Fixed
+* Agents now return `time.INFINITY` when dead, instead of 'inf'
+* `soil.__init__` does not re-export built-in time (change in `soil.simulation`. It used to create subtle import conflicts when importing soil.time.
+* Parallel simulations were broken because lambdas cannot be pickled properly, which is needed for multiprocessing.
+### Changed
+* Some internal simulation methods do not accept `*args` anymore, to avoid ambiguity and bugs.
+## [0.20.5]
+### Changed
+* Defaults are now set in the agent __init__, not in the environment. This decouples both classes a bit more, and it is more intuitive 
+## [0.20.4]
+### Added
+* Agents can now be given any kwargs, which will be used to set their state
+* Environments have a default logger `self.logger` and a log method, just like agents
+## [0.20.3]
+### Fixed
+* Default state values are now deepcopied again.
+* Seeds for environments only concatenate the trial id (i.e., a number), to provide repeatable results.
+* `Environment.run` now calls `Environment.step`, to allow for easy overloading of the environment step
+### Removed
+* Datacollectors are not being used for now.
+* `time.TimedActivation.step` does not use an `until` parameter anymore.
+### Changed
+* Simulations now run right up to `until` (open interval)
+* Time instants (`time.When`) don't need to be floats anymore. Now we can avoid precision issues with big numbers by using ints.
+* Rabbits simulation is more idiomatic (using subclasses)
+
+## [0.20.2]
+### Fixed
+* CI/CD testing issues
+## [0.20.1]
+### Fixed
+* Agents would run another step after dying.
+## [0.20.0]
+### Added
+* Integration with MESA
+* `not_agent_ids` parameter to get sql in history
+### Changed
+* `soil.Environment` now also inherits from `mesa.Model`
+* `soil.Agent` now also inherits from `mesa.Agent`
+* `soil.time` to replace `simpy` events, delays, duration, etc.
+* `agent.id` is not `agent.unique_id` to be compatible with `mesa`. A property `BaseAgent.id` has been added for compatibility.
+* `agent.environment` is now `agent.model`, for the same reason as above. The parameter name in `BaseAgent.__init__` has also been renamed.
+### Removed
+* `simpy` dependency and compatibility. Each agent used to be a simpy generator, but that made debugging and error handling more complex. That has been replaced by a scheduler within the `soil.Environment` class, similar to how `mesa` does it.
+* `soil.history` is now a separate package named `tsih`. The keys namedtuple uses `dict_id` instead of `agent_id`.
+### Added
+* An option to choose whether a database should be used for history 
+## [0.15.2]
+### Fixed
+* Pass the right known_modules and parameters to stats discovery in simulation
+* The configuration file must exist when launching through the CLI. If it doesn't, an error will be logged
+* Minor changes in the documentation of the CLI arguments
+### Changed
+* Stats are now exported by default
+## [0.15.1]
+### Added
+* read-only `History`
+### Fixed
+* Serialization problem with the `Environment` on parallel mode.
+* Analysis functions now work as they should in the tutorial
+## [0.15.0]
+### Added
+* Control logging level in CLI and simulation
+* `Stats` to calculate trial and simulation-wide statistics
+* Simulation statistics are stored in a separate table in history (see `History.get_stats` and `History.save_stats`, as well as `soil.stats`)
+* Aliased `NetworkAgent.G` to `NetworkAgent.topology`.
+### Changed
+* Templates in config files can be given as dictionaries in addition to strings
+* Samplers are used more explicitly
+* Removed nxsim dependency. We had already made a lot of changes, and nxsim has not been updated in 5 years.
+* Exporter methods renamed to `trial` and `end`. Added `start`.
+* `Distribution` exporter now a stats class
+* `global_topology` renamed to `topology`
+* Moved topology-related methods to `NetworkAgent`
+### Fixed
+* Temporary files used for history in dry_run mode are not longer left open 
+
+## [0.14.9]
+### Changed
+* Seed random before environment initialization
+## [0.14.8]
+### Fixed
+* Invalid directory names in Windows gsi-upm/soil#5
+## [0.14.7]
+### Changed
+* Minor change to traceback handling in async simulations
+### Fixed
+* Incomplete example in the docs (example.yml) caused an exception
+## [0.14.6]
+### Fixed
+* Bug with newer versions of networkx (0.24) where the Graph.node attribute has been removed. We have updated our calls, but the code in nxsim is not under our control, so we have pinned the networkx version until that issue is solved.
+### Changed
+* Explicit yaml.SafeLoader to avoid deprecation warnings when using yaml.load. It should not break any existing setups, but we could move to the FullLoader in the future if needed.
+
+## [0.14.4]
+### Fixed
+* Bug in `agent.get_agents()` when `state_id` is passed as a string. The tests have been modified accordingly.
+## [0.14.3]
+### Fixed
+* Incompatibility with py3.3-3.6 due to ModuleNotFoundError and TypeError in DryRunner
+## [0.14.2]
+### Fixed
+* Output path for exporters is now soil_output
+### Changed 
+* CSV output to stdout in dry_run mode
+## [0.14.1]
+### Changed
+* Exporter names in lower case
+* Add default exporter in runs
 ## [0.14.0]
 ### Added
 * Loading configuration from template definitions in the yaml, in preparation for SALib support.

README.md

@@ -1,9 +1,67 @@
 # [SOIL](https://github.com/gsi-upm/soil)
 
+
 Soil is an extensible and user-friendly Agent-based Social Simulator for Social Networks.
 Learn how to run your own simulations with our [documentation](http://soilsim.readthedocs.io).
 
-Follow our [tutorial](examples/tutorial/soil_tutorial.ipynb) to develop your own agent models.
+Follow our [tutorial](docs/tutorial/soil_tutorial.ipynb) to develop your own agent models.
+
+> **Warning**
+> Soil 1.0 introduced many fundamental changes. Check the [documention on how to update your simulations to work with newer versions](docs/notes_v1.0.rst)
+
+## Features
+
+* Integration with (social) networks (through `networkx`)
+* Convenience functions and methods to easily assign agents to your model (and optionally to its network):
+  * Following a given distribution (e.g., 2 agents of type `Foo`, 10% of the network should be agents of type `Bar`)
+  * Based on the topology of the network
+* **Several types of abstractions for agents**:
+  * Finite state machine, where methods can be turned into a state
+  * Network agents, which have convenience methods to access the model's topology
+  * Generator-based agents, whose state is paused though a `yield` and resumed on the next step
+* **Reporting and data collection**:
+  * Soil models include data collection and record some data by default (# of agents, state of each agent, etc.)
+  * All data collected are exported by default to a SQLite database and a description file
+  * Options to export to other formats, such as CSV, or defining your own exporters
+  * A summary of the data collected is shown in the command line, for easy inspection
+* **An event-based scheduler**
+  * Agents can be explicit about when their next time/step should be, and not all agents run in every step. This avoids unnecessary computation.
+  * Time intervals between each step are flexible.
+  * There are primitives to specify when the next execution of an agent should be (or conditions)
+* **Actor-inspired** message-passing
+* A simulation runner (`soil.Simulation`) that can:
+  * Run models in parallel
+  * Save results to different formats
+* Simulation configuration files 
+* A command line interface (`soil`), to quickly run simulations with different parameters
+* An integrated debugger (`soil --debug`) with custom functions to print agent states and break at specific states
+
+## Mesa compatibility
+
+SOIL has been redesigned to integrate well with [Mesa](https://github.com/projectmesa/mesa).
+For instance, it should be possible to run a `mesa.Model` models using a `soil.Simulation` and the `soil` CLI, or to integrate the `soil.TimedActivation` scheduler on a `mesa.Model`.
+
+Note that some combinations of `mesa` and `soil` components, while technically possible, are much less useful or might yield surprising results.
+For instance, you may add any `soil.agent` agent on a regular `mesa.Model` with a vanilla scheduler from `mesa.time`.
+But in that case the agents will not get any of the advanced event-based scheduling, and most agent behaviors that depend on that may not work. 
+
+
+## Changes in version 0.3
+
+Version 0.3 came packed with many changes to provide much better integration with MESA.
+For a long time, we tried to keep soil backwards-compatible, but it turned out to be a big endeavour and the resulting code was less readable.
+This translates to harder maintenance and a worse experience for newcomers. 
+In the end, we decided to make some breaking changes.
+
+If you have an older Soil simulation, you have two options:
+
+* Update the necessary configuration files and code. You may use the examples in the `examples` folder for reference, as well as the documentation.
+* Keep using a previous `soil` version.
+
+
+
+## Citation 
+
 
 If you use Soil in your research, don't forget to cite this paper:
 
@@ -28,7 +86,6 @@ If you use Soil in your research, don't forget to cite this paper:
 
 ```
 
-@Copyright GSI - Universidad Politécnica de Madrid 2017
-
-[![SOIL](logo_gsi.png)](https://www.gsi.dit.upm.es)
+@Copyright GSI - Universidad Politécnica de Madrid 2017-2021
 
+[![SOIL](logo_gsi.png)](https://www.gsi.upm.es)

benchmarks/noop-bench-async.csv

@@ -0,0 +1,12 @@
+command,mean,stddev,median,user,system,min,max,parameter_sim
+python noop/mesa_batchrunner.py,1.3258325165599998,0.05822826666377271,1.31279976286,1.2978164199999997,0.25767558,1.2780627573599999,1.46763559736,mesa_batchrunner
+python noop/mesa_simulation.py,1.3915081544599999,0.07311646048704976,1.37166811936,1.35267662,0.29222067999999995,1.32746067836,1.58495303336,mesa_simulation
+python noop/soil_step.py,1.9859962588599998,0.12143759641749913,1.93586195486,2.0000750199999997,0.54126188,1.9061700903599998,2.2532835533599997,soil_step
+python noop/soil_step_pqueue.py,2.1347049971600005,0.01336179424666973,2.13492341986,2.1368160200000004,0.56862948,2.11810132936,2.16042739636,soil_step_pqueue
+python noop/soil_gens.py,2.1284937893599998,0.03030587681163665,2.13585231586,2.14158812,0.54900038,2.0768625143599997,2.19043625236,soil_gens
+python noop/soil_gens_pqueue.py,2.3469003942599995,0.019461346004472344,2.3486906343599996,2.36505852,0.54629858,2.31766326036,2.37998102136,soil_gens_pqueue
+python noop/soil_async.py,2.85755484126,0.0314955571121844,2.84774029536,2.86388112,0.55261338,2.81428668936,2.90567961636,soil_async
+python noop/soil_async_pqueue.py,3.1999731134600005,0.04432336803797717,3.20255954186,3.2162337199999995,0.5501872800000001,3.1406816913599997,3.26137401936,soil_async_pqueue
+python noop/soilent_step.py,1.30038977816,0.017973958957989845,1.30187804986,1.3231730199999998,0.5452653799999999,1.27058263436,1.31902240836,soilent_step
+python noop/soilent_step_pqueue.py,1.4708435788599998,0.027193290392962755,1.4707784423599999,1.4900387199999998,0.54749428,1.43498127536,1.53065598436,soilent_step_pqueue
+python noop/soilent_gens.py,1.6338810973599998,0.05752539125688073,1.63513330036,1.65216122,0.51846678,1.54135944036,1.7038832853599999,soilent_gens

benchmarks/noop-bench.csv

@@ -0,0 +1,11 @@
+command,mean,stddev,median,user,system,min,max,parameter_sim
+python noop/mesa1_batchrunner.py,1.2559917394000002,0.012031173494887278,1.2572688413000002,1.2168630799999998,0.31825289999999995,1.2346063853,1.2735512493,mesa1_batchrunner
+python noop/mesa1_simulation.py,1.3024417227,0.022498874113931668,1.2994157323,1.2595484799999999,0.3087897,1.2697029703,1.3350640403,mesa1_simulation
+python noop/soil1.py,1.8789492443,0.18023367899835044,1.8186795393000001,1.86076288,0.5309521,1.7326687413000001,2.2928370642999996,soil1
+python noop/soil1_pqueue.py,1.9841675890000001,0.01735524088843906,1.9884363323,2.01830338,0.5787977999999999,1.9592171483,2.0076169282999996,soil1_pqueue
+python noop/soil2.py,2.0135188921999996,0.02869307129649681,2.0184709453,2.03951308,0.5885591,1.9680417823,2.0567112592999997,soil2
+python noop/soil2_pqueue.py,2.2367320454999997,0.024339667344486046,2.2357249777999995,2.2515216799999997,0.5978869,2.1957917303,2.2688685033,soil2_pqueue
+python noop/soilent1.py,1.1309301329,0.015133005948737871,1.1276461497999999,1.14056688,0.6027519,1.1135821423,1.1625753893,soilent1
+python noop/soilent1_pqueue.py,1.3097537665000003,0.018821977712258842,1.3073709358,1.3270259799999997,0.6000067999999998,1.2874580013,1.3381646823,soilent1_pqueue
+python noop/soilent2.py,1.5055360476,0.05166674417574119,1.4883118568,1.5121205799999997,0.5817363999999999,1.4490918363,1.6005909333000001,soilent2
+python noop/soilent2_pqueue.py,1.6622598218,0.031130739036296016,1.6588702603,1.6862567799999997,0.5854159,1.6289724583,1.7330545383,soilent2_pqueue

benchmarks/noop/_config.py

@@ -0,0 +1,25 @@
+import os
+
+NUM_AGENTS = int(os.environ.get('NUM_AGENTS', 100))
+NUM_ITERS = int(os.environ.get('NUM_ITERS', 10))
+MAX_STEPS = int(os.environ.get('MAX_STEPS', 1000))
+
+
+def run_sim(model, **kwargs):
+    from soil import Simulation
+    opts = dict(model=model,
+                dump=False,
+                num_processes=1,
+                parameters={'num_agents': NUM_AGENTS},
+                max_steps=MAX_STEPS,
+                iterations=NUM_ITERS)
+    opts.update(kwargs)
+    res = Simulation(**opts).run()
+
+    total = sum(a.num_calls for e in res for a in e.schedule.agents)
+    expected = NUM_AGENTS * NUM_ITERS * MAX_STEPS
+    print(total)
+    print(expected)
+
+    assert total == expected
+    return res

benchmarks/noop/mesa_batchrunner.py

@@ -0,0 +1,44 @@
+from mesa import batch_run, DataCollector, Agent, Model
+from mesa.time import RandomActivation
+
+
+class NoopAgent(Agent):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.num_calls = 0
+
+    def step(self):
+        # import pdb;pdb.set_trace()
+        self.num_calls += 1 
+
+
+class NoopModel(Model):
+    def __init__(self, N):
+        super().__init__()
+        self.schedule = RandomActivation(self)
+        for i in range(N):
+            self.schedule.add(NoopAgent(self.next_id(), self))
+        self.datacollector = DataCollector(model_reporters={"num_agents": lambda m: m.schedule.get_agent_count(),
+                                                            "time": lambda m: m.schedule.time},
+                                           agent_reporters={"num_calls": "num_calls"})
+        self.datacollector.collect(self)
+
+    def step(self):
+        self.schedule.step()
+        self.datacollector.collect(self)
+
+
+if __name__ == "__main__":
+    from _config import *
+
+    res = batch_run(model_cls=NoopModel,
+                    max_steps=MAX_STEPS,
+                    iterations=NUM_ITERS,
+                    number_processes=1,
+                    parameters={'N': NUM_AGENTS})
+    total = sum(s["num_calls"] for s in res)
+    total_agents = sum(s["num_agents"] for s in res)
+    assert len(res) == NUM_AGENTS * NUM_ITERS
+    assert total == NUM_AGENTS * NUM_ITERS * MAX_STEPS
+    assert total_agents == NUM_AGENTS * NUM_AGENTS * NUM_ITERS
+

benchmarks/noop/mesa_simulation.py

@@ -0,0 +1,38 @@
+from mesa import batch_run, DataCollector, Agent, Model
+from mesa.time import RandomActivation
+from soil import Simulation
+from _config import *
+
+
+class NoopAgent(Agent):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.num_calls = 0
+
+    def step(self):
+        # import pdb;pdb.set_trace()
+        self.num_calls += 1 
+
+
+class NoopModel(Model):
+    def __init__(self, num_agents, *args, **kwargs):
+        super().__init__()
+        self.schedule = RandomActivation(self)
+        for i in range(num_agents):
+            self.schedule.add(NoopAgent(self.next_id(), self))
+        self.datacollector = DataCollector(model_reporters={"num_agents": lambda m: m.schedule.get_agent_count(),
+                                                            "time": lambda m: m.schedule.time},
+                                           agent_reporters={"num_calls": "num_calls"})
+        self.datacollector.collect(self)
+
+    def step(self):
+        self.schedule.step()
+        self.datacollector.collect(self)
+
+
+def run():
+    run_sim(model=NoopModel)
+
+
+if __name__ == "__main__":
+    run()

benchmarks/noop/noop-bench.csv

@@ -0,0 +1,3 @@
+command,mean,stddev,median,user,system,min,max,parameter_sim
+python mesa1_batchrunner.py,1.2932078178200002,0.05649377020829272,1.2705532802200001,1.25902256,0.27242284,1.22210926572,1.40867459172,mesa1_batchrunner
+python mesa1_simulation.py,1.81112963812,0.015491072368938567,1.81342524572,1.8594407599999996,0.8005329399999999,1.78538603972,1.84176361172,mesa1_simulation

benchmarks/noop/soil_async.py

@@ -0,0 +1,24 @@
+from soil import BaseAgent, Environment, Simulation
+
+
+class NoopAgent(BaseAgent):
+    num_calls = 0
+
+    async def step(self):
+        while True:
+            self.num_calls += 1
+            await self.delay()
+
+
+class NoopEnvironment(Environment):
+    num_agents = 100
+
+    def init(self):
+        self.add_agents(NoopAgent, k=self.num_agents)
+        self.add_agent_reporter("num_calls")
+
+
+if __name__ == "__main__":
+    from _config import *
+
+    run_sim(model=NoopEnvironment)

benchmarks/noop/soil_async_pqueue.py

@@ -0,0 +1,25 @@
+from soil import BaseAgent, Environment, Simulation, PQueueActivation
+
+
+class NoopAgent(BaseAgent):
+    num_calls = 0
+
+    async def step(self):
+        while True:
+            self.num_calls += 1
+            await self.delay()
+
+
+class NoopEnvironment(Environment):
+    num_agents = 100
+    schedule_class = PQueueActivation
+
+    def init(self):
+        self.add_agents(NoopAgent, k=self.num_agents)
+        self.add_agent_reporter("num_calls")
+
+
+if __name__ == "__main__":
+    from _config import *
+
+    run_sim(model=NoopEnvironment)

benchmarks/noop/soil_gens.py

@@ -0,0 +1,24 @@
+from soil import BaseAgent, Environment, Simulation
+
+
+class NoopAgent(BaseAgent):
+    num_calls = 0
+
+    def step(self):
+        while True:
+            self.num_calls += 1
+            yield self.delay()
+
+
+class NoopEnvironment(Environment):
+    num_agents = 100
+
+    def init(self):
+        self.add_agents(NoopAgent, k=self.num_agents)
+        self.add_agent_reporter("num_calls")
+
+
+if __name__ == "__main__":
+    from _config import *
+
+    run_sim(model=NoopEnvironment)

benchmarks/noop/soil_gens_pqueue.py

@@ -0,0 +1,25 @@
+from soil import BaseAgent, Environment, Simulation, PQueueActivation
+
+
+class NoopAgent(BaseAgent):
+    num_calls = 0
+
+    def step(self):
+        while True:
+            self.num_calls += 1
+            yield self.delay()
+
+
+class NoopEnvironment(Environment):
+    num_agents = 100
+    schedule_class = PQueueActivation
+
+    def init(self):
+        self.add_agents(NoopAgent, k=self.num_agents)
+        self.add_agent_reporter("num_calls")
+
+
+if __name__ == "__main__":
+    from _config import *
+
+    run_sim(model=NoopEnvironment)

benchmarks/noop/soil_step.py

@@ -0,0 +1,21 @@
+from soil import BaseAgent, Environment, Simulation
+
+
+class NoopAgent(BaseAgent):
+    num_calls = 0
+
+    def step(self):
+        self.num_calls += 1
+
+class NoopEnvironment(Environment):
+    num_agents = 100
+
+    def init(self):
+        self.add_agents(NoopAgent, k=self.num_agents)
+        self.add_agent_reporter("num_calls")
+
+
+if __name__ == "__main__":
+    from _config import *
+
+    run_sim(model=NoopEnvironment)

benchmarks/noop/soil_step_pqueue.py

@@ -0,0 +1,22 @@
+from soil import BaseAgent, Environment, Simulation, PQueueActivation
+
+
+class NoopAgent(BaseAgent):
+    num_calls = 0
+
+    def step(self):
+        self.num_calls += 1
+
+class NoopEnvironment(Environment):
+    num_agents = 100
+    schedule_class = PQueueActivation
+
+    def init(self):
+        self.add_agents(NoopAgent, k=self.num_agents)
+        self.add_agent_reporter("num_calls")
+
+
+if __name__ == "__main__":
+    from _config import *
+
+    run_sim(model=NoopEnvironment)

benchmarks/noop/soilent_async.py

@@ -0,0 +1,29 @@
+from soil import Agent, Environment, Simulation
+from soilent import Scheduler
+
+
+class NoopAgent(Agent):
+    num_calls = 0
+
+    async def step(self):
+        while True:
+            self.num_calls += 1
+            # yield self.delay(1)
+            await self.delay()
+
+
+class NoopEnvironment(Environment):
+    num_agents = 100
+    schedule_class = Scheduler
+
+    def init(self):
+        self.add_agents(NoopAgent, k=self.num_agents)
+        self.add_agent_reporter("num_calls")
+
+
+if __name__ == "__main__":
+    from _config import *
+
+    res = run_sim(model=NoopEnvironment)
+    for r in res:
+        assert isinstance(r.schedule, Scheduler)

benchmarks/noop/soilent_async_pqueue.py

@@ -0,0 +1,27 @@
+from soil import Agent, Environment
+from soilent import PQueueScheduler
+
+
+class NoopAgent(Agent):
+    num_calls = 0
+
+    async def step(self):
+        while True:
+            self.num_calls += 1
+            await self.delay()
+
+class NoopEnvironment(Environment):
+    num_agents = 100
+    schedule_class = PQueueScheduler
+
+    def init(self):
+        self.add_agents(NoopAgent, k=self.num_agents)
+        self.add_agent_reporter("num_calls")
+
+
+if __name__ == "__main__":
+    from _config import *
+
+    res = run_sim(model=NoopEnvironment)
+    for r in res:
+        assert isinstance(r.schedule, PQueueScheduler)

benchmarks/noop/soilent_gens.py

@@ -0,0 +1,28 @@
+from soil import Agent, Environment, Simulation
+from soilent import Scheduler
+
+
+class NoopAgent(Agent):
+    num_calls = 0
+
+    def step(self):
+        while True:
+            self.num_calls += 1
+            # yield self.delay(1)
+            yield self.delay()
+
+class NoopEnvironment(Environment):
+    num_agents = 100
+    schedule_class = Scheduler
+
+    def init(self):
+        self.add_agents(NoopAgent, k=self.num_agents)
+        self.add_agent_reporter("num_calls")
+
+
+if __name__ == "__main__":
+    from _config import *
+
+    res = run_sim(model=NoopEnvironment)
+    for r in res:
+        assert isinstance(r.schedule, Scheduler)

benchmarks/noop/soilent_gens_pqueue.py

@@ -0,0 +1,28 @@
+from soil import Agent, Environment
+from soilent import PQueueScheduler
+
+
+class NoopAgent(Agent):
+    num_calls = 0
+
+    def step(self):
+        while True:
+            self.num_calls += 1
+            # yield self.delay(1)
+            yield
+
+class NoopEnvironment(Environment):
+    num_agents = 100
+    schedule_class = PQueueScheduler
+
+    def init(self):
+        self.add_agents(NoopAgent, k=self.num_agents)
+        self.add_agent_reporter("num_calls")
+
+
+if __name__ == "__main__":
+    from _config import *
+
+    res = run_sim(model=NoopEnvironment)
+    for r in res:
+        assert isinstance(r.schedule, PQueueScheduler)

benchmarks/noop/soilent_step.py

@@ -0,0 +1,24 @@
+from soil import BaseAgent, Environment, Simulation
+from soilent import Scheduler
+
+
+class NoopAgent(BaseAgent):
+    num_calls = 0
+
+    def step(self):
+        self.num_calls += 1
+
+class NoopEnvironment(Environment):
+    num_agents = 100
+    schedule_class = Scheduler
+
+    def init(self):
+        self.add_agents(NoopAgent, k=self.num_agents)
+        self.add_agent_reporter("num_calls")
+
+
+if __name__ == "__main__":
+    from _config import *
+    res = run_sim(model=NoopEnvironment)
+    for r in res:
+        assert isinstance(r.schedule, Scheduler)

benchmarks/noop/soilent_step_pqueue.py

@@ -0,0 +1,24 @@
+from soil import BaseAgent, Environment, Simulation
+from soilent import PQueueScheduler
+
+
+class NoopAgent(BaseAgent):
+    num_calls = 0
+
+    def step(self):
+        self.num_calls += 1
+
+class NoopEnvironment(Environment):
+    num_agents = 100
+    schedule_class = PQueueScheduler
+
+    def init(self):
+        self.add_agents(NoopAgent, k=self.num_agents)
+        self.add_agent_reporter("num_calls")
+
+
+if __name__ == "__main__":
+    from _config import *
+    res = run_sim(model=NoopEnvironment)
+    for r in res:
+        assert isinstance(r.schedule, PQueueScheduler)

benchmarks/run.py

@@ -0,0 +1,19 @@
+#!/bin/env python
+import sys
+import os
+import subprocess
+import argparse
+parser = argparse.ArgumentParser(
+                    prog='Profiler for soil')
+parser.add_argument('--suffix', default=None)
+parser.add_argument('files', nargs="+")
+
+args = parser.parse_args()
+
+for fname in args.files:
+    suffix = ("_" + args.suffix) if args.suffix else ""
+    simname = f"{fname.replace('/', '-')}{suffix}"
+    profpath = os.path.join("profs", simname + ".prof")
+
+    print(f"Running {fname} and saving profile to {profpath}")
+    subprocess.call(["python", "-m", "cProfile", "-o", profpath, fname])

benchmarks/virusonnetwork.csv

@@ -0,0 +1,4 @@
+command,mean,stddev,median,user,system,min,max,parameter_sim
+python virusonnetwork/mesa_basic.py,3.8381473157,0.0518143371442526,3.8475315791,3.873109219999999,0.55102658,3.7523016936,3.9095182436,mesa_basic.py
+python virusonnetwork/soil_step.py,3.2167258977000004,0.02337131987357665,3.2257620261,3.28374132,0.51343958,3.1792271306,3.2511521286000002,soil_step.py
+python virusonnetwork/soil_states.py,3.4908183217,0.03726734070349347,3.4912775086,3.5684004200000006,0.50416068,3.4272087936,3.5529207346000002,soil_states.py

benchmarks/virusonnetwork/_config.py

@@ -0,0 +1,32 @@
+import os
+
+NUM_AGENTS = int(os.environ.get('NUM_AGENTS', 100))
+NUM_ITERS = int(os.environ.get('NUM_ITERS', 10))
+MAX_STEPS = int(os.environ.get('MAX_STEPS', 1000))
+
+
+def run_sim(model, **kwargs):
+    from soil import Simulation
+    opts = dict(model=model,
+                dump=False,
+                num_processes=1,
+                parameters={'num_nodes': NUM_AGENTS,
+                            "avg_node_degree": 3,
+                            "initial_outbreak_size": 5,
+                            "virus_spread_chance": 0.25,
+                            "virus_check_frequency": 0.25,
+                            "recovery_chance": 0.3,
+                            "gain_resistance_chance": 0.1,
+                            },
+                max_steps=MAX_STEPS,
+                iterations=NUM_ITERS)
+    opts.update(kwargs)
+    its = Simulation(**opts).run()
+
+    assert all(it.schedule.steps == MAX_STEPS for it in its)
+    ratios = list(it.resistant_susceptible_ratio() for it in its)
+    print("Max - Avg - Min ratio:", max(ratios), sum(ratios)/len(ratios), min(ratios))
+    assert all(sum([it.number_susceptible,
+                    it.number_infected,
+                    it.number_resistant]) == NUM_AGENTS for it in its)
+    return its

benchmarks/virusonnetwork/mesa_basic.py

@@ -0,0 +1,180 @@
+# Verbatim copy from mesa
+# https://github.com/projectmesa/mesa/blob/976ddfc8a1e5feaaf8007a7abaa9abc7093881a0/examples/virus_on_network/virus_on_network/model.py
+import math
+from enum import Enum
+import networkx as nx
+
+import mesa
+
+
+class State(Enum):
+    SUSCEPTIBLE = 0
+    INFECTED = 1
+    RESISTANT = 2
+
+
+def number_state(model, state):
+    return sum(1 for a in model.grid.get_all_cell_contents() if a.state is state)
+
+
+def number_infected(model):
+    return number_state(model, State.INFECTED)
+
+
+def number_susceptible(model):
+    return number_state(model, State.SUSCEPTIBLE)
+
+
+def number_resistant(model):
+    return number_state(model, State.RESISTANT)
+
+
+class VirusOnNetwork(mesa.Model):
+    """A virus model with some number of agents"""
+
+    def __init__(
+        self,
+        *args,
+        num_nodes=10,
+        avg_node_degree=3,
+        initial_outbreak_size=1,
+        virus_spread_chance=0.4,
+        virus_check_frequency=0.4,
+        recovery_chance=0.3,
+        gain_resistance_chance=0.5,
+        **kwargs,
+    ):
+
+        self.num_nodes = num_nodes
+        prob = avg_node_degree / self.num_nodes
+        self.G = nx.erdos_renyi_graph(n=self.num_nodes, p=prob)
+        self.grid = mesa.space.NetworkGrid(self.G)
+        self.schedule = mesa.time.RandomActivation(self)
+        self.initial_outbreak_size = (
+            initial_outbreak_size if initial_outbreak_size <= num_nodes else num_nodes
+        )
+        self.virus_spread_chance = virus_spread_chance
+        self.virus_check_frequency = virus_check_frequency
+        self.recovery_chance = recovery_chance
+        self.gain_resistance_chance = gain_resistance_chance
+
+        self.datacollector = mesa.DataCollector(
+            {
+                "Ratio": "resistant_susceptible_ratio",
+                "Infected": number_infected,
+                "Susceptible": number_susceptible,
+                "Resistant": number_resistant,
+            }
+        )
+
+        # Create agents
+        for i, node in enumerate(self.G.nodes()):
+            a = VirusAgent(
+                i,
+                self,
+                State.SUSCEPTIBLE,
+                self.virus_spread_chance,
+                self.virus_check_frequency,
+                self.recovery_chance,
+                self.gain_resistance_chance,
+            )
+            self.schedule.add(a)
+            # Add the agent to the node
+            self.grid.place_agent(a, node)
+
+        # Infect some nodes
+        infected_nodes = self.random.sample(list(self.G), self.initial_outbreak_size)
+        for a in self.grid.get_cell_list_contents(infected_nodes):
+            a.state = State.INFECTED
+
+        self.running = True
+        self.datacollector.collect(self)
+    
+    @property
+    def number_susceptible(self):
+        return number_susceptible(self)
+    @property
+    def number_resistant(self):
+        return number_resistant(self)
+    @property
+    def number_infected(self):
+        return number_infected(self)
+
+    def resistant_susceptible_ratio(self):
+        try:
+            return number_state(self, State.RESISTANT) / number_state(
+                self, State.SUSCEPTIBLE
+            )
+        except ZeroDivisionError:
+            return math.inf
+
+    def step(self):
+        self.schedule.step()
+        # collect data
+        self.datacollector.collect(self)
+
+    def run_model(self, n):
+        for i in range(n):
+            self.step()
+
+
+class VirusAgent(mesa.Agent):
+    def __init__(
+        self,
+        unique_id,
+        model,
+        initial_state,
+        virus_spread_chance,
+        virus_check_frequency,
+        recovery_chance,
+        gain_resistance_chance,
+    ):
+        super().__init__(unique_id, model)
+
+        self.state = initial_state
+
+        self.virus_spread_chance = virus_spread_chance
+        self.virus_check_frequency = virus_check_frequency
+        self.recovery_chance = recovery_chance
+        self.gain_resistance_chance = gain_resistance_chance
+
+    def try_to_infect_neighbors(self):
+        neighbors_nodes = self.model.grid.get_neighbors(self.pos, include_center=False)
+        susceptible_neighbors = [
+            agent
+            for agent in self.model.grid.get_cell_list_contents(neighbors_nodes)
+            if agent.state is State.SUSCEPTIBLE
+        ]
+        for a in susceptible_neighbors:
+            if self.random.random() < self.virus_spread_chance:
+                a.state = State.INFECTED
+
+    def try_gain_resistance(self):
+        if self.random.random() < self.gain_resistance_chance:
+            self.state = State.RESISTANT
+
+    def try_remove_infection(self):
+        # Try to remove
+        if self.random.random() < self.recovery_chance:
+            # Success
+            self.state = State.SUSCEPTIBLE
+            self.try_gain_resistance()
+        else:
+            # Failed
+            self.state = State.INFECTED
+
+    def try_check_situation(self):
+        if self.random.random() < self.virus_check_frequency:
+            # Checking...
+            if self.state is State.INFECTED:
+                self.try_remove_infection()
+
+    def step(self):
+        if self.state is State.INFECTED:
+            self.try_to_infect_neighbors()
+        self.try_check_situation()
+
+
+from _config import run_sim
+
+run_sim(model=VirusOnNetwork)

benchmarks/virusonnetwork/soil_states.py

@@ -0,0 +1,92 @@
+# Verbatim copy from mesa
+# https://github.com/projectmesa/mesa/blob/976ddfc8a1e5feaaf8007a7abaa9abc7093881a0/examples/virus_on_network/virus_on_network/model.py
+import math
+from enum import Enum
+import networkx as nx
+
+from soil import *
+
+
+class VirusOnNetwork(Environment):
+    """A virus model with some number of agents"""
+    num_nodes = 10
+    avg_node_degree = 3
+    initial_outbreak_size = 1
+    virus_spread_chance = 0.4
+    virus_check_frequency = 0.4
+    recovery_chance = 0
+    gain_resistance_chance = 0
+
+    def init(self):
+        prob = self.avg_node_degree / self.num_nodes
+        # Use internal seed with the networkx generator
+        self.create_network(generator=nx.erdos_renyi_graph, n=self.num_nodes, p=prob)
+
+        self.initial_outbreak_size = min(self.initial_outbreak_size, self.num_nodes)
+        self.populate_network(VirusAgent)
+
+        # Infect some nodes
+        infected_nodes = self.random.sample(list(self.G), self.initial_outbreak_size)
+        for a in self.get_agents(node_id=infected_nodes):
+            a.set_state(VirusAgent.infected)
+        assert self.number_infected == self.initial_outbreak_size
+
+    @report
+    def resistant_susceptible_ratio(self):
+        try:
+            return self.number_resistant / self.number_susceptible
+        except ZeroDivisionError:
+            return math.inf
+
+    @report
+    @property
+    def number_infected(self):
+        return self.count_agents(state_id=VirusAgent.infected.id)
+
+    @report
+    @property
+    def number_susceptible(self):
+        return self.count_agents(state_id=VirusAgent.susceptible.id)
+
+    @report
+    @property
+    def number_resistant(self):
+        return self.count_agents(state_id=VirusAgent.resistant.id)
+
+
+class VirusAgent(Agent):
+    virus_spread_chance = None # Inherit from model
+    virus_check_frequency = None # Inherit from model
+    recovery_chance = None # Inherit from model
+    gain_resistance_chance = None # Inherit from model
+    just_been_infected = False
+
+    @state(default=True)
+    def susceptible(self):
+        if self.just_been_infected:
+            self.just_been_infected = False
+            return self.infected
+
+    @state
+    def infected(self):
+        susceptible_neighbors = self.get_neighbors(state_id=self.susceptible.id)
+        for a in susceptible_neighbors:
+            if self.prob(self.virus_spread_chance):
+                a.just_been_infected = True
+        if self.prob(self.virus_check_frequency):
+            if self.prob(self.recovery_chance):
+                if self.prob(self.gain_resistance_chance):
+                    return self.resistant
+                else:
+                    return self.susceptible
+            else:
+                return self.infected
+
+    @state
+    def resistant(self):
+        return self.at(INFINITY)
+
+
+if __name__ == "__main__":
+    from _config import run_sim
+    run_sim(model=VirusOnNetwork)

benchmarks/virusonnetwork/soil_step.py

@@ -0,0 +1,104 @@
+# Verbatim copy from mesa
+# https://github.com/projectmesa/mesa/blob/976ddfc8a1e5feaaf8007a7abaa9abc7093881a0/examples/virus_on_network/virus_on_network/model.py
+import math
+from enum import Enum
+import networkx as nx
+
+from soil import *
+
+
+class State(Enum):
+    SUSCEPTIBLE = 0
+    INFECTED = 1
+    RESISTANT = 2
+
+
+class VirusOnNetwork(Environment):
+    """A virus model with some number of agents"""
+    num_nodes = 10
+    avg_node_degree = 3
+    initial_outbreak_size = 1
+    virus_spread_chance = 0.4
+    virus_check_frequency = 0.4
+    recovery_chance = 0
+    gain_resistance_chance = 0
+
+    def init(self):
+        prob = self.avg_node_degree / self.num_nodes
+        # Use internal seed with the networkx generator
+        self.create_network(generator=nx.erdos_renyi_graph, n=self.num_nodes, p=prob)
+
+        self.initial_outbreak_size = min(self.initial_outbreak_size, self.num_nodes)
+        self.populate_network(VirusAgent)
+
+        # Infect some nodes
+        infected_nodes = self.random.sample(list(self.G), self.initial_outbreak_size)
+        for a in self.get_agents(node_id=infected_nodes):
+            a.status = State.INFECTED
+        assert self.number_infected == self.initial_outbreak_size
+
+    @report
+    def resistant_susceptible_ratio(self):
+        try:
+            return self.number_resistant / self.number_susceptible
+        except ZeroDivisionError:
+            return math.inf
+
+    @report
+    @property
+    def number_infected(self):
+        return self.count_agents(status=State.INFECTED)
+
+    @report
+    @property
+    def number_susceptible(self):
+        return self.count_agents(status=State.SUSCEPTIBLE)
+
+    @report
+    @property
+    def number_resistant(self):
+        return self.count_agents(status=State.RESISTANT)
+
+
+
+class VirusAgent(Agent):
+    status = State.SUSCEPTIBLE
+    virus_spread_chance = None # Inherit from model
+    virus_check_frequency = None # Inherit from model
+    recovery_chance = None # Inherit from model
+    gain_resistance_chance = None # Inherit from model
+
+    def try_to_infect_neighbors(self):
+        susceptible_neighbors = self.get_neighbors(status=State.SUSCEPTIBLE)
+        for a in susceptible_neighbors:
+            if self.prob(self.virus_spread_chance):
+                a.status = State.INFECTED
+
+    def try_gain_resistance(self):
+        if self.prob(self.gain_resistance_chance):
+            self.status = State.RESISTANT
+            return self.at(INFINITY)
+
+    def try_remove_infection(self):
+        # Try to remove
+        if self.prob(self.recovery_chance):
+            # Success
+            self.status = State.SUSCEPTIBLE
+            return self.try_gain_resistance()
+
+    def try_check_situation(self):
+        if self.prob(self.virus_check_frequency):
+            # Checking...
+            if self.status is State.INFECTED:
+                return self.try_remove_infection()
+
+    def step(self):
+        if self.status is State.INFECTED:
+            self.try_to_infect_neighbors()
+        return self.try_check_situation()
+
+
+
+if __name__ == "__main__":
+    from _config import run_sim
+    run_sim(model=VirusOnNetwork)

docs/conf.py

@@ -31,7 +31,10 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = []
+extensions = [
+    "IPython.sphinxext.ipython_console_highlighting",
+    "nbsphinx",
+]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -64,12 +67,12 @@ release = '0.1'
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
@@ -152,6 +155,3 @@ texinfo_documents = [
      author, 'Soil', 'One line description of project.',
      'Miscellaneous'),
 ]
-
-
-

docs/configuration.rst

@@ -1,244 +0,0 @@
-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.

docs/index.rst

@@ -1,12 +1,21 @@
-.. Soil documentation master file, created by
-   sphinx-quickstart on Tue Apr 25 12:48:56 2017.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
 Welcome to Soil's documentation!
 ================================
 
-Soil is an Agent-based Social Simulator in Python focused on Social Networks.
+Soil is an opinionated Agent-based Social Simulator in Python focused on Social Networks.
+To get started developing your own simulations and agent behaviors, check out our :doc:`Tutorial <tutorial/soil_tutorial>` and the `examples on GitHub <https://github.com/gsi-upm/soil/tree/master/examples>`.
+
+Soil can be installed through pip (see more details in the :doc:`installation` page):.
+
+.. image:: soil.png
+  :width: 80%
+  :align: center
+
+
+.. code:: bash
+
+    pip install soil
+
+
 
 If you use Soil in your research, do not forget to cite this paper:
 
@@ -38,9 +47,9 @@ If you use Soil in your research, do not forget to cite this paper:
    :caption: Learn more about soil:
 
    installation
-   quickstart
-   configuration
-   Tutorial <soil_tutorial>
+   Tutorial <tutorial/soil_tutorial>
+   notes_v1.0
+   soil-vs
 
 ..
 

docs/installation.rst

@@ -1,7 +1,10 @@
 Installation
 ------------
 
-The easiest way to install Soil is through pip, with Python >= 3.4:
+Through pip
+===========
+
+The easiest way to install Soil is through pip, with Python >= 3.8:
 
 .. code:: bash
 
@@ -14,11 +17,49 @@ Now test that it worked by running the command line tool
 
    soil --help
 
-Or using soil programmatically:
+   #or
+
+   python -m soil --help
+
+Or, if you're using using soil programmatically:
 
 .. code:: python
 
    import soil
    print(soil.__version__)
 
-The latest version can be installed through `GitLab <https://lab.cluster.gsi.dit.upm.es/soil/soil.git>`_.
+
+
+Web UI
+======
+
+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:
+
+.. code::
+
+  pip install soil[web]
+
+Once installed, the soil web UI can be run in two ways:
+
+.. code::
+
+  soil-web
+
+  # OR
+
+  python -m soil.web
+
+
+Development
+===========
+
+The latest version can be downloaded from `GitHub <https://github.com/gsi-upm/soil>`_ and installed manually:
+
+.. code:: bash
+
+   git clone https://github.com/gsi-upm/soil
+   cd soil
+   python -m venv .venv
+   source .venv/bin/activate
+   pip install --editable .

docs/make.bat

@@ -12,7 +12,7 @@ set BUILDDIR=_build
 set SPHINXPROJ=Soil
 
 if "%1" == "" goto help
-
+eE
 %SPHINXBUILD% >NUL 2>NUL
 if errorlevel 9009 (
 	echo.

docs/notes_v1.0.rst

@@ -0,0 +1,38 @@
+Upgrading to Soil 1.0
+---------------------
+
+What are the main changes in version 1.0?
+#########################################
+
+Version 1.0 is a major rewrite of the Soil system, focused on simplifying the API, aligning it with Mesa, and making it easier to use.
+Unfortunately, this comes at the cost of backwards compatibility.
+
+We drew several lessons from the previous version of Soil, and tried to address them in this version.
+Mainly:
+
+- The split between simulation configuration and simulation code was overly complicated for most use cases. As a result, most users ended up reusing configuration.
+- Storing **all** the simulation data in a database is costly and unnecessary for most use cases. For most use cases, only a handful of variables need to be stored. This fits nicely with Mesa's data collection system.
+- The API was too complex, and it was difficult to understand how to use it.
+- Most parts of the API were not aligned with Mesa, which made it difficult to use Mesa's features or to integrate Soil modules with Mesa code, especially for newcomers.
+- Many parts of the API were tightly coupled, which made it difficult to find bugs, test the system and add new features.
+
+The 0.30 rewrite should provide a middle ground between Soil's opinionated approach and Mesa's flexibility.
+The new Soil is less configuration-centric.
+It aims to provide more modular and convenient functions, most of which can be used in vanilla Mesa.
+
+How are agents assigned to nodes in the network
+###############################################
+
+The constructor of the `NetworkAgent` class has two arguments: `node_id` and `topology`.
+If `topology` is not provided, it will default to `self.model.topology`.
+This assignment might err if the model does not have a `topology` attribute, but most Soil environments derive from `NetworkEnvironment`, so they include a topology by default.
+If `node_id` is not provided, a random node will be selected from the topology, until a node with no agent is found.
+Then, the `node_id` of that node is assigned to the agent.
+If no node with no agent is found, a new node is automatically added to the topology.
+
+
+Can Soil environments include more than one network / topology?
+###############################################################
+
+Yes, but each network has to be included manually.
+Somewhere between 0.20 and 0.30 we included the ability to include multiple networks, but it was deemed too complex and was removed.

docs/quickstart.rst

@@ -1,93 +0,0 @@
-Quickstart
-----------
-
-This section shows how to run your first simulation with Soil.
-For installation instructions, see :doc:`installation`.
-
-There are mainly two parts in a simulation: agent classes and simulation configuration.
-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.
-
-
-.. image:: soil.png
-  :width: 80%
-  :align: center
-
-
-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`.
-
-Configuration
-=============
-To get you started, we will use this configuration (:download:`download the file <quickstart.yml>` directly):
-
-.. literalinclude:: quickstart.yml
-   :language: yaml
-
-The agent type used, SISa, is a very simple model.
-It only has three states (neutral, content and discontent),
-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::
-
-    ❯ soil --graph --csv quickstart.yml                                                          [13:35:29]
-    INFO:soil:Using config(s): quickstart
-    INFO:soil:Dumping results to soil_output/quickstart : ['csv', 'gexf']
-    INFO:soil:Starting simulation quickstart at 13:35:30.
-    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
-
-
-The ``CSV`` file should look like this:
-
-.. 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/>`__.
-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:
-
-.. code::
-
-  pip install soil[web]
-
-Once installed, the soil web UI can be run in two ways:
-
-.. code::
-
-  soil-web
-
-  # OR
-
-  python -m soil.web

docs/quickstart.yml

@@ -1,30 +0,0 @@
----
-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

docs/requirements.txt

@@ -0,0 +1,2 @@
+ipython>=7.31.1
+nbsphinx==0.9.1

docs/soil-vs.rst

@@ -0,0 +1,55 @@
+Soil vs other ABM frameworks
+============================
+
+MESA
+----
+
+Starting with version 0.3, Soil has been redesigned to complement Mesa, while remaining compatible with it.
+That means that every component in Soil (i.e., Models, Environments, etc.) can be mixed with existing mesa components.
+In fact, there are examples that show how that integration may be used, in the `examples/mesa` folder in the repository.
+
+Here are some reasons to use Soil instead of plain mesa:
+
+- Less boilerplate for common scenarios (by some definitions of common)
+- Functions to automatically populate a topology with an agent distribution (i.e., different ratios of agent class and state)
+- The `soil.Simulation` class allows you to run multiple instances of the same experiment (i.e., multiple trials with the same parameters but a different randomness seed)
+- Reporting functions that aggregate multiple
+
+Mesa compatibility
+~~~~~~~~~~~~~~~~~~
+
+Soil is in the process of becoming fully compatible with MESA.
+The idea is to provide a set of modular classes and functions that extend the functionality of mesa, whilst staying compatible.
+In the end, it should be possible to add regular mesa agents to a soil simulation, or use a soil agent within a mesa simulation/model.
+
+This is a non-exhaustive list of tasks to achieve compatibility:
+
+.. |check| raw:: html
+
+    ☑
+
+.. |uncheck| raw:: html
+
+    ☐
+
+- |check| Integrate `soil.Simulation` with mesa's runners:
+
+  - |check| `soil.Simulation` can replace `mesa.batchrunner`
+
+- |check| Integrate `soil.Environment` with `mesa.Model`:
+
+  - |check| `Soil.Environment` inherits from `mesa.Model`
+  - |check| `Soil.Environment` includes a Mesa-like Scheduler (see the `soil.time` module.
+  - |check| Allow for `mesa.Model` to be used in a simulation.
+
+- |check| Integrate `soil.Agent` with `mesa.Agent`:
+
+  - |check| Rename agent.id to unique_id
+  - |check| mesa agents can be used in soil simulations (see `examples/mesa`)
+
+- |check| Provide examples
+
+  - |check| Using mesa modules in a soil simulation (see `examples/mesa`)
+  - |uncheck| Using soil modules in a mesa simulation (see `examples/mesa`)
+
+- |uncheck| Document the new APIs and usage

docs/tutorial/soil_tutorial.html

@@ -12330,11 +12330,11 @@ Notice how node 0 is the only one with a TV.</p>
 <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">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_class&#39;</span><span class="p">:</span> <span class="n">NewsEnvironmentAgent</span><span class="p">,</span>
                                                          <span class="s1">&#39;state&#39;</span><span class="p">:</span> <span class="p">{</span>
                                                              <span class="s1">&#39;event_time&#39;</span><span class="p">:</span> <span class="n">EVENT_TIME</span>
                                                          <span class="p">}}],</span>
-                                     <span class="n">network_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">NewsSpread</span><span class="p">,</span>
+                                     <span class="n">network_agents</span><span class="o">=</span><span class="p">[{</span><span class="s1">&#39;agent_class&#39;</span><span class="p">:</span> <span class="n">NewsSpread</span><span class="p">,</span>
                                                       <span class="s1">&#39;weight&#39;</span><span class="p">:</span> <span class="mi">1</span><span class="p">}],</span>
                                      <span class="n">states</span><span class="o">=</span><span class="p">{</span><span class="mi">0</span><span class="p">:</span> <span class="p">{</span><span class="s1">&#39;has_tv&#39;</span><span class="p">:</span> <span class="kc">True</span><span class="p">}},</span>
                                      <span class="n">default_state</span><span class="o">=</span><span class="p">{</span><span class="s1">&#39;has_tv&#39;</span><span class="p">:</span> <span class="kc">False</span><span class="p">},</span>
@@ -12468,14 +12468,14 @@ For this demo, we will use a python dictionary:</p>
     <span class="p">},</span>
     <span class="s1">&#39;network_agents&#39;</span><span class="p">:</span> <span class="p">[</span>
         <span class="p">{</span>
-            <span class="s1">&#39;agent_type&#39;</span><span class="p">:</span> <span class="n">NewsSpread</span><span class="p">,</span>
+            <span class="s1">&#39;agent_class&#39;</span><span class="p">:</span> <span class="n">NewsSpread</span><span class="p">,</span>
             <span class="s1">&#39;weight&#39;</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
             <span class="s1">&#39;state&#39;</span><span class="p">:</span> <span class="p">{</span>
                 <span class="s1">&#39;has_tv&#39;</span><span class="p">:</span> <span class="kc">False</span>
             <span class="p">}</span>
         <span class="p">},</span>
         <span class="p">{</span>
-            <span class="s1">&#39;agent_type&#39;</span><span class="p">:</span> <span class="n">NewsSpread</span><span class="p">,</span>
+            <span class="s1">&#39;agent_class&#39;</span><span class="p">:</span> <span class="n">NewsSpread</span><span class="p">,</span>
             <span class="s1">&#39;weight&#39;</span><span class="p">:</span> <span class="mi">2</span><span class="p">,</span>
             <span class="s1">&#39;state&#39;</span><span class="p">:</span> <span class="p">{</span>
                 <span class="s1">&#39;has_tv&#39;</span><span class="p">:</span> <span class="kc">True</span>
@@ -12483,7 +12483,7 @@ For this demo, we will use a python dictionary:</p>
         <span class="p">}</span>
     <span class="p">],</span>
     <span class="s1">&#39;environment_agents&#39;</span><span class="p">:[</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="p">{</span><span class="s1">&#39;agent_class&#39;</span><span class="p">:</span> <span class="n">NewsEnvironmentAgent</span><span class="p">,</span>
          <span class="s1">&#39;state&#39;</span><span class="p">:</span> <span class="p">{</span>
              <span class="s1">&#39;event_time&#39;</span><span class="p">:</span> <span class="mi">10</span>
          <span class="p">}</span>

examples/README.md

@@ -0,0 +1 @@
+Some of these examples are close to real life simulations, whereas some others are only a demonstration of Soil's capatibilities.

examples/cars/README.md

@@ -0,0 +1,9 @@
+This example can be run like with command-line options, like this:
+
+```bash
+python cars.py --level DEBUG  -e summary --csv
+#or
+soil cars.py -e summary
+```
+
+This will set the `CSV` (save the agent and model data to a CSV) and `summary` (print the a summary of the data to stdout) exporters, and set the log level to DEBUG.

examples/cars/cars_sim.py

@@ -0,0 +1,232 @@
+"""
+This is an example of a simplified city, where there are Passengers and Drivers that can take those passengers
+from their location to their desired location.
+
+An example scenario could play like the following:
+
+- Drivers start in the `wandering` state, where they wander around the city until they have been assigned a journey
+- Passenger(1) tells every driver that it wants to request a Journey.
+- Each driver receives the request.
+  If Driver(2) is interested in providing the Journey, it asks Passenger(1) to confirm that it accepts Driver(2)'s request
+- When Passenger(1) accepts the request, two things happen:
+    - Passenger(1) changes its state to `driving_home`
+    - Driver(2) starts moving towards the origin of the Journey
+- Once Driver(2) reaches the origin, it starts moving itself and Passenger(1) to the destination of the Journey
+- When Driver(2) reaches the destination (carrying Passenger(1) along):
+    - Driver(2) starts wondering again
+    - Passenger(1) dies, and is removed from the simulation
+- If there are no more passengers available in the simulation, Drivers die
+"""
+from __future__ import annotations
+from typing import Optional
+from soil import *
+from soil import events
+from mesa.space import MultiGrid
+
+
+# More complex scenarios may use more than one type of message  between objects.
+# A common pattern is to use `enum.Enum` to represent state changes in a request.
+@dataclass
+class Journey:
+    """
+    This represents a request for a journey. Passengers and drivers exchange this object.
+
+    A journey may have a driver assigned or not. If the driver has not been assigned, this
+    object is considered a "request for a journey".
+    """
+
+    origin: (int, int)
+    destination: (int, int)
+    tip: float
+
+    passenger: Passenger
+    driver: Optional[Driver] = None
+
+
+class City(EventedEnvironment):
+    """
+    An environment with a grid where drivers and passengers will be placed.
+
+    The number of drivers and riders is configurable through its parameters:
+
+    :param str n_cars: The total number of drivers to add
+    :param str n_passengers: The number of passengers in the simulation
+    :param list agents: Specific agents to use in the simulation. It overrides the `n_passengers`
+    and `n_cars` params.
+    :param int height: Height of the internal grid
+    :param int width: Width of the internal grid
+    """
+    n_cars = 1
+    n_passengers = 10
+    height = 100
+    width = 100
+
+    def init(self):
+        self.grid = MultiGrid(width=self.width, height=self.height, torus=False)
+        if not self.get_agents():
+            self.add_agents(Driver, k=self.n_cars)
+            self.add_agents(Passenger, k=self.n_passengers)
+
+        for agent in self.get_agents():
+            self.grid.place_agent(agent, (0, 0))
+            self.grid.move_to_empty(agent)
+        
+        self.total_earnings = 0
+        self.add_model_reporter("total_earnings")
+
+    @report
+    @property
+    def number_passengers(self):
+        return self.count_agents(agent_class=Passenger)
+
+
+class Driver(Evented, FSM):
+    pos = None
+    journey = None
+    earnings = 0
+
+    def on_receive(self, msg, sender):
+        """This is not a state. It will run (and block) every time process_messages is invoked"""
+        if self.journey is None and isinstance(msg, Journey) and msg.driver is None:
+            msg.driver = self
+            self.journey = msg
+
+    def check_passengers(self):
+        """If there are no more passengers, stop forever"""
+        c = self.count_agents(agent_class=Passenger)
+        self.debug(f"Passengers left {c}")
+        return c
+
+    @state(default=True)
+    async def wandering(self):
+        """Move around the city until a journey is accepted"""
+        target = None
+        if not self.check_passengers():
+            return self.die("No passengers left")
+        self.journey = None
+        while self.journey is None:  # No potential journeys detected (see on_receive)
+            if target is None or not self.move_towards(target):
+                target = self.random.choice(
+                    self.model.grid.get_neighborhood(self.pos, moore=False)
+                )
+
+            if not self.check_passengers():
+                return self.die("No passengers left")
+            # This will call on_receive behind the scenes, and the agent's status will be updated
+            self.process_messages()
+            await self.delay(30)  # Wait at least 30 seconds before checking again
+
+        try:
+            # Re-send the journey to the passenger, to confirm that we have been selected
+            self.journey = await self.journey.passenger.ask(self.journey, timeout=60, delay=5)
+        except events.TimedOut:
+            # No journey has been accepted. Try again
+            self.journey = None
+            return
+
+        return self.driving
+
+    @state
+    async def driving(self):
+        """The journey has been accepted. Pick them up and take them to their destination"""
+        self.info(f"Driving towards Passenger {self.journey.passenger.unique_id}")
+        while self.move_towards(self.journey.origin):
+            await self.delay()
+        self.info(f"Driving {self.journey.passenger.unique_id} from {self.journey.origin} to {self.journey.destination}")
+        while self.move_towards(self.journey.destination, with_passenger=True):
+            await self.delay()
+        self.info("Arrived at destination")
+        self.earnings += self.journey.tip
+        self.model.total_earnings += self.journey.tip
+        if not self.check_passengers():
+            return self.die("No passengers left")
+        return self.wandering
+
+    def move_towards(self, target, with_passenger=False):
+        """Move one cell at a time towards a target"""
+        self.debug(f"Moving { self.pos } -> { target }")
+        if target[0] == self.pos[0] and target[1] == self.pos[1]:
+            return False
+
+        next_pos = [self.pos[0], self.pos[1]]
+        for idx in [0, 1]:
+            if self.pos[idx] < target[idx]:
+                next_pos[idx] += 1
+                break
+            if self.pos[idx] > target[idx]:
+                next_pos[idx] -= 1
+                break
+        self.model.grid.move_agent(self, tuple(next_pos))
+        if with_passenger:
+            self.journey.passenger.pos = (
+                self.pos
+            )  # This could be communicated through messages
+        return True
+
+
+class Passenger(Evented, FSM):
+    pos = None
+
+    def on_receive(self, msg, sender):
+        """This is not a state. It will be run synchronously every time `process_messages` is run"""
+
+        if isinstance(msg, Journey):
+            self.journey = msg
+            return msg
+
+    @default_state
+    @state
+    async def asking(self):
+        destination = (
+            self.random.randint(0, self.model.grid.height-1),
+            self.random.randint(0, self.model.grid.width-1),
+        )
+        self.journey = None
+        journey = Journey(
+            origin=self.pos,
+            destination=destination,
+            tip=self.random.randint(10, 100),
+            passenger=self,
+        )
+
+        timeout = 60
+        expiration = self.now + timeout
+        self.info(f"Asking for journey at: { self.pos }")
+        self.model.broadcast(journey, ttl=timeout, sender=self, agent_class=Driver)
+        while not self.journey:
+            self.debug(f"Waiting for responses at: { self.pos }")
+            try:
+                # This will call process_messages behind the scenes, and the agent's status will be updated
+                # If you want to avoid that, you can call it with: check=False
+                await self.received(expiration=expiration, delay=10)
+            except events.TimedOut:
+                self.info(f"Still no response. Waiting at: { self.pos }")
+                self.model.broadcast(
+                    journey, ttl=timeout, sender=self, agent_class=Driver
+                )
+                expiration = self.now + timeout
+        self.info(f"Got a response! Waiting for driver")
+        return self.driving_home
+
+    @state
+    async def driving_home(self):
+        while (
+            self.pos[0] != self.journey.destination[0]
+            or self.pos[1] != self.journey.destination[1]
+        ):
+            try:
+                await self.received(timeout=60)
+            except events.TimedOut:
+                pass
+
+        self.die("Got home safe!")
+
+
+simulation = Simulation(name="RideHailing",
+                        model=City,
+                        seed="carsSeed",
+                        max_time=1000,
+                        parameters=dict(n_passengers=2))
+
+if __name__ == "__main__":
+    easy(simulation)

examples/complete.yml

@@ -1,27 +0,0 @@
----
-name: simple
-group: tests
-dir_path: "/tmp/"
-num_trials: 3
-max_time: 100
-interval: 1
-seed: "CompleteSeed!"
-network_params:
-  generator: complete_graph
-  n: 10
-network_agents:
-  - agent_type: CounterModel
-    weight: 1
-    state:
-      id: 0
-  - agent_type: AggregatedCounter
-    weight: 0.2
-environment_agents: []
-environment_class: Environment
-environment_params:
-  am_i_complete: true
-default_state:
-  incidents: 0
-states:
-  - name: 'The first node'
-  - name: 'The second node'

examples/custom_generator/custom_generator.yml

@@ -1,16 +0,0 @@
----
-name: custom-generator
-description: Using a custom generator for the network
-num_trials: 3
-max_time: 100
-interval: 1
-network_params:
-  generator: mymodule.mygenerator
-# These are custom parameters
-  n: 10
-  n_edges: 5  
-network_agents:
-  - agent_type: CounterModel
-    weight: 1
-    state:
-      id: 0

examples/custom_generator/generator_sim.py

@@ -0,0 +1,39 @@
+from networkx import Graph
+import random
+import networkx as nx
+from soil import Simulation, Environment, CounterModel, parameters
+
+
+def mygenerator(n=5, n_edges=5):
+    """
+    Just a simple generator that creates a network with n nodes and
+    n_edges edges. Edges are assigned randomly, only avoiding self loops.
+    """
+    G = nx.Graph()
+
+    for i in range(n):
+        G.add_node(i)
+
+    for i in range(n_edges):
+        nodes = list(G.nodes)
+        n_in = random.choice(nodes)
+        nodes.remove(n_in)  # Avoid loops
+        n_out = random.choice(nodes)
+        G.add_edge(n_in, n_out)
+    return G
+
+
+class GeneratorEnv(Environment):
+    """Using a custom generator for the network"""
+
+    generator: parameters.function = staticmethod(mygenerator)
+
+    def init(self):
+        self.create_network(generator=self.generator, n=10, n_edges=5)
+        self.add_agents(CounterModel)
+
+
+sim = Simulation(model=GeneratorEnv, max_steps=10)
+
+if __name__ == '__main__':
+    sim.run(dump=False)

examples/custom_generator/mymodule.py

@@ -1,27 +0,0 @@
-from networkx import Graph
-import networkx as nx
-from random import choice
-
-def mygenerator(n=5, n_edges=5):
-    '''
-    Just a simple generator that creates a network with n nodes and
-    n_edges edges. Edges are assigned randomly, only avoiding self loops.
-    '''
-    G = nx.Graph()
-
-    for i in range(n):
-        G.add_node(i)
-    
-    for i in range(n_edges):
-        nodes = list(G.nodes)
-        n_in = choice(nodes)
-        nodes.remove(n_in)  # Avoid loops
-        n_out = choice(nodes)
-        G.add_edge(n_in, n_out)
-    return G
-    
-
-
-
-
-    

examples/custom_timeouts/custom_timeouts.py

@@ -1,35 +0,0 @@
-from soil.agents import FSM, state, default_state
-
-
-class Fibonacci(FSM):
-    '''Agent that only executes in t_steps that are Fibonacci numbers'''
-
-    defaults = {
-        'prev': 1
-    }
-
-    @default_state
-    @state
-    def counting(self):
-        self.log('Stopping at {}'.format(self.now))
-        prev, self['prev'] = self['prev'], max([self.now, self['prev']])
-        return None, self.env.timeout(prev)
-
-class Odds(FSM):
-    '''Agent that only executes in odd t_steps'''
-    @default_state
-    @state
-    def odds(self):
-        self.log('Stopping at {}'.format(self.now))
-        return None, self.env.timeout(1+self.now%2)
-
-if __name__ == '__main__':
-    import logging
-    logging.basicConfig(level=logging.INFO)
-    from soil import Simulation
-    s = Simulation(network_agents=[{'ids': [0], 'agent_type': Fibonacci},
-                                   {'ids': [1], 'agent_type': Odds}],
-                   network_params={"generator": "complete_graph", "n": 2},
-                   max_time=100,
-                   )
-    s.run(dry_run=True)

examples/custom_timeouts/custom_timeouts_sim.py

@@ -0,0 +1,40 @@
+from soil.agents import FSM, state, default_state
+
+
+class Fibonacci(FSM):
+    """Agent that only executes in t_steps that are Fibonacci numbers"""
+    prev = 1
+
+    @default_state
+    @state
+    def counting(self):
+        self.log("Stopping at {}".format(self.now))
+        prev, self["prev"] = self["prev"], max([self.now, self["prev"]])
+        return self.delay(prev)
+    
+
+
+class Odds(FSM):
+    """Agent that only executes in odd t_steps"""
+
+    @state(default=True)
+    def odds(self):
+        self.log("Stopping at {}".format(self.now))
+        return self.delay(1 + (self.now % 2))
+
+
+from soil import Environment, Simulation
+from networkx import complete_graph
+
+
+class TimeoutsEnv(Environment):
+    def init(self):
+        self.create_network(generator=complete_graph, n=2)
+        self.add_agent(agent_class=Fibonacci, node_id=0)
+        self.add_agent(agent_class=Odds, node_id=1)
+
+
+sim = Simulation(model=TimeoutsEnv, max_steps=10)
+
+if __name__ == "__main__":
+    sim.run(dump=False)

examples/markov_chains/MarkovChains.ipynb

@@ -0,0 +1,355 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "7641396c-a602-477e-bf03-09e1191ff549",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%load_ext autoreload"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "4f12285c-78db-4ee8-b9c6-7799d34f10f5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%autoreload 1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "7710bb03-0cb9-413a-a407-fe48855ff917",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%aimport markov_sim"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "2dffca0f-da9e-4f69-ac43-7afe52ad2d32",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%aimport soil\n",
+    "%aimport soil.visualization"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "12871006-70ca-4c6f-8a3e-0aae1d0bce31",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "G = markov_sim.load_city_graph(\"Chamberi, Madrid\", network_type=\"drive\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "31e96cc5-b703-4d2a-a006-7b9a2cedc365",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# env = markov_sim.CityEnv(G=G, n_assets=20, side=10, max_weight=1, seed=10)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "id": "5e070b36-0ba6-4780-8fd4-3c72fa3bb240",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# for i in range(2):\n",
+    "#     env.step()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 35,
+   "id": "56f8b997-65b0-431d-9517-b93edb1cfcd8",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/j/.cache/pypoetry/virtualenvs/soil-cCX5yKRx-py3.10/lib/python3.10/site-packages/osmnx/plot.py:955: UserWarning: FigureCanvasAgg is non-interactive, and thus cannot be shown\n",
+      "  plt.show()\n",
+      "/home/j/.cache/pypoetry/virtualenvs/soil-cCX5yKRx-py3.10/lib/python3.10/site-packages/osmnx/plot.py:955: UserWarning: FigureCanvasAgg is non-interactive, and thus cannot be shown\n",
+      "  plt.show()\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "86e45bd44e434674b11805fd94e98414",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/html": [
+       "Cannot show widget. You probably want to rerun the code cell above (<i>Click in the code cell, and press Shift+Enter <kbd>⇧</kbd>+<kbd>↩</kbd></i>)."
+      ],
+      "text/plain": [
+       "Cannot show ipywidgets in text"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "from soil.visualization import JupyterViz, GeoNetworkDrawer, Controller\n",
+    "from soil import visualization\n",
+    "from matplotlib import colors\n",
+    "from matplotlib import colormaps\n",
+    "plasma = colormaps.get_cmap('plasma')\n",
+    "model_params = {\n",
+    "    \"n_assets\": {\n",
+    "        \"type\": \"SliderInt\",\n",
+    "        \"value\": 100,\n",
+    "        \"label\": \"Number of assets:\",\n",
+    "        \"min\": 1,\n",
+    "        \"max\": 1000,\n",
+    "        \"step\": 1,\n",
+    "    },\n",
+    "    \"max_weight\": {\n",
+    "        \"type\": \"SliderInt\",\n",
+    "        \"value\": 3,\n",
+    "        \"label\": \"Maximum edge weight:\",\n",
+    "        \"min\": 1,\n",
+    "        \"max\": 20,\n",
+    "        \"step\": 1,\n",
+    "    },\n",
+    "    \"ratio_lazy\": {\n",
+    "        \"type\": \"SliderFloat\",\n",
+    "        \"value\": 0,\n",
+    "        \"label\": \"Ratio of lazy agents (they prefer shorter streets):\",\n",
+    "        \"min\": 0,\n",
+    "        \"max\": 1,\n",
+    "        \"step\": 0.05,\n",
+    "    },\n",
+    "    \"side\": {\n",
+    "        \"type\": \"SliderInt\",\n",
+    "        \"value\": 10,\n",
+    "        \"label\": \"Size of the side:\",\n",
+    "        \"min\": 2,\n",
+    "        \"max\": 20,\n",
+    "        \"step\": 1,\n",
+    "    },\n",
+    "    \"gradual_move\": {\n",
+    "        \"type\": \"Checkbox\",\n",
+    "        \"value\": True,\n",
+    "        \"label\": \"Use gradual movement\",\n",
+    "    }, \n",
+    "    \"lockstep\": {\n",
+    "        \"type\": \"Checkbox\",\n",
+    "        \"value\": True,\n",
+    "        \"label\": \"Run in locksteps\",\n",
+    "    },\n",
+    "    \"G\": G,\n",
+    "    # \"width\": 10,\n",
+    "}\n",
+    "\n",
+    "def colorize(d):\n",
+    "    # print(d)\n",
+    "    if any(a.waiting for a in d):\n",
+    "        return 'red'\n",
+    "    else:\n",
+    "        return 'blue'\n",
+    "\n",
+    "def network_portrayal(graph, spring=True):\n",
+    "    global pos, l\n",
+    "    node_size = [10*(len(node[1][\"agent\"])) for node in graph.nodes(data=True)]\n",
+    "    node_color = [colorize(d[\"agent\"]) for (k, d) in graph.nodes(data=True)]\n",
+    "    # pos = {node: (d[\"x\"], d[\"y\"]) for node, d in graph.nodes(data=True)}\n",
+    "    edge_width = [graph.edges[k]['travel_time']/100 for k in graph.edges]\n",
+    "    # print(edge_width)\n",
+    "    weights = [graph.edges[k]['occupation'] for k in graph.edges]\n",
+    "    norm = colors.Normalize(vmin=0, vmax=max(weights))\n",
+    "    color = plasma(norm(weights))\n",
+    "    # print(color)\n",
+    "    return dict(node_size=node_size, node_color=node_color, edge_linewidth=edge_width, edge_color=color)\n",
+    "\n",
+    "page = visualization.JupyterViz(\n",
+    "    markov_sim.CityEnv,\n",
+    "    model_params,\n",
+    "    measures=[\"NodeGini\", \"EdgeGini\", \"EdgeOccupation\"],\n",
+    "    name=\"City Environment\",\n",
+    "    space_drawer=GeoNetworkDrawer,\n",
+    "    agent_portrayal=network_portrayal,\n",
+    "    columns=3,\n",
+    ")\n",
+    "# This is required to render the visualization in the Jupyter notebook\n",
+    "page"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 39,
+   "id": "70da18d7-66bd-4710-89a6-aca14707c56e",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>NodeGini</th>\n",
+       "      <th>EdgeGini</th>\n",
+       "      <th>EdgeOccupation</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>0.866567</td>\n",
+       "      <td>0.927276</td>\n",
+       "      <td>0.087624</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>0.866567</td>\n",
+       "      <td>0.933494</td>\n",
+       "      <td>0.081301</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>0.863867</td>\n",
+       "      <td>0.933163</td>\n",
+       "      <td>0.078591</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>0.866567</td>\n",
+       "      <td>0.929943</td>\n",
+       "      <td>0.084914</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>0.869433</td>\n",
+       "      <td>0.934949</td>\n",
+       "      <td>0.076784</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>...</th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>127</th>\n",
+       "      <td>0.880367</td>\n",
+       "      <td>0.934185</td>\n",
+       "      <td>0.075881</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>128</th>\n",
+       "      <td>0.881400</td>\n",
+       "      <td>0.933038</td>\n",
+       "      <td>0.078591</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>129</th>\n",
+       "      <td>0.881400</td>\n",
+       "      <td>0.936299</td>\n",
+       "      <td>0.078591</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>130</th>\n",
+       "      <td>0.881400</td>\n",
+       "      <td>0.929784</td>\n",
+       "      <td>0.086721</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>131</th>\n",
+       "      <td>0.876733</td>\n",
+       "      <td>0.932746</td>\n",
+       "      <td>0.082204</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "<p>132 rows × 3 columns</p>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "     NodeGini  EdgeGini  EdgeOccupation\n",
+       "0    0.866567  0.927276        0.087624\n",
+       "1    0.866567  0.933494        0.081301\n",
+       "2    0.863867  0.933163        0.078591\n",
+       "3    0.866567  0.929943        0.084914\n",
+       "4    0.869433  0.934949        0.076784\n",
+       "..        ...       ...             ...\n",
+       "127  0.880367  0.934185        0.075881\n",
+       "128  0.881400  0.933038        0.078591\n",
+       "129  0.881400  0.936299        0.078591\n",
+       "130  0.881400  0.929784        0.086721\n",
+       "131  0.876733  0.932746        0.082204\n",
+       "\n",
+       "[132 rows x 3 columns]"
+      ]
+     },
+     "execution_count": 39,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "page.controller.model.datacollector.get_model_vars_dataframe()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d9a7d3c8-2f87-47d5-8d27-a7387ea3457d",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

examples/markov_chains/app.py

@@ -0,0 +1,11 @@
+from flask import Flask
+import solara.server.flask
+
+app = Flask(__name__)
+app.register_blueprint(solara.server.flask.blueprint, url_prefix="/solara/")
+
+
+@app.route("/")
+def hello_world():
+    return "<p>Hello, World!</p>"
+

examples/markov_chains/markov_sim.py

@@ -0,0 +1,159 @@
+'''
+This scenario has drivers driving around a city.
+In this model, drivers can only be at intersections, which are treated as nodes in the City Graph (grid).
+
+At the start of the simulation, drivers are randomly positioned in the city grid.
+
+The following models for agent behavior are included:
+
+* DummyDriver: In each simulation step, this type of driver can instantly move to any of the neighboring nodes in the grid, or stay in its place.
+
+'''
+
+import networkx as nx
+from soil import Environment, BaseAgent, state, time
+from mesa.space import NetworkGrid
+import mesa
+import statistics
+
+
+class CityGrid(NetworkGrid):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args,  **kwargs)
+
+        for (u, v, d) in self.G.edges(data=True):
+            d["occupation"] = 0
+        # self.dijkstras = dict(nx.all_pairs_dijkstra(self.G, weight="length"))
+
+    # def eta(self, pos1, pos2):
+    #     return self.dijkstras[pos1][0][pos2]
+
+    def travel_time(self, pos1, pos2):
+        return float(min(d["travel_time"] for d in self.G.adj[pos1][pos2].values()))
+
+    
+    def node_occupation(self):
+        return {k: len(v.get("agent", [])) for (k, v) in self.G.nodes(data=True)}
+
+    def edge_occupation(self):
+        return {(u,v): d.get('occupation', 1) for (u, v, d) in self.G.edges(data=True)}
+
+
+class Roamer(BaseAgent):
+    waiting = False
+
+    def step(self):
+        '''
+        A simple driver that just moves to a neighboring cell in the city
+        '''
+        yield from self.move_to(None)
+        return self.delay(0)
+    
+    def choose_next(self):
+        opts = self.model.grid.get_neighborhood(self.pos, include_center=False)
+        pos = self.random.choice(opts)
+        delay = self.model.grid.travel_time(self.pos, pos)
+        return pos, delay
+
+    def move_to(self, pos=None):
+        self.waiting = True
+        if pos is None:
+            pos, delay = self.choose_next()
+        if self.model.gradual_move:
+            # Calculate how long it will take, and wait for that long
+            if pos != self.pos:
+                self.model.grid.G.edges[self.pos,pos,0]["occupation"] += 1
+            yield delay
+        if self.model.gradual_move and pos != self.pos:
+            w1 = self.model.grid.G.edges[self.pos,pos,0]["occupation"] 
+            oldpos = self.pos
+            self.model.grid.G.edges[self.pos,pos,0]["occupation"] = w1 - 1
+            assert self.model.grid.G.edges[self.pos,pos,0]["occupation"] == w1-1
+        self.model.grid.move_agent(self, pos)
+        self.waiting = False
+
+
+class LazyRoamer(Roamer):
+    waiting = False
+    def choose_next(self):
+        opts = self.model.grid.get_neighborhood(self.pos, include_center=False)
+        times = [self.model.grid.travel_time(self.pos, other) for other in opts]
+        idx = self.random.choices(range(len(times)), k=1, weights=[1/time for time in times])[0]
+        return opts[idx], times[idx]
+
+
+
+def gini(values):
+    s = sum(values)
+    
+    N = len(values)
+    if s == 0:
+        return 0
+    x = sorted(values)
+
+    B = sum(xi * (N - i) for i, xi in enumerate(x)) / (N * s)
+    return 1 + (1 / N) - 2 * B
+
+
+class CityEnv(Environment):
+    def __init__(self, *, G, side=20, n_assets=100, ratio_lazy=1, lockstep=True, gradual_move=True, max_weight=1, **kwargs):
+        super().__init__(**kwargs)
+        if lockstep:
+            self.schedule = time.Lockstepper(self.schedule)
+        self.n_assets = n_assets
+        self.side = side
+        self.max_weight = max_weight
+        self.gradual_move = gradual_move
+        self.grid = CityGrid(g=G)
+
+        n_lazy = round(self.n_assets * ratio_lazy)
+        n_other = self.n_assets - n_lazy
+        self.add_agents(Roamer, k=n_other)
+        self.add_agents(LazyRoamer, k=n_lazy)
+
+        positions = list(self.grid.G.nodes)
+        for agent in self.get_agents():
+            pos = self.random.choice(positions)
+            self.grid.place_agent(agent, pos)
+        
+        self.datacollector = mesa.DataCollector(
+            model_reporters={
+                "NodeGini": lambda model: gini(model.grid.node_occupation().values()),
+                "EdgeGini": lambda model: gini(model.grid.edge_occupation().values()),            
+                "EdgeOccupation": lambda model: statistics.mean(model.grid.edge_occupation().values()),            
+            }#, agent_reporters={"Wealth": "wealth"}
+        )
+
+class SquareCityEnv(CityEnv):
+    def __init__(self, *, side=20, **kwargs):
+        self.side = side
+        G = nx.grid_graph(dim=[side, side])
+        for (_, _, d) in G.edges(data=True):
+            d["travel_time"] = self.random.randint(1, self.max_weight)
+
+        for (k, d) in G.nodes(data=True):   
+            d["pos"] = k
+        super().__init__(**kwargs, G=G)
+
+import osmnx as ox
+
+
+class NamedCityEnv(CityEnv):
+    def __init__(self, *, location="Chamberi, Madrid", **kwargs):
+        self.location = location
+        super().__init__(**kwargs, G=load_city_graph(location))
+
+
+def load_city_graph(location='Chamberi, Madrid', **kwargs):
+    G = ox.graph.graph_from_place(location, **kwargs)
+    G = ox.add_edge_speeds(G)
+    G = ox.add_edge_travel_times(G)
+    largest = sorted(nx.strongly_connected_components(G), key=lambda x: len(x))[-1]
+    G = G.subgraph(largest)
+    return G
+
+
+if __name__ == "__main__":
+    env = CityEnv()
+    for i in range(100):
+        env.step()

examples/markov_chains/sol.py

@@ -0,0 +1,26 @@
+import solara
+
+@solara.component
+def MainPage(clicks):
+    color = "green"
+    if clicks.value >= 5:
+        color = "red"
+
+    def increment():
+        clicks.value += 1
+        print("clicks", clicks)  # noqa
+
+    solara.Button(label=f"Clicked: {clicks}", on_click=increment, color=color)
+
+@solara.component
+def Page():
+    v = Visualization()
+    v.viz()
+
+class Visualization:
+    def __init__(self):
+        self.clicks = solara.reactive(0)
+
+    def viz(self):
+        from sol_lib import MainPage
+        return MainPage(self.clicks)

examples/markov_chains/sol_lib.py

@@ -0,0 +1,13 @@
+import solara
+
+@solara.component
+def MainPage(clicks):
+    color = "green"
+    if clicks.value >= 5:
+        color = "red"
+
+    def increment():
+        clicks.value += 1
+        print("clicks", clicks)  # noqa
+
+    solara.Button(label=f"Clicked: {clicks}", on_click=increment, color=color)

examples/mesa/mesa_sim.py

@@ -0,0 +1,7 @@
+from soil import Simulation
+from social_wealth import MoneyEnv, graph_generator
+
+sim = Simulation(name="mesa_sim", dump=False, max_steps=10, model=MoneyEnv, parameters=dict(generator=graph_generator, N=10, width=50, height=50))
+
+if __name__ == "__main__":
+    sim.run()

examples/mesa/server.py

@@ -0,0 +1,111 @@
+from mesa.visualization.ModularVisualization import ModularServer
+from mesa.visualization.UserParam import Slider, Choice
+from mesa.visualization.modules import ChartModule, NetworkModule, CanvasGrid
+from social_wealth import MoneyEnv, graph_generator, SocialMoneyAgent
+import networkx as nx
+
+
+class MyNetwork(NetworkModule):
+    def render(self, model):
+        return self.portrayal_method(model)
+
+
+def network_portrayal(env):
+    # The model ensures there is 0 or 1 agent per node
+
+    portrayal = dict()
+    wealths = {
+        node_id: data["agent"].wealth for (node_id, data) in env.G.nodes(data=True)
+    }
+    portrayal["nodes"] = [
+        {
+            "id": node_id,
+            "size": 2 * (wealth + 1),
+            "color": "#CC0000" if wealth == 0 else "#007959",
+            # "color": "#CC0000",
+            "label": f"{node_id}: {wealth}",
+        }
+        for (node_id, wealth) in wealths.items()
+    ]
+
+    portrayal["edges"] = [
+        {"id": edge_id, "source": source, "target": target, "color": "#000000"}
+        for edge_id, (source, target) in enumerate(env.G.edges)
+    ]
+
+    return portrayal
+
+
+def gridPortrayal(agent):
+    """
+    This function is registered with the visualization server to be called
+    each tick to indicate how to draw the agent in its current state.
+    :param agent:  the agent in the simulation
+    :return: the portrayal dictionary
+    """
+    color = max(10, min(agent.wealth * 10, 100))
+    return {
+        "Shape": "rect",
+        "w": 1,
+        "h": 1,
+        "Filled": "true",
+        "Layer": 0,
+        "Label": agent.unique_id,
+        "Text": agent.unique_id,
+        "x": agent.pos[0],
+        "y": agent.pos[1],
+        "Color": f"rgba(31, 10, 255, 0.{color})",
+    }
+
+
+grid = MyNetwork(network_portrayal, 500, 500)
+chart = ChartModule(
+    [{"Label": "Gini", "Color": "Black"}], data_collector_name="datacollector"
+)
+
+parameters = {
+    "N": Slider(
+        "N",
+        5,
+        1,
+        10,
+        1,
+        description="Choose how many agents to include in the model",
+    ),
+    "height": Slider(
+        "height",
+        5,
+        5,
+        10,
+        1,
+        description="Grid height",
+    ),
+    "width": Slider(
+        "width",
+        5,
+        5,
+        10,
+        1,
+        description="Grid width",
+    ),
+    "agent_class": Choice(
+        "Agent class",
+        value="MoneyAgent",
+        choices=["MoneyAgent", "SocialMoneyAgent"],
+    ),
+    "generator": graph_generator,
+}
+
+
+canvas_element = CanvasGrid(
+    gridPortrayal, parameters["width"].value, parameters["height"].value, 500, 500
+)
+
+
+server = ModularServer(
+    MoneyEnv, [grid, chart, canvas_element], "Money Model", parameters
+)
+server.port = 8521
+
+if __name__ == '__main__':
+    server.launch(open_browser=False)

examples/mesa/social_wealth.py

@@ -0,0 +1,135 @@
+"""
+This is an example that adds soil agents and environment in a normal
+mesa workflow.
+"""
+from mesa import Agent as MesaAgent
+from mesa.space import MultiGrid
+
+# from mesa.time import RandomActivation
+from mesa.datacollection import DataCollector
+from mesa.batchrunner import batch_run
+
+import networkx as nx
+
+from soil import NetworkAgent, Environment, serialization
+
+
+def compute_gini(model):
+    agent_wealths = [agent.wealth for agent in model.agents]
+    x = sorted(agent_wealths)
+    N = len(list(model.agents))
+    B = sum(xi * (N - i) for i, xi in enumerate(x)) / (N * sum(x))
+    return 1 + (1 / N) - 2 * B
+
+
+class MoneyAgent(MesaAgent):
+    """
+    A MESA agent with fixed initial wealth.
+    It will only share wealth with neighbors based on grid proximity
+    """
+
+    def __init__(self, unique_id, model, wealth=1, **kwargs):
+        super().__init__(unique_id=unique_id, model=model)
+        self.wealth = wealth
+
+    def move(self):
+        possible_steps = self.model.grid.get_neighborhood(
+            self.pos, moore=True, include_center=False
+        )
+        new_position = self.random.choice(possible_steps)
+        self.model.grid.move_agent(self, new_position)
+
+    def give_money(self):
+        cellmates = self.model.grid.get_cell_list_contents([self.pos])
+        if len(cellmates) > 1:
+            other = self.random.choice(cellmates)
+            other.wealth += 1
+            self.wealth -= 1
+
+    def step(self):
+        print("Crying wolf", self.pos)
+        self.move()
+        if self.wealth > 0:
+            self.give_money()
+
+
+class SocialMoneyAgent(MoneyAgent, NetworkAgent):
+    wealth = 1
+
+    def give_money(self):
+        cellmates = set(self.model.grid.get_cell_list_contents([self.pos]))
+        friends = set(self.get_neighbors())
+        self.info("Trying to give money")
+        self.info("Cellmates: ", cellmates)
+        self.info("Friends: ", friends)
+
+        nearby_friends = list(cellmates & friends)
+
+        if len(nearby_friends):
+            other = self.random.choice(nearby_friends)
+            other.wealth += 1
+            self.wealth -= 1
+
+
+def graph_generator(n=5):
+    G = nx.Graph()
+    for ix in range(n):
+        G.add_edge(0, ix)
+    return G
+
+
+class MoneyEnv(Environment):
+    """A model with some number of agents."""
+
+    def __init__(
+        self,
+        width,
+        height,
+        N,
+        generator=graph_generator,
+        agent_class=SocialMoneyAgent,
+        topology=None,
+        **kwargs
+    ):
+
+        generator = serialization.deserialize(generator)
+        agent_class = serialization.deserialize(agent_class, globs=globals())
+        topology = generator(n=N)
+        super().__init__(topology=topology, N=N, **kwargs)
+        self.grid = MultiGrid(width, height, False)
+
+        self.populate_network(agent_class=agent_class)
+
+        # Create agents
+        for agent in self.get_agents():
+            x = self.random.randrange(self.grid.width)
+            y = self.random.randrange(self.grid.height)
+            self.grid.place_agent(agent, (x, y))
+
+        self.datacollector = DataCollector(
+            model_reporters={"Gini": compute_gini}, agent_reporters={"Wealth": "wealth"}
+        )
+
+
+if __name__ == "__main__":
+
+    fixed_params = {
+        "generator": nx.complete_graph,
+        "width": 10,
+        "network_agents": [{"agent_class": SocialMoneyAgent, "weight": 1}],
+        "height": 10,
+    }
+
+    variable_params = {"N": range(10, 100, 10)}
+
+    results = batch_run(
+        MoneyEnv,
+        variable_parameters=variable_params,
+        fixed_parameters=fixed_params,
+        iterations=5,
+        max_steps=100
+    )  
+
+    run_data = pd.DataFrame(results)
+    print(run_data.head())
+    print(run_data.Gini)

examples/mesa/wealth.py

@@ -0,0 +1,87 @@
+from mesa import Agent, Model
+from mesa.space import MultiGrid
+from mesa.time import RandomActivation
+from mesa.datacollection import DataCollector
+from mesa.batchrunner import BatchRunner
+
+
+def compute_gini(model):
+    agent_wealths = [agent.wealth for agent in model.schedule.agents]
+    x = sorted(agent_wealths)
+    N = model.num_agents
+    B = sum(xi * (N - i) for i, xi in enumerate(x)) / (N * sum(x))
+    return 1 + (1 / N) - 2 * B
+
+
+class MoneyAgent(Agent):
+    """An agent with fixed initial wealth."""
+
+    def __init__(self, unique_id, model):
+        super().__init__(unique_id, model)
+        self.wealth = 1
+
+    def move(self):
+        possible_steps = self.model.grid.get_neighborhood(
+            self.pos, moore=True, include_center=False
+        )
+        new_position = self.random.choice(possible_steps)
+        self.model.grid.move_agent(self, new_position)
+
+    def give_money(self):
+        cellmates = self.model.grid.get_cell_list_contents([self.pos])
+        if len(cellmates) > 1:
+            other = self.random.choice(cellmates)
+            other.wealth += 1
+            self.wealth -= 1
+
+    def step(self):
+        self.move()
+        if self.wealth > 0:
+            self.give_money()
+
+
+class MoneyModel(Model):
+    """A model with some number of agents."""
+
+    def __init__(self, N, width, height):
+        self.num_agents = N
+        self.grid = MultiGrid(width, height, True)
+        self.schedule = RandomActivation(self)
+        self.running = True
+
+        # Create agents
+        for i in range(self.num_agents):
+            a = MoneyAgent(i, self)
+            self.schedule.add(a)
+            # Add the agent to a random grid cell
+            x = self.random.randrange(self.grid.width)
+            y = self.random.randrange(self.grid.height)
+            self.grid.place_agent(a, (x, y))
+
+        self.datacollector = DataCollector(
+            model_reporters={"Gini": compute_gini}, agent_reporters={"Wealth": "wealth"}
+        )
+
+    def step(self):
+        self.datacollector.collect(self)
+        self.schedule.step()
+
+
+if __name__ == "__main__":
+
+    fixed_params = {"width": 10, "height": 10}
+    variable_params = {"N": range(10, 500, 10)}
+
+    batch_run = BatchRunner(
+        MoneyModel,
+        variable_params,
+        fixed_params,
+        iterations=5,
+        max_steps=100,
+        model_reporters={"Gini": compute_gini},
+    )
+    batch_run.run_all()
+
+    run_data = batch_run.get_model_vars_dataframe()
+    run_data.head()
+    print(run_data.Gini)