README.md

@@ -4,7 +4,7 @@
 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](docs/tutorial/soil_tutorial.ipynb) to develop your own agent models.
+Follow our [tutorial](examples/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)

docs/conf.py

@@ -31,10 +31,7 @@
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = [
-    "IPython.sphinxext.ipython_console_highlighting",
-    "nbsphinx",
-]
+extensions = ['IPython.sphinxext.ipython_console_highlighting']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -67,7 +64,7 @@ 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 = "en"
+language = None
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -155,3 +152,6 @@ texinfo_documents = [
      author, 'Soil', 'One line description of project.',
      'Miscellaneous'),
 ]
+
+
+

docs/index.rst

@@ -2,20 +2,19 @@ Welcome to Soil's documentation!
 ================================
 
 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 <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
 
+Soil can be installed through pip (see more details in the :doc:`installation` page):
 
 .. code:: bash
 
     pip install soil
 
 
+To get started developing your own simulations and agent behaviors, check out our :doc:`Tutorial <soil_tutorial>` and the `examples on GitHub <https://github.com/gsi-upm/soil/tree/master/examples>.
 
 If you use Soil in your research, do not forget to cite this paper:
 
@@ -47,8 +46,7 @@ If you use Soil in your research, do not forget to cite this paper:
    :caption: Learn more about soil:
 
    installation
-   Tutorial <tutorial/soil_tutorial>
-   notes_v1.0
+   Tutorial <soil_tutorial>
 
 ..
 

docs/notes_v1.0.rst

@@ -1,6 +1,3 @@
-Upgrading to Soil 1.0
----------------------
-
 What are the main changes in version 1.0?
 #########################################
 

docs/requirements.txt

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

setup.py

@@ -17,9 +17,9 @@ def parse_requirements(filename):
 install_reqs = parse_requirements("requirements.txt")
 test_reqs = parse_requirements("test-requirements.txt")
 extras_require={
+    'mesa': ['mesa>=0.8.9'],
     'geo': ['scipy>=1.3'],
-    'web': ['tornado'],
-    'ipython': ['ipython==8.12', 'nbformat==5.8'],
+    'web': ['tornado']
 }
 extras_require['all'] = [dep for package in extras_require.values() for dep in package]
 

soil/analysis.py

@@ -1,11 +1,12 @@
 import os
-import sys
 import sqlalchemy
 import pandas as pd
 from collections import namedtuple
 
 def plot(env, agent_df=None, model_df=None, steps=False, ignore=["agent_count", ]):
     """Plot the model dataframe and agent dataframe together."""
+    if agent_df is None:
+        agent_df = env.agent_df()
     if model_df is None:
         model_df = env.model_df()
     ignore = list(ignore)
@@ -15,17 +16,9 @@ def plot(env, agent_df=None, model_df=None, steps=False, ignore=["agent_count",
         ignore.append("time")
 
     ax = model_df.drop(ignore, axis='columns').plot();
-    if agent_df is None:
-        try:
-            agent_df = env.agent_df()
-        except UserWarning:
-            print("No agent dataframe provided and no agent reporters found. Skipping agent plot.", file=sys.stderr)
-            return
     if not agent_df.empty:
         agent_df.unstack().apply(lambda x: x.value_counts(),
-                                 axis=1).fillna(0).plot(ax=ax,
-                                                        secondary_y=True)
-
+                                 axis=1).fillna(0).plot(ax=ax, secondary_y=True);
 
 Results = namedtuple("Results", ["config", "parameters", "env", "agents"])
 #TODO implement reading from CSV and SQLITE

soil/environment.py

@@ -216,11 +216,10 @@ class BaseEnvironment(Model):
 
     @classmethod
     def run(cls, *,
-            name=None,
             iterations=1,
             num_processes=1, **kwargs):
         from .simulation import Simulation
-        return Simulation(name=name or cls.__name__,
+        return Simulation(name=cls.__name__,
                           model=cls, iterations=iterations,
                           num_processes=num_processes, **kwargs).run()
 

soil/serialization.py

@@ -8,8 +8,6 @@ import importlib.machinery, importlib.util
 from glob import glob
 from itertools import product, chain
 
-from contextlib import contextmanager
-
 import yaml
 import networkx as nx
 
@@ -112,12 +110,12 @@ KNOWN_MODULES = {
 
 MODULE_FILES = {}
 
-def _add_source_file(file):
+def add_source_file(file):
     """Add a file to the list of known modules"""
     file = os.path.abspath(file)
     if file in MODULE_FILES:
         logger.warning(f"File {file} already added as module {MODULE_FILES[file]}. Reloading")
-        _remove_source_file(file)
+        remove_source_file(file)
     modname = f"imported_module_{len(MODULE_FILES)}"
     loader = importlib.machinery.SourceFileLoader(modname, file)
     spec = importlib.util.spec_from_loader(loader.name, loader)
@@ -126,7 +124,7 @@ def _add_source_file(file):
     MODULE_FILES[file] = modname
     KNOWN_MODULES[modname] = my_module
 
-def _remove_source_file(file):
+def remove_source_file(file):
     """Remove a file from the list of known modules"""
     file = os.path.abspath(file)
     modname = None
@@ -136,18 +134,6 @@ def _remove_source_file(file):
     except KeyError as ex:
         raise ValueError(f"File {file} had not been added as a module: {ex}")
 
-
-@contextmanager
-def with_source(file=None):
-    """Add a file to the list of known modules, and remove it afterwards"""
-    if file:
-        _add_source_file(file)
-    try:
-        yield
-    finally:
-        if file:
-            _remove_source_file(file)
-
 def get_module(modname):
     """Get a module from the list of known modules"""
     if modname not in KNOWN_MODULES or KNOWN_MODULES[modname] is None:

soil/simulation.py

@@ -119,23 +119,28 @@ class Simulation:
         self.logger = logger.getChild(self.name)
         self.logger.setLevel(self.level)
 
-        if self.source_file and (not os.path.isabs(self.source_file)):
-            self.source_file = os.path.abspath(os.path.join(self.dir_path, self.source_file))
-        with serialization.with_source(self.source_file):
+        if self.source_file:
+            source_file = self.source_file
+            if not os.path.isabs(source_file):
+                source_file = os.path.abspath(os.path.join(self.dir_path, source_file))
+            serialization.add_source_file(source_file)
+            self.source_file = source_file
 
-            if isinstance(self.model, str):
-                self.model = serialization.deserialize(self.model)
+        if isinstance(self.model, str):
+            self.model = serialization.deserialize(self.model)
 
-            def deserialize_reporters(reporters):
-                for (k, v) in reporters.items():
-                    if isinstance(v, str) and v.startswith("py:"):
-                        reporters[k] = serialization.deserialize(v.split(":", 1)[1])
-                return reporters
+        def deserialize_reporters(reporters):
+            for (k, v) in reporters.items():
+                if isinstance(v, str) and v.startswith("py:"):
+                    reporters[k] = serialization.deserialize(v.split(":", 1)[1])
+            return reporters
 
-            self.agent_reporters = deserialize_reporters(self.agent_reporters)
-            self.model_reporters = deserialize_reporters(self.model_reporters)
-            self.tables = deserialize_reporters(self.tables)
-            self.id = f"{self.name}_{current_time()}"
+        self.agent_reporters = deserialize_reporters(self.agent_reporters)
+        self.model_reporters = deserialize_reporters(self.model_reporters)
+        self.tables = deserialize_reporters(self.tables)
+        if self.source_file:
+            serialization.remove_source_file(self.source_file)
+        self.id = f"{self.name}_{current_time()}"
 
     def run(self, **kwargs):
         """Run the simulation and return the list of resulting environments"""
@@ -212,7 +217,10 @@ class Simulation:
     ):
         """Run the simulation and yield the resulting environments."""
 
-        with serialization.with_source(self.source_file):
+        try:
+            if self.source_file:
+                serialization.add_source_file(self.source_file)
+
             with utils.timer(f"running for config {params}"):
                 if self.dry_run:
                     def func(*args, **kwargs):
@@ -229,6 +237,9 @@ class Simulation:
                         continue
 
                     yield env
+        finally:
+            if self.source_file:
+                serialization.remove_source_file(self.source_file)
 
     def _get_env(self, iteration_id, params):
         """Create an environment for a iteration of the simulation"""

test-requirements.txt

@@ -2,6 +2,3 @@ pytest
 pytest-profiling
 scipy>=1.3
 tornado
-nbconvert==7.3.1
-nbformat==5.8.0
-jupyter==1.0.0

tests/test_ipython.py

@@ -1,18 +0,0 @@
-from unittest import TestCase
-import os
-import nbformat
-from nbconvert.preprocessors import ExecutePreprocessor
-
-ROOT = os.path.abspath(os.path.dirname(__file__))
-
-class TestNotebooks(TestCase):
-    def test_tutorial(self):
-        notebook = os.path.join(ROOT, "../docs/tutorial/soil_tutorial.ipynb")
-        with open(notebook) as f:
-            nb = nbformat.read(f, as_version=4)
-            ep = ExecutePreprocessor(timeout=60000)
-            try:
-                assert ep.preprocess(nb) is not None, f"Got empty notebook for {notebook}"
-            except Exception:
-                assert False, f"Failed executing {notebook}"
-