v0.15.2

See CHANGELOG.md for a complete list of changes

CHANGELOG.md

@@ -3,6 +3,13 @@ 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).
 
+## [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`

soil/VERSION

@@ -1 +1 @@
-0.15.1
+0.15.2

soil/__init__.py

@@ -23,13 +23,15 @@ def main():
     import argparse
     from . import simulation
 
-    logging.info('Running SOIL version: {}'.format(__version__))
+    logger.info('Running SOIL version: {}'.format(__version__))
 
     parser = argparse.ArgumentParser(description='Run a SOIL simulation')
     parser.add_argument('file', type=str,
                         nargs="?",
                         default='simulation.yml',
-                        help='python module containing the simulation configuration.')
+                        help='Configuration file for the simulation (e.g., YAML or JSON)')
+    parser.add_argument('--version', action='store_true',
+                        help='Show version info and exit')
     parser.add_argument('--module', '-m', type=str,
                         help='file containing the code of any custom agents.')
     parser.add_argument('--dry-run', '--dry', action='store_true',
@@ -52,12 +54,15 @@ def main():
     args = parser.parse_args()
     logging.basicConfig(level=getattr(logging, (args.level or 'INFO').upper()))
 
+    if args.version:
+        return
+
     if os.getcwd() not in sys.path:
         sys.path.append(os.getcwd())
     if args.module:
         importlib.import_module(args.module)
 
-    logging.info('Loading config file: {}'.format(args.file))
+    logger.info('Loading config file: {}'.format(args.file))
 
     try:
         exporters = list(args.exporter or ['default', ])
@@ -68,6 +73,10 @@ def main():
         exp_params = {}
         if args.dry_run:
             exp_params['copy_to'] = sys.stdout
+
+        if not os.path.exists(args.file):
+            logger.error('Please, input a valid file')
+            return
         simulation.run_from_config(args.file,
                                    dry_run=args.dry_run,
                                    exporters=exporters,

soil/exporters.py

@@ -14,15 +14,6 @@ from .utils import open_or_reuse, logger, timer
 from . import utils
 
 
-def for_sim(simulation, names, *args, **kwargs):
-    '''Return the set of exporters for a simulation, given the exporter names'''
-    exporters = []
-    for name in names:
-        mod = deserialize(name, known_modules=['soil.exporters'])
-        exporters.append(mod(simulation, *args, **kwargs))
-    return exporters
-
-
 class DryRunner(BytesIO):
     def __init__(self, fname, *args, copy_to=None, **kwargs):
         super().__init__(*args, **kwargs)
@@ -38,8 +29,12 @@ class DryRunner(BytesIO):
             super().write(bytes(txt, 'utf-8'))
 
     def close(self):
-        logger.info('**Not** written to {} (dry run mode):\n\n{}\n\n'.format(self.__fname,
+        content = '(binary data not shown)'
-                                                                       self.getvalue().decode()))
+        try:
+            content = self.getvalue().decode()
+        except UnicodeDecodeError:
+            pass
+        logger.info('**Not** written to {} (dry run mode):\n\n{}\n\n'.format(self.__fname, content))
         super().close()
 
 
@@ -99,6 +94,12 @@ class default(Exporter):
                 with self.output('{}.sqlite'.format(env.name), mode='wb') as f:
                     env.dump_sqlite(f)
 
+    def end(self, stats):
+          with timer('Dumping simulation {}\'s stats'.format(self.simulation.name)):
+              with self.output('{}.sqlite'.format(self.simulation.name), mode='wb') as f:
+                  self.simulation.dump_sqlite(f)
+
+
 
 class csv(Exporter):
     '''Export the state of each environment (and its agents) in a separate CSV file'''

soil/serialization.py

@@ -208,3 +208,13 @@ def deserialize(type_, value=None, **kwargs):
     if value is None:
         return des
     return des(value)
+
+
+def deserialize_all(names, *args, known_modules=['soil'], **kwargs):
+    '''Return the set of exporters for a simulation, given the exporter names'''
+    exporters = []
+    for name in names:
+        mod = deserialize(name, known_modules=known_modules)
+        exporters.append(mod(*args, **kwargs))
+    return exporters
+

soil/simulation.py

@@ -15,7 +15,7 @@ import pickle
 from . import serialization, utils, basestring, agents
 from .environment import Environment
 from .utils import logger
-from .exporters import default, for_sim as exporters_for_sim
+from .exporters import default
 from .stats import defaultStats
 from .history import History
 
@@ -133,7 +133,7 @@ class Simulation:
                                               self.topology)
 
         self._history = History(name=self.name,
-                               backup=False)
+                                backup=False)
 
     def run_simulation(self, *args, **kwargs):
         return self.run(*args, **kwargs)
@@ -167,14 +167,16 @@ class Simulation:
             logger.setLevel(log_level)
         logger.info('Using exporters: %s', exporters or [])
         logger.info('Output directory: %s', outdir)
-        exporters = exporters_for_sim(self,
+        exporters = serialization.deserialize_all(exporters,
-                                      exporters,
+                                                  simulation=self,
-                                      dry_run=dry_run,
+                                                  known_modules=['soil.exporters',],
-                                      outdir=outdir,
+                                                  dry_run=dry_run,
-                                      **exporter_params)
+                                                  outdir=outdir,
-        stats = exporters_for_sim(self,
+                                                  **exporter_params)
-                                  stats,
+        stats = serialization.deserialize_all(simulation=self,
-                                  **stats_params)
+                                              names=stats,
+                                              known_modules=['soil.stats',],
+                                              **stats_params)
 
         with utils.timer('simulation {}'.format(self.name)):
             for stat in stats:
@@ -293,6 +295,9 @@ class Simulation:
         with utils.open_or_reuse(f, 'wb') as f:
             pickle.dump(self, f)
 
+    def dump_sqlite(self, f):
+        return self._history.dump(f)
+
     def __getstate__(self):
         state={}
         for k, v in self.__dict__.items():

tests/test_exporters.py

@@ -74,10 +74,10 @@ class Exporters(TestCase):
         s = simulation.from_config(config)
         tmpdir = tempfile.mkdtemp()
         envs = s.run_simulation(exporters=[
-            exporters.default,
+                                    exporters.default,
-            exporters.csv,
+                                    exporters.csv,
-            exporters.gexf,
+                                    exporters.gexf,
-        ],
+                                ],
                                 stats=[distribution,],
                                 outdir=tmpdir,
                                 exporter_params={'copy_to': output})