Improve exporters

examples/rabbits/basic/rabbit_agents.py

@@ -1,4 +1,4 @@
-from soil.agents import FSM, state, default_state, BaseAgent, NetworkAgent
+from soil import FSM, state, default_state, BaseAgent, NetworkAgent, Environment
 from soil.time import Delta
 from enum import Enum
 from collections import Counter
@@ -6,7 +6,23 @@ import logging
 import math
 
 
-class RabbitModel(FSM, NetworkAgent):
+class RabbitEnv(Environment):
+
+    @property
+    def num_rabbits(self):
+        return self.count_agents(agent_class=Rabbit)
+
+    @property
+    def num_males(self):
+        return self.count_agents(agent_class=Male)
+
+    @property
+    def num_females(self):
+        return self.count_agents(agent_class=Female)
+
+
+
+class Rabbit(FSM, NetworkAgent):
 
     sexual_maturity = 30
     life_expectancy = 300
@@ -35,7 +51,7 @@ class RabbitModel(FSM, NetworkAgent):
         self.die()
 
 
-class Male(RabbitModel):
+class Male(Rabbit):
     max_females = 5
     mating_prob = 0.001
 
@@ -56,7 +72,7 @@ class Male(RabbitModel):
                 break  # Take a break
 
 
-class Female(RabbitModel):
+class Female(Rabbit):
     gestation = 30
 
     @state
@@ -119,7 +135,7 @@ class RandomAccident(BaseAgent):
 
         prob_death = self.model.get('prob_death', 1e-100)*math.floor(math.log10(max(1, rabbits_alive)))
         self.debug('Killing some rabbits with prob={}!'.format(prob_death))
-        for i in self.iter_agents(agent_class=RabbitModel):
+        for i in self.iter_agents(agent_class=Rabbit):
             if i.state_id == i.dead.id:
                 continue
             if self.prob(prob_death):

examples/rabbits/basic/rabbits.yml

@@ -7,11 +7,10 @@ description: null
 group: null
 interval: 1.0
 max_time: 100
-model_class: soil.environment.Environment
+model_class: rabbit_agents.RabbitEnv
 model_params:
   agents:
     topology: true
-    agent_class: rabbit_agents.RabbitModel
     distribution:
     - agent_class: rabbit_agents.Male
       weight: 1
@@ -34,5 +33,10 @@ model_params:
       nodes:
       - id: 1
       - id: 0
+  model_reporters:
+    num_males: 'num_males'
+    num_females: 'num_females'
+    num_rabbits: |
+      py:lambda env: env.num_males + env.num_females
 extra:
   visualization_params: {}

soil/exporters.py

@@ -10,7 +10,7 @@ import networkx as nx
 
 
 from .serialization import deserialize
-from .utils import open_or_reuse, logger, timer
+from .utils import try_backup, open_or_reuse, logger, timer
 
 
 from . import utils, network
@@ -91,12 +91,14 @@ class default(Exporter):
     """Default exporter. Writes sqlite results, as well as the simulation YAML"""
 
     def sim_start(self):
-        if not self.dry_run:
+        if self.dry_run:
-            logger.info("Dumping results to %s", self.outdir)
-            with self.output(self.simulation.name + ".dumped.yml") as f:
-                f.write(self.simulation.to_yaml())
-        else:
             logger.info("NOT dumping results")
+            return
+        logger.info("Dumping results to %s", self.outdir)
+        with self.output(self.simulation.name + ".dumped.yml") as f:
+            f.write(self.simulation.to_yaml())
+        self.dbpath = os.path.join(self.outdir, f"{self.simulation.name}.sqlite")
+        try_backup(self.dbpath, move=True)
 
     def trial_end(self, env):
         if self.dry_run:
@@ -107,21 +109,23 @@ class default(Exporter):
             "Dumping simulation {} trial {}".format(self.simulation.name, env.id)
         ):
 
-            fpath = os.path.join(self.outdir, f"{env.id}.sqlite")
+            engine = create_engine(f"sqlite:///{self.dbpath}", echo=False)
-            engine = create_engine(f"sqlite:///{fpath}", echo=False)
 
             dc = env.datacollector
-            for (t, df) in get_dc_dfs(dc):
+            for (t, df) in get_dc_dfs(dc, trial_id=env.id):
                 df.to_sql(t, con=engine, if_exists="append")
 
 
-def get_dc_dfs(dc):
+def get_dc_dfs(dc, trial_id=None):
     dfs = {
         "env": dc.get_model_vars_dataframe(),
         "agents": dc.get_agent_vars_dataframe(),
     }
     for table_name in dc.tables:
         dfs[table_name] = dc.get_table_dataframe(table_name)
+    if trial_id:
+        for (name, df) in dfs.items():
+            df['trial_id'] = trial_id
     yield from dfs.items()
 
 
@@ -135,7 +139,7 @@ class csv(Exporter):
                 self.simulation.name, env.id, self.outdir
             )
         ):
-            for (df_name, df) in get_dc_dfs(env.datacollector):
+            for (df_name, df) in get_dc_dfs(env.datacollector, trial_id=env.id):
                 with self.output("{}.{}.csv".format(env.id, df_name)) as f:
                     df.to_csv(f)
 

soil/serialization.py

@@ -197,7 +197,7 @@ def deserializer(type_, known_modules=KNOWN_MODULES):
             return getattr(cls, "deserialize", cls)
         except (ImportError, AttributeError) as ex:
             errors.append((modname, tname, ex))
-    raise Exception('Could not find type "{}". Tried: {}'.format(type_, errors))
+    raise ValueError('Could not find type "{}". Tried: {}'.format(type_, errors))
 
 
 def deserialize(type_, value=None, globs=None, **kwargs):
@@ -207,7 +207,13 @@ def deserialize(type_, value=None, globs=None, **kwargs):
     if globs and type_ in globs:
         des = globs[type_]
     else:
-        des = deserializer(type_, **kwargs)
+        try:
+            des = deserializer(type_, **kwargs)
+        except ValueError as ex:
+            try:
+                des = eval(type_)
+            except Exception:
+                raise ex
     if value is None:
         return des
     return des(value)

soil/simulation.py

@@ -151,7 +151,7 @@ class Simulation:
         def deserialize_reporters(reporters):
             for (k, v) in reporters.items():
                 if isinstance(v, str) and v.startswith("py:"):
-                    reporters[k] = serialization.deserialize(value.lsplit(":", 1)[1])
+                    reporters[k] = serialization.deserialize(v.split(":", 1)[1])
             return reporters
 
         params = self.model_params.copy()

soil/utils.py

@@ -4,7 +4,7 @@ import os
 import traceback
 
 from functools import partial
-from shutil import copyfile
+from shutil import copyfile, move
 from multiprocessing import Pool
 
 from contextlib import contextmanager
@@ -47,21 +47,34 @@ def timer(name="task", pre="", function=logger.info, to_object=None):
         to_object.end = end
 
 
-def safe_open(path, mode="r", backup=True, **kwargs):
+def try_backup(path, move=False):
+    if not os.path.exists(path):
+        return None
     outdir = os.path.dirname(path)
     if outdir and not os.path.exists(outdir):
         os.makedirs(outdir)
-    if backup and "w" in mode and os.path.exists(path):
+    creation = os.path.getctime(path)
-        creation = os.path.getctime(path)
+    stamp = strftime("%Y-%m-%d_%H.%M.%S", localtime(creation))
-        stamp = strftime("%Y-%m-%d_%H.%M.%S", localtime(creation))
+
-
+    backup_dir = os.path.join(outdir, "backup")
-        backup_dir = os.path.join(outdir, "backup")
+    if not os.path.exists(backup_dir):
-        if not os.path.exists(backup_dir):
+        os.makedirs(backup_dir)
-            os.makedirs(backup_dir)
+    newpath = os.path.join(
-        newpath = os.path.join(
+        backup_dir, "{}@{}".format(os.path.basename(path), stamp)
-            backup_dir, "{}@{}".format(os.path.basename(path), stamp)
+    )
-        )
+    if move:
+        move(path, newpath)
+    else:
         copyfile(path, newpath)
+    return newpath
+
+
+def safe_open(path, mode="r", backup=True, **kwargs):
+    outdir = os.path.dirname(path)
+    if outdir and not os.path.exists(outdir):
+        os.makedirs(outdir)
+    if backup and "w" in mode:
+        try_backup(path)
     return open(path, mode=mode, **kwargs)
 
 
@@ -70,7 +83,7 @@ def open_or_reuse(f, *args, **kwargs):
     try:
         with safe_open(f, *args, **kwargs) as f:
             yield f
-    except (AttributeError, TypeError):
+    except (AttributeError, TypeError) as ex:
         yield f
 
 

tests/test_exporters.py

@@ -99,7 +99,7 @@ class Exporters(TestCase):
 
         try:
             for e in envs:
-                db = sqlite3.connect(os.path.join(simdir, f"{e.id}.sqlite"))
+                db = sqlite3.connect(os.path.join(simdir, f"{s.name}.sqlite"))
                 cur = db.cursor()
                 agent_entries = cur.execute("SELECT * from agents").fetchall()
                 env_entries = cur.execute("SELECT * from env").fetchall()