Incorporate SimulationMetadata in wc simulation

tests/core/test_sim_metadata.py

@@ -36,7 +36,7 @@ def setUp(self):
 
         ip_address = socket.gethostbyname(socket.gethostname())
         self.author = author = AuthorMetadata(name='Test user', email='test@test.com',
-                                                organization='Test organization', ip_address=ip_address)
+            username='Test username', organization='Test organization', ip_address=ip_address)
 
         self.run = run = RunMetadata()
         run.record_start()

tests/multialgorithm/test_multialgorithm_main.py

@@ -44,6 +44,11 @@ def test_parse_args(self):
         for arg, value in args.__dict__.items():
             self.assertEqual(getattr(original_args, arg), value)
 
+        args.dataframe_file = os.path.join(self.checkpoints_dir, 'dataframe_file_no_suffix')
+        original_args = copy(args)
+        SimController.process_and_validate_args(args)
+        self.assertEqual(args.dataframe_file, original_args.dataframe_file + '.h5')
+
         # test error detection
         errors = dict(
             end_time=[-3, 0],
@@ -66,7 +71,8 @@ def test_parse_args(self):
             checkpoints_dir=None,
             fba_time_step=10,
         )
-        with self.assertRaisesRegexp(ValueError, 'dataframe_file cannot be specified unless checkpoints_dir is provided'):
+        with self.assertRaisesRegexp(ValueError,
+            'dataframe_file cannot be specified unless checkpoints_dir is provided'):
             SimController.process_and_validate_args(args)
 
     def test_simulate(self):
@@ -77,14 +83,16 @@ def test_simulate(self):
             '--checkpoint-period', '3',
             '--checkpoints-dir', self.checkpoints_dir,
             '--dataframe-file', os.path.join(self.checkpoints_dir, 'dataframe_file.h5'),
-            '--fba-time-step', '5.5',
+            '--fba-time-step', '5',
         ]
         with __main__.App(argv=argv) as app:
             with CaptureOutput() as capturer:
                 app.run()
-                match = re.match('^Saved (\d+) events to (.*?)$', capturer.get_text())
+                events = re.search('^Simulated (\d+) events', capturer.get_text())
+                checkpoints = re.search("Saved chcekpoints in '(.*?)'$", capturer.get_text())
 
-        num_events = int(match.group(1))
-        res_dirname = match.group(2)
+        num_events = int(events.group(1))
+        res_dirname = checkpoints.group(1)
+        # TODO(Arthur): stronger assertions
         self.assertTrue(0 < num_events)
         self.assertTrue(res_dirname.startswith(self.checkpoints_dir))

tests/multialgorithm/test_multialgorithm_simulation.py

@@ -261,8 +261,8 @@ def test_run_ssa_suite(self):
             delta=0,
             init_vol=1E-22)
 
-    # TODO(Arthur): check the random state in checkpoints
     # TODO(Arthur): include metadata in checkpoints
+    # TODO(Arthur): check the random state in checkpoints
     # TODO(Arthur): review the cement programs
     # TODO(Arthur): put specie pop, random state, time, and metadata in the dataframe
     # TODO(Arthur): graphs of a variety of models

wc_sim/core/sim_metadata.py

@@ -200,22 +200,24 @@ class AuthorMetadata(object):
     Attributes:
         name (:obj:`str`): authors' name
         email (:obj:`str`): author's email address
+        username (:obj:`str`): authors' username
         organization (:obj:`str`): author's organization
         ip_address (:obj:`str`): author's ip address
     """
 
-    def __init__(self, name, email, organization, ip_address):
+    def __init__(self, name, email, username, organization, ip_address):
         """ Construct a representation of the author of a simulation run
 
         Args:
             name (:obj:`str`): authors' name
             email (:obj:`str`): author's email address
+            username (:obj:`str`): authors' username
             organization (:obj:`str`): author's organization
             ip_address (:obj:`str`): author's ip address
         """
-
         self.name = name
         self.email = email
+        self.username = username
         self.organization = organization
         self.ip_address = ip_address
 
@@ -231,7 +233,7 @@ def __eq__(self, other):
         if other.__class__ is not self.__class__:
             return False
 
-        attrs = ['name', 'email', 'organization', 'ip_address']
+        attrs = ['name', 'email', 'username', 'organization', 'ip_address']
         for attr in attrs:
             if getattr(other, attr) != getattr(self, attr):
                 return False

wc_sim/multialgorithm/__main__.py

@@ -2,20 +2,24 @@
 """ Command line program for WC simulation
 
 :Author: Arthur Goldberg, Arthur.Goldberg@mssm.edu
+:Author: Jonathan Karr <karr@mssm.edu>
 :Date: 2018-04-18
 :Copyright: 2018, Karr Lab
 :License: MIT
 """
 
 import argparse
 import os
+import getpass
 import sys
+import socket
 import datetime
 import warnings
 import pandas
-
-from .config.core import get_config
 from cement.core.controller import CementBaseController, expose
+
+from wc_sim.core.sim_metadata import SimulationMetadata, ModelMetadata, AuthorMetadata, RunMetadata
+from wc_sim.sim_config import SimulationConfig
 from wc_sim.multialgorithm.multialgorithm_simulation import MultialgorithmSimulation
 from wc_sim.multialgorithm.multialgorithm_errors import MultialgorithmError
 from wc_lang.io import Reader
@@ -26,6 +30,7 @@
 warnings.filterwarnings('ignore', '.*setting concentration.*', )
 
 # get config
+from .config.core import get_config
 config = get_config()['wc_sim']['multialgorithm']
 
 
@@ -42,13 +47,13 @@ class Meta:
             (['end_time'], dict(
                 type=float,
                 help="End time for the simulation (sec)")),
+            (['--checkpoints-dir'], dict(
+                type=str,
+                help="Store simulation results; if provided, a timestamped sub-directory will hold results")),
             (['--checkpoint-period'], dict(
                 type=float,
                 default=config['checkpoint_period'],
                 help="Checkpointing period (sec)")),
-            (['--checkpoints-dir'], dict(
-                type=str,
-                help="Store simulation results; if provided, a timestamped sub-directory will hold results")),
             (['--dataframe-file'], dict(
                 type=str,
                 help="File for storing Pandas DataFrame of checkpoints; written in HDF5; requires checkpoints_dir")),
@@ -72,13 +77,12 @@ def process_and_validate_args(args):
             args (:obj:`object`): parsed command line arguments
 
         Raises:
-            :obj:`ValueError`: if any fo the command line arguments are invalid
+            :obj:`ValueError`: if any of the command line arguments are invalid
         """
 
         # process dataframe_file
-        if args.dataframe_file:
-            if not args.dataframe_file.endswith('.h5'):
-                args.dataframe_file = args.dataframe_file + '.h5'
+        if args.dataframe_file and not args.dataframe_file.endswith('.h5'):
+            args.dataframe_file = args.dataframe_file + '.h5'
 
         # validate args
         if args.end_time <= 0:
@@ -95,6 +99,39 @@ def process_and_validate_args(args):
         if args.dataframe_file and not args.checkpoints_dir:
             raise ValueError("dataframe_file cannot be specified unless checkpoints_dir is provided")
 
+    @staticmethod
+    def create_metadata(args):
+        """ Initialize metadata for this simulation run
+
+        Args:
+            args (:obj:`object`): parsed command line arguments
+        """
+        model = ModelMetadata.create_from_repository()
+
+        # author metadata
+        # TODO: collect more comprehensive and specific author information
+        ip_address = socket.gethostbyname(socket.gethostname())
+        try:
+            username = getpass.getuser() + '(username)'
+        except:
+            username = 'Unknown username'
+        author = AuthorMetadata(name='Unknown name', email='Unknown email', username=username,
+                                organization='Unknown organization', ip_address=ip_address)
+
+        # simulation config metadata
+        time_step = None
+        if args.fba_time_step:
+            time_step = args.fba_time_step
+        simulation_config = SimulationConfig(time_max=args.end_time, time_step=time_step)
+
+        # run metadata
+        run = RunMetadata()
+        run.record_start()
+        run.record_ip_address()
+
+        simulation_metadata = SimulationMetadata(model, simulation_config, run, author)
+        return simulation_metadata
+
     @staticmethod
     def simulate(args):
         """ Run multialgorithmic simulation of a wc_lang model
@@ -103,7 +140,7 @@ def simulate(args):
             args (:obj:`object`): parsed command line arguments
 
         Raises:
-            :obj:`MultialgorithmError`: if a model cannot be read from the model file, or ...
+            :obj:`MultialgorithmError`: if a model cannot be read from the model file
         """
         # read model
         model_file = os.path.abspath(os.path.expanduser(args.model_file))
@@ -116,34 +153,41 @@ def simulate(args):
         CheckModel(model).run()
 
         # create results directory
-        results_sup_dir = os.path.abspath(os.path.expanduser(args.checkpoints_dir))
-        res_dirname = os.path.join(results_sup_dir, datetime.datetime.now().strftime('%Y-%m-%d-%H-%M-%S'))
-        if not os.path.isdir(res_dirname):
-            os.makedirs(res_dirname)
+        res_dirname = None
+        if args.checkpoints_dir:
+            results_sup_dir = os.path.abspath(os.path.expanduser(args.checkpoints_dir))
+            res_dirname = os.path.join(results_sup_dir, datetime.datetime.now().strftime('%Y-%m-%d-%H-%M-%S'))
+            if not os.path.isdir(res_dirname):
+                os.makedirs(res_dirname)
+
+        # create metadata
+        simulation_metadata = SimController.create_metadata(args)
 
         # create a multi-algorithmic simulator
         simulation_args = dict(
             checkpoint_dir=res_dirname,
             checkpoint_period=args.checkpoint_period,
-            # TODO(Arthur): provide metadata
-            metadata={},
+            metadata=simulation_metadata
         )
 
-        # run simulation        
-        multialgorithm_simulation = MultialgorithmSimulation(model, simulation_args)        
+        # run simulation
+        multialgorithm_simulation = MultialgorithmSimulation(model, simulation_args)
         simulation_engine, dynamic_model = multialgorithm_simulation.build_simulation()
-        simulation_engine.initialize()        
+        simulation_engine.initialize()
 
         # run simulation
         num_events = simulation_engine.simulate(args.end_time)
+        simulation_metadata.run.record_end()
 
         if args.dataframe_file:
             pred_species_pops = MultialgorithmCheckpoint.convert_checkpoints(res_dirname)
             store = pandas.HDFStore(args.dataframe_file)
             store['dataframe'] = pred_species_pops
             store.close()
 
-        print('Saved {} events to {}'.format(num_events, res_dirname))
+        print('Simulated {} events'.format(num_events))
+        if args.checkpoints_dir:
+            print("Saved chcekpoints in '{}'".format(res_dirname))
 
 
 handlers = [

wc_sim/multialgorithm/multialgorithm_checkpointing.py

@@ -10,6 +10,7 @@
 
 from wc_sim.log.checkpoint import Checkpoint
 from wc_sim.core.simulation_checkpoint_object import CheckpointSimulationObject, AccessStateObjectInterface
+from wc_sim.core.sim_metadata import SimulationMetadata
 from wc_sim.multialgorithm.submodels.ssa import SSASubmodel
 
 
@@ -98,7 +99,7 @@ def __init__(self, name, checkpoint_period, checkpoint_dir, metadata, local_spec
             name (:obj:`str`): name
             checkpoint_period (:obj:`float`): checkpoint period
             checkpoint_dir (:obj:`str`): checkpoint directory
-            metadata (:obj:``): metadata
+            metadata (:obj:`SimulationMetadata`): metadata
             local_species_population (:obj:`LocalSpeciesPopulation`): the `LocalSpeciesPopulation`
             dynamic_model (:obj:`DynamicModel`): the `DynamicModel`
             multialgorithm_simulation (:obj:`MultialgorithmSimulation`): the `MultialgorithmSimulation`

wc_sim/sim_config.py

@@ -76,7 +76,8 @@ def __init__(self, time_init=0, time_max=3600, time_step=1, changes=None, pertur
             raise SimulationConfigError('time_step must be positive')
 
         if (time_max - time_init) / time_step % 1 != 0:
-            raise SimulationConfigError('(time_max - time_init) must be a multiple of time_step')
+            raise SimulationConfigError('(time_max - time_init) ({} - {}) must be a multiple of time_step ({})'.format(
+                time_max, time_init, time_step))
 
         # random_seed
         if random_seed is not None: