log simulation results to the specified directory rather than a subdi…

…rectory whose name is a timestamp; issue #48; also fix excessive indentation

examples/simulation_run.py

@@ -8,6 +8,7 @@
 
 import os
 import matplotlib.pyplot as plt
+import tempfile
 
 # import simulation and run results
 from wc_sim.simulation import Simulation
@@ -17,7 +18,7 @@
 # use a toy model
 model_filename = os.path.join(os.path.dirname(__file__), '../tests/fixtures',
                                    '2_species_1_reaction.xlsx')
-results_dir = os.path.expanduser('~/tmp/checkpoints_dir')
+results_dir = tempfile.mkdtemp(dir=os.path.join(os.path.expanduser('~/tmp/checkpoints_dir')))
 
 # create and run simulation
 simulation = Simulation(model_filename)

tests/test_simulation.py

@@ -76,7 +76,8 @@ def test_simulate(self):
         end_time = 30
         with CaptureOutput(relay=False):
             num_events, results_dir = Simulation(TOY_MODEL_FILENAME).run(end_time=end_time,
-                                                                         results_dir=self.results_dir, checkpoint_period=10)
+                                                                         results_dir=self.results_dir,
+                                                                         checkpoint_period=10)
 
         # check time, and simulation config in checkpoints
         for time in Checkpoint.list_checkpoints(results_dir):
@@ -93,7 +94,8 @@ def test_reseed(self):
             tmp_results_dir = tempfile.mkdtemp()
             with CaptureOutput(relay=False):
                 num_events, results_dir = Simulation(TOY_MODEL_FILENAME).run(end_time=20,
-                                                                             results_dir=tmp_results_dir, checkpoint_period=5, seed=seed)
+                                                                             results_dir=tmp_results_dir,
+                                                                             checkpoint_period=5, seed=seed)
             results[seed] = {}
             results[seed]['num_events'] = num_events
             run_results[seed] = RunResults(results_dir)
@@ -109,7 +111,8 @@ def test_reseed(self):
             tmp_results_dir = tempfile.mkdtemp()
             with CaptureOutput(relay=False):
                 num_events, results_dir = Simulation(TOY_MODEL_FILENAME).run(end_time=20,
-                                                                             results_dir=tmp_results_dir, checkpoint_period=5, seed=seed)
+                                                                             results_dir=tmp_results_dir,
+                                                                             checkpoint_period=5, seed=seed)
             results[rep] = {}
             results[rep]['num_events'] = num_events
             run_results[rep] = RunResults(results_dir)
@@ -160,43 +163,27 @@ def test_create_metadata_2(self):
         self.assertEqual(simulation_metadata.simulation.time_step, 1)
 
     def test_ckpt_dir_processing_1(self):
-        # checkpoints_dir does not exist
+        # checkpoints_dir gets created because it does not exist
         self.args['results_dir'] = os.path.join(self.results_dir, 'no_such_dir', 'no_such_sub_dir')
         self.simulation.process_and_validate_args(self.args)
         self.assertTrue(os.path.isdir(self.args['results_dir']))
 
     def test_ckpt_dir_processing_2(self):
-        # checkpoints_dir exists, and is empty
-        root_dir = self.args['results_dir']
-        self.simulation.process_and_validate_args(self.args)
-        # process_and_validate_args creates 1 timestamped sub-dir
-        self.assertEqual(len(os.listdir(root_dir)), 1)
-
-    def test_ckpt_dir_processing_3(self):
         # checkpoints_dir is a file
-        self.args['results_dir'] = os.path.join(self.args['results_dir'], 'new_file')
-        try:
-            open(self.args['results_dir'], 'x')
-            with self.assertRaises(MultialgorithmError):
-                self.simulation.process_and_validate_args(self.args)
-        except FileExistsError:
+        path = os.path.join(self.args['results_dir'], 'new_file')
+        self.args['results_dir'] = path
+        with open(path, 'w'):
             pass
+        with self.assertRaises(MultialgorithmError):
+            self.simulation.process_and_validate_args(self.args)
 
-    def test_ckpt_dir_processing_4(self):
-        # timestamped sub-directory of checkpoints-dir already exists
-        root_dir = self.args['results_dir']
-        self.simulation.process_and_validate_args(self.args)
-        # given the chance, albeit small, that the second has advanced and
-        # a different timestamped sub-directory is made, try repeatedly to create the error
-        # the for loop takes about 0.01 sec
-        raised = False
-        for i in range(10):
-            self.args['results_dir'] = root_dir
-            try:
-                self.simulation.process_and_validate_args(self.args)
-            except:
-                raised = True
-        self.assertTrue(raised)
+    def test_ckpt_dir_processing_3(self):
+        # checkpoints_dir is not empty
+        path = os.path.join(self.args['results_dir'], 'new_file')
+        with open(path, 'w'):
+            pass
+        with self.assertRaises(MultialgorithmError):
+            self.simulation.process_and_validate_args(self.args)
 
     def test_process_and_validate_args1(self):
         original_args = copy(self.args)

wc_sim/multialgorithm_simulation.py

@@ -98,8 +98,8 @@ class MultialgorithmSimulation(object):
 
     Attributes:
         model (:obj:`Model`): a model description
-        args (:obj:`dict`): parameters for the simulation; if `results_dir` is provided, then also
-            must include checkpoint_period
+        args (:obj:`dict`): parameters for the simulation; if `results_dir` is an entry in `args`,
+            then `checkpoint_period` must also be included
         simulation (:obj:`SimulationEngine`): the initialized simulation
         checkpointing_sim_obj (:obj:`MultialgorithmicCheckpointingSimObj`): the checkpointing object;
             `None` if absent

wc_sim/simulation.py

@@ -138,25 +138,19 @@ def process_and_validate_args(self, args):
         if 'results_dir' in args:
             results_sup_dir = os.path.abspath(os.path.expanduser(args['results_dir']))
 
-            # if results_sup_dir is a file, raise error
-            if os.path.isfile(results_sup_dir):
-                raise MultialgorithmError("results_dir ({}) is a file, not a dir".format(results_sup_dir))
+            if os.path.exists(results_sup_dir):
+                # raise error if results_sup_dir exists and is not a dir
+                if not os.path.isdir(results_sup_dir):
+                    raise MultialgorithmError(f"results_dir ({results_sup_dir}) is not a dir")
+
+                # raise error if results_sup_dir is not empty
+                if os.listdir(results_sup_dir):
+                    raise MultialgorithmError(f"results_dir ({results_sup_dir}) is not empty")
 
             # if results_sup_dir does not exist, make it
             if not os.path.exists(results_sup_dir):
                 os.makedirs(results_sup_dir)
 
-            # make a time-stamped sub-dir for this run
-            time_stamped_sub_dir = os.path.join(results_sup_dir, datetime.datetime.now().strftime(
-                '%Y-%m-%d-%H-%M-%S'))
-            if os.path.exists(time_stamped_sub_dir):
-                raise MultialgorithmError("timestamped sub-directory of results_dir ({}) already exists".format(
-                    time_stamped_sub_dir))
-            else:
-                os.makedirs(time_stamped_sub_dir)
-            # update results_dir
-            args['results_dir'] = time_stamped_sub_dir
-
         # validate args
         if 'end_time' not in args:
             raise MultialgorithmError("Simulation end time, end_time, must be provided")
@@ -166,8 +160,9 @@ def process_and_validate_args(self, args):
 
         if 'checkpoint_period' in args:
             if args['checkpoint_period'] <= 0 or args['end_time'] < args['checkpoint_period']:
-                raise MultialgorithmError("Checkpointing period ({}) must be positive and less than or equal to end time".format(
-                    args['checkpoint_period']))
+                raise MultialgorithmError("Checkpointing period ({}) must be positive and "
+                                          "less than or equal to end time".format(
+                                          args['checkpoint_period']))
 
             if args['end_time'] / args['checkpoint_period'] % 1 != 0:
                 raise MultialgorithmError('end_time ({}) must be a multiple of checkpoint_period ({})'.format(
@@ -211,16 +206,13 @@ def run(self, end_time, results_dir=None, checkpoint_period=None, time_step=1, s
             simulation_args['checkpoint_period'] = checkpoint_period
 
         self.process_and_validate_args(simulation_args)
-        timestamped_results_dir = None
-        if results_dir:
-            timestamped_results_dir = simulation_args['results_dir']
 
         multialgorithm_simulation = MultialgorithmSimulation(self.model, simulation_args)
         self.simulation_engine, self.dynamic_model = multialgorithm_simulation.build_simulation()
         self.simulation_engine.initialize()
 
-        if timestamped_results_dir:
-            SimulationMetadata.write_metadata(self.simulation_metadata, timestamped_results_dir)
+        if results_dir:
+            SimulationMetadata.write_metadata(self.simulation_metadata, results_dir)
 
         # run simulation
         try:
@@ -234,15 +226,15 @@ def run(self, end_time, results_dir=None, checkpoint_period=None, time_step=1, s
 
         self.simulation_metadata.run.record_end()
         # update metadata in file
-        if timestamped_results_dir:
-            SimulationMetadata.write_metadata(self.simulation_metadata, timestamped_results_dir)
+        if results_dir:
+            SimulationMetadata.write_metadata(self.simulation_metadata, results_dir)
 
         print('Simulated {} events'.format(num_events))
-        if timestamped_results_dir:
-            # summarize results in an HDF5 file in timestamped_results_dir
-            RunResults(timestamped_results_dir)
-            print("Saved checkpoints and run results in '{}'".format(timestamped_results_dir))
-            return (num_events, timestamped_results_dir)
+        if results_dir:
+            # summarize results in an HDF5 file in results_dir
+            RunResults(results_dir)
+            print("Saved checkpoints and run results in '{}'".format(results_dir))
+            return (num_events, results_dir)
         else:
             return (num_events, None)
 

wc_sim/testing/utils.py

@@ -8,6 +8,7 @@
 
 from collections import defaultdict
 import numpy as np
+import os
 
 from wc_lang import Model
 from wc_lang.io import Reader
@@ -234,7 +235,12 @@ def define_trajectory_classes(model):
 
 
 def verify_closed_form_model(test_case, model_filename, results_dir):
-    # alternatively, just load the SpeciesTrajectory & AggregateTrajectory worksheets into pandas
+    # empty results_dir
+    for file in os.listdir(results_dir):
+        file_path = os.path.join(results_dir, file)
+        if os.path.isfile(file_path):
+            os.unlink(file_path)
+
     # read model while ignoring missing models, with std dev = 0
     model = read_model_and_set_all_std_devs_to_0(model_filename)
     # simulate model