Merge pull request #112 from UCL-CCS/dev

Pre-release version

docs/tutorial_files/gauss_tutorial.py

@@ -82,7 +82,8 @@
 
 # 8. Run Application
 #    - gauss is executed for each sample
-my_campaign.apply_for_each_run_dir(uq.actions.ExecuteLocal(cmd))
+my_campaign.apply_for_each_run_dir(uq.actions.ExecuteLocal(cmd,
+                                                           interpret='python3'))
 
 # 9. Collate output
 my_campaign.collate()

easyvvuq/actions/execute_local.py

@@ -33,7 +33,7 @@
 
 class ExecuteLocal(BaseAction):
 
-    def __init__(self, run_cmd):
+    def __init__(self, run_cmd, interpret=None):
         """
         Provides an action element to run a shell command in a specified
         directory.
@@ -43,6 +43,8 @@ def __init__(self, run_cmd):
 
         run_cmd : str
             Command to execute.
+        interpret : str or None
+            Interpreter to use to execute cmd.
 
         """
 
@@ -54,6 +56,7 @@ def __init__(self, run_cmd):
 
         # Need to expand users, get absolute path and dereference symlinks
         self.run_cmd = os.path.realpath(os.path.expanduser(run_cmd))
+        self.interpreter = interpret
 
     def act_on_dir(self, target_dir):
         """
@@ -64,7 +67,10 @@ def act_on_dir(self, target_dir):
 
         """
 
-        full_cmd = f'cd {target_dir}\n{self.run_cmd}\n'
+        if self.interpreter is None:
+            full_cmd = f'cd {target_dir}\n{self.run_cmd}\n'
+        else:
+            full_cmd = f'cd {target_dir}\n{self.interpreter} {self.run_cmd}\n'
         result = os.system(full_cmd)
         if result != 0:
             sys.exit(f'Non-zero exit code from command "{full_cmd}"\n')

easyvvuq/campaign.py

@@ -7,10 +7,11 @@
 import logging
 import tempfile
 import json
-import easyvvuq as uq
-from easyvvuq import constants
-from easyvvuq.constants import default_campaign_prefix
-from easyvvuq.data_structs import RunInfo
+import easyvvuq
+from easyvvuq.constants import default_campaign_prefix, Status
+from easyvvuq.data_structs import RunInfo, CampaignInfo, AppInfo
+from easyvvuq.sampling import BaseSamplingElement
+from easyvvuq.collate import BaseCollationElement
 
 __copyright__ = """
 
@@ -188,10 +189,10 @@ def init_fresh(self, name, db_type='sql',
             logger.critical(message)
             raise RuntimeError(message)
 
-        info = uq.data_structs.CampaignInfo(
+        info = CampaignInfo(
             name=name,
             campaign_dir_prefix=default_campaign_prefix,
-            easyvvuq_version=uq.__version__,
+            easyvvuq_version=easyvvuq.__version__,
             campaign_dir=self.campaign_dir)
         self.campaign_db = CampaignDB(location=self.db_location,
                                       new_campaign=True,
@@ -364,7 +365,7 @@ def add_app(self, name=None, params=None, fixtures=None,
                 raise Exception(msg)
 
         # validate application input
-        app = uq.data_structs.AppInfo(
+        app = AppInfo(
             name=name,
             params=params,
             fixtures=fixtures,
@@ -411,7 +412,7 @@ def set_sampler(self, sampler):
         -------
 
         """
-        if not isinstance(sampler, uq.sampling.BaseSamplingElement):
+        if not isinstance(sampler, BaseSamplingElement):
             msg = "set_sampler() must be passed a sampling element"
             logging.error(msg)
             raise Exception(msg)
@@ -431,7 +432,7 @@ def set_collater(self, collater):
         -------
 
         """
-        if not isinstance(collater, uq.collate.BaseCollationElement):
+        if not isinstance(collater, BaseCollationElement):
             msg = "set_collater() must be passed a collation element"
             logging.error(msg)
             raise Exception(msg)
@@ -572,7 +573,7 @@ def scan_completed(self, *args, **kwargs):
         -------
 
         """
-        return self.list_runs(status=uq.constants.Status.COLLATED)
+        return self.list_runs(status=Status.COLLATED)
 
     def all_complete(self):
         """
@@ -584,7 +585,7 @@ def all_complete(self):
 
         """
 
-        num = self.campaign_db.get_num_runs(not_status=constants.Status.COLLATED)
+        num = self.campaign_db.get_num_runs(not_status=Status.COLLATED)
         if num == 0:
             return True
         return False
@@ -614,7 +615,7 @@ def populate_runs_dir(self):
         runs_dir = self.campaign_db.runs_dir()
 
         # Loop through all runs with status NEW
-        for run_id, run_data in self.campaign_db.runs(status=constants.Status.NEW):
+        for run_id, run_data in self.campaign_db.runs(status=Status.NEW):
 
             # Make run directory
             target_dir = os.path.join(runs_dir, run_id)
@@ -632,7 +633,7 @@ def populate_runs_dir(self):
                 active_encoder.encode(params=run_data['params'],
                                       target_dir=target_dir)
 
-            self.campaign_db.set_run_statuses([run_id], constants.Status.ENCODED)
+            self.campaign_db.set_run_statuses([run_id], Status.ENCODED)
 
     def get_campaign_runs_dir(self):
         """Get the runs directory from the CampaignDB.
@@ -663,7 +664,7 @@ def apply_for_each_run_dir(self, action):
         runs_dir = self.campaign_db.runs_dir()
 
         # Loop through all runs in this campaign with status ENCODED
-        for run_id, run_data in self.campaign_db.runs(status=constants.Status.ENCODED):
+        for run_id, run_data in self.campaign_db.runs(status=Status.ENCODED):
 
             dir_name = os.path.join(runs_dir, run_id)
             print("Applying " + action.__module__ + " to " + dir_name + "...")

easyvvuq/collate/base.py

@@ -1,4 +1,4 @@
-from .. import BaseElement
+from easyvvuq.base_element import BaseElement
 import json
 import logging
 

easyvvuq/data_structs.py

@@ -4,8 +4,9 @@
 import os
 import logging
 import json
-import easyvvuq as uq
 from easyvvuq import constants
+from easyvvuq.encoders import BaseEncoder
+from easyvvuq.decoders import BaseDecoder
 
 __copyright__ = """
 
@@ -235,7 +236,7 @@ def input_encoder(self):
 
     @input_encoder.setter
     def input_encoder(self, encoder):
-        if not isinstance(encoder, uq.encoders.BaseEncoder):
+        if not isinstance(encoder, BaseEncoder):
             msg = f"Provided 'encoder' must be derived from type BaseEncoder"
             logger.error(msg)
             raise Exception(msg)
@@ -248,7 +249,7 @@ def output_decoder(self):
 
     @output_decoder.setter
     def output_decoder(self, decoder):
-        if not isinstance(decoder, uq.decoders.BaseDecoder):
+        if not isinstance(decoder, BaseDecoder):
             msg = f"Provided 'decoder' must be derived from type BaseDecoder"
             logger.error(msg)
             raise Exception(msg)

easyvvuq/sampling/base.py

@@ -1,4 +1,4 @@
-from .. import BaseElement
+from easyvvuq.base_element import BaseElement
 import logging
 import json
 import jsonpickle

setup.py

@@ -25,7 +25,8 @@
 
     author='CCS',
 
-    install_requires=['numpy', 'pandas', 'pytest', 'SQLAlchemy', 'chaospy',
+    install_requires=['numpy', 'pandas>=0.24', 'scipy==1.2.1', 
+                      'pytest', 'SQLAlchemy', 'chaospy',
                       'sqlalchemy-utils', 'matplotlib', 'jsonpickle'],
 
     packages=find_packages(),