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easyvvuq/_version.py

@@ -154,7 +154,7 @@ def git_get_keywords(versionfile_abs):
                     keywords["date"] = mo.group(1)
         f.close()
     except EnvironmentError:
-        pass
+        print('EnvironmentError raised and ignored')
     return keywords
 
 
@@ -513,7 +513,7 @@ def get_versions():
         if cfg.parentdir_prefix:
             return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
     except NotThisMethod:
-        pass
+        print('NotThisMethod raised and ignored')
 
     return {"version": "0+unknown", "full-revisionid": None,
             "dirty": None,

easyvvuq/actions/execute_local.py

@@ -116,7 +116,7 @@ def start(self, previous=None):
         try:
             previous['encoder_filename'] = self.encoder.target_filename
         except AttributeError:
-            pass
+            print('AttributeError raised and ignored')
         return previous
 
     def finished(self):
@@ -233,6 +233,8 @@ def start(self, previous=None):
         self.ret = subprocess.run(
             self.full_cmd, cwd=target_dir,
             stdout=stdout, stderr=stderr)
+        if isinstance(self.stdout, str): close(stdout)
+        if isinstance(self.stderr, str): close(stderr)
         return previous
 
     def finished(self):

easyvvuq/db/sql.py

@@ -9,10 +9,8 @@
 import numpy as np
 from sqlalchemy.sql import case
 from sqlalchemy import create_engine, Column, Integer, String, ForeignKey
-from sqlalchemy.ext.declarative import declarative_base
-from sqlalchemy.orm import sessionmaker
+from sqlalchemy.orm import sessionmaker, declarative_base
 from sqlalchemy import MetaData
-from sqlalchemy.ext.declarative import declarative_base
 from sqlalchemy import text
 from sqlalchemy.engine import Engine
 from sqlalchemy import event

easyvvuq/sampling/mcmc.py

@@ -142,12 +142,12 @@ def update(self, result, invalid):
                 ignored_runs += list(result.loc[result[('chain_id', 0)]
                                                 == chain_id]['run_id'].values)
             except KeyError:
-                pass
+                print('KeyError raised and ignored')
             try:
                 ignored_runs += list(invalid.loc[invalid[('chain_id', 0)]
                                                  == chain_id]['run_id'].values)
             except KeyError:
-                pass
+                print('KeyError raised and ignored')
         ignored_runs = [run[0] for run in ignored_runs]
         self.iteration += 1
         return ignored_runs

tests/sc/test_sobol.py

@@ -4,7 +4,7 @@
 import easyvvuq as uq
 import numpy as np
 import chaospy as cp
-
+from easyvvuq.actions import CreateRunDirectory, Encode, Decode, CleanUp, ExecuteLocal, Actions
 
 def print_exact_sobols():
     V_i = np.zeros(d)
@@ -18,9 +18,7 @@
     print('Exact 1st-order Sobol indices: ', V_i / V)
 
 
-if __name__ == '__main__':
-    import matplotlib.pyplot as plt
-    plt.close('all')
+def test_sobol_basic():
 
     # number of unknown variables
     d = 5
@@ -79,20 +77,17 @@
         target_filename='sobol_in.json')
     decoder = uq.decoders.SimpleCSV(target_filename=output_filename,
                                     output_columns=output_columns)
+    execute = ExecuteLocal(f"{HOME}/sobol_model.py sobol_in.json")
 
-    # Add the SC app (automatically set as current app)
-    my_campaign.add_app(name="sc",
-                        params=params,
-                        encoder=encoder,
-                        decoder=decoder)
+    actions = Actions(CreateRunDirectory(HOME),
+                  Encode(encoder), execute, Decode(decoder))
+
+    campaign = uq.Campaign(name='sc', params=params, actions=actions)
 
     # Create the sampler
     vary = {
         "x1": cp.Uniform(0.0, 1.0),
-        "x2": cp.Uniform(0.0, 1.0),
-        "x3": cp.Uniform(0.0, 1.0),
-        "x4": cp.Uniform(0.0, 1.0),
-        "x5": cp.Uniform(0.0, 1.0)}
+        "x2": cp.Uniform(0.0, 1.0)}
 
     """
     SPARSE GRID PARAMETERS
@@ -102,32 +97,23 @@
       of 1D collocation points per level. Used to make e.g. clenshaw-curtis
       quadrature nested.
     """
+
     my_sampler = uq.sampling.SCSampler(vary=vary, polynomial_order=2,
                                        quadrature_rule="G", sparse=False,
                                        growth=False)
 
-    # Associate the sampler with the campaign
-    my_campaign.set_sampler(my_sampler)
+    campaign.set_sampler(my_sampler)
 
-    # Will draw all (of the finite set of samples)
-    my_campaign.draw_samples()
-    my_campaign.populate_runs_dir()
-
-    # Use this instead to run the samples using EasyVVUQ on the localhost
-    my_campaign.apply_for_each_run_dir(uq.actions.ExecuteLocal(
-        "tests/sc/sobol_model.py sobol_in.json"))
-
-    my_campaign.collate()
+    campaign.execute().collate()
 
     # Post-processing analysis
     analysis = uq.analysis.SCAnalysis(sampler=my_sampler, qoi_cols=output_columns)
 
-    my_campaign.apply_analysis(analysis)
-
-    results = my_campaign.get_last_analysis()
+    results = campaign.analyse(qoi_cols=output_columns)
 
     print(results.sobols_first())
 
-    print_exact_sobols()
+    assert results.sobols_first()["f"]["x1"] > 0.5
 
-    plt.show()
+if __name__ == '__main__':
+    test_sobol_basic()

tests/test_actions_execute_slurm.py

@@ -32,6 +32,6 @@ def test_action_status_slurm(mock_subprocess_run):
     mock_subprocess_run.return_value = slurm_result
 
     action = ExecuteSLURM('tutorials/epidemic/example.slurm', '$target_dir')
-    previous = {'rundir': '/tmp'}
+    # previous = {'rundir': '/tmp'}
     # action.start(previous)
     # assert(status.job_id == '65541')

tests/test_ensemble_boot.py

@@ -30,7 +30,7 @@
 def test_confidence_interval():
     dist = np.array([])
     with pytest.raises(ValueError):
-        stat, low, high = confidence_interval(dist, 0.0, 0.05)
+        confidence_interval(dist, 0.0, 0.05)
     dist = np.array([0.0])
     stat, low, high = confidence_interval(dist, 0.0, 0.05)
     assert (stat == low == high == 0.0)

tests/test_mcmc.py

@@ -3,7 +3,6 @@
 import numpy as np
 import chaospy as cp
 import json
-import matplotlib.pyplot as plt
 import pytest
 import sys
 from easyvvuq.actions import ExecutePython, Actions

tests/test_sampling_mc.py

@@ -1,7 +1,6 @@
 import pytest
 import chaospy as cp
 from easyvvuq.sampling import MCSampler
-from easyvvuq.sampling.base import Vary
 
 
 def test_sampling():

tests/test_sampling_qmc.py

@@ -1,7 +1,6 @@
 import pytest
 import chaospy as cp
 from easyvvuq.sampling import QMCSampler
-from easyvvuq.sampling.base import Vary
 
 
 def test_init():

tests/test_vector.py

@@ -1,13 +1,8 @@
 import easyvvuq as uq
 import chaospy as cp
 import os
-import sys
-import pytest
 import logging
 from pprint import pformat, pprint
-from .gauss.encoder_gauss import GaussEncoder
-from .gauss.decoder_gauss import GaussDecoder
-from easyvvuq.decoders.json import JSONDecoder
 from easyvvuq.actions import Actions, Encode, Decode, CreateRunDirectory
 
 __copyright__ = """
@@ -88,7 +83,7 @@ def test_gauss_vector_sc(tmpdir):
     data = my_campaign.get_collation_result()
     analysis = uq.analysis.SCAnalysis(sampler=sampler, qoi_cols=["numbers"])
     my_campaign.apply_analysis(analysis)
-    results = my_campaign.get_last_analysis()
+    my_campaign.get_last_analysis()
 
 
 def test_gauss_vector_pce(tmpdir):

tutorials/fusion.py

@@ -121,7 +121,7 @@ def solve_Te(Qe_tot=2e6, H0=0, Hw=0.1, Te_bc=100, chi=1, a0=1, R0=3, E0=1.5, b_p
     return Te.value, ne.value, mesh.cellCenters.value[0], mesh.cellCenters.value[0]/a
 
 if __name__ == '__main__':
-    Te, ne, rho, rho_norm = solve_Te()
+    solve_Te()
 
 """
 to test:

versioneer.py

@@ -328,7 +328,7 @@ def get_root():
             print("Warning: build in %s is using versioneer.py from %s"
                   % (os.path.dirname(me), versioneer_py))
     except NameError:
-        pass
+        print('NameError raised and ignored')
     return root
 
 
@@ -574,7 +574,7 @@ def git_get_keywords(versionfile_abs):
                     keywords["date"] = mo.group(1)
         f.close()
     except EnvironmentError:
-        pass
+        print('EnvironmentError raised and ignored')
     return keywords
 
 
@@ -908,7 +908,7 @@ def get_versions():
         return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
                                           verbose)
     except NotThisMethod:
-        pass
+        print('NotThisMethod raised and ignored')
 
     try:
         root = os.path.realpath(__file__)
@@ -927,13 +927,13 @@ def get_versions():
         pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
         return render(pieces, cfg.style)
     except NotThisMethod:
-        pass
+        print('NotThisMethod raised and ignored')
 
     try:
         if cfg.parentdir_prefix:
             return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
     except NotThisMethod:
-        pass
+        print('NotThisMethod raised and ignored')
 
     return {"version": "0+unknown", "full-revisionid": None,
             "dirty": None,
@@ -966,7 +966,7 @@ def git_get_keywords(versionfile_abs):
                     keywords["date"] = mo.group(1)
         f.close()
     except EnvironmentError:
-        pass
+        print('EnvironmentError raised and ignored')
     return keywords
 
 
@@ -1146,7 +1146,7 @@ def do_vcs_install(manifest_in, versionfile_source, ipy):
                     present = True
         f.close()
     except EnvironmentError:
-        pass
+        print('EnvironmentError raised and ignored')
     if not present:
         f = open(".gitattributes", "a+")
         f.write("%s export-subst\n" % versionfile_source)
@@ -1437,15 +1437,15 @@ def get_versions(verbose=False):
                 print("got version from expanded keyword %s" % ver)
             return ver
         except NotThisMethod:
-            pass
+            print('NotThisMethod raised and ignored')
 
     try:
         ver = versions_from_file(versionfile_abs)
         if verbose:
             print("got version from file %s %s" % (versionfile_abs, ver))
         return ver
     except NotThisMethod:
-        pass
+        print('NotThisMethod raised and ignored')
 
     from_vcs_f = handlers.get("pieces_from_vcs")
     if from_vcs_f:
@@ -1456,7 +1456,7 @@ def get_versions(verbose=False):
                 print("got version from VCS %s" % ver)
             return ver
         except NotThisMethod:
-            pass
+            print('NotThisMethod raised and ignored')
 
     try:
         if cfg.parentdir_prefix:
@@ -1465,7 +1465,7 @@ def get_versions(verbose=False):
                 print("got version from parentdir %s" % ver)
             return ver
     except NotThisMethod:
-        pass
+        print('NotThisMethod raised and ignored')
 
     if verbose:
         print("unable to compute version")
@@ -1750,7 +1750,8 @@ def do_setup():
                     for include in line.split()[1:]:
                         simple_includes.add(include)
     except EnvironmentError:
-        pass
+        print('EnvironmentError raised and ignored')
+
     # That doesn't cover everything MANIFEST.in can do
     # (http://docs.python.org/2/distutils/sourcedist.html#commands), so
     # it might give some false negatives. Appending redundant 'include'