Add test for Chain.from_endf. Remove tqdm dependence.

docs/source/conf.py

@@ -26,7 +26,7 @@ MOCK_MODULES = [
     'numpy.ctypeslib', 'scipy', 'scipy.sparse', 'scipy.sparse.linalg',
     'scipy.interpolate', 'scipy.integrate', 'scipy.optimize', 'scipy.special',
     'scipy.stats', 'scipy.spatial', 'h5py', 'pandas', 'uncertainties',
-    'matplotlib', 'matplotlib.pyplot', 'tqdm', 'openmoc',
+    'matplotlib', 'matplotlib.pyplot', 'openmoc',
     'openmc.data.reconstruct'
 ]
 sys.modules.update((mod_name, MagicMock()) for mod_name in MOCK_MODULES)

openmc/data/endf.py

@@ -10,6 +10,7 @@ import io
 import re
 import os
 from math import pi
+from pathlib import PurePath
 from collections import OrderedDict
 from collections.abc import Iterable
 
@@ -299,8 +300,8 @@ class Evaluation(object):
 
     """
     def __init__(self, filename_or_obj):
-        if isinstance(filename_or_obj, str):
-            fh = open(filename_or_obj, 'r')
+        if isinstance(filename_or_obj, (str, PurePath)):
+            fh = open(str(filename_or_obj), 'r')
         else:
             fh = filename_or_obj
         self.section = {}

openmc/deplete/chain.py

@@ -20,7 +20,6 @@ try:
 except ImportError:
     import xml.etree.ElementTree as ET
     _have_lxml = False
-from tqdm import tqdm
 import scipy.sparse as sp
 
 import openmc.data
@@ -153,34 +152,31 @@ class Chain(object):
         chain = cls()
 
         # Create dictionary mapping target to filename
+        print('Processing neutron sub-library files...')
         reactions = {}
-        with tqdm(neutron_files) as pbar:
-            for f in pbar:
-                pbar.set_description('Processing {}'.format(os.path.basename(f)))
-                evaluation = openmc.data.endf.Evaluation(f)
-                name = evaluation.gnd_name
-                reactions[name] = {}
-                for mf, mt, nc, mod in evaluation.reaction_list:
-                    if mf == 3:
-                        file_obj = StringIO(evaluation.section[3, mt])
-                        openmc.data.endf.get_head_record(file_obj)
-                        q_value = openmc.data.endf.get_cont_record(file_obj)[1]
-                        reactions[name][mt] = q_value
+        for f in neutron_files:
+            evaluation = openmc.data.endf.Evaluation(f)
+            name = evaluation.gnd_name
+            reactions[name] = {}
+            for mf, mt, nc, mod in evaluation.reaction_list:
+                if mf == 3:
+                    file_obj = StringIO(evaluation.section[3, mt])
+                    openmc.data.endf.get_head_record(file_obj)
+                    q_value = openmc.data.endf.get_cont_record(file_obj)[1]
+                    reactions[name][mt] = q_value
 
         # Determine what decay and FPY nuclides are available
+        print('Processing decay sub-library files...')
         decay_data = {}
-        with tqdm(decay_files) as pbar:
-            for f in pbar:
-                pbar.set_description('Processing {}'.format(os.path.basename(f)))
-                data = openmc.data.Decay(f)
-                decay_data[data.nuclide['name']] = data
+        for f in decay_files:
+            data = openmc.data.Decay(f)
+            decay_data[data.nuclide['name']] = data
 
+        print('Processing fission product yield sub-library files...')
         fpy_data = {}
-        with tqdm(fpy_files) as pbar:
-            for f in pbar:
-                pbar.set_description('Processing {}'.format(os.path.basename(f)))
-                data = openmc.data.FissionProductYields(f)
-                fpy_data[data.nuclide['name']] = data
+        for f in fpy_files:
+            data = openmc.data.FissionProductYields(f)
+            fpy_data[data.nuclide['name']] = data
 
         print('Creating depletion_chain...')
         missing_daughter = []

setup.py

@@ -57,7 +57,7 @@ kwargs = {
     # Required dependencies
     'install_requires': [
         'numpy>=1.9', 'h5py', 'scipy', 'ipython', 'matplotlib',
-        'pandas', 'lxml', 'uncertainties', 'tqdm'
+        'pandas', 'lxml', 'uncertainties'
     ],
 
     # Optional dependencies

tests/unit_tests/test_deplete_chain.py

@@ -5,11 +5,13 @@ import os
 from pathlib import Path
 
 import numpy as np
+from openmc.data import zam, ATOMIC_SYMBOL
 from openmc.deplete import comm, Chain, reaction_rates, nuclide
 import pytest
 
 from tests import cdtemp
 
+_ENDF_DATA = Path(os.environ['OPENMC_ENDF_DATA'])
 
 _TEST_CHAIN = """\
 <depletion_chain>
@@ -63,9 +65,15 @@ def test_len():
 
 
 def test_from_endf():
-    """Test depletion chain building from ENDF. Empty at the moment until we figure
-    out a good way to unit-test this."""
-    pass
+    """Test depletion chain building from ENDF files"""
+    decay_data = (_ENDF_DATA / 'decay').glob('*.endf')
+    fpy_data = (_ENDF_DATA / 'nfy').glob('*.endf')
+    neutron_data = (_ENDF_DATA / 'neutrons').glob('*.endf')
+    chain = Chain.from_endf(decay_data, fpy_data, neutron_data)
+
+    assert len(chain) == len(chain.nuclides) == len(chain.nuclide_dict) == 3821
+    for nuc in chain.nuclides:
+        assert nuc == chain[nuc.name]
 
 
 def test_from_xml(simple_chain):