git commit -m "[Cython/Test] Make cython testing portable.

Rather than changing to the work directory, ensure all input/output files come from
the the in-package test/data directory. This makes the Cython test suite standalone
and the tests can be run using unittest as: python -m unittest -v cantera.test

interfaces/cython/cantera/test/__init__.py

@@ -2,6 +2,7 @@
 import cantera
 
 cantera.add_directory(os.path.join(os.path.dirname(__file__), 'data'))
+cantera.add_directory(os.path.join(os.path.dirname(__file__), '..', 'examples', 'surface_chemistry'))
 
 from .test_thermo import *
 from .test_purefluid import *
@@ -12,4 +13,4 @@
 from .test_func1 import *
 from .test_reactor import *
 from .test_onedim import *
-from .test_convert import *
+from .test_convert import *

interfaces/cython/cantera/test/test_equilibrium.py

@@ -2,13 +2,14 @@
 
 import unittest
 import os
-import warnings
+from os.path import join as pjoin
 
 import numpy as np
 
 import cantera as ct
 from . import utilities
 
+
 class EquilTestCases(object):
     def __init__(self, solver):
         self.solver = solver
@@ -158,7 +159,8 @@ def test_equil_TP(self):
 
             data[i,1:] = self.mix.species_moles
 
-        self.compare(data, '../data/koh-equil-TP.csv')
+        p = self.get_test_data_directory()
+        self.compare(data, pjoin(p, 'koh-equil-TP.csv'))
 
     def test_equil_HP(self):
         temperatures = range(350, 5000, 300)
@@ -181,7 +183,8 @@ def test_equil_HP(self):
             data[i,1] = self.mix.T # equilibrated temperature
             data[i,2:] = self.mix.species_moles
 
-        self.compare(data, '../data/koh-equil-HP.csv')
+        p = self.get_test_data_directory()
+        self.compare(data, pjoin(p, 'koh-equil-HP.csv'))
 
 
 class TestEquil_GasCarbon(utilities.CanteraTest):
@@ -212,7 +215,8 @@ def solve(self, solver, **kwargs):
             data[i,:2] = (phi[i], mix.T)
             data[i,2:] = mix.species_moles
 
-        self.compare(data, '../data/gas-carbon-equil.csv')
+        p = self.get_test_data_directory()
+        self.compare(data, pjoin(p, 'gas-carbon-equil.csv'))
 
     def test_gibbs(self):
         self.solve('gibbs')

interfaces/cython/cantera/test/test_kinetics.py

@@ -1,11 +1,14 @@
-import unittest
+# import unittest
 import numpy as np
 import re
 import itertools
+from os.path import join as pjoin
+import os
 
 import cantera as ct
 from . import utilities
 
+
 class TestKinetics(utilities.CanteraTest):
     def setUp(self):
         self.phase = ct.Solution('h2o2.xml')
@@ -607,7 +610,8 @@ def cathode_curr(E):
                              cathode_bulk.electric_potential -
                              anode_bulk.electric_potential])
 
-        self.compare(data, '../data/sofc-test.csv')
+        p = self.get_test_data_directory()
+        self.compare(data, pjoin(p, 'sofc-test.csv'))
 
 
 class TestDuplicateReactions(utilities.CanteraTest):
@@ -673,7 +677,8 @@ def test_fromCti(self):
 
     def test_fromXml(self):
         import xml.etree.ElementTree as ET
-        root = ET.parse('../../build/data/h2o2.xml').getroot()
+        p = os.path.dirname(__file__)
+        root = ET.parse(pjoin(p, '..', 'data', 'h2o2.xml')).getroot()
         rxn_node = root.find('.//reaction[@id="0001"]')
         r = ct.Reaction.fromXml(ET.tostring(rxn_node))
 
@@ -690,14 +695,16 @@ def test_listFromFile(self):
         self.assertEqual(eq1, eq2)
 
     def test_listFromCti(self):
-        with open('../../build/data/h2o2.cti') as f:
+        p = os.path.dirname(__file__)
+        with open(pjoin(p, '..', 'data', 'h2o2.cti')) as f:
             R = ct.Reaction.listFromCti(f.read())
         eq1 = [r.equation for r in R]
         eq2 = [r.equation for r in self.gas.reactions()]
         self.assertEqual(eq1, eq2)
 
     def test_listFromXml(self):
-        with open('../../build/data/h2o2.xml') as f:
+        p = os.path.dirname(__file__)
+        with open(pjoin(p, '..', 'data', 'h2o2.xml')) as f:
             R = ct.Reaction.listFromCti(f.read())
         eq1 = [r.equation for r in R]
         eq2 = [r.equation for r in self.gas.reactions()]
@@ -997,15 +1004,16 @@ def test_modify_sticking(self):
         self.assertNear(k1, 4*k2)
 
     def test_motz_wise(self):
+        p = self.get_test_data_directory()
         # Motz & Wise off for all reactions
         gas1 = ct.Solution('ptcombust.xml', 'gas')
         surf1 = ct.Interface('ptcombust.xml', 'Pt_surf', [gas1])
         surf1.coverages = 'O(S):0.1, PT(S):0.5, H(S):0.4'
         gas1.TP = surf1.TP
 
         # Motz & Wise correction on for some reactions
-        gas2 = ct.Solution('../data/ptcombust-motzwise.cti', 'gas')
-        surf2 = ct.Interface('../data/ptcombust-motzwise.cti', 'Pt_surf', [gas2])
+        gas2 = ct.Solution(pjoin(p, 'ptcombust-motzwise.cti'), 'gas')
+        surf2 = ct.Interface(pjoin(p, 'ptcombust-motzwise.cti'), 'Pt_surf', [gas2])
         surf2.TPY = surf1.TPY
 
         k1 = surf1.forward_rate_constants

interfaces/cython/cantera/test/test_onedim.py

@@ -2,6 +2,7 @@
 from . import utilities
 import numpy as np
 import os
+from os.path import join as pjoin
 
 
 class TestOnedim(utilities.CanteraTest):
@@ -303,13 +304,14 @@ def test_prune(self):
         # residual satisfies the error tolerances) on the new grid.
 
     def test_save_restore(self):
+        test_data_dir = self.get_test_data_directory()
         reactants= 'H2:1.1, O2:1, AR:5'
         p = 2 * ct.one_atm
         Tin = 400
 
         self.create_sim(p, Tin, reactants)
         self.solve_fixed_T()
-        filename = 'onedim-fixed-T{0}.xml'.format(utilities.python_version)
+        filename = pjoin(test_data_dir, 'onedim-fixed-T{0}.xml'.format(utilities.python_version))
         if os.path.exists(filename):
             os.remove(filename)
 
@@ -370,7 +372,8 @@ def test_save_restore_add_species(self):
         p = 2 * ct.one_atm
         Tin = 400
 
-        filename = 'onedim-add-species{0}.xml'.format(utilities.python_version)
+        test_data_dir = self.get_test_data_directory()
+        filename = pjoin(test_data_dir, 'onedim-add-species{0}.xml'.format(utilities.python_version))
         if os.path.exists(filename):
             os.remove(filename)
 
@@ -398,7 +401,8 @@ def test_save_restore_remove_species(self):
         p = 2 * ct.one_atm
         Tin = 400
 
-        filename = 'onedim-add-species{0}.xml'.format(utilities.python_version)
+        test_data_dir = self.get_test_data_directory()
+        filename = pjoin(test_data_dir, 'onedim-add-species{0}.xml'.format(utilities.python_version))
         if os.path.exists(filename):
             os.remove(filename)
 
@@ -422,7 +426,8 @@ def test_save_restore_remove_species(self):
             self.assertArrayNear(Y1[k1], Y2[k2])
 
     def test_write_csv(self):
-        filename = 'onedim-write_csv{0}.csv'.format(utilities.python_version)
+        p = self.get_test_data_directory()
+        filename = pjoin(p, 'onedim-write_csv{0}.csv'.format(utilities.python_version))
         if os.path.exists(filename):
             os.remove(filename)
 
@@ -509,7 +514,8 @@ def solve_mix(self, ratio=3.0, slope=0.1, curve=0.12, prune=0.0):
         self.assertEqual(self.sim.transport_model, 'Mix')
 
     def test_mixture_averaged(self, saveReference=False):
-        referenceFile = '../data/DiffusionFlameTest-h2-mix.csv'
+        p = self.get_test_data_directory()
+        referenceFile = pjoin(p, 'DiffusionFlameTest-h2-mix.csv')
         self.create_sim(p=ct.one_atm)
 
         nPoints = len(self.sim.grid)
@@ -534,7 +540,8 @@ def test_mixture_averaged(self, saveReference=False):
             self.assertFalse(bad, bad)
 
     def test_auto(self, saveReference=False):
-        referenceFile = '../data/DiffusionFlameTest-h2-auto.csv'
+        p = self.get_test_data_directory()
+        referenceFile = pjoin(p, 'DiffusionFlameTest-h2-auto.csv')
         self.create_sim(p=ct.one_atm, mdot_fuel=2, mdot_ox=3)
 
         nPoints = []
@@ -599,7 +606,8 @@ def test_extinction_case7(self):
         self.run_extinction(mdot_fuel=0.2, mdot_ox=2.0, T_ox=600, width=0.2, P=0.05)
 
     def test_mixture_averaged_rad(self, saveReference=False):
-        referenceFile = '../data/DiffusionFlameTest-h2-mix-rad.csv'
+        p = self.get_test_data_directory()
+        referenceFile = pjoin(p, 'DiffusionFlameTest-h2-mix-rad.csv')
         self.create_sim(p=ct.one_atm)
 
         nPoints = len(self.sim.grid)
@@ -664,7 +672,6 @@ def test_mixture_fraction(self):
 
 
 class TestCounterflowPremixedFlame(utilities.CanteraTest):
-    referenceFile = '../data/CounterflowPremixedFlame-h2-mix.csv'
     # Note: to re-create the reference file:
     # (1) set PYTHONPATH to build/python2 or build/python3.
     # (2) Start Python in the test/work directory and run:
@@ -707,10 +714,13 @@ def test_mixture_averaged(self, saveReference=False):
         data[:,3] = sim.T
         data[:,4:] = sim.Y.T
 
+        p = self.get_test_data_directory()
+        referenceFile = pjoin(p, 'CounterflowPremixedFlame-h2-mix.csv')
+
         if saveReference:
-            np.savetxt(self.referenceFile, data, '%11.6e', ', ')
+            np.savetxt(referenceFile, data, '%11.6e', ', ')
         else:
-            bad = utilities.compareProfiles(self.referenceFile, data,
+            bad = utilities.compareProfiles(referenceFile, data,
                                             rtol=1e-2, atol=1e-8, xtol=1e-2)
             self.assertFalse(bad, bad)
 
@@ -768,9 +778,10 @@ def test_case5(self):
 
 class TestImpingingJet(utilities.CanteraTest):
     def run_reacting_surface(self, xch4, tsurf, mdot, width):
+        p = self.get_test_data_directory()
         # Simplified version of the example 'catalytic_combustion.py'
-        gas = ct.Solution('../data/ptcombust-simple.cti', 'gas')
-        surf_phase = ct.Interface('../data/ptcombust-simple.cti',
+        gas = ct.Solution(pjoin(p, 'ptcombust-simple.cti'), 'gas')
+        surf_phase = ct.Interface(pjoin(p, 'ptcombust-simple.cti'),
                                   'Pt_surf', [gas])
 
         tinlet = 300.0  # inlet temperature

interfaces/cython/cantera/test/test_reactor.py

@@ -1,5 +1,7 @@
 import math
 import re
+from os.path import join as pjoin
+import os
 
 import numpy as np
 from .utilities import unittest
@@ -917,8 +919,9 @@ def test_coverages_regression1(self):
         surf1.coverages = C
         self.assertArrayNear(surf1.coverages, C)
         data = []
-        test_file = 'test_coverages_regression1.csv'
-        reference_file = '../data/WallKinetics-coverages-regression1.csv'
+        p = self.get_test_data_directory()
+        test_file = pjoin(p, 'test_coverages_regression1.csv')
+        reference_file = pjoin(p, 'WallKinetics-coverages-regression1.csv')
         data = []
         for t in np.linspace(1e-6, 1e-3):
             self.net.advance(t)
@@ -942,8 +945,9 @@ def test_coverages_regression2(self):
         surf.coverages = C
         self.assertArrayNear(surf.coverages, C)
         data = []
-        test_file = 'test_coverages_regression2.csv'
-        reference_file = '../data/WallKinetics-coverages-regression2.csv'
+        p = self.get_test_data_directory()
+        test_file = pjoin(p, 'test_coverages_regression2.csv')
+        reference_file = pjoin(p, 'WallKinetics-coverages-regression2.csv')
         data = []
         for t in np.linspace(1e-6, 1e-3):
             self.net.advance(t)
@@ -1281,8 +1285,9 @@ class CombustorTestImplementation(object):
     consistent output.
     """
 
-    referenceFile = '../data/CombustorTest-integrateWithAdvance.csv'
     def setUp(self):
+        p = os.path.dirname(__file__)
+        self.referenceFile = pjoin(p, 'data', 'CombustorTest-integrateWithAdvance.csv')
         self.gas = ct.Solution('h2o2.xml')
 
         # create a reservoir for the fuel inlet, and set to pure methane.
@@ -1369,8 +1374,9 @@ class WallTestImplementation(object):
     consistent output.
     """
 
-    referenceFile = '../data/WallTest-integrateWithAdvance.csv'
     def setUp(self):
+        p = os.path.dirname(__file__)
+        self.referenceFile = pjoin(p, 'data', 'WallTest-integrateWithAdvance.csv')
         # reservoir to represent the environment
         self.gas0 = ct.Solution('air.xml')
         self.gas0.TP = 300, ct.one_atm