Replace deprecated yaml.safe_load / simplify paths

interfaces/cython/cantera/__init__.py

@@ -11,10 +11,11 @@
 
 import os
 import sys
+from pathlib import Path
 import warnings
 
 warnings.filterwarnings('default', module='cantera')
-add_directory(os.path.join(os.path.dirname(__file__), 'data'))
+add_directory(Path(__file__).parent / "data")
 add_directory('.')  # Move current working directory to the front of the path
 
 # Python interpreter used for converting mechanisms

interfaces/cython/cantera/base.pyx

@@ -2,6 +2,7 @@
 # at https://cantera.org/license.txt for license and copyright information.
 
 from collections import defaultdict as _defaultdict
+from pathlib import PurePath
 
 cdef class _SolutionBase:
     def __cinit__(self, infile='', name='', adjacent=(), origin=None,
@@ -53,6 +54,8 @@ cdef class _SolutionBase:
         self.transport = NULL
 
         # Parse inputs
+        if isinstance(infile, PurePath):
+            infile = str(infile)
         if infile.endswith('.yml') or infile.endswith('.yaml') or yaml:
             self._init_yaml(infile, name, adjacent, yaml)
         elif infile or source:

interfaces/cython/cantera/onedim.pyx

@@ -1411,7 +1411,7 @@ cdef class Sim1D:
         ...        description='solution with energy eqn. disabled')
 
         """
-        self.sim.save(stringify(filename), stringify(name),
+        self.sim.save(stringify(str(filename)), stringify(name),
                       stringify(description), loglevel)
 
     def restore(self, filename='soln.xml', name='solution', loglevel=2):
@@ -1427,7 +1427,7 @@ cdef class Sim1D:
 
         >>> s.restore(filename='save.xml', name='energy_off')
         """
-        self.sim.restore(stringify(filename), stringify(name), loglevel)
+        self.sim.restore(stringify(str(filename)), stringify(name), loglevel)
         self._initialized = True
 
     def restore_time_stepping_solution(self):

interfaces/cython/cantera/test/__init__.py

@@ -1,4 +1,4 @@
-import os
+from pathlib import Path
 import cantera
 
 from .test_composite import *
@@ -15,5 +15,5 @@
 from .test_transport import *
 from .test_utils import *
 
-cantera.add_directory(os.path.join(os.path.dirname(__file__), 'data'))
-cantera.add_directory(os.path.join(os.path.dirname(__file__), '..', 'examples', 'surface_chemistry'))
+cantera.add_directory(Path(__file__) / "data")
+cantera.add_directory(Path(__file__).parents[1] / "examples" / "surface_chemistry")

interfaces/cython/cantera/test/test_composite.py

@@ -1,16 +1,7 @@
-from os.path import join as pjoin
-import os
 import sys
 
 import numpy as np
 from collections import OrderedDict
-import warnings
-
-try:
-    import ruamel_yaml as yaml
-except ImportError:
-    from ruamel import yaml
-
 
 import cantera as ct
 from cantera.composite import _h5py, _pandas
@@ -22,9 +13,8 @@ class TestModels(utilities.CanteraTest):
     @classmethod
     def setUpClass(cls):
         utilities.CanteraTest.setUpClass()
-        cls.yml_file = pjoin(cls.test_data_dir, "thermo-models.yaml")
-        with open(cls.yml_file, 'rt', encoding="utf-8") as stream:
-            cls.yml = yaml.safe_load(stream)
+        cls.yml_file = cls.test_data_path / "thermo-models.yaml"
+        cls.yml = utilities.load_yaml(cls.yml_file)
 
     def test_load_thermo_models(self):
         for ph in self.yml['phases']:
@@ -150,7 +140,7 @@ def test_write_csv(self):
         states.TPX = np.linspace(300, 1000, 7), 2e5, 'H2:0.5, O2:0.4'
         states.equilibrate('HP')
 
-        outfile = pjoin(self.test_work_dir, 'solutionarray.csv')
+        outfile = self.test_work_path / "solutionarray.csv"
         states.write_csv(outfile)
 
         data = np.genfromtxt(outfile, names=True, delimiter=',')
@@ -167,7 +157,7 @@ def test_write_csv(self):
     def test_write_csv_str_column(self):
         states = ct.SolutionArray(self.gas, 3, extra={'spam': 'eggs'})
 
-        outfile = pjoin(self.test_work_dir, 'solutionarray.csv')
+        outfile = self.test_work_path / "solutionarray.csv"
         states.write_csv(outfile)
 
         b = ct.SolutionArray(self.gas, extra={'spam'})
@@ -177,7 +167,7 @@ def test_write_csv_str_column(self):
     def test_write_csv_multidim_column(self):
         states = ct.SolutionArray(self.gas, 3, extra={'spam': np.zeros((3, 5,))})
 
-        outfile = pjoin(self.test_work_dir, 'solutionarray.csv')
+        outfile = self.test_work_path / "solutionarray.csv"
         with self.assertRaisesRegex(NotImplementedError, 'not supported'):
             states.write_csv(outfile)
 
@@ -194,9 +184,10 @@ def test_to_pandas(self):
 
     @utilities.unittest.skipIf(isinstance(_h5py, ImportError), "h5py is not installed")
     def test_write_hdf(self):
-        outfile = pjoin(self.test_work_dir, 'solutionarray.h5')
-        if os.path.exists(outfile):
-            os.remove(outfile)
+        outfile = self.test_work_path / "solutionarray.h5"
+        # In Python >= 3.8, this can be replaced by the missing_ok argument
+        if outfile.is_file():
+            outfile.unlink()
 
         extra = {'foo': range(7), 'bar': range(7)}
         meta = {'spam': 'eggs', 'hello': 'world'}
@@ -239,9 +230,10 @@ def test_write_hdf(self):
 
     @utilities.unittest.skipIf(isinstance(_h5py, ImportError), "h5py is not installed")
     def test_write_hdf_str_column(self):
-        outfile = pjoin(self.test_work_dir, 'solutionarray.h5')
-        if os.path.exists(outfile):
-            os.remove(outfile)
+        outfile = self.test_work_path / "solutionarray.h5"
+        # In Python >= 3.8, this can be replaced by the missing_ok argument
+        if outfile.is_file():
+            outfile.unlink()
 
         states = ct.SolutionArray(self.gas, 3, extra={'spam': 'eggs'})
         states.write_hdf(outfile, mode='w')
@@ -252,9 +244,10 @@ def test_write_hdf_str_column(self):
 
     @utilities.unittest.skipIf(isinstance(_h5py, ImportError), "h5py is not installed")
     def test_write_hdf_multidim_column(self):
-        outfile = pjoin(self.test_work_dir, 'solutionarray.h5')
-        if os.path.exists(outfile):
-            os.remove(outfile)
+        outfile = self.test_work_path / "solutionarray.h5"
+        # In Python >= 3.8, this can be replaced by the missing_ok argument
+        if outfile.is_file():
+            outfile.unlink()
 
         states = ct.SolutionArray(self.gas, 3, extra={'spam': [[1, 2], [3, 4], [5, 6]]})
         states.write_hdf(outfile, mode='w')
@@ -478,8 +471,7 @@ def test_yaml_simple(self):
         gas.equilibrate('HP')
         gas.TP = 1500, ct.one_atm
         gas.write_yaml('h2o2-generated.yaml')
-        with open('h2o2-generated.yaml', 'r') as infile:
-            generated = yaml.safe_load(infile)
+        generated = utilities.load_yaml("h2o2-generated.yaml")
         for key in ('generator', 'date', 'phases', 'species', 'reactions'):
             self.assertIn(key, generated)
         self.assertEqual(generated['phases'][0]['transport'], 'mixture-averaged')
@@ -503,10 +495,8 @@ def test_yaml_outunits(self):
         gas.TP = 1500, ct.one_atm
         units = {'length': 'cm', 'quantity': 'mol', 'energy': 'cal'}
         gas.write_yaml('h2o2-generated.yaml', units=units)
-        with open('h2o2-generated.yaml') as infile:
-            generated = yaml.safe_load(infile)
-        with open(pjoin(self.cantera_data, "h2o2.yaml")) as infile:
-            original = yaml.safe_load(infile)
+        generated = utilities.load_yaml("h2o2-generated.yaml")
+        original = utilities.load_yaml(self.cantera_data_path / "h2o2.yaml")
         self.assertEqual(generated['units'], units)
 
         for r1, r2 in zip(original['reactions'], generated['reactions']):
@@ -529,8 +519,7 @@ def test_yaml_surface(self):
         surf.coverages = np.ones(surf.n_species)
         surf.write_yaml('ptcombust-generated.yaml')
 
-        with open('ptcombust-generated.yaml') as infile:
-            generated = yaml.safe_load(infile)
+        generated = utilities.load_yaml("ptcombust-generated.yaml")
         for key in ('phases', 'species', 'gas-reactions', 'Pt_surf-reactions'):
             self.assertIn(key, generated)
         self.assertEqual(len(generated['gas-reactions']), gas.n_reactions)