[unittests] Add coverage for CSV SolutionArray.save

test/python/test_composite.py

@@ -461,7 +461,23 @@ def test_import_no_norm_data(self):
         self.assertArrayNear(states.P, b.P)
         self.assertArrayNear(states.X, b.X)
 
-    def test_write_csv(self):
+    def check_arrays(self, a, b, rtol=1e-8):
+        self.assertArrayNear(a.T, b.T, rtol=rtol)
+        self.assertArrayNear(a.P, b.P, rtol=rtol)
+        self.assertArrayNear(a.X, b.X, rtol=rtol)
+        for key in a.extra:
+            value = getattr(a, key)
+            if isinstance(value[0], str):
+                assert (getattr(b, key) == value).all()
+            else:
+                self.assertArrayNear(getattr(b, key), value, rtol=rtol)
+        if b.meta:
+            # not all output formats preserve metadata
+            for key, value in a.meta.items():
+                assert b.meta[key] == value
+
+    @pytest.mark.usefixtures("allow_deprecated")
+    def test_write_csv_legacy(self):
         states = ct.SolutionArray(self.gas, 7)
         states.TPX = np.linspace(300, 1000, 7), 2e5, 'H2:0.5, O2:0.4'
         states.equilibrate('HP')
@@ -476,10 +492,9 @@ def test_write_csv(self):
 
         b = ct.SolutionArray(self.gas)
         b.read_csv(outfile)
-        self.assertArrayNear(states.T, b.T)
-        self.assertArrayNear(states.P, b.P)
-        self.assertArrayNear(states.X, b.X)
+        self.check_arrays(states, b)
 
+    @pytest.mark.usefixtures("allow_deprecated")
     def test_write_csv_single_row(self):
         gas = ct.Solution("gri30.yaml")
         states = ct.SolutionArray(gas)
@@ -491,10 +506,9 @@ def test_write_csv_single_row(self):
 
         b = ct.SolutionArray(gas)
         b.read_csv(outfile)
-        self.assertArrayNear(states.T, b.T)
-        self.assertArrayNear(states.P, b.P)
-        self.assertArrayNear(states.X, b.X)
+        self.check_arrays(states, b)
 
+    @pytest.mark.usefixtures("allow_deprecated")
     def test_write_csv_str_column(self):
         states = ct.SolutionArray(self.gas, 3, extra={'spam': 'eggs'})
 
@@ -504,14 +518,103 @@ def test_write_csv_str_column(self):
         b = ct.SolutionArray(self.gas, extra={'spam'})
         b.read_csv(outfile)
         self.assertEqual(list(states.spam), list(b.spam))
+        self.check_arrays(states, b)
 
+    @pytest.mark.usefixtures("allow_deprecated")
     def test_write_csv_multidim_column(self):
         states = ct.SolutionArray(self.gas, 3, extra={'spam': np.zeros((3, 5,))})
 
         outfile = self.test_work_path / "solutionarray.csv"
         with self.assertRaisesRegex(NotImplementedError, 'not supported'):
             states.write_csv(outfile)
 
+    def test_write_csv(self):
+        outfile = self.test_work_path / "solutionarray_new.csv"
+        outfile.unlink(missing_ok=True)
+
+        arr = ct.SolutionArray(self.gas, 7)
+        arr.TPX = np.linspace(300, 1000, 7), 2e5, "H2:0.5, O2:0.4"
+        arr.equilibrate("HP")
+        arr.save(outfile, basis="mole")
+
+        with open(outfile, "r") as fid:
+            header = fid.readline()
+        assert "X_H2" in header.split(",")
+
+        b = ct.SolutionArray(self.gas)
+        b.read_csv(outfile)
+        self.check_arrays(arr, b)
+
+        with pytest.raises(ct.CanteraError, match="already exists"):
+            arr.save(outfile)
+
+    def test_write_csv_fancy(self):
+        outfile = self.test_work_path / "solutionarray_fancy.csv"
+        outfile.unlink(missing_ok=True)
+
+        extra = {"foo": range(7), "bar": range(7), "spam": "eggs"}
+        arr = ct.SolutionArray(self.gas, 7, extra=extra)
+        arr.TPX = np.linspace(300, 1000, 7), 2e5, "H2:0.5, O2:0.4"
+        arr.equilibrate("HP")
+        arr.save(outfile)
+
+        with open(outfile, "r") as fid:
+            header = fid.readline()
+        assert "Y_H2" in header.split(",")
+
+        b = ct.SolutionArray(self.gas)
+        b.read_csv(outfile)
+        self.check_arrays(arr, b)
+
+    def test_write_csv_escaped(self):
+        outfile = self.test_work_path / "solutionarray_escaped.csv"
+        outfile.unlink(missing_ok=True)
+
+        extra = {"foo": range(7), "bar": range(7), "spam,eggs": "a,b,"}
+        arr = ct.SolutionArray(self.gas, 7, extra=extra)
+        arr.TPX = np.linspace(300, 1000, 7), 2e5, "H2:0.5, O2:0.4"
+        arr.equilibrate("HP")
+        with pytest.warns(UserWarning, match="escaped"):
+            arr.save(outfile, basis="mass")
+
+        with open(outfile, "r") as fid:
+            header = fid.readline()
+        assert "Y_H2" in header.split(",")
+
+        b = ct.SolutionArray(self.gas)
+        if _pandas is None:
+            with pytest.raises(ValueError):
+                # np.genfromtxt does not support escaped characters
+                b.read_csv(outfile)
+            return
+
+        b.read_csv(outfile)
+        self.check_arrays(arr, b)
+
+        df = _pandas.read_csv(outfile)
+        b.from_pandas(df)
+        self.check_arrays(arr, b)
+
+    def test_write_csv_exceptions(self):
+        outfile = self.test_work_path / f"solutionarray_invalid.csv"
+        outfile.unlink(missing_ok=True)
+
+        arr = ct.SolutionArray(self.gas, (2, 5))
+        with pytest.raises(ct.CanteraError, match="only works for 1D SolutionArray"):
+            arr.save(outfile)
+
+        arr = ct.SolutionArray(self.gas, 10, extra={'spam"eggs': "foo"})
+        with pytest.raises(NotImplementedError, match="double quotes or line feeds"):
+            arr.save(outfile)
+
+        arr = ct.SolutionArray(self.gas, 10, extra={"foo": 'spam\neggs'})
+        with pytest.raises(NotImplementedError, match="double quotes or line feeds"):
+            arr.save(outfile)
+
+        arr = ct.SolutionArray(self.gas, 10)
+        with pytest.raises(ct.CanteraError, match="Invalid species basis"):
+            arr.save(outfile, basis="foo")
+
     @utilities.unittest.skipIf(_pandas is None, "pandas is not installed")
     def test_to_pandas(self):
         states = ct.SolutionArray(self.gas, 7, extra={"props": range(7)})
@@ -524,7 +627,6 @@ def test_to_pandas(self):
 
     @pytest.mark.skipif("native" not in ct.hdf_support(),
                         reason="Cantera compiled without HDF support")
-    @utilities.unittest.skipIf(_h5py is None, "h5py is not installed")
     def test_write_hdf(self):
         outfile = self.test_work_path / "solutionarray_fancy.h5"
         outfile.unlink(missing_ok=True)
@@ -539,13 +641,7 @@ def test_write_hdf(self):
 
         b = ct.SolutionArray(self.gas)
         attr = b.restore(outfile, "group0")
-        self.assertArrayNear(states.T, b.T)
-        self.assertArrayNear(states.P, b.P)
-        self.assertArrayNear(states.X, b.X)
-        self.assertArrayNear(states.foo, b.foo)
-        self.assertArrayNear(states.bar, b.bar)
-        self.assertEqual(b.meta['spam'], 'eggs')
-        self.assertEqual(b.meta['hello'], 'world')
+        self.check_arrays(states, b)
 
     @pytest.mark.skipif("native" not in ct.hdf_support(),
                         reason="Cantera compiled without HDF support")
@@ -564,7 +660,7 @@ def run_write_str_column(self, mode):
 
         b = ct.SolutionArray(self.gas, extra={'spam'})
         b.restore(outfile, "arr")
-        self.assertEqual(list(states.spam), list(b.spam))
+        self.check_arrays(states, b)
 
     @pytest.mark.skipif("native" not in ct.hdf_support(),
                         reason="Cantera compiled without HDF support")
@@ -583,7 +679,7 @@ def run_write_multidim_column(self, mode):
 
         b = ct.SolutionArray(self.gas, extra={'spam'})
         b.restore(outfile, "arr")
-        self.assertArrayNear(states.spam, b.spam)
+        self.check_arrays(states, b)
 
     @pytest.mark.skipif("native" not in ct.hdf_support(),
                         reason="Cantera compiled without HDF support")
@@ -604,6 +700,7 @@ def run_write_2d(self, mode):
         b.restore(outfile, "arr")
         assert b.shape == states.shape
 
+
 class TestLegacyHDF(utilities.CanteraTest):
     # Test SolutionArray legacy HDF file input
     #

test/python/test_onedim.py

@@ -335,7 +335,7 @@ def run_restart(self, mode):
             data = self.test_work_path / f"freeflame_restart.{mode}"
             data.unlink(missing_ok=True)
             if mode == "csv":
-                self.sim.write_csv(data)
+                self.sim.save(data, basis="mole")
             else:
                 self.sim.save(data, group)
 
@@ -761,7 +761,8 @@ def test_save_restore_remove_species_yaml(self):
             k1 = gas1.species_index(species)
             self.assertArrayNear(Y1[k1], Y2[k2])
 
-    def test_write_csv(self):
+    @pytest.mark.usefixtures("allow_deprecated")
+    def test_write_csv_legacy(self):
         filename = self.test_work_path / "onedim-write_csv.csv"
         # In Python >= 3.8, this can be replaced by the missing_ok argument
         if filename.is_file():
@@ -776,6 +777,19 @@ def test_write_csv(self):
         k = self.gas.species_index('H2')
         self.assertArrayNear(data.X[:, k], self.sim.X[k, :])
 
+    def test_write_csv(self):
+        filename = self.test_work_path / "onedim-save.csv"
+        filename.unlink(missing_ok=True)
+
+        self.create_sim(2e5, 350, 'H2:1.0, O2:2.0', mech="h2o2.yaml")
+        self.sim.save(filename, basis="mole")
+        data = ct.SolutionArray(self.gas)
+        data.read_csv(filename)
+        self.assertArrayNear(data.grid, self.sim.grid)
+        self.assertArrayNear(data.T, self.sim.T)
+        k = self.gas.species_index('H2')
+        self.assertArrayNear(data.X[:, k], self.sim.X[k, :])
+
     @pytest.mark.usefixtures("allow_deprecated")
     @utilities.unittest.skipIf("h5py" not in ct.hdf_support(), "h5py not installed")
     def test_restore_legacy_hdf_h5py(self):
@@ -1139,7 +1153,7 @@ def test_mixture_averaged_rad(self, saveReference=False):
         if filename.is_file():
             filename.unlink()
 
-        self.sim.write_csv(filename) # check output
+        self.sim.save(filename, basis="mole") # check output
         self.assertTrue(filename.is_file())
         csv_data = np.genfromtxt(filename, dtype=float, delimiter=',', names=True)
         self.assertIn('radiativeheatloss', csv_data.dtype.names)
@@ -1245,11 +1259,9 @@ def test_mixture_averaged(self, saveReference=False):
             self.assertFalse(bad, bad)
 
         filename = self.test_work_path / "CounterflowPremixedFlame-h2-mix.csv"
-        # In Python >= 3.8, this can be replaced by the missing_ok argument
-        if filename.is_file():
-            filename.unlink()
+        filename.unlink(missing_ok=True)
 
-        sim.write_csv(filename) # check output
+        sim.save(filename) # check output
         self.assertTrue(filename.is_file())
         csv_data = np.genfromtxt(filename, dtype=float, delimiter=',', names=True)
         self.assertNotIn('qdot', csv_data.dtype.names)