invoke format

keurfonluu · Jun 12, 2022 · 00b4ca7 · 00b4ca7
1 parent e6bb2d8
commit 00b4ca7
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Showing 30 changed files with 66 additions and 215 deletions.
diff --git a/test/helpers.py b/test/helpers.py
@@ -134,7 +134,7 @@ def random_label(label_length):
     n = label_length - 3
     fmt = "{{:0{}d}}".format(n)
 
-    return random_string(3) + fmt.format(np.random.randint(10**n))
+    return random_string(3) + fmt.format(np.random.randint(10 ** n))
 
 
 def allclose_dict(a, b, atol=1.0e-8):

diff --git a/test/test_input.py b/test/test_input.py
@@ -9,15 +9,11 @@
 )
 
 write_read_tough = lambda x: write_read(
-    x,
-    writer_kws={"file_format": "tough"},
-    reader_kws={"file_format": "tough"},
+    x, writer_kws={"file_format": "tough"}, reader_kws={"file_format": "tough"},
 )
 
 write_read_json = lambda x: write_read(
-    x,
-    writer_kws={"file_format": "json"},
-    reader_kws={"file_format": "json"},
+    x, writer_kws={"file_format": "json"}, reader_kws={"file_format": "json"},
 )
 
 
@@ -244,8 +240,7 @@ def test_ncgas(write_read):
 
 
 @pytest.mark.parametrize(
-    "write_read, isothermal",
-    [(write_read_tough, True), (write_read_tough, False)],
+    "write_read, isothermal", [(write_read_tough, True), (write_read_tough, False)],
 )
 def test_multi(write_read, isothermal):
     import random
@@ -409,9 +404,7 @@ def test_indom(write_read, num_pvars, num_items):
     num_items = num_items if num_items else np.random.randint(10) + 1
     parameters_ref = {
         "rocks": {
-            helpers.random_string(5): {
-                "initial_condition": np.random.rand(num_pvars),
-            }
+            helpers.random_string(5): {"initial_condition": np.random.rand(num_pvars),}
             for _ in range(num_items)
         },
     }
@@ -785,18 +778,9 @@ def test_meshm_xyz():
                     "n_increment": np.random.randint(100) + 1,
                     "sizes": np.random.rand(),
                 },
-                {
-                    "type": "ny",
-                    "sizes": np.random.rand(np.random.randint(100) + 1),
-                },
-                {
-                    "type": "nz",
-                    "sizes": np.random.rand(np.random.randint(100) + 1),
-                },
-                {
-                    "type": "nx",
-                    "sizes": np.random.rand(np.random.randint(100) + 1),
-                },
+                {"type": "ny", "sizes": np.random.rand(np.random.randint(100) + 1),},
+                {"type": "nz", "sizes": np.random.rand(np.random.randint(100) + 1),},
+                {"type": "nx", "sizes": np.random.rand(np.random.randint(100) + 1),},
             ],
             "angle": np.random.rand(),
         }
@@ -830,10 +814,7 @@ def test_meshm_rz2d(layer):
         "meshmaker": {
             "type": "rz2dl" if layer else "rz2d",
             "parameters": [
-                {
-                    "type": "radii",
-                    "radii": np.random.rand(np.random.randint(100) + 1),
-                },
+                {"type": "radii", "radii": np.random.rand(np.random.randint(100) + 1),},
                 {
                     "type": "equid",
                     "n_increment": np.random.randint(100) + 1,
@@ -875,9 +856,7 @@ def test_tmvoc():
         "eos": "tmvoc",
         "n_component": 1,
         "n_phase": 1,
-        "default": {
-            "phase_composition": np.random.randint(10),
-        },
+        "default": {"phase_composition": np.random.randint(10),},
         "rocks": {
             helpers.random_string(5): {
                 "initial_condition": np.random.rand(4),
@@ -894,9 +873,7 @@ def test_tmvoc():
         },
     }
     parameters = write_read(
-        parameters_ref,
-        writer_kws={"eos": "tmvoc"},
-        reader_kws={"eos": "tmvoc"},
+        parameters_ref, writer_kws={"eos": "tmvoc"}, reader_kws={"eos": "tmvoc"},
     )
 
     helpers.allclose_dict(parameters_ref["default"], parameters["default"])

diff --git a/test/test_mesh_methods.py b/test/test_mesh_methods.py
@@ -10,24 +10,12 @@
 
 output_ref = {
     "element": {
-        0: {
-            "PRES": 9641264.130638,
-            "TEMP": 149.62999493,
-        },
-        -1: {
-            "PRES": 635804.12294844,
-            "TEMP": 142.89449866,
-        },
+        0: {"PRES": 9641264.130638, "TEMP": 149.62999493,},
+        -1: {"PRES": 635804.12294844, "TEMP": 142.89449866,},
     },
     "connection": {
-        0: {
-            "HEAT": -1.64908253e-07,
-            "FLOW": -2.85760551e-13,
-        },
-        -1: {
-            "HEAT": -5.54750914e-08,
-            "FLOW": -4.68234504e-14,
-        },
+        0: {"HEAT": -1.64908253e-07, "FLOW": -2.85760551e-13,},
+        -1: {"HEAT": -5.54750914e-08, "FLOW": -4.68234504e-14,},
     },
 }
 
@@ -227,8 +215,7 @@ def test_near():
 
 @pytest.mark.skipif(sys.version_info < (3, 6), reason="Order of keys in dictionary")
 @pytest.mark.parametrize(
-    "num_pvars, eos",
-    [(4, None), (6, None), (4, "tmvoc")],
+    "num_pvars, eos", [(4, None), (6, None), (4, "tmvoc")],
 )
 def test_write_tough(num_pvars, eos):
     this_dir = os.path.dirname(os.path.abspath(__file__))

diff --git a/test/test_meshio.py b/test/test_meshio.py
@@ -41,9 +41,7 @@ def test_meshio(mesh_ref, file_format, binary):
         writer_kws["binary"] = binary
 
     mesh = write_read(
-        mesh=mesh_ref,
-        writer_kws=writer_kws,
-        reader_kws={"file_format": file_format},
+        mesh=mesh_ref, writer_kws=writer_kws, reader_kws={"file_format": file_format},
     )
     if file_format == "flac3d":
         mesh_ref.cell_data.pop("c", None)

diff --git a/test/test_output.py b/test/test_output.py
@@ -101,8 +101,7 @@ def test_output_eleme(filename, filename_ref):
 
 
 @pytest.mark.parametrize(
-    "filename",
-    ["OUTPUT_CONNE.csv", "OUTPUT.out", "OUTPUT_6.out"],
+    "filename", ["OUTPUT_CONNE.csv", "OUTPUT.out", "OUTPUT_6.out"],
 )
 def test_output_conne(filename):
     this_dir = os.path.dirname(os.path.abspath(__file__))
@@ -147,9 +146,7 @@ def test_output_conne(filename):
 )
 def test_output(output_ref, file_format):
     output = write_read(
-        output=output_ref,
-        writer_kws={"file_format": file_format},
-        reader_kws={},
+        output=output_ref, writer_kws={"file_format": file_format}, reader_kws={},
     )
 
     output_ref = output_ref if isinstance(output_ref, list) else [output_ref]

diff --git a/test/test_react.py b/test/test_react.py
@@ -359,10 +359,7 @@ def write_read(x):
     parameters_ref = {
         "title": helpers.random_string(80),
         "primary_species": [
-            {
-                "name": helpers.random_string(20),
-                "transport": np.random.randint(2),
-            }
+            {"name": helpers.random_string(20), "transport": np.random.randint(2),}
             for _ in range(np.random.randint(5) + 1)
         ],
         "aqueous_kinetics": [
@@ -513,10 +510,7 @@ def write_read(x):
             },
         ],
         "gaseous_species": [
-            {
-                "name": helpers.random_string(20),
-                "fugacity": np.random.randint(2),
-            }
+            {"name": helpers.random_string(20), "fugacity": np.random.randint(2),}
             for _ in range(np.random.randint(5) + 1)
         ],
         "surface_complexes": [
@@ -673,10 +667,7 @@ def write_read(x):
         pp = "partial_pressure" if key == "initial_gases" else "mole_fraction"
         parameters_ref["zones"][key] = [
             [
-                {
-                    "name": helpers.random_string(20),
-                    pp: np.random.rand(),
-                }
+                {"name": helpers.random_string(20), pp: np.random.rand(),}
                 for _ in range(np.random.randint(5) + 1)
             ]
             for _ in range(np.random.randint(5) + 1)

diff --git a/toughio/_cli/_co2tab.py b/toughio/_cli/_co2tab.py
@@ -33,9 +33,7 @@ def _get_parser():
 
     # Output path
     parser.add_argument(
-        "path",
-        type=str,
-        help="directory path",
+        "path", type=str, help="directory path",
     )
 
     return parser
diff --git a/toughio/_cli/_export.py b/toughio/_cli/_export.py
@@ -84,8 +84,7 @@ def export(argv=None):
         print("{} ...".format(msg), end="")
         sys.stdout.flush()
         points, axis = _get_points(
-            output if args.file_format != "xdmf" else output[0],
-            args.ignore_elements,
+            output if args.file_format != "xdmf" else output[0], args.ignore_elements,
         )
         ndim = len(axis)
         print(" Done!")
@@ -131,7 +130,7 @@ def export(argv=None):
 
                     if args.ignore_elements:
                         data = data[mask]
-                    
+
                     mesh.add_cell_data(label, data[idx])
 
             voxelized = True
@@ -149,7 +148,7 @@ def export(argv=None):
                 for label, data in output.data.items():
                     if label in {"X", "Y", "Z"}:
                         continue
-                    
+
                     if args.ignore_elements:
                         data = data[mask]
 
@@ -233,36 +232,22 @@ def _get_parser():
 
     # Input file
     parser.add_argument(
-        "infile",
-        type=str,
-        help="TOUGH output file",
+        "infile", type=str, help="TOUGH output file",
     )
 
     # Mesh file
     parser.add_argument(
-        "--mesh",
-        "-m",
-        type=str,
-        default=None,
-        help="pickled toughio.Mesh",
+        "--mesh", "-m", type=str, default=None, help="pickled toughio.Mesh",
     )
 
     # Time step
     parser.add_argument(
-        "--time-step",
-        "-t",
-        type=int,
-        default=None,
-        help="time step to export",
+        "--time-step", "-t", type=int, default=None, help="time step to export",
     )
 
     # Output file
     parser.add_argument(
-        "--output-file",
-        "-o",
-        type=str,
-        default=None,
-        help="exported file",
+        "--output-file", "-o", type=str, default=None, help="exported file",
     )
 
     # File format

diff --git a/toughio/_cli/_extract.py b/toughio/_cli/_extract.py
@@ -101,16 +101,12 @@ def _get_parser():
 
     # Input file
     parser.add_argument(
-        "infile",
-        type=str,
-        help="TOUGH output file",
+        "infile", type=str, help="TOUGH output file",
     )
 
     # Mesh file
     parser.add_argument(
-        "mesh",
-        type=str,
-        help="TOUGH MESH file (can be INFILE)",
+        "mesh", type=str, help="TOUGH MESH file (can be INFILE)",
     )
 
     # Output file

diff --git a/toughio/_cli/_merge.py b/toughio/_cli/_merge.py
@@ -76,9 +76,7 @@ def _get_parser():
 
     # Input file
     parser.add_argument(
-        "infile",
-        type=str,
-        help="TOUGH input file",
+        "infile", type=str, help="TOUGH input file",
     )
 
     # Output file

diff --git a/toughio/_cli/_save2incon.py b/toughio/_cli/_save2incon.py
@@ -42,25 +42,17 @@ def _get_parser():
 
     # Input file
     parser.add_argument(
-        "infile",
-        type=str,
-        help="SAVE file to convert",
+        "infile", type=str, help="SAVE file to convert",
     )
 
     # Output file
     parser.add_argument(
-        "outfile",
-        type=str,
-        help="converted INCON file",
+        "outfile", type=str, help="converted INCON file",
     )
 
     # Reset
     parser.add_argument(
-        "--reset",
-        "-r",
-        default=False,
-        action="store_true",
-        help="reset all counters",
+        "--reset", "-r", default=False, action="store_true", help="reset all counters",
     )
 
     return parser
diff --git a/toughio/_common.py b/toughio/_common.py
@@ -15,11 +15,7 @@
         2: "10d,10.3e,10.3e,10.3e,10.3e,10.3e,10.3e,10.3e",
         3: "5d,5s,10.3e,10.3e,10.3e,10.3e,10.3e,10.3e,10.3e",
     },
-    "CHEMP": {
-        1: "5d",
-        2: "20s",
-        3: ",".join(5 * ["10.3e"]),
-    },
+    "CHEMP": {1: "5d", 2: "20s", 3: ",".join(5 * ["10.3e"]),},
     "NCGAS": {1: "5d", 2: "10s"},
     "MULTI": ",".join(5 * ["5d"]),
     "SELEC": {1: ",".join(16 * ["5d"]), 2: ",".join(8 * ["10.3e"])},
@@ -89,23 +85,13 @@
     },
     "MESHM": {
         1: "5s",
-        "XYZ": {
-            1: "10.3e",
-            2: "5s,5d,10.4e",
-            3: ",".join(8 * ["10.4e"]),
-        },
+        "XYZ": {1: "10.3e", 2: "5s,5d,10.4e", 3: ",".join(8 * ["10.4e"]),},
         "RZ2D": {
             1: "5s",
-            "RADII": {
-                1: "5d",
-                2: ",".join(8 * ["10.3e"]),
-            },
+            "RADII": {1: "5d", 2: ",".join(8 * ["10.3e"]),},
             "EQUID": "5d,5s,10.4e",
             "LOGAR": "5d,5s,10.4e,10.4e",
-            "LAYER": {
-                1: "5d",
-                2: ",".join(8 * ["10.4e"]),
-            },
+            "LAYER": {1: "5d", 2: ",".join(8 * ["10.4e"]),},
         },
     },
     "REACT": "25S",