Merge pull request #144 from keurfonluu/devel

Fixes and enhancements

README.rst

@@ -139,7 +139,7 @@ TOUGH simulation output can also be imported into Python as a list of *namedtupl
 -  ``toughio-co2tab``: copy file *CO2TAB* to the target directory,
 -  ``toughio-export``: export TOUGH simulation results to a file for visualization (VTK, VTU, Tecplot or XDMF),
 -  ``toughio-extract``: extract results from TOUGH main output file and reformat as a TOUGH3 element or connection output file (mostly useful for TOUGH2 output *before* calling ``toughio-export``),
--  ``toughio-merge``: merge input file, MESH and/or INCON into a single file (for storage or sharing),
+-  ``toughio-merge``: merge input file, GENER and/or MESH and/or INCON into a single file,
 -  ``toughio-save2incon``: convert a *SAVE* file to an *INCON* file (mostly useful to automatically restart a simulation and reset the counters).
 
 Contributing

doc/source/api/index.rst

@@ -7,6 +7,7 @@ API Reference
 
    io
    mesh
+   run
    rpcap
    cli
 

doc/source/api/io.rst

@@ -14,10 +14,12 @@ Input parameters
 Simulation outputs
 ------------------
 
-.. autofunction:: toughio.read_history
-
 .. autofunction:: toughio.read_output
 
+.. autofunction:: toughio.read_table
+
+.. autofunction:: toughio.write_h5
+
 .. autofunction:: toughio.write_output
 
 .. autofunction:: toughio.register_output

doc/source/api/run.rst

@@ -0,0 +1,4 @@
+Run
+===
+
+.. autofunction:: toughio.run

doc/source/guide/input.rst

@@ -78,6 +78,7 @@ A TOUGH input file is defined as follows:
         "connections": dict,
         "initial_conditions": dict,
         "meshmaker": dict,
+        "minc": dict,
         "chemical_properties": dict,
         "non_condensible_gas": list[str],
         "start": bool,
@@ -365,6 +366,8 @@ The keyword ``"type"`` denotes the type of mesh to generate. The following value
  - ``"rz2d"``
  - ``"rz2dl"``
 
+Note that the keyword ``"angle"`` is only used when ``"type"`` is ``"xyz"``.
+
 If ``"type"`` is set to ``"xyz"``, each dictionary in ``"parameters"`` is defined as follows:
 
 .. code-block::
@@ -397,6 +400,23 @@ The keyword ``"type"`` denotes here the type of increments to generate. The foll
  - ``"layer"``: keyword ``"thicknesses"`` is required
 
 
+MINC
+****
+
+MINC parameters are defined in a separate dictionary from ``"meshmaker"`` by the keyword ``"minc"``, and is organized as follows:
+
+.. code-block::
+
+    {
+        "type": str,
+        "dual": str,
+        "n_minc": int,
+        "where": str,
+        "parameters": list[float],
+        "volumes": list[float],
+    }
+
+
 TMVOC
 *****
 
@@ -449,6 +469,33 @@ Non-condensible gases (block NCGAS) can be listed using keyword ``"non_condensib
     For TMVOC input files, the argument ``eos="tmvoc"`` **must** be provided to the functions :func:`toughio.read_input` and :func:`toughio.write_input`.
 
 
+Array dimensions (iTOUGH2)
+**************************
+
+iTOUGH2 allows users to provide array dimensions if an array is insufficiently dimensioned. An additional keyword ``"array_dimensions"`` can be used to specify such values, as follows:
+
+.. code-block::
+
+    "array_dimensions": {
+        "n_rocks": int,
+        "n_times": int,
+        "n_generators": int,
+        "n_rates": int,
+        "n_increment_x": int,
+        "n_increment_y": int,
+        "n_increment_z": int,
+        "n_increment_rad": int,
+        "n_properties": int,
+        "n_properties_times": int,
+        "n_regions": int,
+        "n_regions_parameters": int,
+        "n_ltab": int,
+        "n_rpcap": int,
+        "n_elements_timbc": int,
+        "n_timbc": int,
+    }
+
+
 TOUGHREACT (flow.inp)
 ---------------------
 
@@ -537,33 +584,6 @@ The permeability of an element called ``"AAA00"`` is defined as follows:
     }
 
 
-Array dimensions (iTOUGH2)
-**************************
-
-iTOUGH2 allows users to provide array dimensions if an array is insufficiently dimensioned. An additional keyword ``"array_dimensions"`` can be used to specify such values, as follows:
-
-.. code-block::
-
-    "array_dimensions": {
-        "n_rocks": int,
-        "n_times": int,
-        "n_generators": int,
-        "n_rates": int,
-        "n_increment_x": int,
-        "n_increment_y": int,
-        "n_increment_z": int,
-        "n_increment_rad": int,
-        "n_properties": int,
-        "n_properties_times": int,
-        "n_regions": int,
-        "n_regions_parameters": int,
-        "n_ltab": int,
-        "n_rpcap": int,
-        "n_elements_timbc": int,
-        "n_timbc": int,
-    }
-
-
 TOUGHREACT (solute.inp)
 -----------------------
 

tasks.py

@@ -1,6 +1,7 @@
 import glob
 import os
 import shutil
+import tarfile
 
 from invoke import task
 
@@ -70,3 +71,22 @@ def isort(c):
 @task
 def format(c):
     c.run("invoke isort black docstring")
+
+
+@task
+def tar(c):
+    patterns = [
+        "__pycache__",
+    ]
+
+    def filter(filename):
+        for pattern in patterns:
+            if filename.name.endswith(pattern):
+                return None
+
+        return filename
+
+    with tarfile.open("toughio.tar.gz", "w:gz") as tf:
+        tf.add("toughio", arcname="toughio/toughio", filter=filter)
+        tf.add("pyproject.toml", arcname="toughio/pyproject.toml")
+        tf.add("setup.cfg", arcname="toughio/setup.cfg")

tests/helpers.py

@@ -74,7 +74,6 @@
 output_eleme = [
     toughio.Output(
         "element",
-        None,
         float(time),
         np.array([f"AAA0{i}" for i in range(10)]),
         {
@@ -91,7 +90,6 @@
 output_conne = [
     toughio.Output(
         "connection",
-        None,
         float(time),
         np.array([[f"AAA0{i}", f"AAA0{i}"] for i in range(10)]),
         {

tests/test_h5.py

@@ -0,0 +1,32 @@
+import pathlib
+
+import h5py
+import helpers
+
+import toughio
+
+
+def test_h5():
+    this_dir = pathlib.Path(__file__).parent
+    path = this_dir / "support_files" / "outputs"
+    filename = helpers.tempdir("output.h5")
+
+    toughio.write_h5(
+        filename=filename,
+        elements=path / "OUTPUT_ELEME.csv",
+        connections=path / "OUTPUT_CONNE.csv",
+        element_history={"A1912": path / "FOFT_A1912.csv"},
+        connection_history={"A1912": path / "FOFT_A1912.csv"},
+        generator_history={"A1162": path / "GOFT_A1162.csv"},
+        rock_history={"ROCK": path / "ROFT.csv"},
+    )
+
+    with h5py.File(filename, "r") as f:
+        assert list(f.keys()) == [
+            "connection_history",
+            "connections",
+            "element_history",
+            "elements",
+            "generator_history",
+            "rock_history",
+        ]

tests/test_input.py

@@ -767,8 +767,10 @@ def test_meshm_xyz():
     assert helpers.allclose(parameters_ref, parameters, atol=1.0e-4)
 
 
-@pytest.mark.parametrize("layer", [True, False])
-def test_meshm_rz2d(layer):
+@pytest.mark.parametrize(
+    "layer, minc", [(True, False), (False, False), (True, True), (False, True)]
+)
+def test_meshm_rz2d(layer, minc):
     parameters_ref = {
         "meshmaker": {
             "type": "rz2dl" if layer else "rz2d",
@@ -795,6 +797,35 @@ def test_meshm_rz2d(layer):
             ],
         }
     }
+
+    if minc:
+        parameters_ref["minc"] = {
+            "type": helpers.random_string(5),
+            "dual": helpers.random_string(5),
+            "n_minc": np.random.randint(100) + 1,
+            "where": helpers.random_string(4),
+            "parameters": np.random.rand(7),
+            "volumes": np.random.rand(np.random.randint(100) + 1),
+        }
+
+    parameters = write_read(parameters_ref)
+
+    assert helpers.allclose(parameters_ref, parameters, atol=1.0e-4)
+
+
+def test_minc():
+    n_volume = np.random.randint(100) + 1
+
+    parameters_ref = {
+        "minc": {
+            "type": helpers.random_string(5),
+            "dual": helpers.random_string(5),
+            "n_minc": np.random.randint(100) + 1,
+            "where": helpers.random_string(4),
+            "parameters": np.random.rand(7),
+            "volumes": np.random.rand(n_volume),
+        }
+    }
     parameters = write_read(parameters_ref)
 
     assert helpers.allclose(parameters_ref, parameters, atol=1.0e-4)

tests/test_output.py

@@ -17,16 +17,16 @@
 
 
 @pytest.mark.parametrize(
-    "filename, filename_ref",
+    "filename, filename_ref, file_format",
     [
-        ("OUTPUT_ELEME.csv", "SAVE.out"),
-        ("OUTPUT_ELEME.tec", "SAVE.out"),
-        ("OUTPUT_ELEME_PETRASIM.csv", "SAVE.out"),
-        ("OUTPUT.out", "SAVE.out"),
-        ("OUTPUT_6.out", "SAVE_6.out"),
+        ("OUTPUT_ELEME.csv", "SAVE.out", "csv"),
+        ("OUTPUT_ELEME.tec", "SAVE.out", "tecplot"),
+        ("OUTPUT_ELEME_PETRASIM.csv", "SAVE.out", "petrasim"),
+        ("OUTPUT.out", "SAVE.out", "tough"),
+        ("OUTPUT_6.out", "SAVE_6.out", "tough"),
     ],
 )
-def test_output_eleme(filename, filename_ref):
+def test_output_eleme(filename, filename_ref, file_format):
     this_dir = os.path.dirname(os.path.abspath(__file__))
     filename = os.path.join(this_dir, "support_files", "outputs", filename)
     outputs = toughio.read_output(filename)
@@ -48,10 +48,10 @@ def test_output_eleme(filename, filename_ref):
         assert time_ref == output.time
         assert (
             save.labels.tolist() == output.labels.tolist()
-            if output.format in {"csv", "petrasim", "tough"}
+            if file_format in {"csv", "petrasim", "tough"}
             else len(output.labels) == 0
         )
-        if output.format != "tough":
+        if file_format != "tough":
             assert keys_ref == sorted(list(output.data))
 
     assert helpers.allclose(save.data["X1"], outputs[-1].data["PRES"])

toughio/VERSION

@@ -1 +1 @@
-1.12.2
+1.13.0

toughio/__init__.py

@@ -9,6 +9,7 @@
     register_input,
     register_output,
     register_table,
+    write_h5,
     write_input,
     write_output,
 )
@@ -18,6 +19,7 @@
 from ._mesh import register as register_mesh
 from ._mesh import write as write_mesh
 from ._mesh import write_time_series
+from ._run import run
 
 __all__ = [
     "Mesh",
@@ -31,6 +33,7 @@
     "read_input",
     "read_output",
     "read_table",
+    "write_h5",
     "write_input",
     "write_output",
     "from_meshio",
@@ -42,6 +45,7 @@
     "relative_permeability",
     "capillarity",
     "convert_labels",
+    "run",
     "_cli",
     "__version__",
 ]

toughio/_cli/_export.py

@@ -54,25 +54,13 @@ def export(argv=None):
             output = output[args.time_step]
         else:
             output = output[-1]
-        input_format = output.format
         labels = output.labels
     else:
-        input_format = output[-1].format
         labels = output[-1].labels
     print(" Done!")
 
-    # Display warning if mesh is provided but input file format is 'tecplot'
-    # Continue as if mesh was not provided
-    if input_format == "tecplot":
-        with_mesh = False
-        msg = (
-            "Cannot use mesh file with Tecplot TOUGH output, inferring dimensionality"
-            if args.mesh
-            else "Inferring dimensionality"
-        )
-    else:
-        with_mesh = bool(args.mesh)
-        msg = "Mesh file not specified, inferring dimensionality"
+    with_mesh = bool(args.mesh)
+    msg = "Mesh file not specified, inferring dimensionality"
 
     # Triangulate or voxelize if no mesh
     voxelized = False
@@ -225,7 +213,7 @@ def _get_parser():
     parser.add_argument(
         "infile",
         type=str,
-        help="TOUGH output file",
+        help="TOUGH input file",
     )
 
     # Mesh file

toughio/_cli/_extract.py

@@ -41,8 +41,6 @@ def extract(argv=None):
 
     # Read TOUGH output file
     output = read_output(args.infile, connection=args.connection)
-    if output[-1].format != "tough":
-        raise ValueError(f"Invalid TOUGH output file '{args.infile}'.")
 
     try:
         if not args.connection: