Merge pull request #171 from keurfonluu/devel

Support flag option for OFT blocks

.github/workflows/doc.yml

@@ -22,11 +22,10 @@ jobs:
             python-version: '3.9'
       - name: Install OSMesa VTK
         run: |
-          sudo apt update
-          sudo apt install libosmesa6-dev libgl1-mesa-dev retry --option="APT::Acquire::Retries=3"
-          pip install https://github.com/pyvista/pyvista-wheels/raw/main/vtk-osmesa-9.1.0-cp39-cp39-linux_x86_64.whl
+          pip install vtk-osmesa==9.3.0 --index-url https://gitlab.kitware.com/api/v4/projects/13/packages/pypi/simple
       - name: Install libGLU for pygmsh
         run: |
+          sudo apt update
           sudo apt install libglu1
       - name: Install toughio
         run: |

doc/source/api/io.rst

@@ -14,6 +14,12 @@ Input parameters
 Simulation outputs
 ------------------
 
+.. autoclass:: toughio.ElementOutput
+   :members:
+
+.. autoclass:: toughio.ConnectionOutput
+   :members:
+
 .. autofunction:: toughio.read_output
 
 .. autofunction:: toughio.read_table

tests/test_input.py

@@ -446,10 +446,20 @@ def test_hyste(write_read):
 )
 def test_oft(write_read, oft, n):
     parameters_ref = {
-        oft: [helpers.random_string(n) for _ in range(np.random.randint(10) + 1)]
+        oft: [
+            helpers.random_string(n),
+            helpers.random_string(n),
+            {"label": helpers.random_string(n)},
+            {"label": helpers.random_string(n), "flag": np.random.randint(10)},
+        ]
     }
     parameters = write_read(parameters_ref)
 
+    if write_read == write_read_tough:
+        for i, v in enumerate(parameters_ref[oft]):
+            if not isinstance(v, dict):
+                parameters_ref[oft][i] = {"label": v}
+
     assert helpers.allclose(parameters_ref, parameters)
 
 

toughio/VERSION

@@ -1 +1 @@
-1.15.0
+1.15.1

toughio/_common.py

@@ -38,9 +38,15 @@
     "MOMOP": "50S",
     "TIMES": {1: "5d,5d,10f,10f", 2: ",".join(8 * ["10f"])},
     "HYSTE": ",".join(3 * ["5d"]),
-    "FOFT": {5: "5s", 6: "6s", 7: "7s", 8: "8s", 9: "9s"},
-    "COFT": {5: "10s", 6: "12s", 7: "14s", 8: "16s", 9: "18s"},
-    "GOFT": {5: "5s", 6: "6s", 7: "7s", 8: "8s", 9: "9s"},
+    "FOFT": {5: "5s,5s,5d", 6: "6s,4s,5d", 7: "7s,3s,5d", 8: "8s,2s,5d", 9: "9s,1s,5d"},
+    "COFT": {
+        5: "10s,10s,5d",
+        6: "12s,8s,5d",
+        7: "14s,6s,5d",
+        8: "16s,4s,5d",
+        9: "18s,2s,5d",
+    },
+    "GOFT": {5: "5s,5s,5d", 6: "6s,4s,5d", 7: "7s,3s,5d", 8: "8s,2s,5d", 9: "9s,1s,5d"},
     "ROFT": "5s,5s",
     "GENER": {
         0: ",".join(4 * ["14f"]),

toughio/_io/input/tough/_common.py

@@ -166,6 +166,11 @@
     "eps": 1.0e-6,
 }
 
+histories = {
+    "label": None,
+    "flag": None,
+}
+
 generators = {
     "label": None,
     "name": None,

toughio/_io/input/tough/_read.py

@@ -841,7 +841,12 @@ def _read_oft(f, oft, label_length):
     while True:
         if line.strip():
             data = read_record(line, fmt[label_length])
-            history[key].append(label_format.format(data[0]))
+            tmp = {"label": label_format.format(data[0])}
+
+            if data[2] is not None:
+                tmp["flag"] = data[2]
+
+            history[key].append(tmp)
 
         else:
             break

toughio/_io/input/tough/_write.py

@@ -1056,43 +1056,56 @@ def _write_hyste(parameters, space_between_values):
     return out
 
 
-@block("FOFT", multi=True)
-def _write_foft(parameters, space_between_values):
-    """Write FOFT block data."""
+def _write_oft(oft, parameters, space_between_values):
+    """Write FOFT, COFT, and GOFT blocks data."""
+    from ._common import histories
+
+    keys = {
+        "FOFT": "element",
+        "COFT": "connection",
+        "GOFT": "generator",
+    }
+
     # Formats
-    fmt = block_to_format["FOFT"]
+    fmt = block_to_format[oft]
     fmt = str2format(fmt[5])
 
-    values = [x for x in parameters["element_history"]]
-    out = write_record(values, fmt, space_between_values, multi=True)
+    out = []
+    for oft in parameters[f"{keys[oft]}_history"]:
+        data = deepcopy(histories)
+
+        if isinstance(oft, dict):
+            data.update(oft)
+
+        else:
+            data["label"] = oft
+
+        values = [
+            data["label"],
+            None,
+            data["flag"],
+        ]
+        out += write_record(values, fmt, space_between_values)
 
     return out
 
 
+@block("FOFT", multi=True)
+def _write_foft(parameters, space_between_values):
+    """Write FOFT block data."""
+    return _write_oft("FOFT", parameters, space_between_values)
+
+
 @block("COFT", multi=True)
 def _write_coft(parameters, space_between_values):
     """Write COFT block data."""
-    # Format
-    fmt = block_to_format["COFT"]
-    fmt = str2format(fmt[5])
-
-    values = [x for x in parameters["connection_history"]]
-    out = write_record(values, fmt, space_between_values, multi=True)
-
-    return out
+    return _write_oft("COFT", parameters, space_between_values)
 
 
 @block("GOFT", multi=True)
 def _write_goft(parameters, space_between_values):
     """Write GOFT block data."""
-    # Format
-    fmt = block_to_format["GOFT"]
-    fmt = str2format(fmt[5])
-
-    values = [x for x in parameters["generator_history"]]
-    out = write_record(values, fmt, space_between_values, multi=True)
-
-    return out
+    return _write_oft("GOFT", parameters, space_between_values)
 
 
 @block("ROFT", multi=True)

toughio/_io/output/_common.py

@@ -271,12 +271,17 @@ def to_output(file_type, labels_order, headers, times, labels, data):
                 "Found duplicate connections. Fixing outputs by summing duplicate connections."
             )
 
-            for output in outputs:
-                output.labels = list(connections)
-                output.data = {
-                    k: np.array([v[idx].sum() for idx in connections.values()])
-                    for k, v in output.data.items()
-                }
+            outputs = [
+                ConnectionOutput(
+                    time=output.time,
+                    data={
+                        k: np.array([v[idx].sum() for idx in connections.values()])
+                        for k, v in output.data.items()
+                    },
+                    labels=list(connections),
+                )
+                for output in outputs
+            ]
 
     if file_type == "element" and labels_order is not None:
         outputs = [output[labels_order] for output in outputs]