[1.9.x] Drop trailing commas that made twelve argsDict values 1-tuples

proteus/m_comp_co2/m_comp_co2.py

@@ -3827,7 +3827,7 @@ def getResidual(self,u,r):
         argsDict["boundaryJac_ref"] = self.u[0].femSpace.elementMaps.boundaryJacobians
         argsDict["nElements_global"] = self.mesh.nElements_global
         argsDict["ebqe_penalty_ext"] = self.ebqe['penalty']
-        argsDict["elementMaterialTypes"] = self.mesh.elementMaterialTypes,
+        argsDict["elementMaterialTypes"] = self.mesh.elementMaterialTypes
         argsDict["isSeepageFace"] = self.coefficients.isSeepageFace
         argsDict["a_rowptr"] = self.coefficients.sdInfo[(0,0)][0]
         argsDict["a_colind"] = self.coefficients.sdInfo[(0,0)][1]
@@ -4674,7 +4674,7 @@ def getJacobian(self,jacobian):
         argsDict["boundaryJac_ref"] = self.u[0].femSpace.elementMaps.boundaryJacobians
         argsDict["nElements_global"] = self.mesh.nElements_global
         argsDict["ebqe_penalty_ext"] = self.ebqe['penalty']
-        argsDict["elementMaterialTypes"] = self.mesh.elementMaterialTypes,
+        argsDict["elementMaterialTypes"] = self.mesh.elementMaterialTypes
         argsDict["isSeepageFace"] = self.coefficients.isSeepageFace
         argsDict["a_rowptr"] = self.coefficients.sdInfo[(0,0)][0]
         argsDict["a_colind"] = self.coefficients.sdInfo[(0,0)][1]

proteus/mprans/PresInc.py

@@ -858,7 +858,7 @@ def getResidual(self, u, r):
         argsDict["nExteriorElementBoundaries_global"] = self.mesh.nExteriorElementBoundaries_global
         argsDict["exteriorElementBoundariesArray"] = self.mesh.exteriorElementBoundariesArray
         argsDict["elementBoundaryElementsArray"] = self.mesh.elementBoundaryElementsArray
-        argsDict["elementBoundaryLocalElementBoundariesArray"] = self.mesh.elementBoundaryLocalElementBoundariesArray, 
+        argsDict["elementBoundaryLocalElementBoundariesArray"] = self.mesh.elementBoundaryLocalElementBoundariesArray
         argsDict["INTEGRATE_BY_PARTS_DIV_U"] = self.coefficients.INTEGRATE_BY_PARTS_DIV_U
         argsDict["q_a"] = self.q['a']
         argsDict["ebqe_a"] = self.ebqe['a']

proteus/mprans/RANS2P_IB.py

@@ -1340,7 +1340,7 @@ def getJacobian(self, jacobian):
         argsDict["normal_ref"] = self.u[0].femSpace.elementMaps.boundaryNormals
         argsDict["boundaryJac_ref"] = self.u[0].femSpace.elementMaps.boundaryJacobians
         argsDict["eb_adjoint_sigma"] = self.eb_adjoint_sigma
-        argsDict["elementDiameter"] = self.elementDiameter,  # mesh.elementDiametersArray
+        argsDict["elementDiameter"] = self.elementDiameter  # mesh.elementDiametersArray
         argsDict["nodeDiametersArray"] = self.mesh.nodeDiametersArray
         argsDict["hFactor"] = self.stabilization.hFactor
         argsDict["nElements_global"] = self.mesh.nElements_global
@@ -1394,7 +1394,7 @@ def getJacobian(self, jacobian):
         argsDict["sdInfo_u_u_colind"] = self.coefficients.sdInfo[(1, 1)][1]
         argsDict["sdInfo_u_v_rowptr"] = self.coefficients.sdInfo[(1, 2)][0]
         argsDict["sdInfo_u_v_colind"] = elf.coefficients.sdInfo[(1, 2)][1]
-        argsDict["sdInfo_u_w_rowptr"] = self.coefficients.sdInfo[(1, 3)][0], 
+        argsDict["sdInfo_u_w_rowptr"] = self.coefficients.sdInfo[(1, 3)][0]
         argsDict["sdInfo_u_w_colind"] = self.coefficients.sdInfo[(1, 3)][1]
         argsDict["sdInfo_v_v_rowptr"] = self.coefficients.sdInfo[(2, 2)][0]
         argsDict["sdInfo_v_v_colind"] = self.coefficients.sdInfo[(2, 2)][1]
@@ -1571,7 +1571,7 @@ def beamStep(self):
         argsDict["normal_ref"] = self.u[0].femSpace.elementMaps.boundaryNormals
         argsDict["boundaryJac_ref"] = self.u[0].femSpace.elementMaps.boundaryJacobians
         argsDict["eb_adjoint_sigma"] = self.eb_adjoint_sigma
-        argsDict["elementDiameter"] = self.elementDiameter,  # mesh.elementDiametersArray
+        argsDict["elementDiameter"] = self.elementDiameter  # mesh.elementDiametersArray
         argsDict["nodeDiametersArray"] = self.mesh.nodeDiametersArray
         argsDict["hFactor"] = self.stabilization.hFactor
         argsDict["nElements_global"] = self.mesh.nElements_global

proteus/mprans/RANS3PF.py

@@ -2726,7 +2726,7 @@ def getJacobian(self, jacobian):
         argsDict["sdInfo_u_u_colind"] = self.coefficients.sdInfo[(0, 0)][1]
         argsDict["sdInfo_u_v_rowptr"] = self.coefficients.sdInfo[(0, 1)][0]
         argsDict["sdInfo_u_v_colind"] = self.coefficients.sdInfo[(0, 1)][1]
-        argsDict["sdInfo_u_w_rowptr"] = self.coefficients.sdInfo[(0, 2)][0], 
+        argsDict["sdInfo_u_w_rowptr"] = self.coefficients.sdInfo[(0, 2)][0]
         argsDict["sdInfo_u_w_colind"] = self.coefficients.sdInfo[(0, 2)][1]
         argsDict["sdInfo_v_v_rowptr"] = self.coefficients.sdInfo[(1, 1)][0]
         argsDict["sdInfo_v_v_colind"] = self.coefficients.sdInfo[(1, 1)][1]
@@ -2738,7 +2738,7 @@ def getJacobian(self, jacobian):
         argsDict["sdInfo_w_w_colind"] = self.coefficients.sdInfo[(2, 2)][1]
         argsDict["sdInfo_w_u_rowptr"] = self.coefficients.sdInfo[(2, 0)][0]
         argsDict["sdInfo_w_u_colind"] = self.coefficients.sdInfo[(2, 0)][1]
-        argsDict["sdInfo_w_v_rowptr"] = self.coefficients.sdInfo[(2, 1)][0], 
+        argsDict["sdInfo_w_v_rowptr"] = self.coefficients.sdInfo[(2, 1)][0]
         argsDict["sdInfo_w_v_colind"] = self.coefficients.sdInfo[(2, 1)][1]
         argsDict["csrRowIndeces_p_p"] = self.csrRowIndeces[(0, 0)]
         argsDict["csrColumnOffsets_p_p"] = self.csrColumnOffsets[(0, 0)]

proteus/mprans/RANS3PSed.py

@@ -1995,7 +1995,7 @@ def getJacobian(self, jacobian):
         argsDict["q_numDiff_w_last"] = self.shockCapturing.numDiff_last[2]
         argsDict["sdInfo_u_u_rowptr"] = self.coefficients.sdInfo[(0, 0)][0]
         argsDict["sdInfo_u_u_colind"] = self.coefficients.sdInfo[(0, 0)][1]
-        argsDict["sdInfo_u_v_rowptr"] = self.coefficients.sdInfo[(0, 1)][0], 
+        argsDict["sdInfo_u_v_rowptr"] = self.coefficients.sdInfo[(0, 1)][0]
         argsDict["sdInfo_u_v_colind"] = self.coefficients.sdInfo[(0, 1)][1]
         argsDict["sdInfo_u_w_rowptr"] = self.coefficients.sdInfo[(0, 2)][0]
         argsDict["sdInfo_u_w_colind"] = self.coefficients.sdInfo[(0, 2)][1]

proteus/mprans/SW2D.py

@@ -822,7 +822,7 @@ def getJacobian(self, jacobian):
         argsDict["vel_grad_test_trace_ref"] = self.u[1].femSpace.grad_psi_trace
         argsDict["normal_ref"] = self.u[0].femSpace.elementMaps.boundaryNormals
         argsDict["boundaryJac_ref"] = self.u[0].femSpace.elementMaps.boundaryJacobians
-        argsDict["elementDiameter"] = self.elementDiameter,  # mesh.elementDiametersArray
+        argsDict["elementDiameter"] = self.elementDiameter  # mesh.elementDiametersArray
         argsDict["nElements_global"] = self.mesh.nElements_global
         argsDict["useRBLES"] = self.coefficients.useRBLES
         argsDict["useMetrics"] = self.coefficients.useMetrics

proteus/richards/Richards.py

@@ -1596,7 +1596,7 @@ def getResidual(self,u,r):
         argsDict["boundaryJac_ref"] = self.u[0].femSpace.elementMaps.boundaryJacobians
         argsDict["nElements_global"] = self.mesh.nElements_global
         argsDict["ebqe_penalty_ext"] = self.ebqe['penalty']
-        argsDict["elementMaterialTypes"] = self.mesh.elementMaterialTypes,
+        argsDict["elementMaterialTypes"] = self.mesh.elementMaterialTypes
         argsDict["isSeepageFace"] = self.coefficients.isSeepageFace
         argsDict["a_rowptr"] = self.coefficients.sdInfo[(0,0)][0]
         argsDict["a_colind"] = self.coefficients.sdInfo[(0,0)][1]
@@ -1959,7 +1959,7 @@ def getJacobian(self,jacobian):
         argsDict["boundaryJac_ref"] = self.u[0].femSpace.elementMaps.boundaryJacobians
         argsDict["nElements_global"] = self.mesh.nElements_global
         argsDict["ebqe_penalty_ext"] = self.ebqe['penalty']
-        argsDict["elementMaterialTypes"] = self.mesh.elementMaterialTypes,
+        argsDict["elementMaterialTypes"] = self.mesh.elementMaterialTypes
         argsDict["isSeepageFace"] = self.coefficients.isSeepageFace
         argsDict["a_rowptr"] = self.coefficients.sdInfo[(0,0)][0]
         argsDict["a_colind"] = self.coefficients.sdInfo[(0,0)][1]

test/test_argsdict_values.py

@@ -0,0 +1,117 @@
+"""No argsDict entry is handed a tuple (or another non-array literal).
+
+``argsDict["k"] = arr,`` -- note the trailing comma -- stores the 1-tuple
+``(arr,)``, not ``arr``. ArgumentsDict.__setitem__ only has overloads for
+int/double arrays and int/double scalars. The xtensor-based caster (1.9.x)
+coerced the tuple into a copy, and a tuple of a double array matched the
+int overload first, so the kernel's ``args.array<double>("k")`` then found
+no such key. proteus::pyarray (main) rejects the tuple with a TypeError.
+Either way the mistake only surfaces when that model's residual or Jacobian
+is first evaluated, and several of the models involved have no test that
+does so. This scan catches it in every module without running any of them.
+"""
+import ast
+import os
+import textwrap
+
+import pytest
+
+import proteus
+
+PROTEUS_ROOT = os.path.dirname(os.path.abspath(proteus.__file__))
+
+#: Modules still carrying the bug, each with the issue that tracks it.
+KNOWN = {
+    # Its extension (richards.cADR) is not built, so the module cannot even be
+    # imported; fixed together with that.
+    "richards/ADR.py": "erdc/proteus#1285",
+}
+
+#: Node types that are never a valid ArgumentsDict value.
+_BAD_NODES = (ast.Tuple, ast.List, ast.Set, ast.Dict,
+              ast.ListComp, ast.SetComp, ast.DictComp, ast.GeneratorExp)
+
+
+def _arguments_dict_names(tree):
+    """Names bound to an ArgumentsDict() in this module, plus 'argsDict'."""
+    names = {"argsDict"}
+    for node in ast.walk(tree):
+        if isinstance(node, ast.Assign) and isinstance(node.value, ast.Call):
+            func = node.value.func
+            fname = func.attr if isinstance(func, ast.Attribute) else getattr(func, "id", None)
+            if fname == "ArgumentsDict":
+                for target in node.targets:
+                    if isinstance(target, ast.Name):
+                        names.add(target.id)
+                    elif isinstance(target, ast.Attribute):
+                        names.add(target.attr)
+    return names
+
+
+def _bad_value(value):
+    if isinstance(value, _BAD_NODES):
+        return True
+    # None, strings, bytes: no overload takes them.
+    return isinstance(value, ast.Constant) and not isinstance(value.value, (int, float))
+
+
+def find_bad_assignments(source, filename="<string>"):
+    """(line, text) for each `<argsDict>[...] = <non-array literal>` in source."""
+    tree = ast.parse(source, filename)
+    names = _arguments_dict_names(tree)
+    found = []
+    for node in ast.walk(tree):
+        if not isinstance(node, ast.Assign) or not _bad_value(node.value):
+            continue
+        for target in node.targets:
+            if not isinstance(target, ast.Subscript):
+                continue
+            base = target.value
+            bname = base.id if isinstance(base, ast.Name) else getattr(base, "attr", None)
+            if bname in names:
+                found.append((node.lineno, ast.unparse(node)))
+    return found
+
+
+def _proteus_sources():
+    for dirpath, dirnames, filenames in os.walk(PROTEUS_ROOT):
+        dirnames[:] = sorted(d for d in dirnames if d != "__pycache__")
+        for name in sorted(filenames):
+            if name.endswith(".py"):
+                yield os.path.join(dirpath, name)
+
+
+def test_scanner_catches_trailing_comma():
+    source = textwrap.dedent("""
+        from proteus.mprans import cArgumentsDict
+        argsDict = cArgumentsDict.ArgumentsDict()
+        argsDict["ok_array"] = a
+        argsDict["ok_scalar"] = 1.0
+        argsDict["bad_tuple"] = a,
+        argsDict["bad_commented"] = a,  # trailing comment
+        argsDict["bad_none"] = None
+        self.args = cArgumentsDict.ArgumentsDict()
+        self.args["bad_attr"] = (a,
+                                 )
+    """)
+    lines = [line for line, _ in find_bad_assignments(source)]
+    assert lines == [6, 7, 8, 10]
+
+
+def test_no_tuple_values_assigned_into_argsdict():
+    offenders = []
+    for path in _proteus_sources():
+        with open(path, encoding="utf-8") as f:
+            source = f.read()
+        try:
+            found = find_bad_assignments(source, path)
+        except SyntaxError as e:
+            pytest.fail("could not parse %s: %s" % (path, e))
+        rel = os.path.relpath(path, PROTEUS_ROOT).replace(os.sep, "/")
+        if rel in KNOWN:
+            assert found, "%s is fixed: drop it from KNOWN (%s)" % (rel, KNOWN[rel])
+            continue
+        offenders += ["proteus/%s:%d: %s" % (rel, line, text) for line, text in found]
+    assert not offenders, (
+        "ArgumentsDict values must be ndarrays or int/float scalars "
+        "(check for a stray trailing comma):\n  " + "\n  ".join(offenders))