support for clingo 5.5

caspo/control.py

@@ -114,7 +114,7 @@ def __init__(self, networks, scenarios):
 
         fs = networks.to_funset().union(scenarios.to_funset())
         for v in (n for n in networks.hg.nodes if n not in scenarios.exclude):
-            fs.add(clingo.Function("candidate", [v]))
+            fs.add(clingo.Function("candidate", [clingo.String(v)]))
 
         self.instance = ". ".join(map(str, fs)) + ". #show intervention/2."
 

caspo/core/clamping.py

@@ -53,7 +53,7 @@ def to_funset(self, lname="clamping", cname="clamped"):
         """
         fs = set()
         for i, clamping in enumerate(self):
-            fs.add(clingo.Function(lname, [i]))
+            fs.add(clingo.Function(lname, [clingo.Number(i)]))
             fs = fs.union(clamping.to_funset(i, cname))
 
         return fs
@@ -368,7 +368,7 @@ def to_funset(self, index, name="clamped"):
         """
         fs = set()
         for var, sign in self:
-            fs.add(clingo.Function(name, [index, var, sign]))
+            fs.add(clingo.Function(name, [clingo.Number(index), clingo.String(var), clingo.Number(sign)]))
 
         return fs
 

caspo/core/dataset.py

@@ -159,6 +159,7 @@ def to_funset(self, discrete):
         for i, row in self.readouts.iterrows():
             for var, val in row.items():
                 if not np.isnan(val):
-                    fs.add(clingo.Function('obs', [i, var, discrete(val)]))
+                    fs.add(clingo.Function('obs', [clingo.Number(i),
+                        clingo.String(var), clingo.Number(discrete(val))]))
 
         return fs

caspo/core/hypergraph.py

@@ -174,12 +174,14 @@ def to_funset(self):
         """
         fs = set()
         for i, n in self.nodes.items():
-            fs.add(clingo.Function('node', [n, i]))
+            fs.add(clingo.Function('node', [clingo.String(n), clingo.Number(i)]))
 
         for j, i in self.hyper.items():
-            fs.add(clingo.Function('hyper', [i, j, len(self.edges[self.edges.hyper_idx == j])]))
+            fs.add(clingo.Function('hyper', [clingo.Number(i), clingo.Number(j),
+                clingo.Number(len(self.edges[self.edges.hyper_idx == j]))]))
 
         for j, v, s in self.edges.itertuples(index=False):
-            fs.add(clingo.Function('edge', [j, v, s]))
+            fs.add(clingo.Function('edge', [clingo.Number(j), clingo.String(v),
+                clingo.Number(s)]))
 
         return fs

caspo/core/logicalnetwork.py

@@ -287,7 +287,7 @@ def to_funset(self):
 
         .. _clingo.Function: https://potassco.github.io/clingo/python-api/current/clingo.html#-Function
         """
-        fs = set((clingo.Function("variable", [var]) for var in self.hg.nodes))
+        fs = set((clingo.Function("variable", [clingo.String(var)]) for var in self.hg.nodes))
 
         formulas = set()
         for network in self:
@@ -297,15 +297,18 @@ def to_funset(self):
 
         for i, network in enumerate(self):
             for v, f in network.formulas_iter():
-                fs.add(clingo.Function("formula", [i, v, int(formulas[formulas == f].index[0])]))
+                fs.add(clingo.Function("formula", [clingo.Number(i),
+                    clingo.String(v), clingo.Number(int(formulas[formulas == f].index[0]))]))
 
         for formula_idx, formula in formulas.items():
             for clause in formula:
                 clause_idx = self.hg.clauses_idx[clause]
 
-                fs.add(clingo.Function("dnf", [formula_idx, clause_idx]))
+                fs.add(clingo.Function("dnf", [clingo.Number(formula_idx),
+                    clingo.Number(clause_idx)]))
                 for variable, sign in clause:
-                    fs.add(clingo.Function("clause", [clause_idx, variable, sign]))
+                    fs.add(clingo.Function("clause", [clingo.Number(clause_idx),
+                        clingo.String(variable), clingo.Number(sign)]))
 
         return fs
 

caspo/core/setup.py

@@ -101,9 +101,9 @@ def to_funset(self):
 
         .. _clingo.Function: https://potassco.github.io/clingo/python-api/current/clingo.html#-Function
         """
-        fs = set((clingo.Function('stimulus', [str(var)]) for var in self.stimuli))
-        fs = fs.union((clingo.Function('inhibitor', [str(var)]) for var in self.inhibitors))
-        fs = fs.union((clingo.Function('readout', [str(var)]) for var in self.readouts))
+        fs = set((clingo.Function('stimulus', [clingo.String(str(var))]) for var in self.stimuli))
+        fs = fs.union((clingo.Function('inhibitor', [clingo.String(str(var))]) for var in self.inhibitors))
+        fs = fs.union((clingo.Function('readout', [clingo.String(str(var))]) for var in self.readouts))
 
         return fs
 

caspo/design.py

@@ -59,9 +59,9 @@ def __init__(self, networks, setup, candidates=None):
         fs = networks.to_funset().union(setup.to_funset())
         if candidates:
             fs = fs.union(self.candidates.to_funset("listing", "listed"))
-            fs.add(clingo.Function("mode", [2]))
+            fs.add(clingo.Function("mode", [clingo.Number(2)]))
         else:
-            fs.add(clingo.Function("mode", [1]))
+            fs.add(clingo.Function("mode", [clingo.Number(1)]))
 
         self.instance = ". ".join(map(str, fs)) + ". #show clamped/3."
 
@@ -143,23 +143,25 @@ def design(self, max_stimuli=-1, max_inhibitors=-1, max_experiments=10, relax=Fa
         solver.ground([("base", [])])
 
         if relax:
-            parts = [("step", [step]) for step in range(1, max_experiments+1)]
-            parts.append(("diff", [max_experiments + 1]))
+            parts = [("step", [clingo.Number(step)]) for step in range(1, max_experiments+1)]
+            parts.append(("diff", [clingo.Number(max_experiments + 1)]))
 
             solver.ground(parts)
             solver.solve(on_model=self.__save__)
         else:
             step, sat = 0, False
             while step <= max_experiments and not sat:
                 parts = []
-                parts.append(("check", [step]))
+                parts.append(("check", [clingo.Number(step)]))
                 if step > 0:
-                    solver.release_external(clingo.Function("query", [step-1]))
-                    parts.append(("step", [step]))
+                    solver.release_external(clingo.Function("query",
+                        [clingo.Number(step-1)]))
+                    parts.append(("step", [clingo.Number(step)]))
                     solver.cleanup()
 
                 solver.ground(parts)
-                solver.assign_external(clingo.Function("query", [step]), True)
+                solver.assign_external(clingo.Function("query",
+                    [clingo.Number(step)]), True)
                 sat, step = solver.solve(on_model=self.__save__).satisfiable, step + 1
 
         self.stats['time_optimum'] = solver.statistics['summary']['times']['solve']

caspo/learn.py

@@ -75,7 +75,7 @@ def __init__(self, graph, dataset, length, discrete, factor):
         self.hypergraph = core.HyperGraph.from_graph(self.graph, length)
 
         fs = self.dataset.to_funset(self.discrete).union(self.hypergraph.to_funset())
-        fs.add(clingo.Function('dfactor', [self.factor]))
+        fs.add(clingo.Function('dfactor', [clingo.Number(self.factor)]))
         self.instance = ". ".join(map(str, fs)) + ". #show dnf/2."
 
         self.optimum = None

recipe/meta.yaml

@@ -28,7 +28,7 @@ requirements:
     - pyparsing
     - pydot
     - joblib
-    - clingo 5*
+    - clingo 5.5.*
 
 test:
   commands:

requirements.txt

@@ -8,3 +8,4 @@ pyparsing
 scikit-learn
 scipy
 seaborn
+clingo