update ilpy API to v0.3.0

docs/source/extending.rst

@@ -104,7 +104,7 @@ Adding Constraints
 New constraints are introduced by subclassing :class:`Constraint
 <motile.constraints.Constraint>` and implementing the :func:`instantiate
 <motile.constraints.Constraint.instantiate>` method. This method should return
-a list of ``ilpy.LinearConstraint``.
+a list of ``ilpy.Constraint``.
 
 Imagine we know precisely that we want to track at most :math:`k` objects, but
 we don't know beforehand which of the many objects in the track graph those
@@ -128,7 +128,7 @@ This can be done with a constraint as follows:
 
         appear_indicators = solver.get_variables(NodeAppear)
 
-        constraint = ilpy.LinearConstraint()
+        constraint = ilpy.Constraint()
         for appear_indicator, index in appear_indicators.items():
           constraint.set_coefficient(index, 1.0)
         constraint.set_relation(ilpy.Relation.LessEqual)
@@ -301,15 +301,15 @@ The complete variable declaration looks like this:
             out_edge_index = edge_indicators[out_edge]
 
             # edge pair indicator = 1 <=> in edge = 1 and out edge = 1
-            constraint = ilpy.LinearConstraint()
+            constraint = ilpy.Constraint()
             constraint.set_coefficient(pair_index, 2)
             constraint.set_coefficient(in_edge_index, -1)
             constraint.set_coefficient(out_edge_index, -1)
             constraint.set_relation(ilpy.Relation.LessEqual)
             constraint.set_value(0)
             constraints.append(constraint)
 
-            constraint = ilpy.LinearConstraint()
+            constraint = ilpy.Constraint()
             constraint.set_coefficient(pair_index, -1)
             constraint.set_coefficient(in_edge_index, 1)
             constraint.set_coefficient(out_edge_index, 1)

motile/constraints/constraint.py

@@ -11,7 +11,7 @@
 
 class Constraint(ABC):
     @abstractmethod
-    def instantiate(self, solver: Solver) -> Iterable[ilpy.LinearConstraint]:
+    def instantiate(self, solver: Solver) -> Iterable[ilpy.Constraint]:
         """Create and return specific linear constraints for the given solver.
 
         Args:
@@ -21,5 +21,5 @@ def instantiate(self, solver: Solver) -> Iterable[ilpy.LinearConstraint]:
 
         Returns:
 
-            An iterable of :class:`ilpy.LinearConstraint`.
+            An iterable of :class:`ilpy.Constraint`.
         """

motile/constraints/max_children.py

@@ -30,11 +30,11 @@ class MaxChildren(Constraint):
     def __init__(self, max_children: int) -> None:
         self.max_children = max_children
 
-    def instantiate(self, solver: Solver) -> Iterable[ilpy.LinearConstraint]:
+    def instantiate(self, solver: Solver) -> Iterable[ilpy.Constraint]:
         edge_indicators = solver.get_variables(EdgeSelected)
 
         for node in solver.graph.nodes:
-            constraint = ilpy.LinearConstraint()
+            constraint = ilpy.Constraint()
 
             # all outgoing edges
             for edge in solver.graph.next_edges[node]:

motile/constraints/max_parents.py

@@ -30,11 +30,11 @@ class MaxParents(Constraint):
     def __init__(self, max_parents: int) -> None:
         self.max_parents = max_parents
 
-    def instantiate(self, solver: Solver) -> Iterable[ilpy.LinearConstraint]:
+    def instantiate(self, solver: Solver) -> Iterable[ilpy.Constraint]:
         edge_indicators = solver.get_variables(EdgeSelected)
 
         for node in solver.graph.nodes:
-            constraint = ilpy.LinearConstraint()
+            constraint = ilpy.Constraint()
 
             # all incoming edges
             for edge in solver.graph.prev_edges[node]:

motile/constraints/pin.py

@@ -33,7 +33,7 @@ class Pin(Constraint):
     def __init__(self, attribute: str) -> None:
         self.attribute = attribute
 
-    def instantiate(self, solver: Solver) -> list[ilpy.LinearConstraint]:
+    def instantiate(self, solver: Solver) -> list[ilpy.Constraint]:
         node_indicators = solver.get_variables(NodeSelected)
         edge_indicators = solver.get_variables(EdgeSelected)
 
@@ -57,8 +57,8 @@ def instantiate(self, solver: Solver) -> list[ilpy.LinearConstraint]:
             if self.attribute in attributes and not attributes[self.attribute]
         ]
 
-        must_select_constraint = ilpy.LinearConstraint()
-        must_not_select_constraint = ilpy.LinearConstraint()
+        must_select_constraint = ilpy.Constraint()
+        must_not_select_constraint = ilpy.Constraint()
 
         for index in must_select:
             must_select_constraint.set_coefficient(index, 1)

motile/constraints/select_edge_nodes.py

@@ -24,7 +24,7 @@ class SelectEdgeNodes(Constraint):
     This constraint will be added by default to any :class:`Solver` instance.
     """
 
-    def instantiate(self, solver: Solver) -> Iterable[ilpy.LinearConstraint]:
+    def instantiate(self, solver: Solver) -> Iterable[ilpy.Constraint]:
         node_indicators = solver.get_variables(NodeSelected)
         edge_indicators = solver.get_variables(EdgeSelected)
 
@@ -34,7 +34,7 @@ def instantiate(self, solver: Solver) -> Iterable[ilpy.LinearConstraint]:
             ind_e = edge_indicators[edge]
             nodes_ind = [node_indicators[node] for node in nodes]
 
-            constraint = ilpy.LinearConstraint()
+            constraint = ilpy.Constraint()
             constraint.set_coefficient(ind_e, len(nodes_ind))
             for node_ind in nodes_ind:
                 constraint.set_coefficient(node_ind, -1)

motile/solver.py

@@ -12,7 +12,6 @@
 from .ssvm import fit_weights
 
 logger = logging.getLogger(__name__)
-ILPY_V03 = ilpy.__version__.split(".")[:2] >= ["0", "3"]
 
 if TYPE_CHECKING:
     from motile.costs import Costs
@@ -48,9 +47,9 @@ def __init__(
         self._weights_changed = True
         self.features = Features()
 
-        self.ilp_solver: ilpy.LinearSolver | None = None
-        self.objective: ilpy.LinearObjective | None = None
-        self.constraints = ilpy.LinearConstraints()
+        self.ilp_solver: ilpy.Solver | None = None
+        self.objective: ilpy.Objective | None = None
+        self.constraints = ilpy.Constraints()
 
         self.num_variables: int = 0
         self._costs = np.zeros((0,), dtype=np.float32)
@@ -131,13 +130,13 @@ def solve(self, timeout: float = 0.0, num_threads: int = 1) -> ilpy.Solution:
             vector.
         """
 
-        self.objective = ilpy.LinearObjective(self.num_variables)
+        self.objective = ilpy.Objective(self.num_variables)
         for i, c in enumerate(self.costs):
             logger.debug("Setting cost of var %d to %.3f", i, c)
             self.objective.set_coefficient(i, c)
 
         # TODO: support other variable types
-        self.ilp_solver = ilpy.LinearSolver(
+        self.ilp_solver = ilpy.Solver(
             self.num_variables,
             ilpy.VariableType.Binary,
             variable_types=self.variable_types,
@@ -153,13 +152,8 @@ def solve(self, timeout: float = 0.0, num_threads: int = 1) -> ilpy.Solution:
 
         self.ilp_solver.set_verbose(False)
 
-        solution = self.ilp_solver.solve()
-
-        if ILPY_V03:
-            self.solution, message = solution, solution.get_status()
-        else:
-            self.solution, message = solution
-        if message:
+        self.solution = self.ilp_solver.solve()
+        if message := self.solution.get_status():
             logger.info("ILP solver returned with: %s", message)
 
         return self.solution

motile/variables/node_appear.py

@@ -39,7 +39,7 @@ def instantiate(solver: Solver) -> Collection[NodeId]:
         return solver.graph.nodes
 
     @staticmethod
-    def instantiate_constraints(solver: Solver) -> Iterable[ilpy.LinearConstraint]:
+    def instantiate_constraints(solver: Solver) -> Iterable[ilpy.Constraint]:
         appear_indicators = solver.get_variables(NodeAppear)
         node_indicators = solver.get_variables(NodeSelected)
         edge_indicators = solver.get_variables(EdgeSelected)
@@ -51,7 +51,7 @@ def instantiate_constraints(solver: Solver) -> Iterable[ilpy.LinearConstraint]:
             if num_prev_edges == 0:
                 # special case: no incoming edges, appear indicator is equal to
                 # selection indicator
-                constraint = ilpy.LinearConstraint()
+                constraint = ilpy.Constraint()
                 constraint.set_coefficient(node_indicators[node], 1.0)
                 constraint.set_coefficient(appear_indicators[node], -1.0)
                 constraint.set_relation(ilpy.Relation.Equal)
@@ -72,8 +72,8 @@ def instantiate_constraints(solver: Solver) -> Iterable[ilpy.LinearConstraint]:
             # (1) s - appear <= num_prev - 1
             # (2) s - appear * num_prev >= 0
 
-            constraint1 = ilpy.LinearConstraint()
-            constraint2 = ilpy.LinearConstraint()
+            constraint1 = ilpy.Constraint()
+            constraint2 = ilpy.Constraint()
 
             # set s for both constraints:
 

motile/variables/node_split.py

@@ -36,7 +36,7 @@ def instantiate(solver: Solver) -> Collection[NodeId]:
         return solver.graph.nodes
 
     @staticmethod
-    def instantiate_constraints(solver: Solver) -> Iterable[ilpy.LinearConstraint]:
+    def instantiate_constraints(solver: Solver) -> Iterable[ilpy.Constraint]:
         split_indicators = solver.get_variables(NodeSplit)
         edge_indicators = solver.get_variables(EdgeSelected)
 
@@ -53,8 +53,8 @@ def instantiate_constraints(solver: Solver) -> Iterable[ilpy.LinearConstraint]:
             # (1) 2 * split - sum(next_selected) <= 0
             # (2) (num_next - 1) * split - sum(next_selected) >= -1
 
-            constraint1 = ilpy.LinearConstraint()
-            constraint2 = ilpy.LinearConstraint()
+            constraint1 = ilpy.Constraint()
+            constraint2 = ilpy.Constraint()
 
             constraint1.set_coefficient(split_indicators[node], 2.0)
             constraint2.set_coefficient(split_indicators[node], len(next_edges) - 1.0)

motile/variables/variable.py

@@ -89,7 +89,7 @@ def instantiate(solver):
         pass
 
     @staticmethod
-    def instantiate_constraints(solver: Solver) -> Iterable[ilpy.LinearConstraint]:
+    def instantiate_constraints(solver: Solver) -> Iterable[ilpy.Constraint]:
         """Add linear constraints to the solver to ensure that these variables
         are coupled to other variables of the solver.
 
@@ -100,7 +100,7 @@ def instantiate_constraints(solver: Solver) -> Iterable[ilpy.LinearConstraint]:
 
         Returns:
 
-            A iterable of :class:`ilpy.LinearConstraint`. See
+            A iterable of :class:`ilpy.Constraint`. See
             :class:`motile.constraints.Constraint` for how to create linear
             constraints.
         """

pyproject.toml

@@ -17,7 +17,7 @@ authors = [
     { name = 'Florian Jug', email = 'florian.jug@fht.org' },
 ]
 dynamic = ["version"]
-dependencies = ['networkx', 'ilpy', 'numpy', 'structsvm']
+dependencies = ['networkx', 'ilpy>=0.3.0', 'numpy', 'structsvm']
 
 [project.optional-dependencies]
 dev = ["pre-commit", "pytest", "pytest-cov", "ruff", "twine", "build"]
@@ -50,6 +50,15 @@ select = [
     "RUF", # ruff specific rules
 ]
 
+# https://docs.pytest.org/en/6.2.x/customize.html
+[tool.pytest.ini_options]
+minversion = "6.0"
+testpaths = ["tests"]
+filterwarnings = [
+    "error:::motile",
+    "ignore:ilpy.*:DeprecationWarning:structsvm",
+]
+
 # https://coverage.readthedocs.io/en/6.4/config.html
 [tool.coverage.report]
 exclude_lines = [
@@ -61,8 +70,8 @@ exclude_lines = [
 
 [tool.mypy]
 files = "motile"
-strict = true                 # feel free to relax this if it's annoying
-allow_untyped_defs = true     # TODO: can eventually fill out typing and remove this
+strict = true             # feel free to relax this if it's annoying
+allow_untyped_defs = true # TODO: can eventually fill out typing and remove this
 # allow_untyped_calls = true    # TODO: can eventually fill out typing and remove this
 disallow_any_generics = false
 ignore_missing_imports = true