Succession api and docs

balm/_sd_algorithms/compute_attractor_seeds.py

@@ -30,7 +30,7 @@ def compute_attractor_seeds(
     if balm.succession_diagram.DEBUG:
         print(f"[{node_id}] Start computing attractor seeds.")
 
-    node_space = sd.node_space(node_id)
+    node_space = sd.node_data(node_id)["space"]
 
     if len(node_space) == sd.network.variable_count():
         # This node is a fixed-point.
@@ -39,8 +39,8 @@ def compute_attractor_seeds(
     # Compute the list of child spaces if the node is expanded. Otherwise
     # "pretend" that there are no children.
     child_spaces = []
-    if sd.node_is_expanded(node_id):
-        child_spaces = [sd.node_space(s) for s in sd.node_successors(node_id)]
+    if sd.node_data(node_id)["expanded"]:
+        child_spaces = [sd.node_data(s)["space"] for s in sd.node_successors(node_id)]
 
     # Fix everything in the NFVS to zero, as long as
     # it isn't already fixed by our `node_space`.

balm/_sd_algorithms/expand_attractor_seeds.py

@@ -47,7 +47,7 @@ def expand_attractor_seeds(sd: SuccessionDiagram, size_limit: int | None = None)
 
         # Retrieve the stable motifs of children that are already expanded.
         expanded_children = [
-            x for x in sd.node_successors(node) if sd.node_is_expanded(x)
+            x for x in sd.node_successors(node) if sd.node_data(x)["expanded"]
         ]
         expanded_motifs = [
             sd.edge_stable_motif(node, child) for child in expanded_children
@@ -61,15 +61,15 @@ def expand_attractor_seeds(sd: SuccessionDiagram, size_limit: int | None = None)
                 # and continue to the next one.
                 successors.pop()
                 continue
-            if sd.node_is_expanded(successors[-1]):
+            if sd.node_data(successors[-1])["expanded"]:
                 # The next node to explore is expanded (by some previous procedure)
                 # but not "seen" in this search yet. We need to visit this node
                 # regardless of other conditions
                 break
             # Now, we need to asses if the next successor has some candidate states which
             # are not covered by the already expanded children.
 
-            successor_space = sd.node_space(successors[-1])
+            successor_space = sd.node_data(successors[-1])["space"]
             retained_set = make_retained_set(
                 sd.symbolic, sd.node_nfvs(node), successor_space
             )

balm/_sd_algorithms/expand_minimal_spaces.py

@@ -34,7 +34,7 @@ def expand_minimal_spaces(sd: SuccessionDiagram, size_limit: int | None = None)
             successors = sorted(successors, reverse=True)  # For determinism!
             # (reversed because we explore the list from the back)
 
-        node_space = sd.node_space(node)
+        node_space = sd.node_data(node)["space"]
 
         # Remove all immediate successors that are already visited or those who
         # do not cover any new minimal trap space.
@@ -52,7 +52,7 @@ def expand_minimal_spaces(sd: SuccessionDiagram, size_limit: int | None = None)
         # of this node is already in the succession diagram.
         if len(successors) == 0:
             if sd.node_is_minimal(node):
-                minimal_traps.remove(sd.node_space(node))
+                minimal_traps.remove(sd.node_data(node)["space"])
             continue
 
         # At this point, we know that `s` is not visited and it contains

balm/_sd_algorithms/expand_to_target.py

@@ -25,7 +25,7 @@ def expand_to_target(
 
     while len(current_level) > 0:
         for node in current_level:
-            node_space = sd.node_space(node)
+            node_space = sd.node_data(node)["space"]
 
             if intersect(node_space, target) is None:
                 # If `node_space` does not intersect with `target`, it is not relevant

balm/control.py

@@ -58,7 +58,7 @@ def __init__(
         Example
         -------
         >>> import balm
-        >>> sd = balm.SuccessionDiagram.from_bnet(
+        >>> sd = balm.SuccessionDiagram.from_rules(
         ...     \"\"\"
         ...     A, B & C
         ...     B, A & C
@@ -87,7 +87,7 @@ def __init__(
         self._control: list[ControlOverrides] = []
         for c in control:
             cs = sorted(map(lambda x: sorted(x.items()), c))
-            self._control.append(list(map(dict, cs)))
+            self._control.append(list(map(dict, cs)))  # type: ignore
 
         self._strategy = strategy
         self._succession = succession
@@ -198,7 +198,7 @@ def succession_control(
     -------
     >>> import balm
     >>> from balm.control import succession_control
-    >>> sd = balm.SuccessionDiagram.from_bnet(
+    >>> sd = balm.SuccessionDiagram.from_rules(
     ...     \"\"\"
     ...     S, S
     ...     A, S | B
@@ -237,7 +237,7 @@ def succession_control(
     -------
     >>> import balm
     >>> from balm.control import succession_control
-    >>> sd = balm.SuccessionDiagram.from_bnet(
+    >>> sd = balm.SuccessionDiagram.from_rules(
     ...         \"\"\"
     ...     S, S
     ...     A, S | B
@@ -335,7 +335,7 @@ def successions_to_target(
         )
 
     for s in succession_diagram.node_ids():
-        fixed_vars = succession_diagram.node_space(s)
+        fixed_vars = succession_diagram.node_data(s)["space"]
         if not is_subspace(fixed_vars, target):
             continue
 

balm/drivers.py

@@ -40,7 +40,7 @@ def find_single_node_LDOIs(
     Example
     _______
     >>> import balm
-    >>> sd = balm.SuccessionDiagram.from_bnet('A, A\\nB, A')
+    >>> sd = balm.SuccessionDiagram.from_rules('A, A\\nB, A')
     >>> ldois = balm.drivers.find_single_node_LDOIs(sd.network)
     >>> for k in sorted(ldois):
     ...     print(f'{k} ==> {sorted(ldois[k].items())}')
@@ -107,7 +107,7 @@ def find_single_drivers(
     Example
     -------
     >>> import balm
-    >>> sd = balm.SuccessionDiagram.from_bnet('A, A\\nB, A')
+    >>> sd = balm.SuccessionDiagram.from_rules('A, A\\nB, A')
     >>> drivers = balm.drivers.find_single_drivers({'B': 0}, sd.network)
     >>> sorted(list(drivers))
     [('A', 0), ('B', 0)]

balm/interaction_graph_utils.py

@@ -96,7 +96,7 @@ def feedback_vertex_set(
     --------
     >>> import balm
     >>> from balm.interaction_graph_utils import feedback_vertex_set
-    >>> sd = balm.SuccessionDiagram.from_bnet(\"\"\"
+    >>> sd = balm.SuccessionDiagram.from_rules(\"\"\"
     ...     A, B
     ...     B, A
     ...     C, D

balm/motif_avoidant.py

@@ -1,5 +1,5 @@
 """
-    A module responsible for detecting motif-avoidant attractors within terminal restriction space.
+A module responsible for detecting motif-avoidant attractors within terminal restriction space.
 """
 
 from __future__ import annotations
@@ -103,13 +103,16 @@ def detect_motif_avoidant_attractors(
     """
     Compute a sub-list of `candidates` which correspond to motif-avoidant
     attractors. Other method inputs:
-     - `graph` and `petri_net` represent the model in which the property
-       should be checked.
-     - `terminal_restriction_space` is a symbolic set of states which contains
-       all motif avoidant attractors (i.e. if a candidate state can leave this
-       set, the candidate cannot be an attractor).
-     - `max_iterations` specifies how much time should be spent on the "simpler"
-       preprocessing before applying a more complete method.
+
+    `graph` and `petri_net` represent the model in which the property
+    should be checked.
+
+    `terminal_restriction_space` is a symbolic set of states which contains
+    all motif avoidant attractors (i.e. if a candidate state can leave this
+    set, the candidate cannot be an attractor).
+
+    `max_iterations` specifies how much time should be spent on the "simpler"
+    preprocessing before applying a more complete method.
     """
     if ensure_subspace is None:
         ensure_subspace = {}