merged sd import methods and updated tests

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
@@ -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

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/succession_diagram.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, cast
+from typing import TYPE_CHECKING, Any, Literal, cast
 
 if TYPE_CHECKING:
     from typing import Iterator
@@ -44,7 +44,7 @@ class SuccessionDiagram:
     Examples
     --------
     >>> import balm
-    >>> sd = balm.SuccessionDiagram.from_bnet(\"""
+    >>> sd = balm.SuccessionDiagram.from_rules(\"""
     ...     A, B
     ...     B, A & C
     ...     C, !A | B
@@ -158,25 +158,35 @@ def __len__(self) -> int:
         return self.dag.number_of_nodes()
 
     @staticmethod
-    def from_aeon(model: str) -> SuccessionDiagram:
+    def from_rules(
+        rules: str,
+        format: Literal["bnet", "aeon", "sbml"] = "bnet",
+    ) -> SuccessionDiagram:
         """
-        Read a `BooleanNetwork` from the string contents of an `.aeon` model.
-        """
-        return SuccessionDiagram(BooleanNetwork.from_aeon(model))
+        Generate a succession diagram from the given string.
 
-    @staticmethod
-    def from_bnet(model: str) -> SuccessionDiagram:
-        """
-        Read a `BooleanNetwork` from the string contents of a `.bnet` model.
-        """
-        return SuccessionDiagram(BooleanNetwork.from_bnet(model))
+        Parameters
+        ----------
+        rules : str
+            The string representation of the network rules.
+        format : Literal['bnet', 'aeon', 'sbml']
+            The format of the string. One of `"bnet"`, `"aeon"`, or `"sbml"`.
+            Defaults to `"bnet"`.
 
-    @staticmethod
-    def from_sbml(model: str) -> SuccessionDiagram:
-        """
-        Read a `BooleanNetwork` from the string contents of an `.sbml` model.
+        Returns
+        -------
+        SuccessionDiagram
+            The generated succession diagram. Initially unexpanded.
         """
-        return SuccessionDiagram(BooleanNetwork.from_sbml(model))
+
+        if format == "bnet":
+            return SuccessionDiagram(BooleanNetwork.from_bnet(rules))
+        elif format == "aeon":
+            return SuccessionDiagram(BooleanNetwork.from_aeon(rules))
+        elif format == "sbml":
+            return SuccessionDiagram(BooleanNetwork.from_sbml(rules))
+        else:
+            raise ValueError(f"Unknown format: {format}")
 
     @staticmethod
     def from_file(path: str) -> SuccessionDiagram:
@@ -207,7 +217,7 @@ def expanded_attractor_seeds(self) -> dict[int, list[BooleanSpace]]:
         Example
         -------
         >>> import balm
-        >>> sd = balm.SuccessionDiagram.from_bnet(\"""
+        >>> sd = balm.SuccessionDiagram.from_rules(\"""
         ...     A, B
         ...     B, A & C
         ...     C, !A | B

tests/control_test.py

@@ -101,7 +101,7 @@ def test_basic_succession_finding():
 
 
 def test_internal_succession_control():
-    sd = SuccessionDiagram.from_bnet(
+    sd = SuccessionDiagram.from_rules(
         """
     S, S
     A, S | B
@@ -143,7 +143,7 @@ def test_internal_succession_control():
 
 
 def test_all_succession_control():
-    sd = SuccessionDiagram.from_bnet(
+    sd = SuccessionDiagram.from_rules(
         """
     S, S
     A, S | B
@@ -185,7 +185,7 @@ def test_all_succession_control():
 
 
 def test_forbidden_drivers():
-    sd = SuccessionDiagram.from_bnet(
+    sd = SuccessionDiagram.from_rules(
         """
     A, B & C
     B, A & C
@@ -255,7 +255,7 @@ def test_forbidden_drivers():
 
 
 def test_size_restriction():
-    sd = SuccessionDiagram.from_bnet(
+    sd = SuccessionDiagram.from_rules(
         """
     A, B & C
     B, A & C

tests/drivers_test.py

@@ -1,6 +1,7 @@
-from balm.drivers import find_single_drivers, find_single_node_LDOIs
 from biodivine_aeon import BooleanNetwork
 
+from balm.drivers import find_single_drivers, find_single_node_LDOIs
+
 
 def test_find_single_node_LDOIs():
     bn = BooleanNetwork.from_bnet(

tests/motif_avoidant_test.py

@@ -1,4 +1,4 @@
-from biodivine_aeon import BooleanNetwork, AsynchronousGraph
+from biodivine_aeon import AsynchronousGraph, BooleanNetwork
 
 from balm.motif_avoidant import _filter_candidates  # type: ignore
 from balm.motif_avoidant import _Pint_reachability  # type: ignore

tests/petri_net_translation_test.py

@@ -1,6 +1,6 @@
 # type: ignore
 import pytest
-from biodivine_aeon import BooleanNetwork, RegulatoryGraph
+from biodivine_aeon import BooleanNetwork
 from networkx import DiGraph, is_isomorphic  # type: ignore
 
 from balm.petri_net_translation import (

tests/space_utils_test.py

@@ -1,13 +1,13 @@
-from biodivine_aeon import BooleanNetwork, BooleanExpression, AsynchronousGraph
+from biodivine_aeon import AsynchronousGraph, BooleanExpression, BooleanNetwork
 
 from balm.space_utils import (
     expression_to_space_list,
     is_subspace,
-    percolate_network,
-    percolation_conflicts,
     percolate_expression,
+    percolate_network,
     percolate_space,
     percolate_space_strict,
+    percolation_conflicts,
     space_unique_key,
 )
 

tests/succession_diagram_test.py

@@ -109,8 +109,8 @@ def test_succession_diagram_structure(self):
 
 
 def test_state():
-    sd1 = SuccessionDiagram.from_bnet("A, B\nB, A")
-    sd2 = SuccessionDiagram.from_bnet("A, B\nB, A\nC, C & B")
+    sd1 = SuccessionDiagram.from_rules("A, B\nB, A")
+    sd2 = SuccessionDiagram.from_rules("A, B\nB, A\nC, C & B")
     sd1.build()
     sd2.__setstate__(sd1.__getstate__())
     slots1 = [x + str(sd1.__getattribute__(x)) for x in sd1.__slots__]
@@ -311,7 +311,7 @@ def test_attractor_expansion(network_file: str):
 
 
 def test_attractor_extraction():
-    sd = balm.SuccessionDiagram.from_bnet(
+    sd = balm.SuccessionDiagram.from_rules(
         """
         A, B
         B, A & C

tests/trappist_core_test.py

@@ -1,12 +1,8 @@
-from biodivine_aeon import (
-    BooleanNetwork,
-    FixedPoints,
-    AsynchronousGraph,
-)
+from biodivine_aeon import AsynchronousGraph, BooleanNetwork, FixedPoints
 
+from balm.interaction_graph_utils import cleanup_network
 from balm.petri_net_translation import network_to_petrinet
 from balm.trappist_core import compute_fixed_point_reduced_STG, trappist
-from balm.interaction_graph_utils import cleanup_network
 from balm.types import BooleanSpace