Merge pull request #130 from jcrozum/daemontus/feat/no-autoexpand

Add option to avoid source node auto expansion

Author: daemontus

.github/workflows/test.yml

@@ -22,9 +22,10 @@ jobs:
         python -m pip install flake8 black mypy
         python -m pip install -r requirements.txt
     - name: Lint with Black
-      uses: rickstaa/action-black@v1
+      uses: psf/black@stable
       with:
-        black_args: ". --check --diff"
+        options: "--check --diff"
+        version: "25.1.0" # If you change this, also update requirements-dev.txt
     - name: Check types
       run: |
         mypy biobalm

biobalm/succession_diagram.py

@@ -185,6 +185,7 @@ def default_config() -> SuccessionDiagramConfiguration:
             "attractor_candidates_limit": 100_000,
             "retained_set_optimization_threshold": 1_000,
             "minimum_simulation_budget": 1_000,
+            "auto_expand_source_nodes": True,
         }
 
     @staticmethod
@@ -1545,7 +1546,7 @@ def _expand_one_node(self, node_id: int):
         # The SD created from the restricted Petri net is technically correct, but can
         # propagate some of the input values further and yields a smaller SD.
         source_nodes = []
-        if node_id == self.root():
+        if node_id == self.root() and self.config["auto_expand_source_nodes"]:
             source_nodes = extract_source_variables(self.petri_net)
 
         sub_spaces: list[BooleanSpace]

biobalm/types.py

@@ -229,6 +229,8 @@ class SuccessionDiagramConfiguration(TypedDict):
     intersect negative cycles to find an NFVS subset. Typically,
     for smaller networks, the trade-off is in favor of
     computing a smaller NFVS.
+
+    [Default: 2_000]
     """
 
     pint_goal_size_limit: int
@@ -242,19 +244,25 @@ class SuccessionDiagramConfiguration(TypedDict):
     The default value was empirically tested as safe on Debian linux, but other operating
     systems may need a different limit to stay safe. Nevertheless, this should not be
     an issue on smaller/simpler networks.
+
+    [Default: 8_192]
     """
 
     attractor_candidates_limit: int
     """
     If more than `attractor_candidates_limit` states are produced during the
     attractor detection process, then the process fails with a `RuntimeError`.
     This is mainly to avoid out-of-memory errors or crashing `clingo`.
+
+    [Default: 100_000]
     """
 
     retained_set_optimization_threshold: int
     """
     If there are more than this amount of attractor candidates, the attractor
     detection process will try to optimize the retained set using ASP (if enabled).
+
+    [Default: 1_000]
     """
 
     minimum_simulation_budget: int
@@ -269,4 +277,16 @@ class SuccessionDiagramConfiguration(TypedDict):
     However, this budget only applies when simulation has not been able to make progress
     in the recent round. That is, if simulation has actively eliminated some candidates in
     the recent round, it will still continue regardless of the budget limit.
+
+    [Default: 1_000]
+    """
+
+    auto_expand_source_nodes: bool
+    """
+    When `biobalm` detects that the network has source nodes, it expands them all simultaneously,
+    instead of expanding them one by one. This is useful for networks with many source nodes,
+    because it produces a much smaller succession diagram without losing any "interesting" behavior.
+    However, this setting needs to be disabled if only specific source nodes are to be expanded.
+
+    [Default: True]
     """

example/attractors.py

@@ -18,12 +18,12 @@
 # Prepare a config which will print progress.
 config = SuccessionDiagram.default_config()
 config["debug"] = True  # Print progress.
-config[
-    "max_motifs_per_node"
-] = 1_000_000  # Maximum number of outgoing edges for each node.
-config[
-    "attractor_candidates_limit"
-] = 100_000  # Maximum number of enumerated attractor candidates.
+config["max_motifs_per_node"] = (
+    1_000_000  # Maximum number of outgoing edges for each node.
+)
+config["attractor_candidates_limit"] = (
+    100_000  # Maximum number of enumerated attractor candidates.
+)
 
 sd = SuccessionDiagram(bn, config)
 

pyproject.toml

@@ -6,7 +6,7 @@ readme = "README.md"
 license = { file = "LICENSE" }
 requires-python = ">=3.11"
 dependencies = [
-    'biodivine_aeon >=1.0.1',
+    'biodivine_aeon >=1.2.5',
     'clingo >=5.6.2',
     'networkx >=2.8.8',    
 ]

requirements-dev.txt

@@ -7,8 +7,8 @@ astroid==3.1.0
 autodocsumm==0.2.12
 Babel==2.14.0
 beautifulsoup4==4.12.3
-biodivine_aeon==1.0.0a8
-black==24.2.0
+biodivine_aeon==1.2.5
+black==25.1.0
 boolean.py==4.0
 CacheControl==0.14.0
 certifi==2024.2.2

requirements.txt

@@ -1,4 +1,4 @@
-biodivine_aeon>=1.0.0
+biodivine_aeon>=1.2.5
 clingo==5.6.2
 networkx==2.8.8
 pypint[pint]==1.6.2

tests/succession_diagram_test.py

@@ -418,3 +418,23 @@ def test_attractor_extraction():
     sd.build()
     eas = sd.expanded_attractor_seeds()
     assert eas == {1: [{"A": 0, "B": 0, "C": 1}], 2: [{"A": 1, "B": 1, "C": 1}]}
+
+
+def test_source_auto_expand():
+    net = """
+        A, A
+        B, B
+        """
+    cfg = biobalm.SuccessionDiagram.default_config()
+    cfg["auto_expand_source_nodes"] = False
+    sd = biobalm.SuccessionDiagram.from_rules(net, config=cfg)
+    sd.expand_dfs()
+    # root, A fixed, B fixed, A+B fixed
+    assert len(sd) == (1 + 2 + 2 + 4)
+
+    cfg = biobalm.SuccessionDiagram.default_config()
+    cfg["auto_expand_source_nodes"] = True
+    sd = biobalm.SuccessionDiagram.from_rules(net, config=cfg)
+    sd.expand_dfs()
+    # root, A+B fixed
+    assert len(sd) == (1 + 4)