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jcrozum · Jun 4, 2024 · 047d448 · 047d448 · github-actions · Jun 4, 2024
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commit 047d448
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Showing 3 changed files with 16 additions and 4 deletions.
diff --git a/biobalm/_sd_algorithms/expand_source_blocks.py b/biobalm/_sd_algorithms/expand_source_blocks.py
@@ -169,7 +169,7 @@ def expand_source_blocks(
                 # can be either in this node, or in any of the child nodes. If a clean block
                 # is found, we know that it is safe to expand it without "missing" any MAAs.
                 clean_block_found = False
-                for (block, block_nodes) in minimal_blocks:
+                for block, block_nodes in minimal_blocks:
                     block_sd = sd.component_subdiagram(list(block), node)
 
                     # The succession diagram "restricted" to the considered block should have
@@ -190,7 +190,9 @@ def expand_source_blocks(
                     )
                     if len(block_sd_candidates) == 0:
                         if sd.config["debug"]:
-                            print(f" > [{node}] Found clean block with no MAAs ({len(block_nodes)}): {block_nodes}")
+                            print(
+                                f" > [{node}] Found clean block with no MAAs ({len(block_nodes)}): {block_nodes}"
+                            )
                         clean_block_found = True
                         next_level = next_level | set(block_nodes)
                         sd.node_data(node)["attractor_seeds"] = []
@@ -204,7 +206,9 @@ def expand_source_blocks(
                 if not clean_block_found:
                     # If all blocks have MAAs, we expand all successors.
                     if sd.config["debug"]:
-                        print(f" > [{node}] No clean block found. Expanding all {len(successors)} successors.")
+                        print(
+                            f" > [{node}] No clean block found. Expanding all {len(successors)} successors."
+                        )
                     next_level = next_level | set(successors)
 
         current_level = next_level

diff --git a/tests/source_SCC_test.py b/tests/source_SCC_test.py
@@ -3,6 +3,7 @@
 from biobalm import SuccessionDiagram
 from biobalm._sd_algorithms.expand_source_SCCs import expand_source_SCCs
 
+
 def expansion(bn: BooleanNetwork):
     sd = SuccessionDiagram(bn)
     fully_expanded = expand_source_SCCs(sd, check_maa=False)

diff --git a/tests/source_block_test.py b/tests/source_block_test.py
@@ -2,12 +2,19 @@
 
 from biobalm import SuccessionDiagram
 
+
 def expansion(bn: BooleanNetwork):
     sd = SuccessionDiagram(bn)
     fully_expanded = sd.expand_block(find_motif_avoidant_attractors=False)
     assert fully_expanded
 
-    return bn.variable_count(), len(sd), len(list(sd.expanded_ids())), sd.depth(), len(sd.minimal_trap_spaces())
+    return (
+        bn.variable_count(),
+        len(sd),
+        len(list(sd.expanded_ids())),
+        sd.depth(),
+        len(sd.minimal_trap_spaces()),
+    )
 
 
 def test_expansion():
File	Stmts	Miss	Cover	Missing
biobalm
_pint_reachability.py	61	50	18%	24, 40–54, 69–93, 101–146
control.py	114	14	88%	107, 119, 125, 129, 134, 143–159, 477, 480, 493
interaction_graph_utils.py	52	6	88%	11–13, 151–152, 206–207
petri_net_translation.py	149	11	93%	22–26, 79, 136, 308–309, 333–334, 343, 452
space_utils.py	132	20	85%	26–28, 104–110, 133–139, 347–350, 414, 462
succession_diagram.py	379	65	83%	6, 120, 210–215, 228, 275–282, 386–393, 410–411, 421, 427, 543, 630–636, 752, 755, 873–891, 923, 933, 936, 976, 983, 1034, 1048, 1170, 1329, 1340, 1348, 1376, 1391, 1403, 1408, 1414
symbolic_utils.py	32	5	84%	10, 39–44, 100, 128
trappist_core.py	184	27	85%	14–18, 55, 57, 92, 215, 217, 219, 247–250, 254–256, 276–282, 340, 342, 372, 420, 422
biobalm/_sd_algorithms
expand_attractor_seeds.py	60	7	88%	6, 28, 42, 109–114, 119
expand_bfs.py	28	1	96%	6
expand_dfs.py	30	1	97%	6
expand_minimal_spaces.py	37	2	95%	6, 31
expand_source_SCCs.py	111	16	86%	11–13, 50, 69, 77, 82, 103, 112, 120, 131, 140, 143, 167, 179, 242–243
expand_source_blocks.py	108	13	88%	11, 26, 41, 49, 54, 78, 128, 154, 163, 193, 203, 209, 218
expand_to_target.py	31	3	90%	6, 38, 43
biobalm/_sd_attractors
attractor_candidates.py	265	90	66%	13–15, 26–27, 93, 101, 107–108, 130, 152, 187, 193–204, 223, 239–320, 325, 329, 335, 341, 356, 383, 388, 392, 398, 400–438, 511, 582–583, 684
attractor_symbolic.py	114	16	86%	6–7, 75, 88–92, 103, 112, 144, 179, 191–193, 202, 230, 236
TOTAL	1974	347	82%