[pre-commit.ci] auto fixes from pre-commit hooks

Author: pre-commit-ci[bot]

profiling/gprof2dot

@@ -1367,7 +1367,7 @@ class AXEParser(Parser):
             attrs[name] = value
         return Struct(attrs)
 
-    _cg_header_re = re.compile("^Index |" "^-----+ ")
+    _cg_header_re = re.compile("^Index |^-----+ ")
 
     _cg_footer_re = re.compile(r"^Index\s+Function\s*$")
 

test/test_big_phi_robust.py

@@ -175,17 +175,17 @@ def test_sia_standard_example_has_repertoires(self, s):
         # Check cause repertoire exists and has required attributes
         assert result.cause is not None, "SIA missing cause repertoire"
         assert hasattr(result.cause, "phi"), "Cause RIA missing phi attribute"
-        assert hasattr(
-            result.cause, "mechanism"
-        ), "Cause RIA missing mechanism attribute"
+        assert hasattr(result.cause, "mechanism"), (
+            "Cause RIA missing mechanism attribute"
+        )
         assert hasattr(result.cause, "purview"), "Cause RIA missing purview attribute"
 
         # Check effect repertoire exists and has required attributes
         assert result.effect is not None, "SIA missing effect repertoire"
         assert hasattr(result.effect, "phi"), "Effect RIA missing phi attribute"
-        assert hasattr(
-            result.effect, "mechanism"
-        ), "Effect RIA missing mechanism attribute"
+        assert hasattr(result.effect, "mechanism"), (
+            "Effect RIA missing mechanism attribute"
+        )
         assert hasattr(result.effect, "purview"), "Effect RIA missing purview attribute"
 
     def test_sia_standard_example_has_system_state(self, s):
@@ -242,9 +242,9 @@ def test_sia_standard_example_partition_type(self, s):
 
         # System has phi > 0, so should have non-null partition
         assert result.phi > 0, "Standard example should have phi > 0"
-        assert not isinstance(
-            result.partition, NullCut
-        ), "Irreducible system has NullCut partition"
+        assert not isinstance(result.partition, NullCut), (
+            "Irreducible system has NullCut partition"
+        )
 
     def test_reducible_system_has_null_partition(self, reducible):
         """Reducible system should have null partition.
@@ -254,12 +254,12 @@ def test_reducible_system_has_null_partition(self, reducible):
         """
         result = reducible.sia()
 
-        assert isinstance(
-            result, NullSystemIrreducibilityAnalysis
-        ), "Reducible system should return NullSIA"
-        assert isinstance(
-            result.partition, NullCut
-        ), "Reducible system should have NullCut partition"
+        assert isinstance(result, NullSystemIrreducibilityAnalysis), (
+            "Reducible system should return NullSIA"
+        )
+        assert isinstance(result.partition, NullCut), (
+            "Reducible system should have NullCut partition"
+        )
         assert result.phi == 0.0, "Reducible system should have phi=0"
 
     def test_empty_subsystem_has_null_partition(self, s_empty):
@@ -270,12 +270,12 @@ def test_empty_subsystem_has_null_partition(self, s_empty):
         """
         result = s_empty.sia()
 
-        assert isinstance(
-            result, NullSystemIrreducibilityAnalysis
-        ), "Empty subsystem should return NullSIA"
-        assert isinstance(
-            result.partition, NullCut
-        ), "Empty subsystem should have NullCut partition"
+        assert isinstance(result, NullSystemIrreducibilityAnalysis), (
+            "Empty subsystem should return NullSIA"
+        )
+        assert isinstance(result.partition, NullCut), (
+            "Empty subsystem should have NullCut partition"
+        )
         assert result.phi == 0.0, "Empty subsystem should have phi=0"
 
 

test/test_iit4_robust.py

@@ -195,9 +195,9 @@ def test_phi_structure_has_distinctions_attribute(self, example_name):
         subsystem = EXAMPLES["subsystem"][example_name]()
         result = new_big_phi.phi_structure(subsystem)
 
-        assert hasattr(
-            result, "distinctions"
-        ), f"PhiStructure for '{example_name}' missing 'distinctions' attribute"
+        assert hasattr(result, "distinctions"), (
+            f"PhiStructure for '{example_name}' missing 'distinctions' attribute"
+        )
 
     @pytest.mark.parametrize(
         "example_name",
@@ -227,9 +227,9 @@ def test_phi_structure_has_relations_attribute(self, example_name):
         subsystem = EXAMPLES["subsystem"][example_name]()
         result = new_big_phi.phi_structure(subsystem)
 
-        assert hasattr(
-            result, "relations"
-        ), f"PhiStructure for '{example_name}' missing 'relations' attribute"
+        assert hasattr(result, "relations"), (
+            f"PhiStructure for '{example_name}' missing 'relations' attribute"
+        )
 
     @pytest.mark.parametrize(
         "example_name",
@@ -255,9 +255,9 @@ def test_phi_structure_distinctions_are_non_empty(self, example_name):
         subsystem = EXAMPLES["subsystem"][example_name]()
         result = new_big_phi.phi_structure(subsystem)
 
-        assert hasattr(
-            result, "distinctions"
-        ), "PhiStructure missing distinctions attribute"
+        assert hasattr(result, "distinctions"), (
+            "PhiStructure missing distinctions attribute"
+        )
 
         distinctions = result.distinctions
         assert distinctions is not None, (
@@ -310,9 +310,9 @@ def test_distinctions_have_mechanism_attribute(self):
 
         # Check each distinction has a mechanism
         for i, distinction in enumerate(concepts):
-            assert hasattr(
-                distinction, "mechanism"
-            ), f"Distinction {i} missing 'mechanism' attribute"
+            assert hasattr(distinction, "mechanism"), (
+                f"Distinction {i} missing 'mechanism' attribute"
+            )
 
     def test_distinctions_mechanisms_are_within_subsystem(self):
         """Distinction mechanisms should be subsets of subsystem nodes.

test/test_invariants.py

@@ -156,21 +156,21 @@ def test_sia_partition_attribute_consistency(self, s, micro_s, reducible):
         # Irreducible systems with phi > 0 should have non-null partitions
         s_result = s.sia()
         if s_result.phi > 0:
-            assert not isinstance(
-                s_result.partition, NullCut
-            ), "System with phi > 0 has NullCut partition (should have real partition)"
+            assert not isinstance(s_result.partition, NullCut), (
+                "System with phi > 0 has NullCut partition (should have real partition)"
+            )
 
         micro_result = micro_s.sia()
         if micro_result.phi > 0:
-            assert not isinstance(
-                micro_result.partition, NullCut
-            ), "System with phi > 0 has NullCut partition (should have real partition)"
+            assert not isinstance(micro_result.partition, NullCut), (
+                "System with phi > 0 has NullCut partition (should have real partition)"
+            )
 
         # Reducible system should have null partition
         reducible_result = reducible.sia()
-        assert isinstance(
-            reducible_result.partition, NullCut
-        ), "Reducible system should have NullCut partition"
+        assert isinstance(reducible_result.partition, NullCut), (
+            "Reducible system should have NullCut partition"
+        )
 
     def test_partition_reduces_or_maintains_phi(self, s, micro_s):
         """Partitioned system cannot have more phi than unpartitioned.
@@ -220,9 +220,9 @@ def test_selfloop_phi_depends_on_config(self, noisy_selfloop_single):
         # With config disabled, phi should be 0
         with config.override(SINGLE_MICRO_NODES_WITH_SELFLOOPS_HAVE_PHI=False):
             result_disabled = noisy_selfloop_single.sia()
-            assert (
-                result_disabled.phi == 0.0
-            ), "Expected phi=0 when SINGLE_MICRO_NODES_WITH_SELFLOOPS_HAVE_PHI=False"
+            assert result_disabled.phi == 0.0, (
+                "Expected phi=0 when SINGLE_MICRO_NODES_WITH_SELFLOOPS_HAVE_PHI=False"
+            )
 
         # With config enabled and EMD, phi should be > 0
         with config.override(
@@ -251,9 +251,9 @@ def test_cache_clearing_option(self, s):
             CACHE_REPERTOIRES=True,
         ):
             _ = s.sia()
-            assert (
-                s._repertoire_cache.cache
-            ), "Cache should have entries when clearing is disabled"
+            assert s._repertoire_cache.cache, (
+                "Cache should have entries when clearing is disabled"
+            )
 
         # Test with cache clearing enabled
         with config.override(
@@ -262,9 +262,9 @@ def test_cache_clearing_option(self, s):
             CACHE_REPERTOIRES=True,
         ):
             _ = s.sia()
-            assert (
-                not s._repertoire_cache.cache
-            ), "Cache should be empty when clearing is enabled"
+            assert not s._repertoire_cache.cache, (
+                "Cache should be empty when clearing is enabled"
+            )
 
 
 class TestPhiStructureInvariants:
@@ -291,12 +291,12 @@ def test_phi_structure_has_distinctions(self, example_name):
 
         # Systems that have phi should have distinctions
         if hasattr(result, "phi") and result.phi > 0:
-            assert hasattr(
-                result, "distinctions"
-            ), f"System '{example_name}' has phi > 0 but no distinctions attribute"
-            assert (
-                len(result.distinctions) > 0
-            ), f"System '{example_name}' has phi > 0 but zero distinctions"
+            assert hasattr(result, "distinctions"), (
+                f"System '{example_name}' has phi > 0 but no distinctions attribute"
+            )
+            assert len(result.distinctions) > 0, (
+                f"System '{example_name}' has phi > 0 but zero distinctions"
+            )
 
     @pytest.mark.parametrize("example_name", ["basic", "fig4"])
     def test_phi_structure_has_relations(self, example_name):