[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"
 
 
@@ -419,14 +419,18 @@ def _noisy_copy_subsystem(p, state):
         Each node copies the other with probability p (LOLI state ordering).
         """
         import numpy as np
-        from pyphi import Network, Subsystem
-
-        tpm = np.array([
-            [1 - p, 1 - p],  # (0,0)
-            [1 - p, p],      # (1,0)
-            [p, 1 - p],      # (0,1)
-            [p, p],          # (1,1)
-        ])
+
+        from pyphi import Network
+        from pyphi import Subsystem
+
+        tpm = np.array(
+            [
+                [1 - p, 1 - p],  # (0,0)
+                [1 - p, p],  # (1,0)
+                [p, 1 - p],  # (0,1)
+                [p, p],  # (1,1)
+            ]
+        )
         cm = np.array([[0, 1], [1, 0]])
         network = Network(tpm, cm=cm, node_labels=["A", "B"])
         return Subsystem(network, state)
@@ -438,7 +442,8 @@ def test_phi_capped_by_ii(self):
         so ii(s) ≈ 0.644 caps phi below GID(MIP).
         """
         from pyphi.direction import Direction
-        from pyphi.new_big_phi import sia, system_intrinsic_information
+        from pyphi.new_big_phi import sia
+        from pyphi.new_big_phi import system_intrinsic_information
 
         subsystem = self._noisy_copy_subsystem(0.8, (1, 1))
         with config.override(**self.II_CONFIG):
@@ -494,9 +499,7 @@ def test_gid_distance_unaffected(self, s):
 
         # Default config uses GENERALIZED_INTRINSIC_DIFFERENCE
         result = sia(s)
-        assert float(result.phi) == pytest.approx(
-            EXPECTED_PHI_VALUES["s"], abs=1e-9
-        )
+        assert float(result.phi) == pytest.approx(EXPECTED_PHI_VALUES["s"], abs=1e-9)
 
 
 # ============================================================================
@@ -522,7 +525,9 @@ class TestPaperExamples:
     def _monad_subsystem(p):
         """Single-node system that stays in current state with probability p."""
         import numpy as np
-        from pyphi import Network, Subsystem
+
+        from pyphi import Network
+        from pyphi import Subsystem
 
         tpm = np.array([[1 - p], [p]])
         cm = np.array([[1]])
@@ -536,6 +541,7 @@ def test_monad_intrinsic_information(self):
         The paper reports φ_s = 0.427 (Figure 2C).
         """
         import numpy as np
+
         from pyphi.new_big_phi import system_intrinsic_information
 
         p = 0.744
@@ -557,17 +563,17 @@ def test_monad_intrinsic_information(self):
         "p,i_diff_expected,i_spec_expected",
         [
             (0.744, 0.426625, 0.426591),  # crossover point (Figure 2C)
-            (0.9, 0.152003, 0.763197),    # high determinism
-            (0.6, 0.736966, 0.157821),    # high noise
+            (0.9, 0.152003, 0.763197),  # high determinism
+            (0.6, 0.736966, 0.157821),  # high noise
         ],
     )
     def test_monad_i_diff_i_spec_tradeoff(self, p, i_diff_expected, i_spec_expected):
         """Verify i_diff and i_spec values across the tradeoff curve (Figure 2C).
 
         i_diff = -log2(p), i_spec = p*log2(2p) for a monad in its ON state.
         """
-        import numpy as np
-        from pyphi import direction, metrics
+        from pyphi import direction
+        from pyphi import metrics
         from pyphi.new_big_phi import system_intrinsic_information
 
         subsystem = self._monad_subsystem(p)

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

@@ -158,21 +158,21 @@ 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.
@@ -222,9 +222,9 @@ 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(
@@ -253,9 +253,9 @@ 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(
@@ -264,9 +264,9 @@ 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:
@@ -293,12 +293,12 @@ 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):