Fix typing

.github/workflows/build_and_test.yml

@@ -91,7 +91,7 @@ jobs:
         pip install .[tests]
         cd tests
     - name: Run mypy
-      run: mypy -p qermit --warn-unused-ignores
+      run: mypy -p qermit tests --warn-unused-ignores
     - name: Linting check
       run: ruff check
     - name: Format check

tests/ccl_test.py

@@ -12,24 +12,24 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-import numpy as np  # type: ignore
+import numpy as np
 from pytket import Circuit, OpType, Qubit
-from pytket.extensions.qiskit import AerBackend  # type: ignore
-from pytket.pauli import Pauli, QubitPauliString  # type: ignore
-from pytket.predicates import CliffordCircuitPredicate  # type: ignore
+from pytket.extensions.qiskit import AerBackend
+from pytket.pauli import Pauli, QubitPauliString
+from pytket.predicates import CliffordCircuitPredicate
 from pytket.utils import QubitPauliOperator
 
-from qermit import (  # type: ignore
+from qermit import (
     AnsatzCircuit,
     MitEx,
     ObservableExperiment,
     ObservableTracker,
     SymbolsDict,
 )
-from qermit.clifford_noise_characterisation import (  # type: ignore
+from qermit.clifford_noise_characterisation import (
     gen_CDR_MitEx,
 )
-from qermit.clifford_noise_characterisation.ccl import (  # type: ignore
+from qermit.clifford_noise_characterisation.ccl import (
     ccl_likelihood_filtering_task_gen,
     ccl_result_batching_task_gen,
     ccl_state_task_gen,

tests/cdr_test.py

@@ -15,13 +15,13 @@
 
 from typing import cast
 
-import numpy as np  # type: ignore
+import numpy as np
 from pytket import Qubit
-from pytket.extensions.qiskit import AerBackend  # type: ignore
-from pytket.pauli import Pauli, QubitPauliString  # type: ignore
+from pytket.extensions.qiskit import AerBackend
+from pytket.pauli import Pauli, QubitPauliString
 from pytket.utils import QubitPauliOperator
 
-from qermit.clifford_noise_characterisation.cdr_post import (  # type: ignore
+from qermit.clifford_noise_characterisation.cdr_post import (
     _PolyCDRCorrect,
     cdr_calibration_task_gen,
     cdr_correction_task_gen,

tests/dfsc_test.py

@@ -16,31 +16,31 @@
 import copy
 
 from pytket import Circuit, Qubit
-from pytket.circuit import fresh_symbol  # type: ignore
-from pytket.extensions.qiskit import AerBackend  # type: ignore
-from pytket.pauli import Pauli, QubitPauliString  # type: ignore
-from pytket.transform import Transform  # type: ignore
+from pytket.circuit import fresh_symbol
+from pytket.extensions.qiskit import AerBackend
+from pytket.pauli import Pauli, QubitPauliString
+from pytket.transform import Transform
 from pytket.utils import QubitPauliOperator
 
-from qermit import (  # type: ignore
+from qermit import (
     MeasurementCircuit,
     MitEx,
     ObservableExperiment,
     ObservableTracker,
     SymbolsDict,
 )
-from qermit.clifford_noise_characterisation import (  # type: ignore
+from qermit.clifford_noise_characterisation import (
     gen_DFSC_MitEx,
 )
-from qermit.clifford_noise_characterisation.dfsc import (  # type: ignore
+from qermit.clifford_noise_characterisation.dfsc import (
     DFSC_characterisation_task_gen,
     DFSC_circuit_task_gen,
     DFSC_collater_task_gen,
     DFSC_correction_task_gen,
     get_clifford_mcs,
     preparation_circuit_for_partition,
 )
-from qermit.taskgraph.mitex import get_basic_measurement_circuit  # type: ignore
+from qermit.taskgraph.mitex import get_basic_measurement_circuit
 
 sym_0 = fresh_symbol("alpha")
 sym_1 = fresh_symbol("beta")

tests/frame_randomisation_test.py

@@ -14,13 +14,13 @@
 
 
 from pytket import Circuit
-from pytket.extensions.qiskit import AerBackend  # type: ignore
+from pytket.extensions.qiskit import AerBackend
 
-from qermit.frame_randomisation import (  # type: ignore
+from qermit.frame_randomisation import (
     FrameRandomisation,
     gen_Frame_Randomisation_MitRes,
 )
-from qermit.frame_randomisation.frame_randomisation import (  # type: ignore
+from qermit.frame_randomisation.frame_randomisation import (
     frame_randomisation_circuits_task_gen,
 )
 

tests/full_spam_test.py

@@ -13,14 +13,14 @@
 # limitations under the License.
 
 
-import numpy as np  # type: ignore
+import numpy as np
 from pytket import Bit, Circuit, Qubit
-from pytket.extensions.qiskit import AerBackend  # type: ignore
+from pytket.extensions.qiskit import AerBackend
 
-from qermit.spam import (  # type: ignore
+from qermit.spam import (
     CorrectionMethod,
 )
-from qermit.spam.full_spam_correction import (  # type: ignore
+from qermit.spam.full_spam_correction import (
     gen_full_tomography_spam_characterisation_task,
     gen_full_tomography_spam_circuits_task,
     gen_full_tomography_spam_correction_task,

tests/measurement_reduction_test.py

@@ -14,20 +14,20 @@
 
 
 from pytket import Bit, Circuit, Qubit
-from pytket.extensions.qiskit import AerBackend  # type: ignore
-from pytket.partition import (  # type: ignore
+from pytket.extensions.qiskit import AerBackend
+from pytket.partition import (
     GraphColourMethod,
     PauliPartitionStrat,
 )
-from pytket.pauli import Pauli, QubitPauliString  # type: ignore
-from pytket.transform import CXConfigType  # type: ignore
+from pytket.pauli import Pauli, QubitPauliString
+from pytket.transform import CXConfigType
 from pytket.utils import QubitPauliOperator
 
-from qermit import (  # type: ignore
+from qermit import (
     ObservableTracker,
     SymbolsDict,
 )
-from qermit.taskgraph.measurement_reduction import (  # type: ignore
+from qermit.taskgraph.measurement_reduction import (
     gen_MeasurementReduction_MitEx,
     measurement_reduction_task_gen,
 )

tests/mitex_test.py

@@ -16,20 +16,20 @@
 import copy
 
 import pytest
-from pytket.circuit import Circuit, OpType, Qubit, fresh_symbol  # type: ignore
-from pytket.extensions.qiskit import AerBackend  # type: ignore
-from pytket.pauli import Pauli, QubitPauliString  # type: ignore
+from pytket.circuit import Circuit, OpType, Qubit, fresh_symbol
+from pytket.extensions.qiskit import AerBackend
+from pytket.pauli import Pauli, QubitPauliString
 from pytket.utils import QubitPauliOperator
 
-from qermit import (  # type: ignore
+from qermit import (
     AnsatzCircuit,
     CircuitShots,
     MitEx,
     ObservableExperiment,
     ObservableTracker,
     SymbolsDict,
 )
-from qermit.taskgraph.mitex import (  # type: ignore
+from qermit.taskgraph.mitex import (
     collate_circuit_shots_task_gen,
     filter_observable_tracker_task_gen,
     gen_compiled_shot_split_MitRes,

tests/mitres_test.py

@@ -14,13 +14,13 @@
 
 
 from pytket import Circuit
-from pytket.extensions.qiskit import AerBackend  # type: ignore
+from pytket.extensions.qiskit import AerBackend
 
-from qermit import (  # type: ignore
+from qermit import (
     CircuitShots,
     MitRes,
 )
-from qermit.taskgraph.mitres import (  # type: ignore
+from qermit.taskgraph.mitres import (
     backend_handle_task_gen,
     backend_res_task_gen,
     gen_shot_split_MitRes,

tests/noise_model_test.py

@@ -57,7 +57,7 @@ def test_to_ptm() -> None:
 
 def test_from_ptm() -> None:
     # Test that the error distribution to and from ptm is the same as the initial
-    distribution = {
+    distribution: dict[tuple[Pauli, ...], float] = {
         (Pauli.X, Pauli.X): 0.1,
         (Pauli.Y, Pauli.Z): 0.2,
         (Pauli.Z, Pauli.X): 0.3,
@@ -150,7 +150,7 @@ def test_qermit_pauli_commute_coeff() -> None:
 def test_noise_model_logical_error_propagation() -> None:
     pytket_ciruit = Circuit(2).H(0).CX(0, 1).measure_all()
 
-    error_distribution_dict = {
+    error_distribution_dict: dict[tuple[Pauli, ...], float] = {
         (Pauli.X, Pauli.I): 0.1,
     }
     error_distribution = ErrorDistribution(
@@ -163,23 +163,23 @@ def test_noise_model_logical_error_propagation() -> None:
         pytket_ciruit, n_rand=10000
     )
 
-    ideal_error = QubitPauliString(map={Qubit(0): Pauli.Z, Qubit(1): Pauli.X})
-    assert list(logical_distribution.distribution.keys()) == [ideal_error]
-    assert abs(logical_distribution.distribution[ideal_error] - 0.1) <= 0.01
+    ideal_error_one = QubitPauliString(map={Qubit(0): Pauli.Z, Qubit(1): Pauli.X})
+    assert list(logical_distribution.distribution.keys()) == [ideal_error_one]
+    assert abs(logical_distribution.distribution[ideal_error_one] - 0.1) <= 0.01
 
-    logical_distribution = noise_model.counter_propagate(
+    error_counter = noise_model.counter_propagate(
         pytket_ciruit, n_counts=10000, direction=Direction.forward
     )
-    ideal_error = QermitPauli.from_qubit_pauli_string(
+    ideal_error_two = QermitPauli.from_qubit_pauli_string(
         QubitPauliString(map={Qubit(0): Pauli.X, Qubit(1): Pauli.I})
     )
-    assert list(logical_distribution.keys()) == [ideal_error]
-    assert abs(logical_distribution[ideal_error] - 1000) <= 1
+    assert list(error_counter.keys()) == [ideal_error_two]
+    assert abs(error_counter[ideal_error_two] - 1000) <= 1
 
 
 def test_error_distribution_utilities(tmp_path_factory) -> None:
     # Test that the probabilities must be less than 1.
-    error_distribution_dict = {(Pauli.X, Pauli.I): 1.1}
+    error_distribution_dict: dict[tuple[Pauli, ...], float] = {(Pauli.X, Pauli.I): 1.1}
     with pytest.raises(Exception):
         error_distribution = ErrorDistribution(
             distribution=error_distribution_dict,
@@ -290,12 +290,12 @@ def test_error_distribution_post_select() -> None:
 
 
 def test_to_dict(tmpdir_factory) -> None:
-    error_distribution_dict_zzmax = {}
+    error_distribution_dict_zzmax: dict[tuple[Pauli, ...], float] = {}
     error_distribution_dict_zzmax[(Pauli.X, Pauli.I)] = 0.0002
     error_distribution_dict_zzmax[(Pauli.I, Pauli.X)] = 0.0002
     error_distribution_dict_zzmax[(Pauli.I, Pauli.I)] = 0.9996
 
-    error_distribution_dict_cz = {}
+    error_distribution_dict_cz: dict[tuple[Pauli, ...], float] = {}
     error_distribution_dict_cz[(Pauli.Z, Pauli.Z)] = 0.002
     error_distribution_dict_cz[(Pauli.I, Pauli.Z)] = 0.002
     error_distribution_dict_cz[(Pauli.I, Pauli.I)] = 0.996
@@ -339,7 +339,7 @@ def test_transpiler_backend() -> None:
         circuit.ZZMax(0, 1).ZZMax(1, 2)
     circuit.measure_all()
 
-    error_distribution_dict = {}
+    error_distribution_dict: dict[tuple[Pauli, ...], float] = {}
     error_distribution_dict[(Pauli.X, Pauli.I)] = 0.002
     error_distribution_dict[(Pauli.I, Pauli.X)] = 0.002
 
@@ -363,14 +363,13 @@ def test_transpiler_backend() -> None:
 
 def test_pauli_error_transpile() -> None:
     error_distribution_dict = {
-        error: 0 for error in product([Pauli.I, Pauli.X, Pauli.Y, Pauli.Z], repeat=2)
+        error: 0.0 for error in product([Pauli.I, Pauli.X, Pauli.Y, Pauli.Z], repeat=2)
     }
 
     error_rate = 0.5
     error_distribution_dict[(Pauli.X, Pauli.I)] = error_rate
     error_distribution_dict[(Pauli.I, Pauli.X)] = error_rate
     error_distribution_dict[(Pauli.I, Pauli.I)] = 1 - 2 * error_rate
-    # error_distribution_dict[(Pauli.I, Pauli.I)] = 1 - 2*error_rate
 
     error_distribution = ErrorDistribution(
         error_distribution_dict, rng=np.random.default_rng(seed=2)
@@ -389,7 +388,7 @@ def test_pauli_error_transpile() -> None:
 def test_noise_model() -> None:
     mp.set_start_method("spawn", force=True)
 
-    error_distribution_dict = {}
+    error_distribution_dict: dict[tuple[Pauli, ...], float] = {}
     error_rate = 0.5
     error_distribution_dict[(Pauli.X, Pauli.I)] = error_rate
     error_distribution_dict[(Pauli.I, Pauli.X)] = error_rate
@@ -454,7 +453,7 @@ def test_back_propagate_random_error() -> None:
     qubit_list = cliff_circ.qubits
 
     error_rate = 0.5
-    error_distribution_dict = {}
+    error_distribution_dict: dict[tuple[Pauli, ...], float] = {}
     error_distribution_dict[(Pauli.X, Pauli.I)] = error_rate
     error_distribution_dict[(Pauli.I, Pauli.X)] = error_rate
     error_distribution_dict[(Pauli.I, Pauli.I)] = 1 - 2 * error_rate
@@ -483,7 +482,7 @@ def test_effective_error_distribution() -> None:
     qubits = cliff_circ.qubits
 
     error_rate = 0.5
-    error_distribution_dict = {}
+    error_distribution_dict: dict[tuple[Pauli, ...], float] = {}
     error_distribution_dict[(Pauli.X, Pauli.I)] = error_rate
     error_distribution_dict[(Pauli.I, Pauli.X)] = error_rate
 
@@ -493,13 +492,13 @@ def test_effective_error_distribution() -> None:
     )
     noise_model = NoiseModel({OpType.CZ: error_distribution})
 
-    error_distribution = noise_model.get_effective_pre_error_distribution(
+    logical_error_distribution = noise_model.get_effective_pre_error_distribution(
         cliff_circ, n_rand=10000
     )
 
     assert all(
         abs(count - 2500) < 100
-        for count in error_distribution.pauli_error_counter.values()
+        for count in logical_error_distribution.pauli_error_counter.values()
     )
 
     cliff_circ = Circuit()

tests/pec_test.py

@@ -18,24 +18,24 @@
 import pytest
 from pytket import Circuit, OpType, Qubit
 from pytket.extensions.qiskit import (
-    AerBackend,  # type: ignore
-    IBMQEmulatorBackend,  # type: ignore
+    AerBackend,
+    IBMQEmulatorBackend,
 )
-from pytket.pauli import Pauli, QubitPauliString  # type: ignore
-from pytket.predicates import CliffordCircuitPredicate, GateSetPredicate  # type: ignore
+from pytket.pauli import Pauli, QubitPauliString
+from pytket.predicates import CliffordCircuitPredicate, GateSetPredicate
 from pytket.utils import QubitPauliOperator
-from qiskit_ibm_provider import IBMProvider
+from qiskit_ibm_provider import IBMProvider  # type: ignore
 
-from qermit import (  # type: ignore
+from qermit import (
     AnsatzCircuit,
     ObservableExperiment,
     ObservableTracker,
     SymbolsDict,
 )
-from qermit.probabilistic_error_cancellation import (  # type: ignore
+from qermit.probabilistic_error_cancellation import (
     gen_PEC_learning_based_MitEx,
 )
-from qermit.probabilistic_error_cancellation.pec_learning_based import (  # type: ignore
+from qermit.probabilistic_error_cancellation.pec_learning_based import (
     collate_results_task_gen,
     gen_get_clifford_training_set,
     gen_get_noisy_circuits,

tests/spam_methods_test.py

@@ -14,13 +14,13 @@
 
 
 from pytket import Circuit, Qubit
-from pytket.architecture import Architecture  # type: ignore
-from pytket.circuit import Node  # type: ignore
-from pytket.extensions.qiskit import AerBackend  # type: ignore
+from pytket.architecture import Architecture
+from pytket.circuit import Node
+from pytket.extensions.qiskit import AerBackend
 
 from qermit import CircuitShots
-from qermit.noise_model import MockQuantinuumBackend  # type: ignore
-from qermit.spam import (  # type: ignore
+from qermit.noise_model import MockQuantinuumBackend
+from qermit.spam import (
     CorrectionMethod,
     gen_FullyCorrelated_SPAM_MitRes,
     gen_UnCorrelated_SPAM_MitRes,