From 827cc08c52a460de759cf5f4772cbabdd9661f8b Mon Sep 17 00:00:00 2001
From: Grace <grace.harper@ibm.com>
Date: Thu, 14 Sep 2023 16:22:45 -0400
Subject: [PATCH] linted

---
 .pylintrc                                     |   3 -
 src/qiskit_qec/circuits/repetition_code.py    | 178 +++++++++++-------
 src/qiskit_qec/circuits/surface_code.py       |   2 +-
 src/qiskit_qec/decoders/decoding_graph.py     |  62 +++---
 src/qiskit_qec/decoders/hdrg_decoders.py      |  66 ++++---
 src/qiskit_qec/linear/symplectic.py           |  67 ++++---
 .../utils/decoding_graph_attributes.py        |   8 +-
 src/qiskit_qec/utils/stim_tools.py            |   2 +-
 test/code_circuits/test_rep_codes.py          |  89 ++++++---
 test/union_find/test_clayg.py                 |  13 +-
 test/utils/test_visualization.py              |  20 +-
 11 files changed, 329 insertions(+), 181 deletions(-)

diff --git a/.pylintrc b/.pylintrc
index 2d44948f..7e2e1dc7 100644
--- a/.pylintrc
+++ b/.pylintrc
@@ -476,9 +476,6 @@ disable=raw-checker-failed,
         missing-raises-doc,
         logging-too-many-args,
         spelling,       # way too noisy
-        no-self-use,        # disabled as it is too verbose
-        bad-continuation, bad-whitespace # differences of opinion with black
-
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option
 # multiple time (only on the command line, not in the configuration file where
diff --git a/src/qiskit_qec/circuits/repetition_code.py b/src/qiskit_qec/circuits/repetition_code.py
index 04b64cb0..cb9d4f2d 100644
--- a/src/qiskit_qec/circuits/repetition_code.py
+++ b/src/qiskit_qec/circuits/repetition_code.py
@@ -15,19 +15,19 @@
 # pylint: disable=invalid-name
 
 """Generates circuits based on repetition codes."""
+from copy import deepcopy
 from typing import List, Optional, Tuple
 
-from copy import deepcopy
 import numpy as np
 import rustworkx as rx
-
-from qiskit import ClassicalRegister, QuantumCircuit, QuantumRegister, transpile
-from qiskit.circuit.library import XGate, RZGate
-from qiskit.transpiler import PassManager, InstructionDurations
+from qiskit import (ClassicalRegister, QuantumCircuit, QuantumRegister,
+                    transpile)
+from qiskit.circuit.library import RZGate, XGate
+from qiskit.transpiler import InstructionDurations, PassManager
 from qiskit.transpiler.passes import DynamicalDecoupling
 
 from qiskit_qec.circuits.code_circuit import CodeCircuit
-from qiskit_qec.utils import DecodingGraphNode, DecodingGraphEdge
+from qiskit_qec.utils import DecodingGraphEdge, DecodingGraphNode
 
 
 def _separate_string(string):
@@ -87,7 +87,8 @@ def __init__(
 
         self.circuit = {}
         for log in ["0", "1"]:
-            self.circuit[log] = QuantumCircuit(self.link_qubit, self.code_qubit, name=log)
+            self.circuit[log] = QuantumCircuit(
+                self.link_qubit, self.code_qubit, name=log)
 
         self._xbasis = xbasis
         self._resets = resets
@@ -184,7 +185,8 @@ def syndrome_measurement(self, final: bool = False, barrier: bool = False, delay
         """
         barrier = barrier or self._barriers
 
-        self.link_bits.append(ClassicalRegister((self.d - 1), "round_" + str(self.T) + "_link_bit"))
+        self.link_bits.append(ClassicalRegister(
+            (self.d - 1), "round_" + str(self.T) + "_link_bit"))
 
         for log in ["0", "1"]:
             self.circuit[log].add_register(self.link_bits[-1])
@@ -196,14 +198,18 @@ def syndrome_measurement(self, final: bool = False, barrier: bool = False, delay
                 self.circuit[log].h(self.link_qubit)
             for j in range(self.d - 1):
                 if self._xbasis:
-                    self.circuit[log].cx(self.link_qubit[j], self.code_qubit[j])
+                    self.circuit[log].cx(
+                        self.link_qubit[j], self.code_qubit[j])
                 else:
-                    self.circuit[log].cx(self.code_qubit[j], self.link_qubit[j])
+                    self.circuit[log].cx(
+                        self.code_qubit[j], self.link_qubit[j])
             for j in range(self.d - 1):
                 if self._xbasis:
-                    self.circuit[log].cx(self.link_qubit[j], self.code_qubit[j + 1])
+                    self.circuit[log].cx(
+                        self.link_qubit[j], self.code_qubit[j + 1])
                 else:
-                    self.circuit[log].cx(self.code_qubit[j + 1], self.link_qubit[j])
+                    self.circuit[log].cx(
+                        self.code_qubit[j + 1], self.link_qubit[j])
             if self._xbasis:
                 self.circuit[log].h(self.link_qubit)
 
@@ -211,7 +217,8 @@ def syndrome_measurement(self, final: bool = False, barrier: bool = False, delay
             if barrier:
                 self.circuit[log].barrier()
             for j in range(self.d - 1):
-                self.circuit[log].measure(self.link_qubit[j], self.link_bits[self.T][j])
+                self.circuit[log].measure(
+                    self.link_qubit[j], self.link_bits[self.T][j])
 
             # resets
             if self._resets and not final:
@@ -245,15 +252,16 @@ def _process_string(self, string):
         measured_log = string[0] + " " + string[self.d - 1]
 
         if self._resets:
-            syndrome = string[self.d :]
+            syndrome = string[self.d:]
         else:
             # if there are no resets, results are cumulative and need to be separated
-            cumsyn_list = string[self.d :].split(" ")
+            cumsyn_list = string[self.d:].split(" ")
             syndrome_list = []
             for tt, cum_syn in enumerate(cumsyn_list[0:-1]):
                 syn = ""
                 for j in range(len(cum_syn)):
-                    syn += str(int(cumsyn_list[tt][j] != cumsyn_list[tt + 1][j]))
+                    syn += str(int(cumsyn_list[tt][j]
+                               != cumsyn_list[tt + 1][j]))
                 syndrome_list.append(syn)
             syndrome_list.append(cumsyn_list[-1])
             syndrome = " ".join(syndrome_list)
@@ -261,7 +269,9 @@ def _process_string(self, string):
         # final syndrome deduced from final code qubit readout
         full_syndrome = ""
         for j in range(self.d - 1):
-            full_syndrome += "0" * (string[j] == string[j + 1]) + "1" * (string[j] != string[j + 1])
+            full_syndrome += "0" * \
+                (string[j] == string[j + 1]) + \
+                "1" * (string[j] != string[j + 1])
         # results from all other syndrome measurements then added
         full_syndrome = full_syndrome + syndrome
 
@@ -310,7 +320,8 @@ def string2nodes(self, string, **kwargs):
             logical = "0"
 
         string = self._process_string(string)
-        separated_string = _separate_string(string)  # [ <boundary>, <syn>, <syn>,...]
+        # [ <boundary>, <syn>, <syn>,...]
+        separated_string = _separate_string(string)
         nodes = []
 
         # boundary nodes
@@ -322,7 +333,8 @@ def string2nodes(self, string, **kwargs):
                     bqubits = [self.css_x_logical[i]]
                 else:
                     bqubits = [self.css_z_logical[i]]
-                bnode = DecodingGraphNode(is_boundary=True, qubits=bqubits, index=bqec_index)
+                bnode = DecodingGraphNode(
+                    is_boundary=True, qubits=bqubits, index=bqec_index)
                 nodes.append(bnode)
 
         # bulk nodes
@@ -335,7 +347,8 @@ def string2nodes(self, string, **kwargs):
                             qubits = self.css_z_gauge_ops[qec_index]
                         else:
                             qubits = self.css_x_gauge_ops[qec_index]
-                        node = DecodingGraphNode(time=syn_round, qubits=qubits, index=qec_index)
+                        node = DecodingGraphNode(
+                            time=syn_round, qubits=qubits, index=qec_index)
                         nodes.append(node)
         return nodes
 
@@ -434,10 +447,11 @@ def check_nodes(self, nodes, ignore_extra_boundary=False, minimal=False):
                     elem = self.css_z_boundary.index(qubits)
                 else:
                     elem = self.css_x_boundary.index(qubits)
-                node = DecodingGraphNode(is_boundary=True, qubits=qubits, index=elem)
+                node = DecodingGraphNode(
+                    is_boundary=True, qubits=qubits, index=elem)
                 flipped_logical_nodes.append(node)
 
-            if neutral and flipped_logical_nodes == []:
+            if neutral and not flipped_logical_nodes:
                 break
 
         return neutral, flipped_logical_nodes, num_errors
@@ -467,7 +481,8 @@ def partition_outcomes(
             for i, layer in enumerate(gauge_outcomes):
                 for j, gauge_op in enumerate(layer):
                     if i > 0:
-                        gauge_outcomes[i][j] = (gauge_op + gauge_outcomes[i - 1][j]) % 2
+                        gauge_outcomes[i][j] = (
+                            gauge_op + gauge_outcomes[i - 1][j]) % 2
         # assign outcomes to the correct gauge ops
         if round_schedule == "z":
             x_gauge_outcomes = []
@@ -574,14 +589,17 @@ def __init__(
         if run_202:
             self.links_202 = []
             for link in self.links:
-                logical_overlap = {link[0], link[2]}.intersection(set(self.z_logicals))
+                logical_overlap = {link[0], link[2]
+                                   }.intersection(set(self.z_logicals))
                 if not logical_overlap:
                     self.links_202.append(link)
             num_links = len(self.links_202)
             if num_links > 0:
                 self.rounds_per_link = int(np.floor(T / num_links))
-                self.metabuffer = np.ceil((T - num_links * self.rounds_per_link) / 2)
-                self.roundbuffer = np.ceil((self.rounds_per_link - self.rounds_per_202) / 2)
+                self.metabuffer = np.ceil(
+                    (T - num_links * self.rounds_per_link) / 2)
+                self.roundbuffer = np.ceil(
+                    (self.rounds_per_link - self.rounds_per_202) / 2)
                 if self.roundbuffer > 0:
                     self.roundbuffer -= 1
                 self.run_202 = self.rounds_per_link >= self.rounds_per_202
@@ -605,7 +623,8 @@ def __init__(
     def _get_link_graph(self, max_dist=1):
         graph = rx.PyGraph()
         for link in self.links:
-            add_edge(graph, (link[0], link[2]), {"distance": 1, "link qubit": link[1]})
+            add_edge(graph, (link[0], link[2]), {
+                     "distance": 1, "link qubit": link[1]})
         distance = rx.distance_matrix(graph)
         edges = graph.edge_list()
         for n0, node0 in enumerate(graph.nodes()):
@@ -627,7 +646,8 @@ def _get_cycles(self):
         lg_edges = set(link_graph.edge_list())
         lg_nodes = link_graph.nodes()
         cycles = rx.cycle_basis(link_graph)
-        cycle_dict = {(lg_nodes[edge[0]], lg_nodes[edge[1]]): list(edge) for edge in lg_edges}
+        cycle_dict = {(lg_nodes[edge[0]], lg_nodes[edge[1]])
+                       : list(edge) for edge in lg_edges}
         for cycle in cycles:
             edges = []
             cl = len(cycle)
@@ -685,7 +705,8 @@ def _get_coupling_graph(self, aux=None):
                 add_edge(graph, (link[1], link[2]), {})
         # we use max degree of the nodes as the edge weight, to delay bottlenecks
         for e, (n0, n1) in enumerate(graph.edge_list()):
-            graph.edges()[e]["weight"] = max(graph.degree(n0), graph.degree(n1))
+            graph.edges()[e]["weight"] = max(
+                graph.degree(n0), graph.degree(n1))
 
         return graph
 
@@ -706,12 +727,14 @@ def weight_fn(edge):
             graph = self._get_coupling_graph(aux)
 
             # find a min weight matching, and then another that exlcudes the pairs from the first
-            matching = [rx.max_weight_matching(graph, max_cardinality=True, weight_fn=weight_fn)]
+            matching = [rx.max_weight_matching(
+                graph, max_cardinality=True, weight_fn=weight_fn)]
             cut_graph = deepcopy(graph)
             for n0, n1 in matching[0]:
                 cut_graph.remove_edge(n0, n1)
             matching.append(
-                rx.max_weight_matching(cut_graph, max_cardinality=True, weight_fn=weight_fn)
+                rx.max_weight_matching(
+                    cut_graph, max_cardinality=True, weight_fn=weight_fn)
             )
 
             # rewrite the matchings to use nodes instead of indices, and to always place
@@ -735,7 +758,8 @@ def weight_fn(edge):
 
             # add these matched pairs to the schedule
             for j in range(2):
-                schedule.append([pair for pair in matching[j] if pair[1] in completed])
+                schedule.append(
+                    [pair for pair in matching[j] if pair[1] in completed])
 
             # update the list of auxilliaries for links yet to be paired
             aux = aux.difference(completed)
@@ -798,7 +822,8 @@ def _preparation(self):
         # create the circuits and initialize the code qubits
         self.circuit = {}
         for basis in list({self.basis, self.basis[::-1]}):
-            self.circuit[basis] = QuantumCircuit(self.link_qubit, self.code_qubit, name=basis)
+            self.circuit[basis] = QuantumCircuit(
+                self.link_qubit, self.code_qubit, name=basis)
             if self.logical == "1":
                 self.circuit[basis].x(self.code_qubit)
             self._basis_change(basis)
@@ -857,7 +882,8 @@ def _get_202(self, t):
                 neighbors = list(graph.incident_edges(n))
                 neighbors.remove(list(edges).index(tuple(ns)))
                 qubit_l_nghbrs.append(
-                    [graph.get_edge_data_by_index(ngbhr)["link qubit"] for ngbhr in neighbors]
+                    [graph.get_edge_data_by_index(
+                        ngbhr)["link qubit"] for ngbhr in neighbors]
                 )
         return tau, qubit_l_202, qubit_l_nghbrs
 
@@ -869,7 +895,8 @@ def _syndrome_measurement(self, final: bool = False):
         """
 
         self.link_bits.append(
-            ClassicalRegister(self.num_qubits[1], "round_" + str(self.T) + "_link_bit")
+            ClassicalRegister(
+                self.num_qubits[1], "round_" + str(self.T) + "_link_bit")
         )
 
         tau, qubit_l_202, qubit_l_nghbrs = self._get_202(self.T)
@@ -910,7 +937,8 @@ def _syndrome_measurement(self, final: bool = False):
             if self.resets and not final:
                 for q_l in links_to_reset:
                     if self.conditional_reset:
-                        qc.x(self.link_qubit[q_l]).c_if(self.link_bits[self.T][q_l], 1)
+                        qc.x(self.link_qubit[q_l]).c_if(
+                            self.link_bits[self.T][q_l], 1)
                     else:
                         qc.reset(self.link_qubit[q_l])
 
@@ -924,7 +952,8 @@ def _syndrome_measurement(self, final: bool = False):
                             # get the first listed neighbouring link
                             control_link = self.links[self.link_index[qubit_l_nghbrs[j][0]]]
                             # find the qubit on which it overlaps with the 202
-                            qubit_t = list(set(target_link).intersection(set(control_link)))[0]
+                            qubit_t = list(set(target_link).intersection(
+                                set(control_link)))[0]
                             # and the qubit whose result controls the feedforward
                             qubit_c = control_link[1]
                             # get their indices
@@ -933,7 +962,8 @@ def _syndrome_measurement(self, final: bool = False):
                             # and the colour of the targeted qubit
                             c = self.color[qubit_t]
                             self._rotate(basis, c, self.code_qubit[q_t], True)
-                            qc.x(self.code_qubit[q_t]).c_if(self.link_bits[self.T][q_c], 1)
+                            qc.x(self.code_qubit[q_t]).c_if(
+                                self.link_bits[self.T][q_c], 1)
                             self._rotate(basis, c, self.code_qubit[q_t], False)
 
             # delay
@@ -965,15 +995,16 @@ def _process_string(self, string):
             measured_log += string[self.num_qubits[0] - j - 1] + " "
 
         if self.resets:
-            syndrome = string[self.num_qubits[0] :]
+            syndrome = string[self.num_qubits[0]:]
         else:
             # if there are no resets, results are cumulative and need to be separated
-            cumsyn_list = string[self.num_qubits[0] :].split(" ")
+            cumsyn_list = string[self.num_qubits[0]:].split(" ")
             syndrome_list = []
             for tt, cum_syn in enumerate(cumsyn_list[0:-1]):
                 syn = ""
                 for j in range(len(cum_syn)):
-                    syn += str(int(cumsyn_list[tt][j] != cumsyn_list[tt + 1][j]))
+                    syn += str(int(cumsyn_list[tt][j]
+                               != cumsyn_list[tt + 1][j]))
                 syndrome_list.append(syn)
             syndrome_list.append(cumsyn_list[-1])
             syndrome = " ".join(syndrome_list)
@@ -981,7 +1012,8 @@ def _process_string(self, string):
         # final syndrome deduced from final code qubit readout
         full_syndrome = ""
         for link in self.links:
-            q = [self.num_qubits[0] - 1 - self.code_index[link[j]] for j in [0, -1]]
+            q = [self.num_qubits[0] - 1 - self.code_index[link[j]]
+                 for j in [0, -1]]
             full_syndrome += "0" * (string[q[0]] == string[q[1]]) + "1" * (
                 string[q[0]] != string[q[1]]
             )
@@ -1033,7 +1065,8 @@ def _process_string(self, string):
                         dt = 1
                 # for those where we now have a dt, calculate the change
                 if dt:
-                    change = syndrome_list[-t - 1][j] != syndrome_list[-t - 1 + dt][j]
+                    change = syndrome_list[-t -
+                                           1][j] != syndrome_list[-t - 1 + dt][j]
                 syndrome_changes += "0" * (not change) + "1" * change
             syndrome_changes += " "
             last_neighbors = all_neighbors.copy()
@@ -1098,7 +1131,8 @@ def string2nodes(self, string, **kwargs) -> List[DecodingGraphNode]:
                             qubits=code_qubits,
                             index=elem_num,
                         )
-                        node.properties["conjugate"] = ((tau % 2) == 1) and tau > 1
+                        node.properties["conjugate"] = (
+                            (tau % 2) == 1) and tau > 1
                         node.properties["link qubit"] = link_qubit
                         nodes.append(node)
         return nodes
@@ -1215,7 +1249,8 @@ def check_nodes(self, nodes, ignore_extra_boundary=False, minimal=False):
                             num_nodes[new_c] += 1
                         # if it is coloured, check the colour is correct
                         else:
-                            base_neutral = base_neutral and (node_color[nn] == (c + dc) % 2)
+                            base_neutral = base_neutral and (
+                                node_color[nn] == (c + dc) % 2)
                 for nn, c in newly_colored.items():
                     node_color[nn] = c
                     if nn in ns_to_do:
@@ -1224,7 +1259,8 @@ def check_nodes(self, nodes, ignore_extra_boundary=False, minimal=False):
                 # process is converged once one colour has stoppped growing
                 # once ns_to_do is empty
                 converged = (not ns_to_do) and (
-                    (num_nodes[0] == last_num[0] != 0) or (num_nodes[1] == last_num[1] != 0)
+                    (num_nodes[0] == last_num[0] != 0) or (
+                        num_nodes[1] == last_num[1] != 0)
                 )
                 fully_converged = converged and last_converged
                 if not fully_converged:
@@ -1239,7 +1275,8 @@ def check_nodes(self, nodes, ignore_extra_boundary=False, minimal=False):
             else:
                 min_color = (conv_color + 1) % 2
             # calculate the number of nodes for the other
-            num_nodes[(min_color + 1) % 2] = link_graph.num_nodes() - num_nodes[min_color]
+            num_nodes[(min_color + 1) %
+                      2] = link_graph.num_nodes() - num_nodes[min_color]
             # get the set of min nodes
             min_ns = set()
             for n, c in node_color.items():
@@ -1280,7 +1317,8 @@ def check_nodes(self, nodes, ignore_extra_boundary=False, minimal=False):
                     flipped_logicals = set()
                 # otherwise, report only needed logicals that aren't given
                 else:
-                    flipped_logicals = flipped_logicals.difference(given_logicals)
+                    flipped_logicals = flipped_logicals.difference(
+                        given_logicals)
 
                 flipped_logical_nodes = []
                 for flipped_logical in flipped_logicals:
@@ -1291,7 +1329,7 @@ def check_nodes(self, nodes, ignore_extra_boundary=False, minimal=False):
                     )
                     flipped_logical_nodes.append(node)
 
-                if neutral and flipped_logical_nodes == []:
+                if neutral and not flipped_logical_nodes:
                     break
 
         else:
@@ -1308,15 +1346,13 @@ def check_nodes(self, nodes, ignore_extra_boundary=False, minimal=False):
 
         return neutral, flipped_logical_nodes, num_errors
 
-    def is_cluster_neutral(self, atypical_nodes):
+    def is_cluster_neutral(self, atypical_nodes: dict):
         """
         Determines whether or not the cluster is neutral, meaning that one or more
         errors could have caused the set of atypical nodes (syndrome changes) passed
         to the method.
         Args:
-            atypical_nodes (dictionary in the form of the return value of string2nodes)
-            ignore_extra_boundary (bool): If `True`, undeeded boundary nodes are
-            ignored.
+            atypical_nodes: dictionary in the form of the return value of string2nodes
         """
         neutral, logicals, _ = self.check_nodes(atypical_nodes)
         return neutral and not logicals
@@ -1361,9 +1397,11 @@ def transpile(self, backend, echo=("X", "X"), echo_num=(2, 0)):
                     dd_sequences.append([XGate()] * echo_num[j])
                     spacings.append(None)
                 elif echo[j] == "XZX":
-                    dd_sequences.append([XGate(), RZGate(np.pi), XGate()] * echo_num)
+                    dd_sequences.append(
+                        [XGate(), RZGate(np.pi), XGate()] * echo_num)
                     d = 1.0 / (2 * echo_num - 1 + 1)
-                    spacing = [d / 2] + ([0, d, d] * echo_num[j])[:-1] + [d / 2]
+                    spacing = [d / 2] + \
+                        ([0, d, d] * echo_num[j])[:-1] + [d / 2]
                     for _ in range(2):
                         spacing[0] += 1 - sum(spacing)
                     spacings.append(spacing)
@@ -1399,7 +1437,9 @@ def transpile(self, backend, echo=("X", "X"), echo_num=(2, 0)):
                         q = gate[1][0]
                         t = gate[0].params[0]
                         total_delay[0][q] += t
-                        new_t = 16 * np.ceil((total_delay[0][q] - total_delay[1][q]) / 16)
+                        new_t = 16 * \
+                            np.ceil(
+                                (total_delay[0][q] - total_delay[1][q]) / 16)
                         total_delay[1][q] += new_t
                         gate[0].params[0] = new_t
 
@@ -1515,7 +1555,8 @@ def get_error_coords(self, counts, decoding_graph, method="spitz"):
                             for dt, pairs in enumerate(self.schedule):
                                 if pair in pairs or tuple(pair) in pairs:
                                     dts.append(dt)
-                        time = [max(0, node0.time - 1 + (max(dts) + 1) / round_length)]
+                        time = [
+                            max(0, node0.time - 1 + (max(dts) + 1) / round_length)]
                         time.append(node0.time + min(dts) / round_length)
                     # error during a round
                     else:
@@ -1533,8 +1574,10 @@ def get_error_coords(self, counts, decoding_graph, method="spitz"):
                                     dts.append(dt)
                         # use to define fractional time
                         if dts[0] < dts[1]:
-                            time = [node_pair[1].time + (dts[0] + 1) / round_length]
-                            time.append(node_pair[1].time + dts[1] / round_length)
+                            time = [node_pair[1].time +
+                                    (dts[0] + 1) / round_length]
+                            time.append(
+                                node_pair[1].time + dts[1] / round_length)
                         else:
                             # impossible cases get no valid time
                             time = []
@@ -1542,25 +1585,30 @@ def get_error_coords(self, counts, decoding_graph, method="spitz"):
                     # measurement error
                     assert node0.time != node1.time and node0.qubits == node1.qubits
                     qubit = node0.properties["link qubit"]
-                    time = [node0.time, node0.time + (round_length - 1) / round_length]
+                    time = [node0.time, node0.time +
+                            (round_length - 1) / round_length]
                     time.sort()
             else:
                 # detected only by one stabilizer
-                boundary_qubits = list(set(node0.qubits).intersection(z_logicals))
+                boundary_qubits = list(
+                    set(node0.qubits).intersection(z_logicals))
                 # for the case of boundary stabilizers
                 if boundary_qubits:
                     qubit = boundary_qubits[0]
                     pair = [qubit, node0.properties["link qubit"]]
                     for dt, pairs in enumerate(self.schedule):
                         if pair in pairs or tuple(pair) in pairs:
-                            time = [max(0, node0.time - 1 + (dt + 1) / round_length)]
+                            time = [
+                                max(0, node0.time - 1 + (dt + 1) / round_length)]
                             time.append(node0.time + dt / round_length)
 
                 else:
-                    qubit = tuple(node0.qubits + [node0.properties["link qubit"]])
-                    time = [node0.time, node0.time + (round_length - 1) / round_length]
+                    qubit = tuple(
+                        node0.qubits + [node0.properties["link qubit"]])
+                    time = [node0.time, node0.time +
+                            (round_length - 1) / round_length]
 
-            if time != []:  # only record if not nan
+            if time:  # only record if not nan
                 if (qubit, time[0], time[1]) not in error_coords:
                     error_coords[qubit, time[0], time[1]] = {}
                 error_coords[qubit, time[0], time[1]][n0, n1] = prob
diff --git a/src/qiskit_qec/circuits/surface_code.py b/src/qiskit_qec/circuits/surface_code.py
index dc800dcb..f6f6a8b1 100644
--- a/src/qiskit_qec/circuits/surface_code.py
+++ b/src/qiskit_qec/circuits/surface_code.py
@@ -478,7 +478,7 @@ def check_nodes(self, nodes, ignore_extra_boundary=False, minimal=False):
                     p = y
                 else:
                     p = x
-                num_errors = min(num_errors, min(p + 1, self.d - p))
+                num_errors = min(num_errors, p + 1, self.d - p)
             flipped_logicals = {1 - int(p < (self.d - 1) / 2)}
 
         # if unneeded logical zs are given, cluster is not neutral
diff --git a/src/qiskit_qec/decoders/decoding_graph.py b/src/qiskit_qec/decoders/decoding_graph.py
index 774cf361..58b4dce0 100644
--- a/src/qiskit_qec/decoders/decoding_graph.py
+++ b/src/qiskit_qec/decoders/decoding_graph.py
@@ -19,13 +19,14 @@
 """
 import itertools
 import logging
-from typing import List, Tuple
+from typing import List, Tuple, Union
 
 import numpy as np
 import rustworkx as rx
+
 from qiskit_qec.analysis.faultenumerator import FaultEnumerator
 from qiskit_qec.exceptions import QiskitQECError
-from qiskit_qec.utils import DecodingGraphNode, DecodingGraphEdge
+from qiskit_qec.utils import DecodingGraphEdge, DecodingGraphNode
 
 
 class DecodingGraph:
@@ -98,7 +99,8 @@ def _make_syndrome_graph(self):
                                 n1 = graph.nodes().index(target)
                                 qubits = []
                                 if not (source.is_boundary and target.is_boundary):
-                                    qubits = list(set(source.qubits).intersection(target.qubits))
+                                    qubits = list(
+                                        set(source.qubits).intersection(target.qubits))
                                     if not qubits:
                                         continue
                                 if (
@@ -161,7 +163,8 @@ def get_error_probs(
 
             for string in counts:
                 # list of i for which v_i=1
-                error_nodes = set(self.code.string2nodes(string, logical=logical))
+                error_nodes = set(self.code.string2nodes(
+                    string, logical=logical))
 
                 for node0 in error_nodes:
                     n0 = self.graph.nodes().index(node0)
@@ -191,9 +194,11 @@ def get_error_probs(
                     boundary.append(n0)
                 else:
                     if (1 - 2 * av_xor[n0, n1]) != 0:
-                        x = (av_vv[n0, n1] - av_v[n0] * av_v[n1]) / (1 - 2 * av_xor[n0, n1])
+                        x = (av_vv[n0, n1] - av_v[n0] * av_v[n1]) / \
+                            (1 - 2 * av_xor[n0, n1])
                         if x < 0.25:
-                            error_probs[n0, n1] = max(0, 0.5 - np.sqrt(0.25 - x))
+                            error_probs[n0, n1] = max(
+                                0, 0.5 - np.sqrt(0.25 - x))
                         else:
                             error_probs[n0, n1] = np.nan
                     else:
@@ -222,7 +227,8 @@ def get_error_probs(
                 for edge in self.graph.edge_list()
             }
             for string in counts:
-                error_nodes = set(self.code.string2nodes(string, logical=logical))
+                error_nodes = set(self.code.string2nodes(
+                    string, logical=logical))
                 for edge in self.graph.edge_list():
                     element = ""
                     for j in range(2):
@@ -293,12 +299,13 @@ def weight_syndrome_graph(self, counts, method: str = METHOD_SPITZ):
             edge_data.weight = w
             self.graph.update_edge(edge[0], edge[1], edge_data)
 
-    def make_error_graph(self, data, all_logicals=True):
+    def make_error_graph(self, data: Union[str, List], all_logicals=True):
         """Returns error graph.
 
         Args:
             data: Either an ouput string of the code, or a list of
             nodes for the code.
+            all_logicals(bool): Whether to do all logicals
 
         Returns:
             The subgraph of graph which corresponds to the non-trivial
@@ -322,7 +329,8 @@ def make_error_graph(self, data, all_logicals=True):
         def weight_fn(edge):
             return int(edge.weight)
 
-        distance_matrix = rx.graph_floyd_warshall_numpy(self.graph, weight_fn=weight_fn)
+        distance_matrix = rx.graph_floyd_warshall_numpy(
+            self.graph, weight_fn=weight_fn)
 
         for source_index in E.node_indexes():
             for target_index in E.node_indexes():
@@ -333,9 +341,11 @@ def weight_fn(edge):
                     nt = self.graph.nodes().index(target)
                     distance = distance_matrix[ns][nt]
                     if np.isfinite(distance):
-                        qubits = list(set(source.qubits).intersection(target.qubits))
+                        qubits = list(
+                            set(source.qubits).intersection(target.qubits))
                         distance = int(distance)
-                        E.add_edge(source_index, target_index, DecodingGraphEdge(qubits, distance))
+                        E.add_edge(source_index, target_index,
+                                   DecodingGraphEdge(qubits, distance))
         return E
 
 
@@ -367,7 +377,8 @@ def __init__(
         self.round_schedule = round_schedule
         self.basis = basis
 
-        self.layer_types = self._layer_types(self.blocks, self.round_schedule, self.basis)
+        self.layer_types = self._layer_types(
+            self.blocks, self.round_schedule, self.basis)
 
         self._decoding_graph()
 
@@ -442,7 +453,8 @@ def _decoding_graph(self):
                 idx += 1
             for index, supp in enumerate(boundary):
                 # Add optional is_boundary property for pymatching
-                node = DecodingGraphNode(is_boundary=True, qubits=supp, index=index)
+                node = DecodingGraphNode(
+                    is_boundary=True, qubits=supp, index=index)
                 node.properties["highlighted"] = False
                 graph.add_node(node)
                 logging.debug("boundary %d t=%d %s", idx, time, supp)
@@ -478,9 +490,11 @@ def _decoding_graph(self):
                         edge.properties["highlighted"] = False
                         edge.properties["measurement_error"] = 0
                         graph.add_edge(
-                            idxmap[(time, tuple(op_g))], idxmap[(time, tuple(op_h))], edge
+                            idxmap[(time, tuple(op_g))], idxmap[(
+                                time, tuple(op_h))], edge
                         )
-                        logging.debug("spacelike t=%d (%s, %s)", time, op_g, op_h)
+                        logging.debug("spacelike t=%d (%s, %s)",
+                                      time, op_g, op_h)
                         logging.debug(
                             " qubits %s",
                             [com[0]],
@@ -497,8 +511,10 @@ def _decoding_graph(self):
                 edge = DecodingGraphEdge(qubits=[], weight=0)
                 edge.properties["highlighted"] = False
                 edge.properties["measurement_error"] = 0
-                graph.add_edge(idxmap[(time, tuple(bound_g))], idxmap[(time, tuple(bound_h))], edge)
-                logging.debug("spacelike boundary t=%d (%s, %s)", time, bound_g, bound_h)
+                graph.add_edge(idxmap[(time, tuple(bound_g))],
+                               idxmap[(time, tuple(bound_h))], edge)
+                logging.debug("spacelike boundary t=%d (%s, %s)",
+                              time, bound_g, bound_h)
 
             # Add (space)time-like edges from t to t-1
             # By construction, the qubit sets of pairs of vertices at graph and T
@@ -543,9 +559,11 @@ def _decoding_graph(self):
                                     idxmap[(time, tuple(op_g))],
                                     edge,
                                 )
-                                logging.debug("timelike t=%d (%s, %s)", time, op_g, op_h)
+                                logging.debug(
+                                    "timelike t=%d (%s, %s)", time, op_g, op_h)
                             else:  # Case (b)
-                                edge = DecodingGraphEdge(qubits=[com[0]], weight=1)
+                                edge = DecodingGraphEdge(
+                                    qubits=[com[0]], weight=1)
                                 edge.properties["highlighted"] = False
                                 edge.properties["measurement_error"] = 1
                                 graph.add_edge(
@@ -553,7 +571,8 @@ def _decoding_graph(self):
                                     idxmap[(time, tuple(op_g))],
                                     edge,
                                 )
-                                logging.debug("spacetime hook t=%d (%s, %s)", time, op_g, op_h)
+                                logging.debug(
+                                    "spacetime hook t=%d (%s, %s)", time, op_g, op_h)
                                 logging.debug(" qubits %s", [com[0]])
                 # Add a single time-like edge between boundary vertices at
                 # time t-1 and t
@@ -561,7 +580,8 @@ def _decoding_graph(self):
                 edge.properties["highlighted"] = False
                 edge.properties["measurement_error"] = 0
                 graph.add_edge(
-                    idxmap[(time - 1, tuple(boundary[0]))], idxmap[(time, tuple(boundary[0]))], edge
+                    idxmap[(time - 1, tuple(boundary[0]))
+                           ], idxmap[(time, tuple(boundary[0]))], edge
                 )
                 logging.debug("boundarylink t=%d", time)
 
diff --git a/src/qiskit_qec/decoders/hdrg_decoders.py b/src/qiskit_qec/decoders/hdrg_decoders.py
index 60a788b7..6c1ed19c 100644
--- a/src/qiskit_qec/decoders/hdrg_decoders.py
+++ b/src/qiskit_qec/decoders/hdrg_decoders.py
@@ -16,15 +16,16 @@
 
 """Hard decision renormalization group decoders."""
 
+from abc import ABC
 from copy import copy, deepcopy
 from dataclasses import dataclass
 from typing import Dict, List, Set, Tuple
-from abc import ABC
-from rustworkx import connected_components, distance_matrix, PyGraph
+
+from rustworkx import PyGraph, connected_components, distance_matrix
 
 from qiskit_qec.circuits.repetition_code import ArcCircuit
 from qiskit_qec.decoders.decoding_graph import DecodingGraph
-from qiskit_qec.utils import DecodingGraphNode, DecodingGraphEdge
+from qiskit_qec.utils import DecodingGraphEdge, DecodingGraphNode
 
 
 class ClusteringDecoder(ABC):
@@ -87,7 +88,8 @@ def get_corrections(self, string, clusters):
             cluster_logicals[c] = z_logicals
 
         # get the net effect on each logical
-        net_z_logicals = {z_logical[0]: 0 for z_logical in self.measured_logicals}
+        net_z_logicals = {
+            z_logical[0]: 0 for z_logical in self.measured_logicals}
         for c, z_logicals in cluster_logicals.items():
             for z_logical in self.measured_logicals:
                 if z_logical[0] in z_logicals:
@@ -99,7 +101,8 @@ def get_corrections(self, string, clusters):
         string = string.split(" ")[0]
         for z_logical in self.measured_logicals:
             raw_logical = int(string[-1 - self.code_index[z_logical[0]]])
-            corrected_logical = (raw_logical + net_z_logicals[z_logical[0]]) % 2
+            corrected_logical = (
+                raw_logical + net_z_logicals[z_logical[0]]) % 2
             corrected_z_logicals.append(corrected_logical)
 
         return corrected_z_logicals
@@ -168,7 +171,8 @@ def _cluster(self, ns, dist_max):
     def _get_boundary_nodes(self):
         boundary_nodes = []
         for element, z_logical in enumerate(self.measured_logicals):
-            node = DecodingGraphNode(is_boundary=True, qubits=z_logical, index=element)
+            node = DecodingGraphNode(
+                is_boundary=True, qubits=z_logical, index=element)
             if isinstance(self.code, ArcCircuit):
                 node.properties["link qubit"] = None
             boundary_nodes.append(node)
@@ -188,7 +192,8 @@ def cluster(self, nodes):
         # get indices for nodes and boundary nodes
         dg = self.decoding_graph.graph
         ns = set(dg.nodes().index(node) for node in nodes)
-        bns = set(dg.nodes().index(node) for node in self._get_boundary_nodes())
+        bns = set(dg.nodes().index(node)
+                  for node in self._get_boundary_nodes())
 
         dist_max = 0
         final_clusters = {}
@@ -327,14 +332,16 @@ def process(self, string: str):
 
         if self.use_peeling:
             self.graph = deepcopy(self.decoding_graph.graph)
-            highlighted_nodes = self.code.string2nodes(string, all_logicals=True)
+            highlighted_nodes = self.code.string2nodes(
+                string, all_logicals=True)
 
             # call cluster to do the clustering, but actually use the peeling form
             self.cluster(highlighted_nodes)
             clusters = self._clusters4peeling
 
             # determine the net logical z
-            net_z_logicals = {tuple(z_logical): 0 for z_logical in self.measured_logicals}
+            net_z_logicals = {
+                tuple(z_logical): 0 for z_logical in self.measured_logicals}
             for cluster_nodes, _ in clusters:
                 erasure = self.graph.subgraph(cluster_nodes)
                 flipped_qubits = self.peeling(erasure)
@@ -350,7 +357,8 @@ def process(self, string: str):
             raw_logicals = self.code.string2raw_logicals(string)
             for j, z_logical in enumerate(self.measured_logicals):
                 raw_logical = int(raw_logicals[j])
-                corrected_logical = (raw_logical + net_z_logicals[tuple(z_logical)]) % 2
+                corrected_logical = (
+                    raw_logical + net_z_logicals[tuple(z_logical)]) % 2
                 corrected_z_logicals.append(corrected_logical)
             return corrected_z_logicals
         else:
@@ -359,16 +367,13 @@ def process(self, string: str):
             clusters = self.cluster(nodes)
             return self.get_corrections(string, clusters)
 
-    def cluster(self, nodes):
+    def cluster(self, nodes: List):
         """
         Create clusters using the union-find algorithm.
 
         Args:
             nodes (List): List of non-typical nodes in the syndrome graph,
             of the type produced by `string2nodes`.
-            standard_form (Bool): Whether to use the standard form of
-            the clusters for clustering decoders, or the form used internally
-            by the class.
 
         Returns:
             clusters (dict): Dictionary with the indices of
@@ -396,7 +401,8 @@ def cluster(self, nodes):
         clusters = {}
         for c, cluster in self.clusters.items():
             # determine which nodes exactly are in the neutral cluster
-            neutral_nodes = list(cluster.atypical_nodes | cluster.boundary_nodes)
+            neutral_nodes = list(cluster.atypical_nodes |
+                                 cluster.boundary_nodes)
             # put them in the required dict
             for n in neutral_nodes:
                 clusters[n] = c
@@ -407,7 +413,8 @@ def cluster(self, nodes):
             if not cluster.atypical_nodes:
                 continue
             self._clusters4peeling.append(
-                (list(cluster.nodes), list(cluster.atypical_nodes | cluster.boundary_nodes))
+                (list(cluster.nodes), list(
+                    cluster.atypical_nodes | cluster.boundary_nodes))
             )
 
         return clusters
@@ -426,7 +433,8 @@ def find(self, u: int) -> int:
         if self.graph[u].properties["root"] == u:
             return self.graph[u].properties["root"]
 
-        self.graph[u].properties["root"] = self.find(self.graph[u].properties["root"])
+        self.graph[u].properties["root"] = self.find(
+            self.graph[u].properties["root"])
         return self.graph[u].properties["root"]
 
     def _create_new_cluster(self, node_index):
@@ -435,11 +443,13 @@ def _create_new_cluster(self, node_index):
             self.odd_cluster_roots.insert(0, node_index)
         boundary_edges = []
         for edge_index, neighbour, data in self.neighbouring_edges(node_index):
-            boundary_edges.append(BoundaryEdge(edge_index, node_index, neighbour, data))
+            boundary_edges.append(BoundaryEdge(
+                edge_index, node_index, neighbour, data))
         self.clusters[node_index] = UnionFindDecoderCluster(
             boundary=boundary_edges,
             fully_grown_edges=set(),
-            atypical_nodes=set([node_index]) if not node.is_boundary else set([]),
+            atypical_nodes=set(
+                [node_index]) if not node.is_boundary else set([]),
             boundary_nodes=set([node_index]) if node.is_boundary else set([]),
             nodes=set([node_index]),
             size=1,
@@ -606,7 +616,8 @@ def peeling(self, erasure: PyGraph) -> List[int]:
         edges = set()
         for edge in tree.edges[::-1]:
             endpoints = erasure.get_edge_endpoints_by_index(edge)
-            pendant_vertex = endpoints[0] if not tree.vertices[endpoints[0]] else endpoints[1]
+            pendant_vertex = endpoints[0] if not tree.vertices[endpoints[0]
+                                                               ] else endpoints[1]
             tree_vertex = endpoints[0] if pendant_vertex == endpoints[1] else endpoints[1]
             tree.vertices[tree_vertex].remove(edge)
             if erasure[pendant_vertex].properties["syndrome"]:
@@ -685,7 +696,8 @@ def process(self, string: str):
             edge.properties["fully_grown"] = False
 
         string = "".join([str(c) for c in string[::-1]])
-        output = [int(bit) for bit in list(string.split(" ", maxsplit=self.code.d)[0])][::-1]
+        output = [int(bit) for bit in list(
+            string.split(" ", maxsplit=self.code.d)[0])][::-1]
         highlighted_nodes = self.code.string2nodes(string, all_logicals=True)
         if not highlighted_nodes:
             return output  # There's nothing for us to do here
@@ -696,7 +708,8 @@ def process(self, string: str):
         flattened_highlighted_nodes: List[DecodingGraphNode] = []
         for highlighted_node in highlighted_nodes:
             highlighted_node.time = 0
-            flattened_highlighted_nodes.append(self.graph.nodes().index(highlighted_node))
+            flattened_highlighted_nodes.append(
+                self.graph.nodes().index(highlighted_node))
 
         for cluster_nodes, cluster_atypical_nodes in clusters:
             if not cluster_nodes:
@@ -725,7 +738,8 @@ def cluster(self, nodes):
         self.clusters: Dict[int, UnionFindDecoderCluster] = {}
         self.odd_cluster_roots = []
 
-        times: List[List[DecodingGraphNode]] = [[] for _ in range(self.code.T + 1)]
+        times: List[List[DecodingGraphNode]] = [[]
+                                                for _ in range(self.code.T + 1)]
         boundaries = []
         for node in deepcopy(nodes):
             if node.is_boundary:
@@ -757,7 +771,8 @@ def cluster(self, nodes):
         clusters = {}
         for c, cluster in enumerate(neutral_clusters):
             # determine which nodes exactly are in the neutral cluster
-            neutral_nodes = list(cluster.atypical_nodes | cluster.boundary_nodes)
+            neutral_nodes = list(cluster.atypical_nodes |
+                                 cluster.boundary_nodes)
             # put them in the required dict
             for n in neutral_nodes:
                 clusters[n] = c
@@ -765,7 +780,8 @@ def cluster(self, nodes):
         neutral_cluster_nodes: List[List[int]] = []
         for cluster in neutral_clusters:
             neutral_cluster_nodes.append(
-                (list(cluster.nodes), list(cluster.atypical_nodes | cluster.boundary_nodes))
+                (list(cluster.nodes), list(
+                    cluster.atypical_nodes | cluster.boundary_nodes))
             )
 
         self._clusters4peeling = neutral_cluster_nodes
diff --git a/src/qiskit_qec/linear/symplectic.py b/src/qiskit_qec/linear/symplectic.py
index 80fe38fe..7222a8c1 100644
--- a/src/qiskit_qec/linear/symplectic.py
+++ b/src/qiskit_qec/linear/symplectic.py
@@ -13,12 +13,11 @@
 """Symplectic functions."""
 
 from collections import deque
-from typing import List, Any, Tuple
-from typing import Union, Optional
+from typing import Any, List, Optional, Tuple, Union
 
 import numpy as np
-
 from qiskit import QiskitError
+
 from qiskit_qec.linear import matrix as mt
 
 
@@ -93,7 +92,8 @@ def symplectic_product(mat1: np.ndarray, mat2: np.ndarray) -> Union[int, np.ndar
     mat2_np_array = np.array(mat2, dtype=np.int8)
 
     if not is_symplectic_form(mat1) or not is_symplectic_form(mat2):
-        raise QiskitError("Input matrices/vectors must be GF(2) symplectic matrices/vectors")
+        raise QiskitError(
+            "Input matrices/vectors must be GF(2) symplectic matrices/vectors")
 
     if not mat1_np_array.ndim == mat2_np_array.ndim:
         raise QiskitError(
@@ -325,14 +325,16 @@ def make_commute_hyper(
     _make_commute_hyper
     """
     if not (is_symplectic_form(a) and is_symplectic_form(x) and is_symplectic_form(z)):
-        raise QiskitError("Input matrices/vectors must be GF(2) symplectic matrices/vectors")
+        raise QiskitError(
+            "Input matrices/vectors must be GF(2) symplectic matrices/vectors")
 
     def make_list(srange):
         if srange is not None:
             try:
                 srange = list(srange)
             except TypeError as terror:
-                raise QiskitError(f"Input range {srange} is not iterable") from terror
+                raise QiskitError(
+                    f"Input range {srange} is not iterable") from terror
 
         return srange
 
@@ -349,7 +351,8 @@ def make_list(srange):
     z = np.atleast_2d(np.array(z))
 
     if not a.shape[1] == x.shape[1] == z.shape[1]:
-        raise QiskitError("Input matrices/vectors must have the same number of columns/length")
+        raise QiskitError(
+            "Input matrices/vectors must have the same number of columns/length")
 
     return _make_commute_hyper(a, x, z, arange, xrange, zrange, squeeze)
 
@@ -618,7 +621,8 @@ def build_hyper_partner(matrix, index: int) -> np.ndarray:
 
     # matrix -> all associated operators must commute
     if not all_commute(matrix):
-        raise QiskitError("Input matrix must represent a set of commuting operators")
+        raise QiskitError(
+            "Input matrix must represent a set of commuting operators")
 
     rank_ = mt.rank(matrix)
     if rank_ != matrix.shape[0]:
@@ -628,7 +632,8 @@ def build_hyper_partner(matrix, index: int) -> np.ndarray:
         )
 
     if index not in range(matrix.shape[1] >> 1):
-        raise QiskitError(f"Input index out or range: {index}>={matrix.shape[1]>>1}")
+        raise QiskitError(
+            f"Input index out or range: {index}>={matrix.shape[1]>>1}")
 
     return _build_hyper_partner(matrix, index)
 
@@ -753,7 +758,8 @@ def symplectic_gram_schmidt(
         x = np.atleast_2d(x)
         x = list(x)
         if not is_symplectic_vector_form(x[0]):
-            raise QiskitError("Input hyperbolic array x is not a GF(2) sympletic matrix")
+            raise QiskitError(
+                "Input hyperbolic array x is not a GF(2) sympletic matrix")
 
     if z is None:
         z = []
@@ -761,7 +767,8 @@ def symplectic_gram_schmidt(
         z = np.atleast_2d(z)
         z = list(z)
         if not is_symplectic_vector_form(z[0]):
-            raise QiskitError("Input hyperbolic array z is not a GF(2) sympletic matrix")
+            raise QiskitError(
+                "Input hyperbolic array z is not a GF(2) sympletic matrix")
 
     if not len(x) == len(z):
         raise QiskitError("Input hyperbolic arrays have different dimensions")
@@ -771,7 +778,8 @@ def symplectic_gram_schmidt(
 
     if x != []:
         if not is_hyper_form(x, z):
-            raise QiskitError("Input hyperbolic matrices do not represent a hyperbolic basis")
+            raise QiskitError(
+                "Input hyperbolic matrices do not represent a hyperbolic basis")
 
     return _symplectic_gram_schmidt(a, x, z)
 
@@ -834,7 +842,7 @@ def _symplectic_gram_schmidt(
 
             # Revove elem_p from a_view
             temp_view = a_view[:-1]
-            temp_view[index:] = a_view[index + 1 :]
+            temp_view[index:] = a_view[index + 1:]
             a_view = temp_view
 
             a_view = make_commute_hyper(a_view, elem, elem_p)
@@ -1496,7 +1504,8 @@ def _make_hyperbolic(
     while center_size > 0:
         hop = _build_hyper_partner(center_[:center_size], center_size - 1)
         # TODO: Change the use of make_commute_hyper to _make_commute_hyper
-        hop = make_commute_hyper(hop, x, z, xrange=range(hyper_size), zrange=range(hyper_size))
+        hop = make_commute_hyper(hop, x, z, xrange=range(
+            hyper_size), zrange=range(hyper_size))
         # hop = _make_element_commute_with_hyper_pairs(
         #    hop, x, z, range(hyper_size), range(hyper_size)
         # )
@@ -1657,7 +1666,8 @@ def hyperbolic_basis_for_pauli_group(
     else:
         if matrix is None:
             if n is None:
-                raise QiskitError("If matrix, x and z are None then n must be provided")
+                raise QiskitError(
+                    "If matrix, x and z are None then n must be provided")
             zero = np.zeros(shape=(n, n), dtype=np.bool_)
             x = mt.augment_mat(zero, "left")
             z = mt.augment_mat(zero, "right")
@@ -1803,7 +1813,8 @@ def remove_hyper_elements_from_hyper_form(
     if center_ is not None:
         center_ = np.atleast_2d(np.array(center_))
         if not is_symplectic_matrix_form(center_):
-            raise QiskitError("Input center is not a GF(2) symplectiv matrix/vector")
+            raise QiskitError(
+                "Input center is not a GF(2) symplectiv matrix/vector")
         if not x.shape[1] == center_.shape[1]:
             raise QiskitError(
                 "x and z must have the same size in the second \
@@ -1888,7 +1899,8 @@ def min_generating(
 
     Args:
         matrix (Optional[np.ndarray]): Input GF(2) symplectic matrix
-        x, z (Optional[np.ndarray]): Input hyperbolic set - pair of GF(2) symplectic matrices
+        x (Optional[np.ndarray]): Input hyperbolic set - pair of GF(2) symplectic matrices
+        z (Optional[np.ndarray]): Input hyperbolic set - pair of GF(2) symplectic matrices
 
     Raises:
         QiskitError: An input matrix is required
@@ -1969,7 +1981,8 @@ def _min_generating_matrix(matrix: np.ndarray) -> np.ndarray:
         return matrix
 
     posns = np.flatnonzero(heads)
-    ext_matrix = np.zeros(shape=(posns.shape[0], matrix.shape[1]), dtype=np.bool_)
+    ext_matrix = np.zeros(
+        shape=(posns.shape[0], matrix.shape[1]), dtype=np.bool_)
     for k, index in enumerate(posns):
         ext_matrix[k] = matrix[index]
     return ext_matrix
@@ -1991,8 +2004,9 @@ def _min_generating_matrix_xz(matrix, x, z) -> np.ndarray:
     heads, _, _, rank_ = mt.rref_complete(tmp_matrix)
     if rank_ < tmp_matrix.shape[0]:
         # Since (x,z) has already been reduced any removal will appear in the matrix part
-        posns = np.flatnonzero(heads[2 * x.shape[0] :])
-        ext_matrix = np.zeros(shape=(posns.shape[0], matrix.shape[1]), dtype=np.bool_)
+        posns = np.flatnonzero(heads[2 * x.shape[0]:])
+        ext_matrix = np.zeros(
+            shape=(posns.shape[0], matrix.shape[1]), dtype=np.bool_)
         for k, index in enumerate(posns):
             ext_matrix[k] = matrix[index]
         matrix = ext_matrix
@@ -2075,7 +2089,8 @@ def normalizer(
         raise QiskitError("x and z must have the same shape")
 
     if not matrix.shape[1] == x.shape[1]:
-        raise QiskitError("All inputs must have the same number of columns/length")
+        raise QiskitError(
+            "All inputs must have the same number of columns/length")
 
     if not is_center(matrix, np.vstack((matrix, x, z))):
         raise QiskitError(
@@ -2106,7 +2121,8 @@ def _normalizer_abelian_group(
 
     matrix_ext = _basis_for_pauli_group(matrix)
     center_, x, z = _symplectic_gram_schmidt(matrix_ext, [], [])
-    center_, x, z = _remove_hyper_elements_from_hyper_form(center_, x, z, list(range(dist_center)))
+    center_, x, z = _remove_hyper_elements_from_hyper_form(
+        center_, x, z, list(range(dist_center)))
 
     if center_.shape[0] > 1:
         center_ = center_[np.where(center_.any(axis=1))[0]]
@@ -2143,7 +2159,8 @@ def _normalizer_group_preserve(
         x, z = _make_hyperbolic(center_, x, z)
 
     matrix_ext = _basis_for_pauli_group(np.vstack((x, z)))
-    matrix_ext = make_commute_hyper(matrix_ext, x, z, range(x.shape[0] << 1, matrix_ext.shape[0]))
+    matrix_ext = make_commute_hyper(
+        matrix_ext, x, z, range(x.shape[0] << 1, matrix_ext.shape[0]))
     # matrix_ext = _make_elements_commute_with_hyper_pairs(
     #    matrix_ext,
     #    range(x.shape[0] << 1, matrix_ext.shape[0]),
@@ -2152,9 +2169,9 @@ def _normalizer_group_preserve(
     #    z,
     #    range(z.shape[0]),
     # )
-    matrix = matrix_ext[x.shape[0] << 1 :]
+    matrix = matrix_ext[x.shape[0] << 1:]
     lx = [item.copy() for item in matrix_ext[: x.shape[0]]]
-    lz = [item.copy() for item in matrix_ext[x.shape[0] : x.shape[0] << 1]]
+    lz = [item.copy() for item in matrix_ext[x.shape[0]: x.shape[0] << 1]]
     center_, x, z = _symplectic_gram_schmidt(matrix, lx, lz)
     indices = list(range(gauge_degree, gauge_degree + center_size))
     return _remove_hyper_elements_from_hyper_form(center_, x, z, indices)
diff --git a/src/qiskit_qec/utils/decoding_graph_attributes.py b/src/qiskit_qec/utils/decoding_graph_attributes.py
index c650e72c..85699053 100644
--- a/src/qiskit_qec/utils/decoding_graph_attributes.py
+++ b/src/qiskit_qec/utils/decoding_graph_attributes.py
@@ -57,11 +57,13 @@ def __getitem__(self, key):
             return self.properties[key]
         else:
             raise QiskitQECError(
-                "'" + str(key) + "'" + " is not an an attribute or property of the node."
+                "'" + str(key) + "'" +
+                " is not an an attribute or property of the node."
             )
 
     def get(self, key, _):
         """A dummy docstring."""
+        # pylint: disable=unnecessary-dunder-call
         return self.__getitem__(key)
 
     def __setitem__(self, key, value):
@@ -117,11 +119,13 @@ def __getitem__(self, key):
             return self.properties[key]
         else:
             raise QiskitQECError(
-                "'" + str(key) + "'" + " is not an an attribute or property of the edge."
+                "'" + str(key) + "'" +
+                " is not an an attribute or property of the edge."
             )
 
     def get(self, key, _):
         """A dummy docstring."""
+        # pylint: disable=unnecessary-dunder-call
         return self.__getitem__(key)
 
     def __setitem__(self, key, value):
diff --git a/src/qiskit_qec/utils/stim_tools.py b/src/qiskit_qec/utils/stim_tools.py
index b5ca721c..17015ab4 100644
--- a/src/qiskit_qec/utils/stim_tools.py
+++ b/src/qiskit_qec/utils/stim_tools.py
@@ -144,7 +144,7 @@ def get_counts_via_stim(
     """Returns a qiskit compatible dictionary of measurement outcomes
 
     Args:
-        circuit: Qiskit circuit compatible with `get_stim_circuits` or list thereof.
+        circuits: Qiskit circuit compatible with `get_stim_circuits` or list thereof.
         shots: Number of samples to be generated.
         noise_model: Pauli noise model for any additional noise to be applied.
 
diff --git a/test/code_circuits/test_rep_codes.py b/test/code_circuits/test_rep_codes.py
index 763fe70d..a84eb9c0 100644
--- a/test/code_circuits/test_rep_codes.py
+++ b/test/code_circuits/test_rep_codes.py
@@ -16,20 +16,23 @@
 
 """Run codes and decoders."""
 
-import unittest
 import itertools
+import unittest
 from random import choices
 
 from qiskit import Aer, QuantumCircuit, execute
 from qiskit.providers.fake_provider import FakeJakarta
 from qiskit_aer.noise import NoiseModel
 from qiskit_aer.noise.errors import depolarizing_error
-from qiskit_qec.circuits.repetition_code import RepetitionCodeCircuit as RepetitionCode
+
+from qiskit_qec.analysis.faultenumerator import FaultEnumerator
 from qiskit_qec.circuits.repetition_code import ArcCircuit
+from qiskit_qec.circuits.repetition_code import \
+    RepetitionCodeCircuit as RepetitionCode
 from qiskit_qec.decoders.decoding_graph import DecodingGraph
+from qiskit_qec.decoders.hdrg_decoders import (BravyiHaahDecoder,
+                                               UnionFindDecoder)
 from qiskit_qec.utils import DecodingGraphNode
-from qiskit_qec.analysis.faultenumerator import FaultEnumerator
-from qiskit_qec.decoders.hdrg_decoders import BravyiHaahDecoder, UnionFindDecoder
 
 
 def get_syndrome(code, noise_model, shots=1024):
@@ -55,7 +58,8 @@ def get_noise(p_meas, p_gate):
     error_gate2 = error_gate1.tensor(error_gate1)
 
     noise_model = NoiseModel()
-    noise_model.add_all_qubit_readout_error([[1 - p_meas, p_meas], [p_meas, 1 - p_meas]])
+    noise_model.add_all_qubit_readout_error(
+        [[1 - p_meas, p_meas], [p_meas, 1 - p_meas]])
     noise_model.add_all_qubit_quantum_error(error_gate1, ["h"])
     noise_model.add_all_qubit_quantum_error(error_gate2, ["cx"])
 
@@ -91,7 +95,7 @@ def single_error_test(
                         temp_qc.name = str((j, qubit, error))
                         temp_qc.data = qc.data[0:j]
                         getattr(temp_qc, error)(qubit)
-                        temp_qc.data += qc.data[j : depth + 1]
+                        temp_qc.data += qc.data[j: depth + 1]
                         circuit_name[(j, qubit, error)] = temp_qc.name
                         error_circuit[temp_qc.name] = temp_qc
 
@@ -125,7 +129,8 @@ def test_string2nodes_1(self):
         s0 = "0 0  01 00 01"
         s1 = "1 1  01 00 01"
         self.assertTrue(
-            code.string2nodes(s0, logical="0") == code.string2nodes(s1, logical="1"),
+            code.string2nodes(s0, logical="0") == code.string2nodes(
+                s1, logical="1"),
             "Error: Incorrect nodes from results string",
         )
 
@@ -197,8 +202,10 @@ def test_weight(self):
                 + "'."
             )
             p = dec.get_error_probs(test_results, method=method)
-            n0 = dec.graph.nodes().index(DecodingGraphNode(time=0, qubits=[0, 1], index=0))
-            n1 = dec.graph.nodes().index(DecodingGraphNode(time=0, qubits=[1, 2], index=1))
+            n0 = dec.graph.nodes().index(
+                DecodingGraphNode(time=0, qubits=[0, 1], index=0))
+            n1 = dec.graph.nodes().index(
+                DecodingGraphNode(time=0, qubits=[1, 2], index=1))
             # edges in graph aren't directed and could be in any order
             if (n0, n1) in p:
                 self.assertTrue(round(p[n0, n1], 2) == 0.33, error)
@@ -224,7 +231,8 @@ def single_error_test(
             edges = link_graph.incident_edges(n)
             incident_links[node] = set()
             for edge in edges:
-                incident_links[node].add(link_graph.edges()[edge]["link qubit"])
+                incident_links[node].add(
+                    link_graph.edges()[edge]["link qubit"])
             if node in code.z_logicals:
                 incident_links[node].add(None)
 
@@ -246,7 +254,8 @@ def single_error_test(
                     minimal = minimal and (max(ts) - min(ts)) <= 1
                 # check that it doesn't extend beyond the neigbourhood of a code qubit
                 flat_nodes = code.flatten_nodes(nodes)
-                link_qubits = set(node.properties["link qubit"] for node in flat_nodes)
+                link_qubits = set(
+                    node.properties["link qubit"] for node in flat_nodes)
                 minimal = minimal and link_qubits in incident_links.values()
                 self.assertTrue(
                     minimal,
@@ -315,23 +324,28 @@ def test_202s(self):
             self.assertTrue(
                 running_202 == run_202,
                 "Error: [[2,0,2]] codes not present when required." * run_202
-                + "Error: [[2,0,2]] codes present when not required." * (not run_202),
+                + "Error: [[2,0,2]] codes present when not required." *
+                (not run_202),
             )
         # second, do they yield non-trivial outputs yet trivial nodes
-        code = ArcCircuit(links, T=T, run_202=True, logical="1", rounds_per_202=5)
+        code = ArcCircuit(links, T=T, run_202=True,
+                          logical="1", rounds_per_202=5)
         backend = Aer.get_backend("aer_simulator")
         counts = backend.run(code.circuit[code.basis]).result().get_counts()
-        self.assertTrue(len(counts) > 1, "No randomness in the results for [[2,0,2]] circuits.")
+        self.assertTrue(len(counts) > 1,
+                        "No randomness in the results for [[2,0,2]] circuits.")
         nodeless = True
         for string in counts:
-            nodeless = nodeless and code.string2nodes(string) == []
-        self.assertTrue(nodeless, "Non-trivial nodes found for noiseless [[2,0,2]] circuits.")
+            nodeless = nodeless and not code.string2nodes(string)
+        self.assertTrue(
+            nodeless, "Non-trivial nodes found for noiseless [[2,0,2]] circuits.")
 
     def test_single_error_202s(self):
         """Test a range of single errors for a code with [[2,0,2]] codes."""
         links = [(0, 1, 2), (2, 3, 4), (4, 5, 0), (2, 7, 6)]
         for T in [21, 25]:
-            code = ArcCircuit(links, T, run_202=True, barriers=True, logical="1", rounds_per_202=5)
+            code = ArcCircuit(links, T, run_202=True,
+                              barriers=True, logical="1", rounds_per_202=5)
             assert code.run_202
             # insert errors on a selection of qubits during a selection of rounds
             qc = code.circuit[code.base]
@@ -348,11 +362,14 @@ def test_single_error_202s(self):
                             barrier_num += 1
                             if barrier_num == 2 * t + 1:
                                 if q % 2 == 0:
-                                    error_qc.z(code.code_qubit[code.code_index[q]])
+                                    error_qc.z(
+                                        code.code_qubit[code.code_index[q]])
                                 else:
-                                    error_qc.x(code.link_qubit[code.link_index[q]])
+                                    error_qc.x(
+                                        code.link_qubit[code.link_index[q]])
                         error_qc.append(gate)
-                    counts = Aer.get_backend("qasm_simulator").run(error_qc).result().get_counts()
+                    counts = Aer.get_backend("qasm_simulator").run(
+                        error_qc).result().get_counts()
                     for string in counts:
                         # look at only bulk non-conjugate nodes
                         nodes = [
@@ -397,7 +414,8 @@ def test_feedforward(self):
             counts = result.get_counts(j)
             for string in counts:
                 # final result should be same as initial
-                correct_final = code.logical + str((int(code.logical) + 1) % 2) + code.logical * 2
+                correct_final = code.logical + \
+                    str((int(code.logical) + 1) % 2) + code.logical * 2
                 correct = correct and string[0:4] == correct_final
         self.assertTrue(correct, "Result string not as required")
 
@@ -420,7 +438,8 @@ def test_bases(self):
                 else:
                     for op in ["s", "sdg"]:
                         rightops = rightops and op not in ops
-        self.assertTrue(rightops, "Error: Required rotations for basis changes not present.")
+        self.assertTrue(
+            rightops, "Error: Required rotations for basis changes not present.")
 
     def test_anisotropy(self):
         """Test that code qubits have neighbors with the opposite color."""
@@ -430,7 +449,8 @@ def test_anisotropy(self):
         color = code.color
         for j in range(1, link_num - 1):
             self.assertTrue(
-                color[2 * j] != color[2 * (j - 1)] or color[2 * j] != color[2 * (j + 1)],
+                color[2 * j] != color[2 *
+                                      (j - 1)] or color[2 * j] != color[2 * (j + 1)],
                 "Error: Code qubit does not have neighbor of oppposite color.",
             )
 
@@ -439,16 +459,20 @@ def test_transpilation(self):
         backend = FakeJakarta()
         links = [(0, 1, 3), (3, 5, 6)]
         schedule = [[(0, 1), (3, 5)], [(3, 1), (6, 5)]]
-        code = ArcCircuit(links, schedule=schedule, T=2, delay=1000, logical="0")
+        code = ArcCircuit(links, schedule=schedule,
+                          T=2, delay=1000, logical="0")
         circuit = code.transpile(backend)
-        self.assertTrue(code.schedule == schedule, "Error: Given schedule not used.")
+        self.assertTrue(code.schedule == schedule,
+                        "Error: Given schedule not used.")
         circuit = code.transpile(backend, echo_num=(0, 2))
         self.assertTrue(
-            circuit[code.base].count_ops()["x"] == 2, "Error: Wrong echo sequence for link qubits."
+            circuit[code.base].count_ops(
+            )["x"] == 2, "Error: Wrong echo sequence for link qubits."
         )
         circuit = code.transpile(backend, echo_num=(2, 0))
         self.assertTrue(
-            circuit[code.base].count_ops()["x"] == 8, "Error: Wrong echo sequence for code qubits."
+            circuit[code.base].count_ops(
+            )["x"] == 8, "Error: Wrong echo sequence for code qubits."
         )
         self.assertTrue(
             circuit[code.base].count_ops()["cx"] == 8,
@@ -526,7 +550,8 @@ def clustering_decoder_test(
         for row in [0, 1]:
             for j in range(half_d - 1):
                 delta = row * (2 * half_d - 1)
-                links_ladder.append((delta + 2 * j, delta + 2 * j + 1, delta + 2 * (j + 1)))
+                links_ladder.append(
+                    (delta + 2 * j, delta + 2 * j + 1, delta + 2 * (j + 1)))
         q = links_ladder[-1][2] + 1
         for j in range(half_d):
             delta = 2 * half_d - 1
@@ -537,15 +562,17 @@ def clustering_decoder_test(
         for c, code in enumerate(codes):
             decoding_graph = DecodingGraph(code)
             if c == 3 and Decoder is UnionFindDecoder:
-                decoder = Decoder(code, decoding_graph=decoding_graph, use_peeling=False)
+                decoder = Decoder(
+                    code, decoding_graph=decoding_graph, use_peeling=False)
             else:
                 decoder = Decoder(code, decoding_graph=decoding_graph)
-            errors = {z_logical[0]: 0 for z_logical in decoder.measured_logicals}
+            errors = {z_logical[0]                      : 0 for z_logical in decoder.measured_logicals}
             min_error_num = code.d
             min_error_string = ""
             for _ in range(N):
                 # generate random string
-                string = "".join([choices(["1", "0"], [1 - p, p])[0] for _ in range(d)])
+                string = "".join([choices(["1", "0"], [1 - p, p])[0]
+                                 for _ in range(d)])
                 for _ in range(code.T):
                     string = string + " " + "0" * (d - 1)
                 # get and check corrected_z_logicals
diff --git a/test/union_find/test_clayg.py b/test/union_find/test_clayg.py
index 6147df34..765456e2 100644
--- a/test/union_find/test_clayg.py
+++ b/test/union_find/test_clayg.py
@@ -15,8 +15,9 @@
 import math
 import random
 import unittest
-from qiskit_qec.decoders import ClAYGDecoder
+
 from qiskit_qec.circuits import RepetitionCodeCircuit
+from qiskit_qec.decoders import ClAYGDecoder
 from qiskit_qec.noise.paulinoisemodel import PauliNoiseModel
 
 
@@ -124,7 +125,8 @@ def test_error_rates(self):
 
         testcases = []
         testcases = [
-            "".join([random.choices(["0", "1"], [1 - p, p])[0] for _ in range(d)])
+            "".join([random.choices(["0", "1"], [1 - p, p])[0]
+                    for _ in range(d)])
             for _ in range(samples)
         ]
         codes = self.construct_codes(d)
@@ -144,10 +146,13 @@ def test_error_rates(self):
                 string += testcases[sample]
                 # get and check corrected_z_logicals
                 outcome = decoder.process(string)
-                logical_outcome = sum([outcome[int(z_logical / 2)] for z_logical in z_logicals]) % 2
+                # pylint: disable=consider-using-generator
+                logical_outcome = sum([outcome[int(z_logical / 2)]
+                                      for z_logical in z_logicals]) % 2
                 if not logical_outcome == 0:
                     logical_errors += 1
-                    min_flips_for_logical = min(min_flips_for_logical, string.count("1"))
+                    min_flips_for_logical = min(
+                        min_flips_for_logical, string.count("1"))
 
             # check that error rates are at least <p^/2
             # and that min num errors to cause logical errors >d/3
diff --git a/test/utils/test_visualization.py b/test/utils/test_visualization.py
index 7635728d..7f83d355 100644
--- a/test/utils/test_visualization.py
+++ b/test/utils/test_visualization.py
@@ -1,5 +1,17 @@
-# """Test pauli rep."""
+# -*- coding: utf-8 -*-
 
+# This code is part of Qiskit.
+#
+# (C) Copyright IBM 2019-2023.
+#
+# This code is licensed under the Apache License, Version 2.0. You may
+# obtain a copy of this license in the LICENSE.txt file in the root directory
+# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
+#
+# Any modifications or derivative works of this code must retain this
+# copyright notice, and modified files need to carry a notice indicating
+# that they have been altered from the originals.
+"""Visualization Module"""
 from unittest import TestCase
 
 from qiskit_qec.utils.visualizations import QiskitGameEngine, Screen
@@ -42,10 +54,12 @@ def next_frame(_):
             "Default color not correct for pixel in game engine.",
         )
         self.assertTrue(
-            engine.screen.pixel[engine.size - 1, 0].button.button_style == "danger",
+            engine.screen.pixel[engine.size - 1,
+                                0].button.button_style == "danger",
             "Pixel in game engine did not turn red when required.",
         )
         self.assertTrue(
-            engine.screen.pixel[0, engine.size - 1].button.description == "hello",
+            engine.screen.pixel[0, engine.size -
+                                1].button.description == "hello",
             "Pixel in game engine not displaying correct text",
         )