From c6704ad8d3e034c25d8aaa5d71f0a8a4c4d7d6eb Mon Sep 17 00:00:00 2001
From: Hayk Sargsyan <52532457+hay-k@users.noreply.github.com>
Date: Wed, 21 Aug 2024 15:30:00 +0400
Subject: [PATCH 01/70] fix kernel based weights being generated multiple times

---
 src/qibolab/instruments/zhinst/executor.py | 74 ++++++++++------------
 1 file changed, 33 insertions(+), 41 deletions(-)

diff --git a/src/qibolab/instruments/zhinst/executor.py b/src/qibolab/instruments/zhinst/executor.py
index bfba7a6d98..995863bf94 100644
--- a/src/qibolab/instruments/zhinst/executor.py
+++ b/src/qibolab/instruments/zhinst/executor.py
@@ -559,6 +559,34 @@ def get_channel_node_path(self, channel_name: str) -> str:
             f"Could not find instrument node corresponding to channel {channel_name}"
         )
 
+    def _calculate_weight(self, pulse, qubit, exp_options):
+        if (
+            qubit.kernel is not None
+            and exp_options.acquisition_type == lo.AcquisitionType.DISCRIMINATION
+        ):
+            return lo.pulse_library.sampled_pulse_complex(
+                samples=qubit.kernel * np.exp(1j * qubit.iq_angle),
+            )
+
+        elif exp_options.acquisition_type == lo.AcquisitionType.DISCRIMINATION:
+            return lo.pulse_library.sampled_pulse_complex(
+                samples=np.ones(
+                    [
+                        int(
+                            pulse.pulse.duration * 2
+                            - 3 * self.smearing * NANO_TO_SECONDS
+                        )
+                    ]
+                )
+                * np.exp(1j * qubit.iq_angle),
+            )
+        else:
+            return lo.pulse_library.const(
+                length=round(pulse.pulse.duration * NANO_TO_SECONDS, 9)
+                - 1.5 * self.smearing * NANO_TO_SECONDS,
+                amplitude=1,
+            )
+
     def select_exp(self, exp, qubits, exp_options):
         """Build Zurich Experiment selecting the relevant sections."""
         # channels that were not split are just applied in parallel to the rest of the experiment
@@ -607,53 +635,17 @@ def select_exp(self, exp, qubits, exp_options):
             with exp.section(uid=section_uid, play_after=previous_section):
                 for ch, pulse in seq.measurements:
                     qubit = qubits[pulse.pulse.qubit]
-                    q = qubit.name
 
                     exp.delay(
                         signal=acquire_channel_name(qubit),
                         time=self.smearing * NANO_TO_SECONDS,
                     )
 
-                    if (
-                        qubit.kernel is not None
-                        and exp_options.acquisition_type
-                        == lo.AcquisitionType.DISCRIMINATION
-                    ):
-                        weight = lo.pulse_library.sampled_pulse_complex(
-                            samples=qubit.kernel * np.exp(1j * qubit.iq_angle),
+                    if qubit.name not in weights:
+                        weights[qubit.name] = self._calculate_weight(
+                            pulse, qubit, exp_options
                         )
 
-                    else:
-                        if i == 0:
-                            if (
-                                exp_options.acquisition_type
-                                == lo.AcquisitionType.DISCRIMINATION
-                            ):
-                                weight = lo.pulse_library.sampled_pulse_complex(
-                                    samples=np.ones(
-                                        [
-                                            int(
-                                                pulse.pulse.duration * 2
-                                                - 3 * self.smearing * NANO_TO_SECONDS
-                                            )
-                                        ]
-                                    )
-                                    * np.exp(1j * qubit.iq_angle),
-                                )
-                                weights[q] = weight
-                            else:
-                                weight = lo.pulse_library.const(
-                                    length=round(
-                                        pulse.pulse.duration * NANO_TO_SECONDS, 9
-                                    )
-                                    - 1.5 * self.smearing * NANO_TO_SECONDS,
-                                    amplitude=1,
-                                )
-
-                                weights[q] = weight
-                        elif i != 0:
-                            weight = weights[q]
-
                     measure_pulse_parameters = {"phase": 0}
 
                     if i == len(self.sequence[measure_channel_name(qubit)]) - 1:
@@ -663,8 +655,8 @@ def select_exp(self, exp, qubits, exp_options):
 
                     exp.measure(
                         acquire_signal=acquire_channel_name(qubit),
-                        handle=f"sequence{q}_{i}",
-                        integration_kernel=weight,
+                        handle=f"sequence{qubit.name}_{i}",
+                        integration_kernel=weights[qubit.name],
                         integration_kernel_parameters=None,
                         integration_length=None,
                         measure_signal=measure_channel_name(qubit),

From cb040762e572642da732a2557e39bb477b4bc146 Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Sun, 15 Sep 2024 11:47:07 +0400
Subject: [PATCH 02/70] fix: Add minus sign to RZ rule

---
 src/qibolab/compilers/default.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/qibolab/compilers/default.py b/src/qibolab/compilers/default.py
index a9bc0a8d3c..b178eefe92 100644
--- a/src/qibolab/compilers/default.py
+++ b/src/qibolab/compilers/default.py
@@ -22,7 +22,7 @@ def z_rule(gate, platform):
 def rz_rule(gate, platform):
     """RZ gate applied virtually."""
     qubit = list(platform.qubits)[gate.target_qubits[0]]
-    return PulseSequence(), {qubit: gate.parameters[0]}
+    return PulseSequence(), {qubit: -gate.parameters[0]}
 
 
 def gpi2_rule(gate, platform):

From 15dce6acc7c283363f9fc67ecde5b9972925d9ed Mon Sep 17 00:00:00 2001
From: Stavros Efthymiou <35475381+stavros11@users.noreply.github.com>
Date: Tue, 8 Oct 2024 15:20:48 +0400
Subject: [PATCH 03/70] fix: change Rust array type to u32

---
 crate/src/lib.rs | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/crate/src/lib.rs b/crate/src/lib.rs
index 3238e6acb6..be73f64552 100644
--- a/crate/src/lib.rs
+++ b/crate/src/lib.rs
@@ -3,7 +3,7 @@ use numpy::PyArray2;
 use pyo3::prelude::*;
 use pyo3::types::PyDict;
 
-pub fn execute_qasm(circuit: String, platform: String, nshots: u32) -> PyResult<Array2<i32>> {
+pub fn execute_qasm(circuit: String, platform: String, nshots: u32) -> PyResult<Array2<u32>> {
     Python::with_gil(|py| {
         let kwargs = PyDict::new(py);
         kwargs.set_item("circuit", circuit)?;
@@ -11,7 +11,7 @@ pub fn execute_qasm(circuit: String, platform: String, nshots: u32) -> PyResult<
         kwargs.set_item("nshots", nshots)?;
 
         let qibolab = PyModule::import(py, "qibolab")?;
-        let pyarray: &PyArray2<i32> = qibolab
+        let pyarray: &PyArray2<u32> = qibolab
             .getattr("execute_qasm")?
             .call((), Some(kwargs))?
             .call_method0("samples")?

From edf8b2574e92e72f7d8ae7ceecf662bb07190498 Mon Sep 17 00:00:00 2001
From: Stavros Efthymiou <35475381+stavros11@users.noreply.github.com>
Date: Mon, 16 Sep 2024 16:26:12 +0400
Subject: [PATCH 04/70] feat: introduce OPX1000 concepts

---
 src/qibolab/instruments/qm/config.py  | 18 +++++++-
 src/qibolab/instruments/qm/devices.py | 62 +++++++++++++++++++++++++--
 src/qibolab/instruments/qm/ports.py   | 30 ++++++++++++-
 3 files changed, 103 insertions(+), 7 deletions(-)

diff --git a/src/qibolab/instruments/qm/config.py b/src/qibolab/instruments/qm/config.py
index 41c1f3e4af..3f528048e4 100644
--- a/src/qibolab/instruments/qm/config.py
+++ b/src/qibolab/instruments/qm/config.py
@@ -6,7 +6,7 @@
 
 from qibolab.pulses import PulseType, Rectangular
 
-from .ports import OPXIQ, OctaveInput, OctaveOutput, OPXOutput
+from .ports import OPXIQ, FEMInput, FEMOutput, OctaveInput, OctaveOutput, OPXOutput
 
 SAMPLING_RATE = 1
 """Sampling rate of Quantum Machines OPX in GSps."""
@@ -48,17 +48,31 @@ def register_port(self, port):
             self.register_port(port.q)
         else:
             is_octave = isinstance(port, (OctaveOutput, OctaveInput))
+            is_fem = isinstance(port, (FEMOutput, FEMInput))
             controllers = self.octaves if is_octave else self.controllers
             if port.device not in controllers:
                 if is_octave:
                     controllers[port.device] = {}
+                elif is_fem:
+                    controllers[port.device] = {"type": "opx1000", "fems": {}}
                 else:
                     controllers[port.device] = {
                         "analog_inputs": DEFAULT_INPUTS,
                         "digital_outputs": {},
                     }
 
-            device = controllers[port.device]
+            if is_fem:
+                fems = controllers[port.device]["fems"]
+                if port.fem_number not in fems:
+                    fems[port.fem_number] = {
+                        "type": port.fem_type,
+                        "analog_inputs": DEFAULT_INPUTS,
+                        "digital_outputs": {},
+                    }
+                device = fems[port.fem_number]
+            else:
+                device = controllers[port.device]
+
             if port.key in device:
                 device[port.key].update(port.config)
             else:
diff --git a/src/qibolab/instruments/qm/devices.py b/src/qibolab/instruments/qm/devices.py
index 6ec0674d88..f314529ac4 100644
--- a/src/qibolab/instruments/qm/devices.py
+++ b/src/qibolab/instruments/qm/devices.py
@@ -1,12 +1,14 @@
 from collections import defaultdict
 from dataclasses import dataclass, field
 from itertools import chain
-from typing import Dict
+from typing import Dict, Literal, Union
 
 from qibolab.instruments.abstract import Instrument
 
 from .ports import (
     OPXIQ,
+    FEMInput,
+    FEMOutput,
     OctaveInput,
     OctaveOutput,
     OPXInput,
@@ -94,13 +96,60 @@ def __post_init__(self):
         self.inputs = PortsDefaultdict(lambda n: OPXInput(self.name, n))
 
 
+@dataclass
+class FEM:
+    """Device handling OPX1000 FEMs."""
+
+    name: int
+    type: Literal["LF", "MF"] = "LF"
+
+
+@dataclass
+class OPX1000(QMDevice):
+    """Device handling OPX1000 controllers."""
+
+    fems: Dict[int, FEM] = field(default_factory=dict)
+
+    def __post_init__(self):
+        def kwargs(fem):
+            return {"fem_number": fem, "fem_type": self.fems[fem].type}
+
+        self.outputs = PortsDefaultdict(
+            lambda fem, n: FEMOutput(self.name, n, **kwargs(fem))
+        )
+        self.inputs = PortsDefaultdict(
+            lambda fem, n: FEMInput(self.name, n, **kwargs(fem))
+        )
+
+    def ports(self, fem_number: int, number: int, output: bool = True):
+        ports_ = self.outputs if output else self.inputs
+        return ports_[(fem_number, number)]
+
+    def connectivity(self, fem_number: int) -> tuple["OPX1000", int]:
+        return (self, fem_number)
+
+    def setup(self, **kwargs):
+        for name, settings in kwargs.items():
+            fem, port = name.split("/")
+            fem = int(fem)
+            number = int(port[1:])
+            if port[0] == "o":
+                self.outputs[(fem, number)].setup(**settings)
+            elif port[0] == "i":
+                self.inputs[(fem, number)].setup(**settings)
+            else:
+                raise ValueError(
+                    f"Invalid port name {name} in instrument settings for {self.name}."
+                )
+
+
 @dataclass
 class Octave(QMDevice):
     """Device handling Octaves."""
 
     port: int
     """Network port of the Octave in the cluster configuration."""
-    connectivity: OPXplus
+    connectivity: Union[OPXplus, tuple[OPX1000, int]]
     """OPXplus that acts as the waveform generator for the Octave."""
 
     def __post_init__(self):
@@ -115,7 +164,12 @@ def ports(self, number, output=True):
         """
         port = super().ports(number, output)
         if port.opx_port is None:
-            iport = self.connectivity.ports(2 * number - 1, output)
-            qport = self.connectivity.ports(2 * number, output)
+            if isinstance(self.connectivity, OPXplus):
+                iport = self.connectivity.ports(2 * number - 1, output)
+                qport = self.connectivity.ports(2 * number, output)
+            else:
+                opx, fem_number = self.connectivity
+                iport = opx.ports(fem_number, 2 * number - 1, output)
+                qport = opx.ports(fem_number, 2 * number, output)
             port.opx_port = OPXIQ(iport, qport)
         return port
diff --git a/src/qibolab/instruments/qm/ports.py b/src/qibolab/instruments/qm/ports.py
index 1d6ce2d444..2d3e54b4b8 100644
--- a/src/qibolab/instruments/qm/ports.py
+++ b/src/qibolab/instruments/qm/ports.py
@@ -1,5 +1,5 @@
 from dataclasses import dataclass, field, fields
-from typing import ClassVar, Dict, Optional, Union
+from typing import ClassVar, Dict, Literal, Optional, Union
 
 DIGITAL_DELAY = 57
 DIGITAL_BUFFER = 18
@@ -131,6 +131,34 @@ class OPXIQ:
     """Port implementing the Q-component of the signal."""
 
 
+@dataclass
+class FEMOutput(OPXOutput):
+    fem_number: int = 0
+    fem_type: Literal["LF", "MF"] = "LF"
+
+    @property
+    def name(self):
+        return f"{self.fem_number}/o{self.number}"
+
+    @property
+    def pair(self):
+        return (self.device, self.fem_number, self.number)
+
+
+@dataclass
+class FEMInput(OPXInput):
+    fem_number: int = 0
+    fem_type: Literal["LF", "MF"] = "LF"
+
+    @property
+    def name(self):
+        return f"{self.fem_number}/i{self.number}"
+
+    @property
+    def pair(self):
+        return (self.device, self.fem_number, self.number)
+
+
 @dataclass
 class OctaveOutput(QMOutput):
     key: ClassVar[str] = "RF_outputs"

From 450624f31523ffa88612858d08f1a099c49df2da Mon Sep 17 00:00:00 2001
From: Stavros Efthymiou <35475381+stavros11@users.noreply.github.com>
Date: Mon, 16 Sep 2024 17:27:52 +0400
Subject: [PATCH 05/70] fix: octave connectivity

---
 src/qibolab/instruments/qm/__init__.py   |  2 +-
 src/qibolab/instruments/qm/config.py     | 32 ++++++++++++------------
 src/qibolab/instruments/qm/controller.py |  4 ++-
 src/qibolab/instruments/qm/devices.py    |  7 ++++--
 src/qibolab/instruments/qm/ports.py      |  9 ++++---
 5 files changed, 31 insertions(+), 23 deletions(-)

diff --git a/src/qibolab/instruments/qm/__init__.py b/src/qibolab/instruments/qm/__init__.py
index e053aa970a..6689872786 100644
--- a/src/qibolab/instruments/qm/__init__.py
+++ b/src/qibolab/instruments/qm/__init__.py
@@ -1,2 +1,2 @@
 from .controller import QMController
-from .devices import Octave, OPXplus
+from .devices import FEM, OPX1000, Octave, OPXplus
diff --git a/src/qibolab/instruments/qm/config.py b/src/qibolab/instruments/qm/config.py
index 3f528048e4..74e69d1084 100644
--- a/src/qibolab/instruments/qm/config.py
+++ b/src/qibolab/instruments/qm/config.py
@@ -79,11 +79,19 @@ def register_port(self, port):
                 device[port.key] = port.config
 
             if is_octave:
-                con = port.opx_port.i.device
-                number = port.opx_port.i.number
-                device["connectivity"] = con
                 self.register_port(port.opx_port)
-                self.controllers[con]["digital_outputs"][number] = {}
+                subport = port.opx_port.i
+                if isinstance(subport, (FEMOutput, FEMInput)):
+                    con = subport.device
+                    fem = subport.fem_number
+                    number = subport.number
+                    device["connectivity"] = (con, fem)
+                    self.controllers[con]["fems"][fem]["digital_outputs"][number] = {}
+                else:
+                    con = subport.device
+                    number = subport.number
+                    device["connectivity"] = con
+                    self.controllers[con]["digital_outputs"][number] = {}
 
     @staticmethod
     def iq_imbalance(g, phi):
@@ -289,10 +297,6 @@ def register_pulse(self, qubit, qmpulse):
                     "waveforms": {"I": serial_i, "Q": serial_q},
                     "digital_marker": "ON",
                 }
-                # register drive pulse in elements
-                self.elements[qmpulse.element]["operations"][
-                    qmpulse.operation
-                ] = qmpulse.operation
 
             elif pulse.type is PulseType.FLUX:
                 serial = self.register_waveform(pulse)
@@ -303,10 +307,6 @@ def register_pulse(self, qubit, qmpulse):
                         "single": serial,
                     },
                 }
-                # register flux pulse in elements
-                self.elements[qmpulse.element]["operations"][
-                    qmpulse.operation
-                ] = qmpulse.operation
 
             elif pulse.type is PulseType.READOUT:
                 serial_i = self.register_waveform(pulse, "i")
@@ -326,14 +326,14 @@ def register_pulse(self, qubit, qmpulse):
                     },
                     "digital_marker": "ON",
                 }
-                # register readout pulse in elements
-                self.elements[qmpulse.element]["operations"][
-                    qmpulse.operation
-                ] = qmpulse.operation
 
             else:
                 raise_error(TypeError, f"Unknown pulse type {pulse.type.name}.")
 
+        self.elements[qmpulse.element]["operations"][
+            qmpulse.operation
+        ] = qmpulse.operation
+
     def register_waveform(self, pulse, mode="i"):
         """Registers waveforms in QM config.
 
diff --git a/src/qibolab/instruments/qm/controller.py b/src/qibolab/instruments/qm/controller.py
index 08d3f23f6e..a8032eea03 100644
--- a/src/qibolab/instruments/qm/controller.py
+++ b/src/qibolab/instruments/qm/controller.py
@@ -189,6 +189,9 @@ def __post_init__(self):
             # convert simulation duration from ns to clock cycles
             self.simulation_duration //= 4
 
+    def __str__(self):
+        return self.name
+
     def ports(self, name, output=True):
         """Provides instrument ports to the user.
 
@@ -255,7 +258,6 @@ def disconnect(self):
         self._reset_temporary_calibration()
         if self.manager is not None:
             self.manager.close_all_quantum_machines()
-            self.manager.close()
             self.is_connected = False
 
     def calibrate_mixers(self, qubits):
diff --git a/src/qibolab/instruments/qm/devices.py b/src/qibolab/instruments/qm/devices.py
index f314529ac4..e8b3a547bd 100644
--- a/src/qibolab/instruments/qm/devices.py
+++ b/src/qibolab/instruments/qm/devices.py
@@ -45,6 +45,9 @@ class QMDevice(Instrument):
     inputs: Dict[int, QMInput] = field(init=False)
     """Dictionary containing the instrument's input ports."""
 
+    def __str__(self):
+        return self.name
+
     def ports(self, number, output=True):
         """Provides instrument's ports to the user.
 
@@ -115,10 +118,10 @@ def kwargs(fem):
             return {"fem_number": fem, "fem_type": self.fems[fem].type}
 
         self.outputs = PortsDefaultdict(
-            lambda fem, n: FEMOutput(self.name, n, **kwargs(fem))
+            lambda pair: FEMOutput(self.name, pair[1], **kwargs(pair[0]))
         )
         self.inputs = PortsDefaultdict(
-            lambda fem, n: FEMInput(self.name, n, **kwargs(fem))
+            lambda pair: FEMInput(self.name, pair[1], **kwargs(pair[0]))
         )
 
     def ports(self, fem_number: int, number: int, output: bool = True):
diff --git a/src/qibolab/instruments/qm/ports.py b/src/qibolab/instruments/qm/ports.py
index 2d3e54b4b8..598f72406f 100644
--- a/src/qibolab/instruments/qm/ports.py
+++ b/src/qibolab/instruments/qm/ports.py
@@ -193,11 +193,14 @@ def digital_inputs(self):
 
         Digital markers are used to switch LOs on in triggered mode.
         """
-        opx = self.opx_port.i.device
-        number = self.opx_port.i.number
+        opx_port = self.opx_port.i
+        if isinstance(opx_port, (FEMOutput, FEMInput)):
+            port = (opx_port.device, opx_port.fem_number, opx_port.number)
+        else:
+            port = (opx_port.device, opx_port.number)
         return {
             "output_switch": {
-                "port": (opx, number),
+                "port": port,
                 "delay": self.digital_delay,
                 "buffer": self.digital_buffer,
             }

From e4bf6e4bd5146c4d70787c5e0c32dbb485a900fa Mon Sep 17 00:00:00 2001
From: Stavros Efthymiou <35475381+stavros11@users.noreply.github.com>
Date: Thu, 26 Sep 2024 16:08:19 +0400
Subject: [PATCH 06/70] feat: amplified output mode

---
 src/qibolab/instruments/qm/ports.py    |  3 +++
 src/qibolab/instruments/qm/sweepers.py | 10 ++++++----
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/qibolab/instruments/qm/ports.py b/src/qibolab/instruments/qm/ports.py
index 598f72406f..fcb50f67d3 100644
--- a/src/qibolab/instruments/qm/ports.py
+++ b/src/qibolab/instruments/qm/ports.py
@@ -135,6 +135,9 @@ class OPXIQ:
 class FEMOutput(OPXOutput):
     fem_number: int = 0
     fem_type: Literal["LF", "MF"] = "LF"
+    output_mode: Literal["direct", "amplified"] = field(
+        default="direct", metadata={"config": "output_mode"}
+    )
 
     @property
     def name(self):
diff --git a/src/qibolab/instruments/qm/sweepers.py b/src/qibolab/instruments/qm/sweepers.py
index 3110e1f3d8..081f682649 100644
--- a/src/qibolab/instruments/qm/sweepers.py
+++ b/src/qibolab/instruments/qm/sweepers.py
@@ -141,16 +141,18 @@ def _sweep_bias(sweepers, qubits, qmsequence, relaxation_time):
     for qubit in sweeper.qubits:
         b0 = qubit.flux.offset
         max_offset = qubit.flux.max_offset
+        if max_offset is None:
+            max_offset = 0.5
         max_value = maximum_sweep_value(sweeper.values, b0)
         check_max_offset(max_value, max_offset)
         offset0.append(declare(fixed, value=b0))
     b = declare(fixed)
     with for_(*from_array(b, sweeper.values)):
         for qubit, b0 in zip(sweeper.qubits, offset0):
-            with qua.if_((b + b0) >= 0.49):
-                qua.set_dc_offset(f"flux{qubit.name}", "single", 0.49)
-            with qua.elif_((b + b0) <= -0.49):
-                qua.set_dc_offset(f"flux{qubit.name}", "single", -0.49)
+            with qua.if_((b + b0) >= max_offset):
+                qua.set_dc_offset(f"flux{qubit.name}", "single", max_offset)
+            with qua.elif_((b + b0) <= -max_offset):
+                qua.set_dc_offset(f"flux{qubit.name}", "single", -max_offset)
             with qua.else_():
                 qua.set_dc_offset(f"flux{qubit.name}", "single", (b + b0))
 

From cb4ed576ce68645babb9697adec771fcb0ab4a09 Mon Sep 17 00:00:00 2001
From: Stavros Efthymiou <35475381+stavros11@users.noreply.github.com>
Date: Wed, 2 Oct 2024 13:21:25 +0400
Subject: [PATCH 07/70] chore: Change LO output mode to always_on

---
 src/qibolab/instruments/qm/ports.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/qibolab/instruments/qm/ports.py b/src/qibolab/instruments/qm/ports.py
index fcb50f67d3..bfdce18c00 100644
--- a/src/qibolab/instruments/qm/ports.py
+++ b/src/qibolab/instruments/qm/ports.py
@@ -180,7 +180,7 @@ class OctaveOutput(QMOutput):
 
     Can be external or internal.
     """
-    output_mode: str = field(default="triggered", metadata={"config": "output_mode"})
+    output_mode: str = field(default="always_on", metadata={"config": "output_mode"})
     """Can be: "always_on" / "always_off"/ "triggered" / "triggered_reversed"."""
     digital_delay: int = DIGITAL_DELAY
     """Delay for digital output channel."""

From 91a9c5bde401f3bc3a5c2a261ee955461843bdee Mon Sep 17 00:00:00 2001
From: Stavros Efthymiou <35475381+stavros11@users.noreply.github.com>
Date: Mon, 7 Oct 2024 17:01:10 +0400
Subject: [PATCH 08/70] fix: force offset setting

---
 src/qibolab/instruments/qm/controller.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/qibolab/instruments/qm/controller.py b/src/qibolab/instruments/qm/controller.py
index a8032eea03..e9017bb4b0 100644
--- a/src/qibolab/instruments/qm/controller.py
+++ b/src/qibolab/instruments/qm/controller.py
@@ -375,6 +375,10 @@ def sweep(self, qubits, couplers, sequence, options, *sweepers):
         # play pulses using QUA
         with qua.program() as experiment:
             n = declare(int)
+            for qubit in qubits.values():
+                if qubit.flux:
+                    qua.set_dc_offset(qubit.flux.name, "single", qubit.sweetspot)
+
             acquisitions = declare_acquisitions(ro_pulses, qubits, options)
             with for_(n, 0, n < options.nshots, n + 1):
                 sweep(

From a2ee33f9a3a58f4569085a6794faf2a7ea081ddc Mon Sep 17 00:00:00 2001
From: Stavros Efthymiou <35475381+stavros11@users.noreply.github.com>
Date: Mon, 7 Oct 2024 17:01:29 +0400
Subject: [PATCH 09/70] fix: output_mode dump

---
 src/qibolab/instruments/qm/ports.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/qibolab/instruments/qm/ports.py b/src/qibolab/instruments/qm/ports.py
index bfdce18c00..5a593746dc 100644
--- a/src/qibolab/instruments/qm/ports.py
+++ b/src/qibolab/instruments/qm/ports.py
@@ -136,7 +136,7 @@ class FEMOutput(OPXOutput):
     fem_number: int = 0
     fem_type: Literal["LF", "MF"] = "LF"
     output_mode: Literal["direct", "amplified"] = field(
-        default="direct", metadata={"config": "output_mode"}
+        default="direct", metadata={"config": "output_mode", "settings": True}
     )
 
     @property

From 721e127a4496f982f6419924c30cea3cb539d83f Mon Sep 17 00:00:00 2001
From: Stavros Efthymiou <35475381+stavros11@users.noreply.github.com>
Date: Tue, 8 Oct 2024 13:08:31 +0400
Subject: [PATCH 10/70] chore: variable definition repeated in if branches

---
 src/qibolab/instruments/qm/config.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/qibolab/instruments/qm/config.py b/src/qibolab/instruments/qm/config.py
index 74e69d1084..578efc24a5 100644
--- a/src/qibolab/instruments/qm/config.py
+++ b/src/qibolab/instruments/qm/config.py
@@ -81,15 +81,13 @@ def register_port(self, port):
             if is_octave:
                 self.register_port(port.opx_port)
                 subport = port.opx_port.i
+                con = subport.device
+                number = subport.number
                 if isinstance(subport, (FEMOutput, FEMInput)):
-                    con = subport.device
                     fem = subport.fem_number
-                    number = subport.number
                     device["connectivity"] = (con, fem)
                     self.controllers[con]["fems"][fem]["digital_outputs"][number] = {}
                 else:
-                    con = subport.device
-                    number = subport.number
                     device["connectivity"] = con
                     self.controllers[con]["digital_outputs"][number] = {}
 

From 9786545de79fcbdc40fc1d3341468eaec6e4d1ee Mon Sep 17 00:00:00 2001
From: Alvaro Orgaz <aorgazf@gmail.com>
Date: Wed, 15 May 2024 23:41:32 +0400
Subject: [PATCH 11/70] qblox support for couplers bias

---
 .../instruments/qblox/cluster_qcm_bb.py       | 42 +++++++++++++++----
 .../instruments/qblox/cluster_qcm_rf.py       |  1 +
 .../instruments/qblox/cluster_qrm_rf.py       |  1 +
 src/qibolab/instruments/qblox/controller.py   | 16 +++++--
 4 files changed, 49 insertions(+), 11 deletions(-)

diff --git a/src/qibolab/instruments/qblox/cluster_qcm_bb.py b/src/qibolab/instruments/qblox/cluster_qcm_bb.py
index e95cf69ef9..8aca5e382a 100644
--- a/src/qibolab/instruments/qblox/cluster_qcm_bb.py
+++ b/src/qibolab/instruments/qblox/cluster_qcm_bb.py
@@ -201,7 +201,7 @@ def setup(self, **settings):
         """
         pass
 
-    def _get_next_sequencer(self, port, frequency, qubits: dict):
+    def _get_next_sequencer(self, port, frequency, qubits: dict, couplers: dict = {}):
         """Retrieves and configures the next avaliable sequencer.
 
         The parameters of the new sequencer are copied from those of the default sequencer, except for the
@@ -209,17 +209,33 @@ def _get_next_sequencer(self, port, frequency, qubits: dict):
         Args:
             port (str):
             frequency ():
-            qubit ():
+            qubits ():
+            couplers ():
         Raises:
             Exception = If attempting to set a parameter without a connection to the instrument.
         """
-        # select the qubit with flux line, if present, connected to the specific port
+        # check if this port is responsible for the flux of any qubit or coupler
         qubit = None
         for _qubit in qubits.values():
-            name = _qubit.flux.port.name
-            module = _qubit.flux.port.module
-            if _qubit.flux is not None and (name, module) == (port, self):
-                qubit = _qubit
+            if _qubit.flux.port is not None:
+                if (
+                    _qubit.flux.port.name == port
+                    and _qubit.flux.port.module.name == self.name
+                ):
+                    qubit = _qubit
+            else:
+                log.warning(f"Qubit {_qubit.name} has no flux line connected")
+
+        coupler = None
+        for _coupler in couplers.values():
+            if _coupler.flux.port is not None:
+                if (
+                    _coupler.flux.port.name == port
+                    and _coupler.flux.port.module.name == self.name
+                ):
+                    coupler = _coupler
+            else:
+                log.warning(f"Coupler {_coupler.name} has no flux line connected")
 
         # select a new sequencer and configure it as required
         next_sequencer_number = self._free_sequencers_numbers.pop(0)
@@ -245,6 +261,13 @@ def _get_next_sequencer(self, port, frequency, qubits: dict):
             # TODO: Throw error in that event or implement for non_overlapping_same_frequency_pulses
             # Even better, set the frequency before each pulse is played (would work with hardware modulation only)
 
+            if qubit:
+                self._ports[port].offset = qubit.sweetspot
+            elif coupler:
+                self._ports[port].offset = coupler.sweetspot
+            else:
+                self._ports[port].offset = 0
+
         # create sequencer wrapper
         sequencer = Sequencer(next_sequencer_number)
         sequencer.qubit = qubit.name if qubit else None
@@ -267,6 +290,7 @@ def get_if(self, pulse):
     def process_pulse_sequence(
         self,
         qubits: dict,
+        couplers: dict,
         instrument_pulses: PulseSequence,
         navgs: int,
         nshots: int,
@@ -349,6 +373,7 @@ def process_pulse_sequence(
                         port=port,
                         frequency=self.get_if(non_overlapping_pulses[0]),
                         qubits=qubits,
+                        couplers=couplers,
                     )
                     # add the sequencer to the list of sequencers required by the port
                     self._sequencers[port].append(sequencer)
@@ -383,12 +408,13 @@ def process_pulse_sequence(
                                 port=port,
                                 frequency=self.get_if(non_overlapping_pulses[0]),
                                 qubits=qubits,
+                                couplers=couplers,
                             )
                             # add the sequencer to the list of sequencers required by the port
                             self._sequencers[port].append(sequencer)
             else:
                 sequencer = self._get_next_sequencer(
-                    port=port, frequency=0, qubits=qubits
+                    port=port, frequency=0, qubits=qubits, couplers=couplers
                 )
                 # add the sequencer to the list of sequencers required by the port
                 self._sequencers[port].append(sequencer)
diff --git a/src/qibolab/instruments/qblox/cluster_qcm_rf.py b/src/qibolab/instruments/qblox/cluster_qcm_rf.py
index cd91832577..0d5aa64abc 100644
--- a/src/qibolab/instruments/qblox/cluster_qcm_rf.py
+++ b/src/qibolab/instruments/qblox/cluster_qcm_rf.py
@@ -289,6 +289,7 @@ def get_if(self, pulse):
     def process_pulse_sequence(
         self,
         qubits: dict,
+        couplers: dict,
         instrument_pulses: PulseSequence,
         navgs: int,
         nshots: int,
diff --git a/src/qibolab/instruments/qblox/cluster_qrm_rf.py b/src/qibolab/instruments/qblox/cluster_qrm_rf.py
index a70d26c428..7c93242faf 100644
--- a/src/qibolab/instruments/qblox/cluster_qrm_rf.py
+++ b/src/qibolab/instruments/qblox/cluster_qrm_rf.py
@@ -337,6 +337,7 @@ def get_if(self, pulse: Pulse):
     def process_pulse_sequence(
         self,
         qubits: dict,
+        couplers: dict,
         instrument_pulses: PulseSequence,
         navgs: int,
         nshots: int,
diff --git a/src/qibolab/instruments/qblox/controller.py b/src/qibolab/instruments/qblox/controller.py
index f125677583..b85719c066 100644
--- a/src/qibolab/instruments/qblox/controller.py
+++ b/src/qibolab/instruments/qblox/controller.py
@@ -120,6 +120,7 @@ def _set_module_channel_map(self, module: QrmRf, qubits: dict):
     def _execute_pulse_sequence(
         self,
         qubits: dict,
+        couplers: dict,
         sequence: PulseSequence,
         options: ExecutionParameters,
         sweepers: list() = [],  # list(Sweeper) = []
@@ -178,6 +179,7 @@ def _execute_pulse_sequence(
             #  ask each module to generate waveforms & program and upload them to the device
             module.process_pulse_sequence(
                 qubits,
+                couplers,
                 module_pulses[name],
                 navgs,
                 nshots,
@@ -228,7 +230,7 @@ def _execute_pulse_sequence(
         return data
 
     def play(self, qubits, couplers, sequence, options):
-        return self._execute_pulse_sequence(qubits, sequence, options)
+        return self._execute_pulse_sequence(qubits, couplers, sequence, options)
 
     def sweep(
         self,
@@ -292,6 +294,7 @@ def sweep(
         # execute the each sweeper recursively
         self._sweep_recursion(
             qubits,
+            couplers,
             sequence_copy,
             options,
             *tuple(sweepers_copy),
@@ -308,6 +311,7 @@ def sweep(
     def _sweep_recursion(
         self,
         qubits,
+        couplers,
         sequence,
         options: ExecutionParameters,
         *sweepers,
@@ -386,6 +390,7 @@ def _sweep_recursion(
                 if len(sweepers) > 1:
                     self._sweep_recursion(
                         qubits,
+                        couplers,
                         sequence,
                         options,
                         *sweepers[1:],
@@ -393,7 +398,10 @@ def _sweep_recursion(
                     )
                 else:
                     result = self._execute_pulse_sequence(
-                        qubits=qubits, sequence=sequence, options=options
+                        qubits=qubits,
+                        couplers=couplers,
+                        sequence=sequence,
+                        options=options,
                     )
                     for pulse in sequence.ro_pulses:
                         if results[pulse.id]:
@@ -440,6 +448,7 @@ def _sweep_recursion(
                         )
                         self._sweep_recursion(
                             qubits,
+                            couplers,
                             sequence,
                             options,
                             *((split_sweeper,) + sweepers[1:]),
@@ -486,7 +495,7 @@ def _sweep_recursion(
                     #                 qubits[pulse.qubit].drive.gain = 1
 
                     result = self._execute_pulse_sequence(
-                        qubits, sequence, options, sweepers
+                        qubits, couplers, sequence, options, sweepers
                     )
                     self._add_to_results(sequence, results, result)
                 else:
@@ -509,6 +518,7 @@ def _sweep_recursion(
 
                         res = self._execute_pulse_sequence(
                             qubits,
+                            couplers,
                             sequence,
                             replace(options, nshots=_nshots),
                             sweepers,

From db433330b5a4e17839bd96aad10dedf8a1ae3d3b Mon Sep 17 00:00:00 2001
From: Alvaro Orgaz <aorgazf@gmail.com>
Date: Sat, 18 May 2024 11:22:54 +0400
Subject: [PATCH 12/70] coupler support for qblox drivers

---
 src/qibolab/instruments/qblox/cluster_qcm_bb.py | 10 +++++++++-
 src/qibolab/instruments/qblox/controller.py     | 10 ++++++++--
 src/qibolab/instruments/qblox/sequencer.py      |  1 +
 src/qibolab/pulses.py                           | 10 ++++++++++
 4 files changed, 28 insertions(+), 3 deletions(-)

diff --git a/src/qibolab/instruments/qblox/cluster_qcm_bb.py b/src/qibolab/instruments/qblox/cluster_qcm_bb.py
index 8aca5e382a..5156e4d9df 100644
--- a/src/qibolab/instruments/qblox/cluster_qcm_bb.py
+++ b/src/qibolab/instruments/qblox/cluster_qcm_bb.py
@@ -271,6 +271,7 @@ def _get_next_sequencer(self, port, frequency, qubits: dict, couplers: dict = {}
         # create sequencer wrapper
         sequencer = Sequencer(next_sequencer_number)
         sequencer.qubit = qubit.name if qubit else None
+        sequencer.coupler = coupler.name if coupler else None
         return sequencer
 
     def get_if(self, pulse):
@@ -519,7 +520,14 @@ def process_pulse_sequence(
                             )
 
                     else:  # qubit_sweeper_parameters
-                        if sequencer.qubit in [qubit.name for qubit in sweeper.qubits]:
+
+                        if (
+                            sweeper.qubits
+                            and sequencer.qubit in [q.name for q in sweeper.qubits]
+                        ) or (
+                            sweeper.couplers
+                            and sequencer.coupler in [c.name for c in sweeper.couplers]
+                        ):
                             # plays an active role
                             if sweeper.parameter == Parameter.bias:
                                 reference_value = self._ports[port].offset
diff --git a/src/qibolab/instruments/qblox/controller.py b/src/qibolab/instruments/qblox/controller.py
index b85719c066..05604d821c 100644
--- a/src/qibolab/instruments/qblox/controller.py
+++ b/src/qibolab/instruments/qblox/controller.py
@@ -102,7 +102,7 @@ def _termination_handler(self, signum, frame):
         log.warning("QbloxController: all modules are disconnected.")
         exit(0)
 
-    def _set_module_channel_map(self, module: QrmRf, qubits: dict):
+    def _set_module_channel_map(self, module: QrmRf, qubits: dict, couplers: dict):
         """Retrieve all the channels connected to a specific Qblox module.
 
         This method updates the `channel_port_map` attribute of the
@@ -115,6 +115,10 @@ def _set_module_channel_map(self, module: QrmRf, qubits: dict):
             for channel in qubit.channels:
                 if channel.port and channel.port.module.name == module.name:
                     module.channel_map[channel.name] = channel
+        for coupler in couplers.values():
+            for channel in coupler.channels:
+                if channel.port and channel.port.module.name == module.name:
+                    module.channel_map[channel.name] = channel
         return list(module.channel_map)
 
     def _execute_pulse_sequence(
@@ -173,7 +177,7 @@ def _execute_pulse_sequence(
         data = {}
         for name, module in self.modules.items():
             # from the pulse sequence, select those pulses to be synthesised by the module
-            module_channels = self._set_module_channel_map(module, qubits)
+            module_channels = self._set_module_channel_map(module, qubits, couplers)
             module_pulses[name] = sequence.get_channel_pulses(*module_channels)
 
             #  ask each module to generate waveforms & program and upload them to the device
@@ -271,6 +275,7 @@ def sweep(
                     values=sweeper.values,
                     pulses=ps,
                     qubits=sweeper.qubits,
+                    couplers=sweeper.couplers,
                     type=sweeper.type,
                 )
             )
@@ -445,6 +450,7 @@ def _sweep_recursion(
                             values=_values,
                             pulses=sweeper.pulses,
                             qubits=sweeper.qubits,
+                            couplers=sweeper.couplers,
                         )
                         self._sweep_recursion(
                             qubits,
diff --git a/src/qibolab/instruments/qblox/sequencer.py b/src/qibolab/instruments/qblox/sequencer.py
index 185375185d..c55a7df904 100644
--- a/src/qibolab/instruments/qblox/sequencer.py
+++ b/src/qibolab/instruments/qblox/sequencer.py
@@ -232,3 +232,4 @@ def __init__(self, number: int):
         self.weights: dict = {}
         self.program: Program = Program()
         self.qubit = None  # self.qubit: int | str = None
+        self.coupler = None  # self.coupler: int | str = None
diff --git a/src/qibolab/pulses.py b/src/qibolab/pulses.py
index 8da469bb9e..001c963934 100644
--- a/src/qibolab/pulses.py
+++ b/src/qibolab/pulses.py
@@ -929,6 +929,15 @@ def copy(self):  # -> Pulse|ReadoutPulse|DrivePulse|FluxPulse:
                 self.channel,
                 self.qubit,
             )
+        elif type(self) == CouplerFluxPulse:
+            return CouplerFluxPulse(
+                self.start,
+                self.duration,
+                self.amplitude,
+                self._shape,
+                self.channel,
+                self.qubit,
+            )
         else:
             # return eval(self.serial)
             return Pulse(
@@ -1221,6 +1230,7 @@ class PulseConstructor(Enum):
     READOUT = ReadoutPulse
     DRIVE = DrivePulse
     FLUX = FluxPulse
+    COUPLERFLUX = CouplerFluxPulse
 
 
 class PulseSequence:

From a751d725a63976053f62d5da689be93f0a6ea6c9 Mon Sep 17 00:00:00 2001
From: Alvaro Orgaz <aorgazf@gmail.com>
Date: Sat, 18 May 2024 11:22:54 +0400
Subject: [PATCH 13/70] coupler support for qblox drivers

---
 src/qibolab/instruments/qblox/cluster_qcm_bb.py | 10 ++++++----
 src/qibolab/instruments/qblox/cluster_qcm_rf.py |  5 ++++-
 src/qibolab/instruments/qblox/cluster_qrm_rf.py | 10 ++++++++--
 src/qibolab/instruments/qblox/sequencer.py      |  2 +-
 src/qibolab/pulses.py                           |  9 +++++++++
 5 files changed, 28 insertions(+), 8 deletions(-)

diff --git a/src/qibolab/instruments/qblox/cluster_qcm_bb.py b/src/qibolab/instruments/qblox/cluster_qcm_bb.py
index 5156e4d9df..9e65262319 100644
--- a/src/qibolab/instruments/qblox/cluster_qcm_bb.py
+++ b/src/qibolab/instruments/qblox/cluster_qcm_bb.py
@@ -520,13 +520,12 @@ def process_pulse_sequence(
                             )
 
                     else:  # qubit_sweeper_parameters
-
                         if (
                             sweeper.qubits
-                            and sequencer.qubit in [q.name for q in sweeper.qubits]
+                            and sequencer.qubit in [_.name for _ in sweeper.qubits]
                         ) or (
                             sweeper.couplers
-                            and sequencer.coupler in [c.name for c in sweeper.couplers]
+                            and sequencer.coupler in [_.name for _ in sweeper.couplers]
                         ):
                             # plays an active role
                             if sweeper.parameter == Parameter.bias:
@@ -650,7 +649,10 @@ def process_pulse_sequence(
                         and pulses[n].sweeper.type == QbloxSweeperType.duration
                     ):
                         RI = pulses[n].sweeper.register
-                        if pulses[n].type == PulseType.FLUX:
+                        if (
+                            pulses[n].type == PulseType.FLUX
+                            or pulses[n].type == PulseType.COUPLERFLUX
+                        ):
                             RQ = pulses[n].sweeper.register
                         else:
                             RQ = pulses[n].sweeper.aux_register
diff --git a/src/qibolab/instruments/qblox/cluster_qcm_rf.py b/src/qibolab/instruments/qblox/cluster_qcm_rf.py
index 0d5aa64abc..f587e609b0 100644
--- a/src/qibolab/instruments/qblox/cluster_qcm_rf.py
+++ b/src/qibolab/instruments/qblox/cluster_qcm_rf.py
@@ -611,7 +611,10 @@ def process_pulse_sequence(
                         and pulses[n].sweeper.type == QbloxSweeperType.duration
                     ):
                         RI = pulses[n].sweeper.register
-                        if pulses[n].type == PulseType.FLUX:
+                        if (
+                            pulses[n].type == PulseType.FLUX
+                            or pulses[n].type == PulseType.COUPLERFLUX
+                        ):
                             RQ = pulses[n].sweeper.register
                         else:
                             RQ = pulses[n].sweeper.aux_register
diff --git a/src/qibolab/instruments/qblox/cluster_qrm_rf.py b/src/qibolab/instruments/qblox/cluster_qrm_rf.py
index 7c93242faf..4705821d51 100644
--- a/src/qibolab/instruments/qblox/cluster_qrm_rf.py
+++ b/src/qibolab/instruments/qblox/cluster_qrm_rf.py
@@ -741,7 +741,10 @@ def process_pulse_sequence(
                             and pulses[n].sweeper.type == QbloxSweeperType.duration
                         ):
                             RI = pulses[n].sweeper.register
-                            if pulses[n].type == PulseType.FLUX:
+                            if (
+                                pulses[n].type == PulseType.FLUX
+                                or pulses[n].type == PulseType.COUPLERFLUX
+                            ):
                                 RQ = pulses[n].sweeper.register
                             else:
                                 RQ = pulses[n].sweeper.aux_register
@@ -788,7 +791,10 @@ def process_pulse_sequence(
                             and pulses[n].sweeper.type == QbloxSweeperType.duration
                         ):
                             RI = pulses[n].sweeper.register
-                            if pulses[n].type == PulseType.FLUX:
+                            if (
+                                pulses[n].type == PulseType.FLUX
+                                or pulses[n].type == PulseType.COUPLERFLUX
+                            ):
                                 RQ = pulses[n].sweeper.register
                             else:
                                 RQ = pulses[n].sweeper.aux_register
diff --git a/src/qibolab/instruments/qblox/sequencer.py b/src/qibolab/instruments/qblox/sequencer.py
index c55a7df904..922e33f9be 100644
--- a/src/qibolab/instruments/qblox/sequencer.py
+++ b/src/qibolab/instruments/qblox/sequencer.py
@@ -127,7 +127,7 @@ def bake_pulse_waveforms(
         # there may be other waveforms stored already, set first index as the next available
         first_idx = len(self.unique_waveforms)
 
-        if pulse.type == PulseType.FLUX:
+        if pulses[n].type == PulseType.FLUX or pulses[n].type == PulseType.COUPLERFLUX:
             # for flux pulses, store i waveforms
             idx_range = np.arange(first_idx, first_idx + len(values), 1)
 
diff --git a/src/qibolab/pulses.py b/src/qibolab/pulses.py
index 001c963934..3468d856dd 100644
--- a/src/qibolab/pulses.py
+++ b/src/qibolab/pulses.py
@@ -938,6 +938,15 @@ def copy(self):  # -> Pulse|ReadoutPulse|DrivePulse|FluxPulse:
                 self.channel,
                 self.qubit,
             )
+        elif type(self) == CouplerFluxPulse:
+            return CouplerFluxPulse(
+                self.start,
+                self.duration,
+                self.amplitude,
+                self._shape,
+                self.channel,
+                self.qubit,
+            )
         else:
             # return eval(self.serial)
             return Pulse(

From 40c53fc2a1cfc89eb3d353181c9fdc6b353aecf1 Mon Sep 17 00:00:00 2001
From: Alvaro Orgaz <aorgazf@gmail.com>
Date: Sat, 18 May 2024 19:47:56 +0400
Subject: [PATCH 14/70] coupler support for qblox drivers

---
 src/qibolab/instruments/qblox/sequencer.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/qibolab/instruments/qblox/sequencer.py b/src/qibolab/instruments/qblox/sequencer.py
index 922e33f9be..304a6b716c 100644
--- a/src/qibolab/instruments/qblox/sequencer.py
+++ b/src/qibolab/instruments/qblox/sequencer.py
@@ -127,7 +127,7 @@ def bake_pulse_waveforms(
         # there may be other waveforms stored already, set first index as the next available
         first_idx = len(self.unique_waveforms)
 
-        if pulses[n].type == PulseType.FLUX or pulses[n].type == PulseType.COUPLERFLUX:
+        if pulse.type == PulseType.FLUX or pulse.type == PulseType.COUPLERFLUX:
             # for flux pulses, store i waveforms
             idx_range = np.arange(first_idx, first_idx + len(values), 1)
 

From e6e7d2f1e81331bc9322cd25a12caac2502a3dff Mon Sep 17 00:00:00 2001
From: Alvaro Orgaz <aorgazf@gmail.com>
Date: Mon, 20 May 2024 10:05:36 +0400
Subject: [PATCH 15/70] support for baking Custom pulses and enhancements in
 their evaluation from a string

---
 src/qibolab/pulses.py | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/src/qibolab/pulses.py b/src/qibolab/pulses.py
index 3468d856dd..0598495b79 100644
--- a/src/qibolab/pulses.py
+++ b/src/qibolab/pulses.py
@@ -705,11 +705,13 @@ class Custom(PulseShape):
     """Arbitrary shape."""
 
     def __init__(self, envelope_i, envelope_q=None):
+        from ast import literal_eval
+
         self.name = "Custom"
         self.pulse: Pulse = None
-        self.envelope_i: np.ndarray = np.array(envelope_i)
+        self.envelope_i: np.ndarray = np.array(literal_eval(envelope_i))
         if envelope_q is not None:
-            self.envelope_q: np.ndarray = np.array(envelope_q)
+            self.envelope_q: np.ndarray = np.array(literal_eval(envelope_q))
         else:
             self.envelope_q = self.envelope_i
 
@@ -717,11 +719,13 @@ def envelope_waveform_i(self, sampling_rate=SAMPLING_RATE) -> Waveform:
         """The envelope waveform of the i component of the pulse."""
 
         if self.pulse:
-            if self.pulse.duration != len(self.envelope_i):
+            if self.pulse.duration > len(self.envelope_i):
                 raise ValueError("Length of envelope_i must be equal to pulse duration")
             num_samples = int(np.rint(self.pulse.duration * sampling_rate))
 
-            waveform = Waveform(self.envelope_i * self.pulse.amplitude)
+            waveform = Waveform(
+                np.clip(self.envelope_i[:num_samples] * self.pulse.amplitude, -1, 1)
+            )
             waveform.serial = f"Envelope_Waveform_I(num_samples = {num_samples}, amplitude = {format(self.pulse.amplitude, '.6f').rstrip('0').rstrip('.')}, shape = {repr(self)})"
             return waveform
         raise ShapeInitError
@@ -730,11 +734,13 @@ def envelope_waveform_q(self, sampling_rate=SAMPLING_RATE) -> Waveform:
         """The envelope waveform of the q component of the pulse."""
 
         if self.pulse:
-            if self.pulse.duration != len(self.envelope_q):
+            if self.pulse.duration > len(self.envelope_q):
                 raise ValueError("Length of envelope_q must be equal to pulse duration")
             num_samples = int(np.rint(self.pulse.duration * sampling_rate))
 
-            waveform = Waveform(self.envelope_q * self.pulse.amplitude)
+            waveform = Waveform(
+                np.clip(self.envelope_q[:num_samples] * self.pulse.amplitude, -1, 1)
+            )
             waveform.serial = f"Envelope_Waveform_Q(num_samples = {num_samples}, amplitude = {format(self.pulse.amplitude, '.6f').rstrip('0').rstrip('.')}, shape = {repr(self)})"
             return waveform
         raise ShapeInitError

From 1d97650e72f262737b453785d3e2dc57c98b6a18 Mon Sep 17 00:00:00 2001
From: Alvaro Orgaz <aorgazf@gmail.com>
Date: Mon, 20 May 2024 23:08:24 +0400
Subject: [PATCH 16/70] add possibility to define shape in
 create_qubit_flux_pulse

---
 src/qibolab/platform/platform.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/qibolab/platform/platform.py b/src/qibolab/platform/platform.py
index 7477405caf..94f2b06440 100644
--- a/src/qibolab/platform/platform.py
+++ b/src/qibolab/platform/platform.py
@@ -385,13 +385,15 @@ def create_qubit_readout_pulse(self, qubit, start):
         qubit = self.get_qubit(qubit)
         return self.create_MZ_pulse(qubit, start)
 
-    def create_qubit_flux_pulse(self, qubit, start, duration, amplitude=1):
+    def create_qubit_flux_pulse(self, qubit, start, duration, amplitude=1, shape=None):
         qubit = self.get_qubit(qubit)
+        if shape is None:
+            shape = "Rectangular()"
         pulse = FluxPulse(
             start=start,
             duration=duration,
             amplitude=amplitude,
-            shape="Rectangular",
+            shape=shape,
             channel=self.qubits[qubit].flux.name,
             qubit=qubit,
         )

From f174b6f115b115c398ff5fd3080984b73f06e614 Mon Sep 17 00:00:00 2001
From: Alvaro Orgaz <aorgazf@gmail.com>
Date: Fri, 31 May 2024 06:12:06 +0400
Subject: [PATCH 17/70] support the creation of coupler flux pulses with a
 particular shape

---
 src/qibolab/platform/platform.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/qibolab/platform/platform.py b/src/qibolab/platform/platform.py
index 94f2b06440..269ec67fa4 100644
--- a/src/qibolab/platform/platform.py
+++ b/src/qibolab/platform/platform.py
@@ -400,8 +400,10 @@ def create_qubit_flux_pulse(self, qubit, start, duration, amplitude=1, shape=Non
         pulse.duration = duration
         return pulse
 
-    def create_coupler_pulse(self, coupler, start, duration=None, amplitude=None):
+    def create_coupler_pulse(self, coupler, start, duration=None, amplitude=None, shape=None):
         coupler = self.get_coupler(coupler)
+        if shape is None:
+            shape = "Rectangular()"
         pulse = self.couplers[coupler].native_pulse.CP.pulse(start)
         if duration is not None:
             pulse.duration = duration

From 9ac640084b1b5ff66e1e6d0e478f9c1d3a062db0 Mon Sep 17 00:00:00 2001
From: Alvaro Orgaz <aorgazf@gmail.com>
Date: Fri, 31 May 2024 06:12:47 +0400
Subject: [PATCH 18/70] fix custom pulse initialisation so that it works both
 with strings and np arrays

---
 src/qibolab/pulses.py | 23 ++++++++++++++++++-----
 1 file changed, 18 insertions(+), 5 deletions(-)

diff --git a/src/qibolab/pulses.py b/src/qibolab/pulses.py
index 0598495b79..f70dec8bd9 100644
--- a/src/qibolab/pulses.py
+++ b/src/qibolab/pulses.py
@@ -709,11 +709,24 @@ def __init__(self, envelope_i, envelope_q=None):
 
         self.name = "Custom"
         self.pulse: Pulse = None
-        self.envelope_i: np.ndarray = np.array(literal_eval(envelope_i))
-        if envelope_q is not None:
-            self.envelope_q: np.ndarray = np.array(literal_eval(envelope_q))
-        else:
-            self.envelope_q = self.envelope_i
+        if isinstance(envelope_i, str):
+            self.envelope_i: np.ndarray = np.array(literal_eval(envelope_i))
+            if envelope_q is not None:
+                self.envelope_q: np.ndarray = np.array(literal_eval(envelope_q))
+            else:
+                self.envelope_q = self.envelope_i
+        elif isinstance(envelope_i, list):
+            self.envelope_i: np.ndarray = np.array(envelope_i)
+            if envelope_q is not None:
+                self.envelope_q: np.ndarray = np.array(envelope_q)
+            else:
+                self.envelope_q = self.envelope_i
+        elif isinstance(envelope_i, np.ndarray):
+            self.envelope_i: np.ndarray = envelope_i
+            if envelope_q is not None:
+                self.envelope_q: np.ndarray = envelope_q
+            else:
+                self.envelope_q = self.envelope_i
 
     def envelope_waveform_i(self, sampling_rate=SAMPLING_RATE) -> Waveform:
         """The envelope waveform of the i component of the pulse."""

From 93559ad5e1ace00a0c787e49580daddc40359e0c Mon Sep 17 00:00:00 2001
From: Alvaro Orgaz <aorgazf@gmail.com>
Date: Mon, 3 Jun 2024 09:27:23 +0400
Subject: [PATCH 19/70] expose i & q offsets properties in qblox port, for
 mixer calibration

---
 .../instruments/qblox/cluster_qcm_rf.py       |  4 ++
 .../instruments/qblox/cluster_qrm_rf.py       |  4 ++
 src/qibolab/instruments/qblox/port.py         | 41 +++++++++++++++++++
 3 files changed, 49 insertions(+)

diff --git a/src/qibolab/instruments/qblox/cluster_qcm_rf.py b/src/qibolab/instruments/qblox/cluster_qcm_rf.py
index f587e609b0..507ac78693 100644
--- a/src/qibolab/instruments/qblox/cluster_qcm_rf.py
+++ b/src/qibolab/instruments/qblox/cluster_qcm_rf.py
@@ -197,6 +197,10 @@ def connect(self, cluster: Cluster = None):
                         self._ports[port].lo_frequency = self.settings[port][
                             "lo_frequency"
                         ]
+                    if "mixer_calibration" in self.settings[port]:
+                        self._ports[port].mixer_calibration = self.settings[port][
+                            "mixer_calibration"
+                        ]
                     self._ports[port].attenuation = self.settings[port]["attenuation"]
                     self._ports[port].hardware_mod_en = True
                     self._ports[port].nco_freq = 0
diff --git a/src/qibolab/instruments/qblox/cluster_qrm_rf.py b/src/qibolab/instruments/qblox/cluster_qrm_rf.py
index 4705821d51..98c0f8fe26 100644
--- a/src/qibolab/instruments/qblox/cluster_qrm_rf.py
+++ b/src/qibolab/instruments/qblox/cluster_qrm_rf.py
@@ -213,6 +213,10 @@ def connect(self, cluster: Cluster = None):
                         self._ports["o1"].lo_frequency = self.settings["o1"][
                             "lo_frequency"
                         ]
+                    if "mixer_calibration" in self.settings["o1"]:
+                        self._ports["o1"].mixer_calibration = self.settings["o1"][
+                            "mixer_calibration"
+                        ]
                     self._ports["o1"].hardware_mod_en = True
                     self._ports["o1"].nco_freq = 0
                     self._ports["o1"].nco_phase_offs = 0
diff --git a/src/qibolab/instruments/qblox/port.py b/src/qibolab/instruments/qblox/port.py
index c83cf391e3..b087b0d345 100644
--- a/src/qibolab/instruments/qblox/port.py
+++ b/src/qibolab/instruments/qblox/port.py
@@ -19,6 +19,8 @@ class QbloxOutputPort_Settings:
     nco_phase_offs: float = 0
     lo_enabled: bool = True
     lo_frequency: int = 2_000_000_000
+    i_offset: float = 0
+    q_offset: float = 0
 
 
 @dataclass
@@ -221,6 +223,45 @@ def lo_frequency(self, value):
             elif self.module.device.is_qcm_type:
                 self.module.device.set(f"out{self.port_number}_lo_freq", value=value)
 
+    @property
+    def mixer_calibration(self):
+        """Parameters for calibrating mixer output.
+
+        i and q offsets are supported.
+        """
+        if self.module.device:
+            self._settings.i_offset = self.module.device.get(
+                f"out{self.port_number}_offset_path0"
+            )
+            self._settings.q_offset = self.module.device.get(
+                f"out{self.port_number}_offset_path1"
+            )
+        return [self._settings.i_offset, self._settings.q_offset]
+
+    @mixer_calibration.setter
+    def mixer_calibration(self, value):
+        if not isinstance(value, list) or len(value) != 2:
+            raise_error(
+                ValueError,
+                f"Invalid mixer calibration parameters {value}. A list [i_offset, q_offset] is required.",
+            )
+        self._settings.i_offset, self._settings.q_offset = value
+
+        if self.module.device:
+            self.module._set_device_parameter(
+                self.module.device,
+                f"out{self.port_number}_offset_path0",
+                value=self._settings.i_offset,
+            )
+            self.module._set_device_parameter(
+                self.module.device,
+                f"out{self.port_number}_offset_path1",
+                value=self._settings.q_offset,
+            )
+        else:
+            pass
+            # TODO: This case regards a connection error of the module
+
 
 class QbloxInputPort:
     def __init__(self, module, port_number: int, port_name: str = None):

From 84c61ccf229de1b127f9c21725bc106ec119f838 Mon Sep 17 00:00:00 2001
From: Alvaro Orgaz <aorgazf@gmail.com>
Date: Tue, 16 Jul 2024 11:03:11 +0400
Subject: [PATCH 20/70] cz_sweep & standard_rb

---
 src/qibolab/instruments/qblox/sequencer.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/qibolab/instruments/qblox/sequencer.py b/src/qibolab/instruments/qblox/sequencer.py
index 304a6b716c..d061d38ebc 100644
--- a/src/qibolab/instruments/qblox/sequencer.py
+++ b/src/qibolab/instruments/qblox/sequencer.py
@@ -121,6 +121,7 @@ def bake_pulse_waveforms(
             NotEnoughMemory: If the memory needed to store the waveforms in more than the memory avalible.
         """
         # In order to generate waveforms for each duration value, the pulse will need to be modified.
+        values = np.round(values).astype(int)
         # To avoid any conflicts, make a copy of the pulse first.
         pulse_copy = pulse.copy()
 

From a18a6f1fa5b53b169f14302bbf30fdd92e19d6ea Mon Sep 17 00:00:00 2001
From: Hayk Sargsyan <52532457+hay-k@users.noreply.github.com>
Date: Tue, 13 Aug 2024 12:14:57 +0400
Subject: [PATCH 21/70] cleanup the cherry-picked commits

---
 .../instruments/qblox/cluster_qcm_bb.py       | 41 ++++++++++---------
 .../instruments/qblox/cluster_qcm_rf.py       |  5 +--
 .../instruments/qblox/cluster_qrm_rf.py       | 12 +++---
 src/qibolab/instruments/qblox/port.py         | 19 +++------
 src/qibolab/instruments/qblox/sequencer.py    | 10 +++--
 src/qibolab/platform/platform.py              | 36 ++++++++++++----
 src/qibolab/pulses.py                         | 20 ++++-----
 7 files changed, 80 insertions(+), 63 deletions(-)

diff --git a/src/qibolab/instruments/qblox/cluster_qcm_bb.py b/src/qibolab/instruments/qblox/cluster_qcm_bb.py
index 9e65262319..4693777022 100644
--- a/src/qibolab/instruments/qblox/cluster_qcm_bb.py
+++ b/src/qibolab/instruments/qblox/cluster_qcm_bb.py
@@ -201,16 +201,18 @@ def setup(self, **settings):
         """
         pass
 
-    def _get_next_sequencer(self, port, frequency, qubits: dict, couplers: dict = {}):
-        """Retrieves and configures the next avaliable sequencer.
+    def _get_next_sequencer(
+        self, port: str, frequency: float, qubits: dict, couplers: dict
+    ):
+        """Retrieves and configures the next available sequencer.
 
         The parameters of the new sequencer are copied from those of the default sequencer, except for the
         intermediate frequency and classification parameters.
         Args:
-            port (str):
-            frequency ():
-            qubits ():
-            couplers ():
+            port: name of the output port
+            frequency: NCO frequency
+            qubits: qubits associated with this sequencer
+            couplers: couplers associated with this sequencer
         Raises:
             Exception = If attempting to set a parameter without a connection to the instrument.
         """
@@ -237,6 +239,17 @@ def _get_next_sequencer(self, port, frequency, qubits: dict, couplers: dict = {}
             else:
                 log.warning(f"Coupler {_coupler.name} has no flux line connected")
 
+        if qubit and coupler:
+            raise ValueError(
+                f"Port {port} of device {self.name} is configured for more than one line (flux lines of qubit {qubit.name} and coupler {coupler.name}"
+            )
+        if qubit:
+            self._ports[port].offset = qubit.sweetspot
+        elif coupler:
+            self._ports[port].offset = coupler.sweetspot
+        else:
+            self._ports[port].offset = 0
+
         # select a new sequencer and configure it as required
         next_sequencer_number = self._free_sequencers_numbers.pop(0)
         if next_sequencer_number != self.DEFAULT_SEQUENCERS[port]:
@@ -261,13 +274,6 @@ def _get_next_sequencer(self, port, frequency, qubits: dict, couplers: dict = {}
             # TODO: Throw error in that event or implement for non_overlapping_same_frequency_pulses
             # Even better, set the frequency before each pulse is played (would work with hardware modulation only)
 
-            if qubit:
-                self._ports[port].offset = qubit.sweetspot
-            elif coupler:
-                self._ports[port].offset = coupler.sweetspot
-            else:
-                self._ports[port].offset = 0
-
         # create sequencer wrapper
         sequencer = Sequencer(next_sequencer_number)
         sequencer.qubit = qubit.name if qubit else None
@@ -522,10 +528,10 @@ def process_pulse_sequence(
                     else:  # qubit_sweeper_parameters
                         if (
                             sweeper.qubits
-                            and sequencer.qubit in [_.name for _ in sweeper.qubits]
+                            and sequencer.qubit in [q.name for q in sweeper.qubits]
                         ) or (
                             sweeper.couplers
-                            and sequencer.coupler in [_.name for _ in sweeper.couplers]
+                            and sequencer.coupler in [c.name for c in sweeper.couplers]
                         ):
                             # plays an active role
                             if sweeper.parameter == Parameter.bias:
@@ -649,10 +655,7 @@ def process_pulse_sequence(
                         and pulses[n].sweeper.type == QbloxSweeperType.duration
                     ):
                         RI = pulses[n].sweeper.register
-                        if (
-                            pulses[n].type == PulseType.FLUX
-                            or pulses[n].type == PulseType.COUPLERFLUX
-                        ):
+                        if pulses[n].type in (PulseType.FLUX, PulseType.COUPLERFLUX):
                             RQ = pulses[n].sweeper.register
                         else:
                             RQ = pulses[n].sweeper.aux_register
diff --git a/src/qibolab/instruments/qblox/cluster_qcm_rf.py b/src/qibolab/instruments/qblox/cluster_qcm_rf.py
index 507ac78693..a8f2c62bd1 100644
--- a/src/qibolab/instruments/qblox/cluster_qcm_rf.py
+++ b/src/qibolab/instruments/qblox/cluster_qcm_rf.py
@@ -615,10 +615,7 @@ def process_pulse_sequence(
                         and pulses[n].sweeper.type == QbloxSweeperType.duration
                     ):
                         RI = pulses[n].sweeper.register
-                        if (
-                            pulses[n].type == PulseType.FLUX
-                            or pulses[n].type == PulseType.COUPLERFLUX
-                        ):
+                        if pulses[n].type in (PulseType.FLUX, PulseType.COUPLERFLUX):
                             RQ = pulses[n].sweeper.register
                         else:
                             RQ = pulses[n].sweeper.aux_register
diff --git a/src/qibolab/instruments/qblox/cluster_qrm_rf.py b/src/qibolab/instruments/qblox/cluster_qrm_rf.py
index 98c0f8fe26..7d930a4e92 100644
--- a/src/qibolab/instruments/qblox/cluster_qrm_rf.py
+++ b/src/qibolab/instruments/qblox/cluster_qrm_rf.py
@@ -745,9 +745,9 @@ def process_pulse_sequence(
                             and pulses[n].sweeper.type == QbloxSweeperType.duration
                         ):
                             RI = pulses[n].sweeper.register
-                            if (
-                                pulses[n].type == PulseType.FLUX
-                                or pulses[n].type == PulseType.COUPLERFLUX
+                            if pulses[n].type in (
+                                PulseType.FLUX,
+                                PulseType.COUPLERFLUX,
                             ):
                                 RQ = pulses[n].sweeper.register
                             else:
@@ -795,9 +795,9 @@ def process_pulse_sequence(
                             and pulses[n].sweeper.type == QbloxSweeperType.duration
                         ):
                             RI = pulses[n].sweeper.register
-                            if (
-                                pulses[n].type == PulseType.FLUX
-                                or pulses[n].type == PulseType.COUPLERFLUX
+                            if pulses[n].type in (
+                                PulseType.FLUX,
+                                PulseType.COUPLERFLUX,
                             ):
                                 RQ = pulses[n].sweeper.register
                             else:
diff --git a/src/qibolab/instruments/qblox/port.py b/src/qibolab/instruments/qblox/port.py
index b087b0d345..9efb4e160f 100644
--- a/src/qibolab/instruments/qblox/port.py
+++ b/src/qibolab/instruments/qblox/port.py
@@ -248,19 +248,12 @@ def mixer_calibration(self, value):
         self._settings.i_offset, self._settings.q_offset = value
 
         if self.module.device:
-            self.module._set_device_parameter(
-                self.module.device,
-                f"out{self.port_number}_offset_path0",
-                value=self._settings.i_offset,
-            )
-            self.module._set_device_parameter(
-                self.module.device,
-                f"out{self.port_number}_offset_path1",
-                value=self._settings.q_offset,
-            )
-        else:
-            pass
-            # TODO: This case regards a connection error of the module
+            self.module.device.set(
+                f"out{self.port_number}_offset_path0", self._settings.i_offset
+            ),
+            self.module.device.set(
+                f"out{self.port_number}_offset_path1", self._settings.q_offset
+            ),
 
 
 class QbloxInputPort:
diff --git a/src/qibolab/instruments/qblox/sequencer.py b/src/qibolab/instruments/qblox/sequencer.py
index d061d38ebc..60a03fd33c 100644
--- a/src/qibolab/instruments/qblox/sequencer.py
+++ b/src/qibolab/instruments/qblox/sequencer.py
@@ -1,3 +1,5 @@
+from typing import Optional, Union
+
 import numpy as np
 from qblox_instruments.qcodes_drivers.sequencer import Sequencer as QbloxSequencer
 
@@ -120,15 +122,15 @@ def bake_pulse_waveforms(
         Raises:
             NotEnoughMemory: If the memory needed to store the waveforms in more than the memory avalible.
         """
-        # In order to generate waveforms for each duration value, the pulse will need to be modified.
         values = np.round(values).astype(int)
+        # In order to generate waveforms for each duration value, the pulse will need to be modified.
         # To avoid any conflicts, make a copy of the pulse first.
         pulse_copy = pulse.copy()
 
         # there may be other waveforms stored already, set first index as the next available
         first_idx = len(self.unique_waveforms)
 
-        if pulse.type == PulseType.FLUX or pulse.type == PulseType.COUPLERFLUX:
+        if pulse.type in (PulseType.FLUX, PulseType.COUPLERFLUX):
             # for flux pulses, store i waveforms
             idx_range = np.arange(first_idx, first_idx + len(values), 1)
 
@@ -232,5 +234,5 @@ def __init__(self, number: int):
         self.acquisitions: dict = {}
         self.weights: dict = {}
         self.program: Program = Program()
-        self.qubit = None  # self.qubit: int | str = None
-        self.coupler = None  # self.coupler: int | str = None
+        self.qubit: Optional[Union[int, str]] = None
+        self.coupler: Optional[Union[int, str]] = None
diff --git a/src/qibolab/platform/platform.py b/src/qibolab/platform/platform.py
index 269ec67fa4..5178978cbc 100644
--- a/src/qibolab/platform/platform.py
+++ b/src/qibolab/platform/platform.py
@@ -10,7 +10,14 @@
 from qibolab.couplers import Coupler
 from qibolab.execution_parameters import ExecutionParameters
 from qibolab.instruments.abstract import Controller, Instrument, InstrumentId
-from qibolab.pulses import Drag, FluxPulse, PulseSequence, ReadoutPulse
+from qibolab.pulses import (
+    CouplerFluxPulse,
+    Drag,
+    FluxPulse,
+    PulseSequence,
+    ReadoutPulse,
+    Rectangular,
+)
 from qibolab.qubits import Qubit, QubitId, QubitPair, QubitPairId
 from qibolab.sweeper import Sweeper
 from qibolab.unrolling import batch
@@ -388,7 +395,7 @@ def create_qubit_readout_pulse(self, qubit, start):
     def create_qubit_flux_pulse(self, qubit, start, duration, amplitude=1, shape=None):
         qubit = self.get_qubit(qubit)
         if shape is None:
-            shape = "Rectangular()"
+            shape = Rectangular()
         pulse = FluxPulse(
             start=start,
             duration=duration,
@@ -400,15 +407,30 @@ def create_qubit_flux_pulse(self, qubit, start, duration, amplitude=1, shape=Non
         pulse.duration = duration
         return pulse
 
-    def create_coupler_pulse(self, coupler, start, duration=None, amplitude=None, shape=None):
+    def create_coupler_pulse(
+        self, coupler, start, duration=None, amplitude=None, shape=None
+    ):
         coupler = self.get_coupler(coupler)
+        native_pulse = self.couplers[coupler].native_pulse.CP.pulse(start)
+
+        if duration is None:
+            duration = native_pulse.duration
+        if amplitude is None:
+            amplitude = native_pulse.amplitude
+
         if shape is None:
-            shape = "Rectangular()"
-        pulse = self.couplers[coupler].native_pulse.CP.pulse(start)
-        if duration is not None:
+            pulse = native_pulse
             pulse.duration = duration
-        if amplitude is not None:
             pulse.amplitude = amplitude
+        else:
+            pulse = CouplerFluxPulse(
+                start=start,
+                duration=duration,
+                amplitude=amplitude,
+                shape=shape,
+                channel=self.qubits[coupler].flux.name,
+                qubit=coupler,
+            )
         return pulse
 
     # TODO Remove RX90_drag_pulse and RX_drag_pulse, replace them with create_qubit_drive_pulse
diff --git a/src/qibolab/pulses.py b/src/qibolab/pulses.py
index f70dec8bd9..6e8213e33c 100644
--- a/src/qibolab/pulses.py
+++ b/src/qibolab/pulses.py
@@ -732,13 +732,13 @@ def envelope_waveform_i(self, sampling_rate=SAMPLING_RATE) -> Waveform:
         """The envelope waveform of the i component of the pulse."""
 
         if self.pulse:
-            if self.pulse.duration > len(self.envelope_i):
-                raise ValueError("Length of envelope_i must be equal to pulse duration")
             num_samples = int(np.rint(self.pulse.duration * sampling_rate))
+            if len(self.envelope_i) != num_samples:
+                raise ValueError(
+                    "Length of envelope_i must be equal to pulse duration in samples"
+                )
 
-            waveform = Waveform(
-                np.clip(self.envelope_i[:num_samples] * self.pulse.amplitude, -1, 1)
-            )
+            waveform = Waveform(self.envelope_i * self.pulse.amplitude)
             waveform.serial = f"Envelope_Waveform_I(num_samples = {num_samples}, amplitude = {format(self.pulse.amplitude, '.6f').rstrip('0').rstrip('.')}, shape = {repr(self)})"
             return waveform
         raise ShapeInitError
@@ -747,13 +747,13 @@ def envelope_waveform_q(self, sampling_rate=SAMPLING_RATE) -> Waveform:
         """The envelope waveform of the q component of the pulse."""
 
         if self.pulse:
-            if self.pulse.duration > len(self.envelope_q):
-                raise ValueError("Length of envelope_q must be equal to pulse duration")
             num_samples = int(np.rint(self.pulse.duration * sampling_rate))
+            if len(self.envelope_q) != num_samples:
+                raise ValueError(
+                    "Length of envelope_q must be equal to pulse duration in samples"
+                )
 
-            waveform = Waveform(
-                np.clip(self.envelope_q[:num_samples] * self.pulse.amplitude, -1, 1)
-            )
+            waveform = Waveform(self.envelope_q * self.pulse.amplitude)
             waveform.serial = f"Envelope_Waveform_Q(num_samples = {num_samples}, amplitude = {format(self.pulse.amplitude, '.6f').rstrip('0').rstrip('.')}, shape = {repr(self)})"
             return waveform
         raise ShapeInitError

From 48e8d2683490b7b8097cb91ad49ba99f12b9c39b Mon Sep 17 00:00:00 2001
From: Hayk Sargsyan <52532457+hay-k@users.noreply.github.com>
Date: Tue, 13 Aug 2024 12:58:34 +0400
Subject: [PATCH 22/70] revert a5013cbb9c0f9145b1889943b245e2b928e4989c

---
 src/qibolab/pulses.py | 24 +++++-------------------
 1 file changed, 5 insertions(+), 19 deletions(-)

diff --git a/src/qibolab/pulses.py b/src/qibolab/pulses.py
index 6e8213e33c..27f5b573f8 100644
--- a/src/qibolab/pulses.py
+++ b/src/qibolab/pulses.py
@@ -705,28 +705,14 @@ class Custom(PulseShape):
     """Arbitrary shape."""
 
     def __init__(self, envelope_i, envelope_q=None):
-        from ast import literal_eval
 
         self.name = "Custom"
         self.pulse: Pulse = None
-        if isinstance(envelope_i, str):
-            self.envelope_i: np.ndarray = np.array(literal_eval(envelope_i))
-            if envelope_q is not None:
-                self.envelope_q: np.ndarray = np.array(literal_eval(envelope_q))
-            else:
-                self.envelope_q = self.envelope_i
-        elif isinstance(envelope_i, list):
-            self.envelope_i: np.ndarray = np.array(envelope_i)
-            if envelope_q is not None:
-                self.envelope_q: np.ndarray = np.array(envelope_q)
-            else:
-                self.envelope_q = self.envelope_i
-        elif isinstance(envelope_i, np.ndarray):
-            self.envelope_i: np.ndarray = envelope_i
-            if envelope_q is not None:
-                self.envelope_q: np.ndarray = envelope_q
-            else:
-                self.envelope_q = self.envelope_i
+        self.envelope_i: np.ndarray = np.array(envelope_i)
+        if envelope_q is not None:
+            self.envelope_q: np.ndarray = np.array(envelope_q)
+        else:
+            self.envelope_q = self.envelope_i
 
     def envelope_waveform_i(self, sampling_rate=SAMPLING_RATE) -> Waveform:
         """The envelope waveform of the i component of the pulse."""

From 39f8fc1cfe36d363fe10c21300205717e43327ce Mon Sep 17 00:00:00 2001
From: Hayk Sargsyan <52532457+hay-k@users.noreply.github.com>
Date: Tue, 13 Aug 2024 13:01:56 +0400
Subject: [PATCH 23/70] remove duplicate block

---
 src/qibolab/pulses.py | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/src/qibolab/pulses.py b/src/qibolab/pulses.py
index 27f5b573f8..b28fc1869e 100644
--- a/src/qibolab/pulses.py
+++ b/src/qibolab/pulses.py
@@ -943,15 +943,6 @@ def copy(self):  # -> Pulse|ReadoutPulse|DrivePulse|FluxPulse:
                 self.channel,
                 self.qubit,
             )
-        elif type(self) == CouplerFluxPulse:
-            return CouplerFluxPulse(
-                self.start,
-                self.duration,
-                self.amplitude,
-                self._shape,
-                self.channel,
-                self.qubit,
-            )
         else:
             # return eval(self.serial)
             return Pulse(

From 169f39751a3179c7f6805e6480c19d53c72d6e41 Mon Sep 17 00:00:00 2001
From: Hayk Sargsyan <52532457+hay-k@users.noreply.github.com>
Date: Wed, 14 Aug 2024 09:45:29 +0400
Subject: [PATCH 24/70] fix reference to shape

---
 src/qibolab/pulses.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/qibolab/pulses.py b/src/qibolab/pulses.py
index b28fc1869e..17c2917148 100644
--- a/src/qibolab/pulses.py
+++ b/src/qibolab/pulses.py
@@ -939,7 +939,7 @@ def copy(self):  # -> Pulse|ReadoutPulse|DrivePulse|FluxPulse:
                 self.start,
                 self.duration,
                 self.amplitude,
-                self._shape,
+                self.shape,
                 self.channel,
                 self.qubit,
             )

From 6110d392b7a1444fcec769f8641300d71268faef Mon Sep 17 00:00:00 2001
From: Hayk Sargsyan <52532457+hay-k@users.noreply.github.com>
Date: Thu, 15 Aug 2024 12:24:58 +0400
Subject: [PATCH 25/70] fix pulse shape deserialization not working for Custom,
 IIR, and SNZ

---
 src/qibolab/pulses.py | 59 +++++++++++++++++++++++++++----------
 tests/test_pulses.py  | 67 +++++++++++++++++++++++++++++++++++++++++--
 2 files changed, 109 insertions(+), 17 deletions(-)

diff --git a/src/qibolab/pulses.py b/src/qibolab/pulses.py
index 17c2917148..62b58614f2 100644
--- a/src/qibolab/pulses.py
+++ b/src/qibolab/pulses.py
@@ -19,6 +19,22 @@
 """
 
 
+def _np_array_from_string_or_array_like(x) -> np.ndarray:
+    """Convert input into numpy array.
+
+    The input can be in one of these forms:
+        1. string in form '[1, 2, 3, ...]'
+        2. list, e.g. [1, 2, 3, ...]
+        3. numpy array. This will be identity conversion.
+    """
+    if isinstance(x, str):
+        return np.fromstring(x[1:-1], sep=",")
+    elif isinstance(x, (list, np.ndarray)):
+        return np.array(x)
+    else:
+        raise ValueError(f"Data in unrecognized format: {x}")
+
+
 class PulseType(Enum):
     """An enumeration to distinguish different types of pulses.
 
@@ -215,12 +231,19 @@ def eval(value: str) -> "PulseShape":
 
             To be replaced by proper serialization.
         """
-        shape_name = re.findall(r"(\w+)", value)[0]
-        if shape_name not in globals():
-            raise ValueError(f"shape {value} not found")
-        shape_parameters = re.findall(r"[-\w+\d\.\d]+", value)[1:]
-        # TODO: create multiple tests to prove regex working correctly
-        return globals()[shape_name](*shape_parameters)
+        match = re.fullmatch(r"(\w+)\((.*)\)", value)
+        shape_name, params = None, None
+        if match is not None:
+            shape_name, params = match.groups()
+        if match is None or shape_name not in globals():
+            raise ValueError(f"shape {value} not recognized")
+
+        single_item_pattern = r"[^,\s\[\]\(\)]+"
+        csv_items_pattern = rf"(?:{single_item_pattern}(?:,\s*)?)*"
+        param_pattern = (
+            rf"\[{csv_items_pattern}\]|\w+\({csv_items_pattern}\)|{single_item_pattern}"
+        )
+        return globals()[shape_name](*re.findall(param_pattern, params))
 
 
 class Rectangular(PulseShape):
@@ -509,12 +532,14 @@ class IIR(PulseShape):
     # p = [b0 = 1−k +k ·α, b1 = −(1−k)·(1−α),a0 = 1 and a1 = −(1−α)]
     # p = [b0, b1, a0, a1]
 
-    def __init__(self, b, a, target: PulseShape):
+    def __init__(self, b, a, target):
         self.name = "IIR"
-        self.target: PulseShape = target
+        self.target: PulseShape = (
+            PulseShape.eval(target) if isinstance(target, str) else target
+        )
         self._pulse: Pulse = None
-        self.a: np.ndarray = np.array(a)
-        self.b: np.ndarray = np.array(b)
+        self.a: np.ndarray = _np_array_from_string_or_array_like(a)
+        self.b: np.ndarray = _np_array_from_string_or_array_like(b)
         # Check len(a) = len(b) = 2
 
     def __eq__(self, item) -> bool:
@@ -596,8 +621,10 @@ class SNZ(PulseShape):
     def __init__(self, t_idling, b_amplitude=None):
         self.name = "SNZ"
         self.pulse: Pulse = None
-        self.t_idling: float = t_idling
-        self.b_amplitude = b_amplitude
+        self.t_idling: float = float(t_idling)
+        self.b_amplitude = (
+            float(b_amplitude) if b_amplitude is not None else b_amplitude
+        )
 
     def __eq__(self, item) -> bool:
         """Overloads == operator."""
@@ -708,9 +735,11 @@ def __init__(self, envelope_i, envelope_q=None):
 
         self.name = "Custom"
         self.pulse: Pulse = None
-        self.envelope_i: np.ndarray = np.array(envelope_i)
+        self.envelope_i: np.ndarray = _np_array_from_string_or_array_like(envelope_i)
         if envelope_q is not None:
-            self.envelope_q: np.ndarray = np.array(envelope_q)
+            self.envelope_q: np.ndarray = _np_array_from_string_or_array_like(
+                envelope_q
+            )
         else:
             self.envelope_q = self.envelope_i
 
@@ -745,7 +774,7 @@ def envelope_waveform_q(self, sampling_rate=SAMPLING_RATE) -> Waveform:
         raise ShapeInitError
 
     def __repr__(self):
-        return f"{self.name}({self.envelope_i[:3]}, ..., {self.envelope_q[:3]}, ...)"
+        return f"{self.name}({self.envelope_i[:3]}, {self.envelope_q[:3]})"
 
 
 @dataclass
diff --git a/tests/test_pulses.py b/tests/test_pulses.py
index 9939b8faec..62f7a64b63 100644
--- a/tests/test_pulses.py
+++ b/tests/test_pulses.py
@@ -12,6 +12,7 @@
     Custom,
     Drag,
     DrivePulse,
+    Exponential,
     FluxPulse,
     Gaussian,
     GaussianSquare,
@@ -275,8 +276,70 @@ def test_pulses_pulseshape_sampling_rate(shape):
 def test_pulseshape_eval():
     shape = PulseShape.eval("Rectangular()")
     assert isinstance(shape, Rectangular)
-    with pytest.raises(ValueError):
-        shape = PulseShape.eval("Ciao()")
+
+    shape = PulseShape.eval("Exponential(1, 2)")
+    assert isinstance(shape, Exponential)
+    assert shape.tau == 1
+    assert shape.upsilon == 2
+
+    shape = PulseShape.eval("Exponential(4, 5, 6)")
+    assert isinstance(shape, Exponential)
+    assert shape.tau == 4
+    assert shape.upsilon == 5
+    assert shape.g == 6
+
+    shape = PulseShape.eval("Gaussian(3.1)")
+    assert isinstance(shape, Gaussian)
+    assert shape.rel_sigma == 3.1
+
+    shape = PulseShape.eval("GaussianSquare(5, 78)")
+    assert isinstance(shape, GaussianSquare)
+    assert shape.rel_sigma == 5
+    assert shape.width == 78
+
+    shape = PulseShape.eval("Drag(4, 0.1)")
+    assert isinstance(shape, Drag)
+    assert shape.rel_sigma == 4
+    assert shape.beta == 0.1
+
+    shape = PulseShape.eval("IIR([1, 2, 3], [5], Drag(3, 0.2))")
+    assert isinstance(shape, IIR)
+    assert np.array_equal(shape.b, np.array([1, 2, 3]))
+    assert np.array_equal(shape.a, np.array([5]))
+    assert isinstance(shape.target, Drag)
+    assert shape.target.rel_sigma == 3
+    assert shape.target.beta == 0.2
+
+    shape = PulseShape.eval("SNZ(10, 20)")
+    assert isinstance(shape, SNZ)
+    assert shape.t_idling == 10
+    assert shape.b_amplitude == 20
+
+    shape = PulseShape.eval("eCap(3.14)")
+    assert isinstance(shape, eCap)
+    assert shape.alpha == 3.14
+
+    shape = PulseShape.eval("Custom([1, 2, 3], [4, 5, 6])")
+    assert isinstance(shape, Custom)
+    assert np.array_equal(shape.envelope_i, np.array([1, 2, 3]))
+    assert np.array_equal(shape.envelope_q, np.array([4, 5, 6]))
+
+    with pytest.raises(ValueError, match="shape .* not recognized"):
+        _ = PulseShape.eval("Ciao()")
+
+
+@pytest.mark.parametrize(
+    "value_str",
+    ["-0.1", "+0.1", "1.", "-3.", "+1.", "-0.1e2", "1e-2", "+1e3", "-3e-1", "-.4"],
+)
+def test_pulse_shape_eval_numeric_varieties(value_str):
+    shape = PulseShape.eval(f"Drag(1, {value_str})")
+    assert isinstance(shape, Drag)
+    assert shape.beta == float(value_str)
+
+    shape = PulseShape.eval(f"Custom([0.1, {value_str}])")
+    assert isinstance(shape, Custom)
+    assert np.array_equal(shape.envelope_i, np.array([0.1, float(value_str)]))
 
 
 @pytest.mark.parametrize("rel_sigma,beta", [(5, 1), (5, -1), (3, -0.03), (4, 0.02)])

From f34b3fb537dc295ecc2ea6436e4383bd3c3db60b Mon Sep 17 00:00:00 2001
From: Hayk Sargsyan <52532457+hay-k@users.noreply.github.com>
Date: Tue, 20 Aug 2024 11:42:21 +0400
Subject: [PATCH 26/70] update qblox test setup

---
 tests/dummy_qrc/qblox/parameters.json      | 88 ++++++++++++++++------
 tests/dummy_qrc/qblox/platform.py          | 22 +++++-
 tests/test_instruments_qblox_controller.py | 19 +++++
 3 files changed, 106 insertions(+), 23 deletions(-)

diff --git a/tests/dummy_qrc/qblox/parameters.json b/tests/dummy_qrc/qblox/parameters.json
index 7a5099b5fe..e8797d7266 100644
--- a/tests/dummy_qrc/qblox/parameters.json
+++ b/tests/dummy_qrc/qblox/parameters.json
@@ -11,24 +11,30 @@
         3,
         4
     ],
-    "topology": [
-        [
+    "couplers": [
+        0,
+        1,
+        3,
+        4
+    ],
+    "topology": {
+        "0": [
             0,
             2
         ],
-        [
+        "1": [
             1,
             2
         ],
-        [
+        "3": [
             2,
             3
         ],
-        [
+        "4": [
             2,
             4
         ]
-    ],
+    },
     "instruments": {
         "qblox_controller": {
             "bounds": {
@@ -76,7 +82,8 @@
             "o1": {
                 "attenuation": 36,
                 "lo_frequency": 7300000000,
-                "gain": 0.6
+                "gain": 0.6,
+                "mixer_calibration": [-3.2, 1.4]
             },
             "i1": {
                 "acquisition_hold_off": 500,
@@ -87,7 +94,8 @@
             "o1": {
                 "attenuation": 36,
                 "lo_frequency": 7850000000,
-                "gain": 0.6
+                "gain": 0.6,
+                "mixer_calibration": [0.3, -3.8]
             },
             "i1": {
                 "acquisition_hold_off": 500,
@@ -243,6 +251,48 @@
                 }
             }
         },
+        "coupler": {
+            "0": {
+                "CP": {
+                    "type": "coupler",
+                    "duration": 0,
+                    "amplitude": 0,
+                    "shape": "Rectangular()",
+                    "coupler": 0,
+                    "relative_start": 0
+                }
+            },
+            "1": {
+                "CP": {
+                    "type": "coupler",
+                    "duration": 0,
+                    "amplitude": 0,
+                    "shape": "Rectangular()",
+                    "coupler": 1,
+                    "relative_start": 0
+                }
+            },
+            "3": {
+                "CP": {
+                    "type": "coupler",
+                    "duration": 0,
+                    "amplitude": 0,
+                    "shape": "Rectangular()",
+                    "coupler": 3,
+                    "relative_start": 0
+                }
+            },
+            "4": {
+                "CP": {
+                    "type": "coupler",
+                    "duration": 0,
+                    "amplitude": 0,
+                    "shape": "Rectangular()",
+                    "coupler": 4,
+                    "relative_start": 0
+                }
+            }
+        },
         "two_qubit": {
             "2-3": {
                 "CZ": [
@@ -401,22 +451,18 @@
                 "threshold": 0.002323
             }
         },
-        "two_qubit":{
-            "0-2": {
-                "gate_fidelity": [0.0, 0.0],
-                "cz_fidelity": [0.0, 0.0]
+        "coupler": {
+            "0": {
+                "sweetspot": 0.1
             },
-            "1-2": {
-                "gate_fidelity": [0.0, 0.0],
-                "cz_fidelity": [0.0, 0.0]
+            "1": {
+                "sweetspot": 0.2
             },
-            "2-3": {
-                "gate_fidelity": [0.0, 0.0],
-                "cz_fidelity": [0.0, 0.0]
+            "3": {
+                "sweetspot": -0.3
             },
-            "2-4": {
-                "gate_fidelity": [0.0, 0.0],
-                "cz_fidelity": [0.0, 0.0]
+            "4": {
+                "sweetspot": 0.0
             }
         }
     }
diff --git a/tests/dummy_qrc/qblox/platform.py b/tests/dummy_qrc/qblox/platform.py
index a60a600d8f..6129c716d9 100644
--- a/tests/dummy_qrc/qblox/platform.py
+++ b/tests/dummy_qrc/qblox/platform.py
@@ -30,6 +30,7 @@ def create():
     modules = {
         "qcm_bb0": QcmBb("qcm_bb0", f"{ADDRESS}:2"),
         "qcm_bb1": QcmBb("qcm_bb1", f"{ADDRESS}:4"),
+        "qcm_bb2": QcmBb("qcm_bb2", f"{ADDRESS}:3"),
         "qcm_rf0": QcmRf("qcm_rf0", f"{ADDRESS}:6"),
         "qcm_rf1": QcmRf("qcm_rf1", f"{ADDRESS}:8"),
         "qcm_rf2": QcmRf("qcm_rf2", f"{ADDRESS}:10"),
@@ -61,12 +62,17 @@ def create():
     channels |= Channel(name="L3-12", port=modules["qcm_rf1"].ports("o1"))
     channels |= Channel(name="L3-13", port=modules["qcm_rf1"].ports("o2"))
     channels |= Channel(name="L3-14", port=modules["qcm_rf2"].ports("o1"))
-    # Flux
+    # Qubit flux
     channels |= Channel(name="L4-5", port=modules["qcm_bb0"].ports("o1"))
     channels |= Channel(name="L4-1", port=modules["qcm_bb0"].ports("o2"))
     channels |= Channel(name="L4-2", port=modules["qcm_bb0"].ports("o3"))
     channels |= Channel(name="L4-3", port=modules["qcm_bb0"].ports("o4"))
     channels |= Channel(name="L4-4", port=modules["qcm_bb1"].ports("o1"))
+    # Coupler flux
+    channels |= Channel(name="L4-12", port=modules["qcm_bb1"].ports("o2"))
+    channels |= Channel(name="L4-13", port=modules["qcm_bb1"].ports("o3"))
+    channels |= Channel(name="L4-14", port=modules["qcm_bb1"].ports("o4"))
+    channels |= Channel(name="L4-5", port=modules["qcm_bb2"].ports("o1"))
     # TWPA
     channels |= Channel(name="L3-28", port=None)
     channels["L3-28"].local_oscillator = twpa_pump
@@ -98,8 +104,20 @@ def create():
     for q in range(5):
         qubits[q].flux.max_bias = 2.5
 
+    for i, coupler in enumerate(couplers):
+        couplers[coupler].flux = (
+            channels[f"L4-{11 + i}"] if i > 0 else channels[f"L4-5"]
+        )
+        couplers[coupler].flux.max_bias = 2.5
+
     settings = load_settings(runcard)
 
     return Platform(
-        str(FOLDER), qubits, pairs, instruments, settings, resonator_type="2D"
+        str(FOLDER),
+        qubits,
+        pairs,
+        instruments,
+        settings,
+        resonator_type="2D",
+        couplers=couplers,
     )
diff --git a/tests/test_instruments_qblox_controller.py b/tests/test_instruments_qblox_controller.py
index fde3682f07..c5c5fba003 100644
--- a/tests/test_instruments_qblox_controller.py
+++ b/tests/test_instruments_qblox_controller.py
@@ -61,6 +61,25 @@ def test_sweep_too_many_sweep_points(platform, controller):
         controller.sweep({0: qubit}, {}, PulseSequence(pulse), params, sweep)
 
 
+def test_sweep_coupler(platform, controller):
+    """Test that coupler related sweep is accepted."""
+    ro_pulse = platform.create_MZ_pulse(qubit=0, start=0)
+    sequence = PulseSequence(ro_pulse)
+
+    sweeper = Sweeper(Parameter.bias, np.random.rand(4), couplers=[0])
+    params = ExecutionParameters(
+        nshots=10, relaxation_time=1000, averaging_mode=AveragingMode.CYCLIC
+    )
+    mock_data = np.array([1, 2, 3, 4])
+    controller._execute_pulse_sequence = Mock(
+        return_value={ro_pulse.serial: IntegratedResults(mock_data)}
+    )
+    res = controller.sweep(
+        platform.qubits, platform.couplers, sequence, params, sweeper
+    )
+    assert np.array_equal(res[ro_pulse.serial].voltage, mock_data)
+
+
 @pytest.mark.qpu
 def connect(connected_controller: QbloxController):
     connected_controller.connect()

From 4074c9d2f84573e849f6e591b18490f4faa39d03 Mon Sep 17 00:00:00 2001
From: Hayk Sargsyan <52532457+hay-k@users.noreply.github.com>
Date: Wed, 18 Sep 2024 15:07:25 +0400
Subject: [PATCH 27/70] workaround to make experiments with start sweeper on
 non RO lines move RO according to the sweep

---
 src/qibolab/instruments/qblox/controller.py | 41 ++++++++++++++++++++-
 1 file changed, 39 insertions(+), 2 deletions(-)

diff --git a/src/qibolab/instruments/qblox/controller.py b/src/qibolab/instruments/qblox/controller.py
index 05604d821c..d4623036f0 100644
--- a/src/qibolab/instruments/qblox/controller.py
+++ b/src/qibolab/instruments/qblox/controller.py
@@ -11,7 +11,7 @@
 from qibolab.instruments.qblox.cluster_qcm_rf import QcmRf
 from qibolab.instruments.qblox.cluster_qrm_rf import QrmRf
 from qibolab.instruments.qblox.sequencer import SAMPLING_RATE
-from qibolab.pulses import PulseSequence, PulseType
+from qibolab.pulses import Custom, PulseSequence, PulseType, ReadoutPulse
 from qibolab.result import SampleResults
 from qibolab.sweeper import Parameter, Sweeper, SweeperType
 from qibolab.unrolling import Bounds
@@ -280,6 +280,43 @@ def sweep(
                 )
             )
 
+        serial_map = {p.serial: p.serial for p in sequence_copy.ro_pulses}
+        for sweeper in sweepers_copy:
+            if sweeper.parameter is Parameter.start and not any(
+                pulse.type is PulseType.READOUT for pulse in sweeper.pulses
+            ):
+                for pulse in sequence_copy:
+                    if pulse.type is PulseType.READOUT:
+                        idx = sequence_copy.index(pulse)
+                        padded_pulse = ReadoutPulse(
+                            start=0,
+                            duration=pulse.start + pulse.duration,
+                            amplitude=pulse.amplitude,
+                            frequency=pulse.frequency,
+                            relative_phase=pulse.relative_phase,
+                            shape=Custom(
+                                envelope_i=np.concatenate(
+                                    (
+                                        np.zeros(pulse.start),
+                                        pulse.envelope_waveform_i().data
+                                        / pulse.amplitude,
+                                    )
+                                ),
+                                envelope_q=np.concatenate(
+                                    (
+                                        np.zeros(pulse.start),
+                                        pulse.envelope_waveform_q().data
+                                        / pulse.amplitude,
+                                    )
+                                ),
+                            ),
+                            channel=pulse.channel,
+                            qubit=pulse.qubit,
+                        )
+                        serial_map[padded_pulse.serial] = pulse.serial
+                        sequence_copy[idx] = padded_pulse
+                        sweeper.pulses.append(padded_pulse)
+
         # reverse sweepers exept for res punchout att
         contains_attenuation_frequency = any(
             sweepers_copy[i].parameter == Parameter.attenuation
@@ -309,7 +346,7 @@ def sweep(
         # return the results using the original serials
         serial_results = {}
         for pulse in sequence_copy.ro_pulses:
-            serial_results[map_id_serial[pulse.id]] = id_results[pulse.id]
+            serial_results[serial_map[map_id_serial[pulse.id]]] = id_results[pulse.id]
             serial_results[pulse.qubit] = id_results[pulse.id]
         return serial_results
 

From 108c3c2ffaa208ee1ec959bff7b799e2430b35a3 Mon Sep 17 00:00:00 2001
From: Hayk Sargsyan <52532457+hay-k@users.noreply.github.com>
Date: Fri, 20 Sep 2024 11:30:28 +0400
Subject: [PATCH 28/70] trim waveforms of pulses with custom shapes for shorter
 pulse durations

---
 src/qibolab/pulses.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/qibolab/pulses.py b/src/qibolab/pulses.py
index 62b58614f2..63fd1b314a 100644
--- a/src/qibolab/pulses.py
+++ b/src/qibolab/pulses.py
@@ -748,12 +748,12 @@ def envelope_waveform_i(self, sampling_rate=SAMPLING_RATE) -> Waveform:
 
         if self.pulse:
             num_samples = int(np.rint(self.pulse.duration * sampling_rate))
-            if len(self.envelope_i) != num_samples:
+            if len(self.envelope_i) < num_samples:
                 raise ValueError(
-                    "Length of envelope_i must be equal to pulse duration in samples"
+                    "Length of envelope_i must not be shorter than pulse duration in samples"
                 )
 
-            waveform = Waveform(self.envelope_i * self.pulse.amplitude)
+            waveform = Waveform(self.envelope_i[:num_samples] * self.pulse.amplitude)
             waveform.serial = f"Envelope_Waveform_I(num_samples = {num_samples}, amplitude = {format(self.pulse.amplitude, '.6f').rstrip('0').rstrip('.')}, shape = {repr(self)})"
             return waveform
         raise ShapeInitError
@@ -763,12 +763,12 @@ def envelope_waveform_q(self, sampling_rate=SAMPLING_RATE) -> Waveform:
 
         if self.pulse:
             num_samples = int(np.rint(self.pulse.duration * sampling_rate))
-            if len(self.envelope_q) != num_samples:
+            if len(self.envelope_q) < num_samples:
                 raise ValueError(
-                    "Length of envelope_q must be equal to pulse duration in samples"
+                    "Length of envelope_q must not be shorter than pulse duration in samples"
                 )
 
-            waveform = Waveform(self.envelope_q * self.pulse.amplitude)
+            waveform = Waveform(self.envelope_q[:num_samples] * self.pulse.amplitude)
             waveform.serial = f"Envelope_Waveform_Q(num_samples = {num_samples}, amplitude = {format(self.pulse.amplitude, '.6f').rstrip('0').rstrip('.')}, shape = {repr(self)})"
             return waveform
         raise ShapeInitError

From 9242c2afe31277b65d7c0693b2a3296261ecff38 Mon Sep 17 00:00:00 2001
From: Hayk Sargsyan <52532457+hay-k@users.noreply.github.com>
Date: Fri, 20 Sep 2024 14:06:36 +0400
Subject: [PATCH 29/70] workaround to make sure RO pulse does not overlap with
 duration-swept pulse

---
 src/qibolab/instruments/qblox/controller.py | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/src/qibolab/instruments/qblox/controller.py b/src/qibolab/instruments/qblox/controller.py
index d4623036f0..a82ca6635f 100644
--- a/src/qibolab/instruments/qblox/controller.py
+++ b/src/qibolab/instruments/qblox/controller.py
@@ -282,11 +282,19 @@ def sweep(
 
         serial_map = {p.serial: p.serial for p in sequence_copy.ro_pulses}
         for sweeper in sweepers_copy:
-            if sweeper.parameter is Parameter.start and not any(
+            if sweeper.parameter in (Parameter.duration, Parameter.start) and not any(
                 pulse.type is PulseType.READOUT for pulse in sweeper.pulses
             ):
-                for pulse in sequence_copy:
-                    if pulse.type is PulseType.READOUT:
+                for pulse in sequence_copy.ro_pulses:
+                    current_serial = pulse.serial
+                    if sweeper.parameter is Parameter.duration:
+                        sweep_values = sweeper.get_values(sweeper.pulses[0].duration)
+                        if (
+                            max_finish := sweeper.pulses[0].start + np.max(sweep_values)
+                        ) > pulse.start:
+                            pulse.start = max_finish
+                            serial_map[pulse.serial] = current_serial
+                    if sweeper.parameter is Parameter.start:
                         idx = sequence_copy.index(pulse)
                         padded_pulse = ReadoutPulse(
                             start=0,
@@ -313,7 +321,7 @@ def sweep(
                             channel=pulse.channel,
                             qubit=pulse.qubit,
                         )
-                        serial_map[padded_pulse.serial] = pulse.serial
+                        serial_map[padded_pulse.serial] = current_serial
                         sequence_copy[idx] = padded_pulse
                         sweeper.pulses.append(padded_pulse)
 

From 730e291af4c5c54a137417970e5f930dc920b232 Mon Sep 17 00:00:00 2001
From: Hayk Sargsyan <52532457+hay-k@users.noreply.github.com>
Date: Fri, 20 Sep 2024 15:04:01 +0400
Subject: [PATCH 30/70] change order of arctan2 arguments

---
 src/qibolab/result.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/qibolab/result.py b/src/qibolab/result.py
index 837d7fba10..19ecb0c7fd 100644
--- a/src/qibolab/result.py
+++ b/src/qibolab/result.py
@@ -38,7 +38,7 @@ def magnitude(self):
     @cached_property
     def phase(self):
         """Signal phase in radians."""
-        return np.unwrap(np.arctan2(self.voltage_i, self.voltage_q))
+        return np.unwrap(np.arctan2(self.voltage_q, self.voltage_i))
 
     @cached_property
     def phase_std(self):
@@ -95,7 +95,7 @@ def phase_std(self):
     @cached_property
     def phase(self):
         """Phase not unwrapped because it is a single value."""
-        return np.arctan2(self.voltage_i, self.voltage_q)
+        return np.arctan2(self.voltage_q, self.voltage_i)
 
 
 class RawWaveformResults(IntegratedResults):

From 1e56825290f21d721e39c12a435135ced2ed92c1 Mon Sep 17 00:00:00 2001
From: Hayk Sargsyan <52532457+hay-k@users.noreply.github.com>
Date: Thu, 26 Sep 2024 14:48:48 +0400
Subject: [PATCH 31/70] take sequencer number from defaults

---
 src/qibolab/instruments/qblox/port.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/qibolab/instruments/qblox/port.py b/src/qibolab/instruments/qblox/port.py
index 9efb4e160f..8827709d99 100644
--- a/src/qibolab/instruments/qblox/port.py
+++ b/src/qibolab/instruments/qblox/port.py
@@ -38,7 +38,7 @@ class QbloxOutputPort(Port):
     def __init__(self, module, port_number: int, port_name: str = None):
         self.name = port_name
         self.module = module
-        self.sequencer_number: int = port_number
+        self.sequencer_number: int = module.DEFAULT_SEQUENCERS[port_name]
         self.port_number: int = port_number
         self._settings = QbloxOutputPort_Settings()
 

From 035b325929ebc1f0d1d503e1fdb9cd34f28f1196 Mon Sep 17 00:00:00 2001
From: jevillegasdatTII <juan.villegas@tii.ae>
Date: Wed, 9 Oct 2024 11:45:11 +0400
Subject: [PATCH 32/70] Fix for frequencies not overlapping. With @aorgazf.

---
 src/qibolab/pulses.py | 55 +++++++++++++++++++++++++------------------
 1 file changed, 32 insertions(+), 23 deletions(-)

diff --git a/src/qibolab/pulses.py b/src/qibolab/pulses.py
index 63fd1b314a..45eae38c28 100644
--- a/src/qibolab/pulses.py
+++ b/src/qibolab/pulses.py
@@ -1587,30 +1587,39 @@ def separate_overlapping_pulses(self):  # -> dict((int,int): PulseSequence):
         """Separates a sequence of overlapping pulses into a list of non-
         overlapping sequences."""
 
-        # This routine separates the pulses of a sequence into non-overlapping sets
-        # but it does not check if the frequencies of the pulses within a set have the same frequency
-
-        separated_pulses = []
-        for new_pulse in self.pulses:
-            stored = False
-            for ps in separated_pulses:
-                overlaps = False
-                for existing_pulse in ps:
-                    if (
-                        new_pulse.start < existing_pulse.finish
-                        and new_pulse.finish > existing_pulse.start
-                    ):
-                        overlaps = True
+        # This routine separates the pulses of a sequence into sets of different frequecy, non-overlapping
+        # pulses
+
+        freqs = set()
+        for pulse in self.pulses:
+            freqs |= {pulse.frequency}
+        PS_freq = {}
+        separated_pulses = {}
+        for freq in freqs:
+            PS_freq[freq] = PulseSequence()
+            separated_pulses[freq] = []
+            for pulse in self.pulses:
+                if pulse.frequency == freq:
+                    PS_freq[freq].add(pulse)
+
+            for new_pulse in PS_freq[freq]:
+                stored = False
+                for ps in separated_pulses[freq]:
+                    overlaps = False
+                    for existing_pulse in ps:
+                        if (
+                            new_pulse.start < existing_pulse.finish
+                            and new_pulse.finish > existing_pulse.start
+                        ):
+                            overlaps = True
+                            break
+                    if not overlaps:
+                        ps.add(new_pulse)
+                        stored = True
                         break
-                if not overlaps:
-                    ps.add(new_pulse)
-                    stored = True
-                    break
-            if not stored:
-                separated_pulses.append(PulseSequence(new_pulse))
-        return separated_pulses
-
-    # TODO: Implement separate_different_frequency_pulses()
+                if not stored:
+                    separated_pulses[freq].append(PulseSequence(new_pulse))
+        return [ps for freq in freqs for ps in separated_pulses[freq]]
 
     @property
     def pulses_overlap(self) -> bool:

From f85447aa9ff231432842e4e26fa1ab0069085e14 Mon Sep 17 00:00:00 2001
From: Hayk Sargsyan <52532457+hay-k@users.noreply.github.com>
Date: Wed, 23 Oct 2024 11:27:26 +0400
Subject: [PATCH 33/70] fix result tests

---
 tests/test_result.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/test_result.py b/tests/test_result.py
index e861f56796..7ba339bbae 100644
--- a/tests/test_result.py
+++ b/tests/test_result.py
@@ -71,7 +71,7 @@ def test_integrated_result_properties(result):
         np.sqrt(results.voltage_i**2 + results.voltage_q**2), results.magnitude
     )
     np.testing.assert_equal(
-        np.unwrap(np.arctan2(results.voltage_i, results.voltage_q)), results.phase
+        np.unwrap(np.arctan2(results.voltage_q, results.voltage_i)), results.phase
     )
 
 
@@ -119,7 +119,7 @@ def test_serialize(average, result):
             "MSR[V]": np.sqrt(avg.voltage_i**2 + avg.voltage_q**2),
             "i[V]": avg.voltage_i,
             "q[V]": avg.voltage_q,
-            "phase[rad]": np.unwrap(np.arctan2(avg.voltage_i, avg.voltage_q)),
+            "phase[rad]": np.unwrap(np.arctan2(avg.voltage_q, avg.voltage_i)),
         }
         assert avg.serialize.keys() == target_dict.keys()
         for key in output:
@@ -155,7 +155,7 @@ def test_serialize_averaged_iq_results(result):
         "MSR[V]": np.sqrt(results.voltage_i**2 + results.voltage_q**2),
         "i[V]": results.voltage_i,
         "q[V]": results.voltage_q,
-        "phase[rad]": np.unwrap(np.arctan2(results.voltage_i, results.voltage_q)),
+        "phase[rad]": np.unwrap(np.arctan2(results.voltage_q, results.voltage_i)),
     }
     assert output.keys() == target_dict.keys()
     for key in output:

From d7e480684820bca0a0be4c57679f9a1b4b837548 Mon Sep 17 00:00:00 2001
From: Alessandro Candido <candido.ale@gmail.com>
Date: Mon, 28 Oct 2024 13:41:52 +0100
Subject: [PATCH 34/70] chore: Switch docformatter hook to master

Waiting for a proper release which will fix the pre-commit 4 incompatibility
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 8896d83bfa..2e3810a89b 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -19,7 +19,7 @@ repos:
       - id: isort
         args: ["--profile", "black"]
   - repo: https://github.com/PyCQA/docformatter
-    rev: v1.7.5
+    rev: master
     hooks:
       - id: docformatter
         additional_dependencies: [tomli]

From 761047c18da0ad49e9e0c4d76481a59b2c77c84e Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Fri, 18 Oct 2024 14:30:29 +0400
Subject: [PATCH 35/70] feat: add properties in QibolabBackend

---
 src/qibolab/backends.py | 19 +++++++++++++++++++
 tests/test_backends.py  | 14 ++++++++++++++
 2 files changed, 33 insertions(+)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index f17ce97f82..fc6aa4d9e7 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -50,6 +50,25 @@ def __init__(self, platform):
         }
         self.compiler = Compiler.default()
 
+    @property
+    def qubits(self) -> list[str | int]:
+        return list(self.platform.qubits.keys())
+
+    @property
+    def connectivity(self) -> list[tuple[str | int, str | int]]:
+        return list(self.platform.pairs)
+
+    @property
+    def natives(self) -> list[str]:    
+        native_gates = set()
+        for _, q in self.platform.qubits.items():
+            native_gates |= {k for k, v in q.native_gates.__dict__.items() if v is not None}
+        
+        for _, p in self.platform.pairs.items():
+            native_gates |= {k for k, v in p.native_gates.__dict__.items() if v is not None}
+
+        return list(native_gates)
+
     def apply_gate(self, gate, state, nqubits):  # pragma: no cover
         raise_error(NotImplementedError, "Qibolab cannot apply gates directly.")
 
diff --git a/tests/test_backends.py b/tests/test_backends.py
index 886d1a5bdc..4c05a55601 100644
--- a/tests/test_backends.py
+++ b/tests/test_backends.py
@@ -22,6 +22,20 @@ def generate_circuit_with_gate(nqubits, gate, **kwargs):
 def connected_backend(connected_platform):
     yield QibolabBackend(connected_platform)
 
+def test_qubits():
+    backend = QibolabBackend("dummy")
+    assert isinstance(backend.qubits, list)
+    assert set(backend.qubits) == set([0, 1, 2, 3, 4])
+
+def test_connectivity():
+    backend = QibolabBackend("dummy")
+    assert isinstance(backend.connectivity, list)
+    assert set(backend.connectivity) == set([(0, 2), (2, 0), (1, 2), (2, 1), (2, 3), (3, 2), (2, 4), (4, 2)])
+
+def test_natives():
+    backend = QibolabBackend("dummy")
+    assert isinstance(backend.natives, list)
+    assert set(backend.natives) == set(['RX12', 'RX', 'CZ', 'iSWAP', 'MZ', 'CNOT'])
 
 def test_execute_circuit_initial_state():
     backend = QibolabBackend("dummy")

From b7e993923741a999d62a78e0d03b068b1ba6d1fa Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Fri, 18 Oct 2024 14:34:34 +0400
Subject: [PATCH 36/70] fix: type hint for python 3.9

---
 src/qibolab/backends.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index fc6aa4d9e7..5baaa39210 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -1,4 +1,5 @@
 from collections import deque
+from typing import Union
 
 import numpy as np
 from qibo import __version__ as qibo_version
@@ -51,11 +52,11 @@ def __init__(self, platform):
         self.compiler = Compiler.default()
 
     @property
-    def qubits(self) -> list[str | int]:
+    def qubits(self) -> list[Union[str, int]]:
         return list(self.platform.qubits.keys())
 
     @property
-    def connectivity(self) -> list[tuple[str | int, str | int]]:
+    def connectivity(self) -> list[tuple[Union[str, int], Union[str, int]]]:
         return list(self.platform.pairs)
 
     @property

From c5381ca6638ac3e2a9d50cd4a35061caa52167d5 Mon Sep 17 00:00:00 2001
From: Changsoo Kim <57739683+csookim@users.noreply.github.com>
Date: Sun, 20 Oct 2024 11:05:23 +0400
Subject: [PATCH 37/70] Update src/qibolab/backends.py

Co-authored-by: Alessandro Candido <candido.ale@gmail.com>
---
 src/qibolab/backends.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index 5baaa39210..7f1cec8ad4 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -60,7 +60,7 @@ def connectivity(self) -> list[tuple[Union[str, int], Union[str, int]]]:
         return list(self.platform.pairs)
 
     @property
-    def natives(self) -> list[str]:    
+    def natives(self) -> list[str]:
         native_gates = set()
         for _, q in self.platform.qubits.items():
             native_gates |= {k for k, v in q.native_gates.__dict__.items() if v is not None}

From 6da1b133f234d482208b6a03b741e7e69cd2cfcf Mon Sep 17 00:00:00 2001
From: Changsoo Kim <57739683+csookim@users.noreply.github.com>
Date: Sun, 20 Oct 2024 11:05:48 +0400
Subject: [PATCH 38/70] Update src/qibolab/backends.py

Co-authored-by: Alessandro Candido <candido.ale@gmail.com>
---
 src/qibolab/backends.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index 7f1cec8ad4..c3703b21fd 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -53,7 +53,7 @@ def __init__(self, platform):
 
     @property
     def qubits(self) -> list[Union[str, int]]:
-        return list(self.platform.qubits.keys())
+        return list(self.platform.qubits)
 
     @property
     def connectivity(self) -> list[tuple[Union[str, int], Union[str, int]]]:

From fd6ff6e13c5a4c435524c5edf8caca61c2c0a66b Mon Sep 17 00:00:00 2001
From: Changsoo Kim <57739683+csookim@users.noreply.github.com>
Date: Sun, 20 Oct 2024 11:06:26 +0400
Subject: [PATCH 39/70] Update src/qibolab/backends.py

Co-authored-by: Alessandro Candido <candido.ale@gmail.com>
---
 src/qibolab/backends.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index c3703b21fd..f662b26f0b 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -63,7 +63,7 @@ def connectivity(self) -> list[tuple[Union[str, int], Union[str, int]]]:
     def natives(self) -> list[str]:
         native_gates = set()
         for _, q in self.platform.qubits.items():
-            native_gates |= {k for k, v in q.native_gates.__dict__.items() if v is not None}
+            native_gates |= {k for k, v in asdict(q.native_gates).items() if v is not None}
         
         for _, p in self.platform.pairs.items():
             native_gates |= {k for k, v in p.native_gates.__dict__.items() if v is not None}

From cbc5943214d18a94a7bd181794c64cd58651e495 Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Sun, 20 Oct 2024 17:01:43 +0400
Subject: [PATCH 40/70] fix: replace __dict__ with flelds()

---
 src/qibolab/backends.py | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index f662b26f0b..dfe30ad80b 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -1,4 +1,5 @@
 from collections import deque
+from dataclasses import fields
 from typing import Union
 
 import numpy as np
@@ -63,11 +64,18 @@ def connectivity(self) -> list[tuple[Union[str, int], Union[str, int]]]:
     def natives(self) -> list[str]:
         native_gates = set()
         for _, q in self.platform.qubits.items():
-            native_gates |= {k for k, v in asdict(q.native_gates).items() if v is not None}
-        
-        for _, p in self.platform.pairs.items():
-            native_gates |= {k for k, v in p.native_gates.__dict__.items() if v is not None}
+            native_gates |= {
+                fld.name
+                for fld in fields(q.native_gates)
+                if getattr(q.native_gates, fld.name) is not None
+            }
 
+        for _, p in self.platform.pairs.items():
+            native_gates |= {
+                fld.name
+                for fld in fields(p.native_gates)
+                if getattr(p.native_gates, fld.name) is not None
+            }
         return list(native_gates)
 
     def apply_gate(self, gate, state, nqubits):  # pragma: no cover

From 86e836e240e3f08a60d7326adba73aa443e6e89b Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Tue, 22 Oct 2024 09:32:03 +0400
Subject: [PATCH 41/70] feat: add _rename_gates

---
 src/qibolab/backends.py | 20 +++++++++++++++++++-
 tests/test_backends.py  | 30 +++++++++++++++++++++++++++---
 2 files changed, 46 insertions(+), 4 deletions(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index dfe30ad80b..1d3231c5e1 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -76,7 +76,25 @@ def natives(self) -> list[str]:
                 for fld in fields(p.native_gates)
                 if getattr(p.native_gates, fld.name) is not None
             }
-        return list(native_gates)
+
+        return self._rename_gates(list(native_gates))
+
+    def _rename_gates(self, natives: list[str]):
+        gates = []
+        for native in natives:
+            if native == "RX12":
+                pass
+            elif native == "RX":
+                gates.append("RX")
+            elif native == "CZ":
+                gates.append("CZ")
+            elif native == "iSWAP":
+                gates.append("iSWAP")
+            elif native == "MZ":
+                gates.append("M")
+            elif native == "CNOT":
+                gates.append("CNOT")
+        return gates
 
     def apply_gate(self, gate, state, nqubits):  # pragma: no cover
         raise_error(NotImplementedError, "Qibolab cannot apply gates directly.")
diff --git a/tests/test_backends.py b/tests/test_backends.py
index 4c05a55601..9f09771c48 100644
--- a/tests/test_backends.py
+++ b/tests/test_backends.py
@@ -22,20 +22,44 @@ def generate_circuit_with_gate(nqubits, gate, **kwargs):
 def connected_backend(connected_platform):
     yield QibolabBackend(connected_platform)
 
+
 def test_qubits():
     backend = QibolabBackend("dummy")
     assert isinstance(backend.qubits, list)
-    assert set(backend.qubits) == set([0, 1, 2, 3, 4])
+    assert set(backend.qubits) == {0, 1, 2, 3, 4}
+
 
 def test_connectivity():
     backend = QibolabBackend("dummy")
     assert isinstance(backend.connectivity, list)
-    assert set(backend.connectivity) == set([(0, 2), (2, 0), (1, 2), (2, 1), (2, 3), (3, 2), (2, 4), (4, 2)])
+    assert set(backend.connectivity) == {
+        (0, 2),
+        (2, 0),
+        (1, 2),
+        (2, 1),
+        (2, 3),
+        (3, 2),
+        (2, 4),
+        (4, 2),
+    }
+
 
 def test_natives():
     backend = QibolabBackend("dummy")
     assert isinstance(backend.natives, list)
-    assert set(backend.natives) == set(['RX12', 'RX', 'CZ', 'iSWAP', 'MZ', 'CNOT'])
+    assert set(backend.natives) == {"RX", "CZ", "iSWAP", "M", "CNOT"}
+
+
+def test_rename_gates():
+    backend = QibolabBackend("dummy")
+    assert backend._rename_gates(["RX12", "RX", "CZ", "iSWAP", "MZ", "CNOT"]) == [
+        "RX",
+        "CZ",
+        "iSWAP",
+        "M",
+        "CNOT",
+    ]
+
 
 def test_execute_circuit_initial_state():
     backend = QibolabBackend("dummy")

From 8166c419ff1de4b555a6cc827f251316f212967c Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Wed, 23 Oct 2024 11:17:29 +0400
Subject: [PATCH 42/70] fix: update natives() and add two-qubit gate filter

---
 src/qibolab/backends.py | 63 +++++++++++++++++++----------------------
 tests/test_backends.py  | 18 ++++++------
 2 files changed, 37 insertions(+), 44 deletions(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index 1d3231c5e1..e67b137722 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -1,9 +1,9 @@
 from collections import deque
-from dataclasses import fields
 from typing import Union
 
 import numpy as np
 from qibo import __version__ as qibo_version
+from qibo import gates
 from qibo.backends import NumpyBackend
 from qibo.config import raise_error
 from qibo.models import Circuit
@@ -54,47 +54,42 @@ def __init__(self, platform):
 
     @property
     def qubits(self) -> list[Union[str, int]]:
+        """Returns the qubits in the platform."""
         return list(self.platform.qubits)
 
     @property
     def connectivity(self) -> list[tuple[Union[str, int], Union[str, int]]]:
+        """Returns the list of connected qubits."""
         return list(self.platform.pairs)
 
     @property
     def natives(self) -> list[str]:
-        native_gates = set()
-        for _, q in self.platform.qubits.items():
-            native_gates |= {
-                fld.name
-                for fld in fields(q.native_gates)
-                if getattr(q.native_gates, fld.name) is not None
-            }
-
-        for _, p in self.platform.pairs.items():
-            native_gates |= {
-                fld.name
-                for fld in fields(p.native_gates)
-                if getattr(p.native_gates, fld.name) is not None
-            }
-
-        return self._rename_gates(list(native_gates))
-
-    def _rename_gates(self, natives: list[str]):
-        gates = []
-        for native in natives:
-            if native == "RX12":
-                pass
-            elif native == "RX":
-                gates.append("RX")
-            elif native == "CZ":
-                gates.append("CZ")
-            elif native == "iSWAP":
-                gates.append("iSWAP")
-            elif native == "MZ":
-                gates.append("M")
-            elif native == "CNOT":
-                gates.append("CNOT")
-        return gates
+        """Returns the list of native gates supported by the platform."""
+        compiler = Compiler.default()
+        natives = [g.__name__ for g in list(compiler.rules)]
+
+        if "CZ" in natives and "CNOT" in natives:
+            for pair in self.connectivity:
+                cz = gates.CZ(*pair)
+                cnot = gates.CNOT(*pair)
+
+                if not self._is_gate_calibrated(cz, compiler):
+                    natives.remove("CZ")
+                    break
+
+                if not self._is_gate_calibrated(cnot, compiler):
+                    natives.remove("CNOT")
+                    break
+
+        return natives
+
+    def _is_gate_calibrated(self, gate, compiler) -> bool:
+        """Helper method to check if a gate is calibrated."""
+        try:
+            compiler[gate.__class__](gate, self.platform)
+            return True
+        except ValueError:
+            return False
 
     def apply_gate(self, gate, state, nqubits):  # pragma: no cover
         raise_error(NotImplementedError, "Qibolab cannot apply gates directly.")
diff --git a/tests/test_backends.py b/tests/test_backends.py
index 9f09771c48..94a01887a3 100644
--- a/tests/test_backends.py
+++ b/tests/test_backends.py
@@ -47,18 +47,16 @@ def test_connectivity():
 def test_natives():
     backend = QibolabBackend("dummy")
     assert isinstance(backend.natives, list)
-    assert set(backend.natives) == {"RX", "CZ", "iSWAP", "M", "CNOT"}
-
-
-def test_rename_gates():
-    backend = QibolabBackend("dummy")
-    assert backend._rename_gates(["RX12", "RX", "CZ", "iSWAP", "MZ", "CNOT"]) == [
-        "RX",
+    assert set(backend.natives) == {
+        "I",
+        "Z",
+        "RZ",
+        "U3",
         "CZ",
-        "iSWAP",
+        "GPI2",
+        "GPI",
         "M",
-        "CNOT",
-    ]
+    }
 
 
 def test_execute_circuit_initial_state():

From 1a1899c8aa96a7c87c1bf2aaf113295f3b034e78 Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Wed, 23 Oct 2024 11:25:47 +0400
Subject: [PATCH 43/70] fix: add pragma and remove commented pre commit

---
 src/qibolab/backends.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index e67b137722..81d6ce1c52 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -73,7 +73,7 @@ def natives(self) -> list[str]:
                 cz = gates.CZ(*pair)
                 cnot = gates.CNOT(*pair)
 
-                if not self._is_gate_calibrated(cz, compiler):
+                if not self._is_gate_calibrated(cz, compiler):  # pragma: no cover
                     natives.remove("CZ")
                     break
 

From 030a7b96960a61e2ffe6dd3c8aa0ba7f80aa820b Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Thu, 24 Oct 2024 09:41:46 +0400
Subject: [PATCH 44/70] fix: natives() find uniformly supported gates

---
 src/qibolab/backends.py | 22 ++++++++--------------
 1 file changed, 8 insertions(+), 14 deletions(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index 81d6ce1c52..09e9847465 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -68,25 +68,19 @@ def natives(self) -> list[str]:
         compiler = Compiler.default()
         natives = [g.__name__ for g in list(compiler.rules)]
 
-        if "CZ" in natives and "CNOT" in natives:
-            for pair in self.connectivity:
-                cz = gates.CZ(*pair)
-                cnot = gates.CNOT(*pair)
-
-                if not self._is_gate_calibrated(cz, compiler):  # pragma: no cover
-                    natives.remove("CZ")
-                    break
-
-                if not self._is_gate_calibrated(cnot, compiler):
-                    natives.remove("CNOT")
-                    break
-
+        check_2q = ["CZ", "CNOT"]
+        for gate in check_2q:
+            if gate in natives and any(
+                not self._is_gate_calibrated(getattr(gates, gate)(*pair), compiler)
+                for pair in self.connectivity
+            ):
+                natives.remove(gate)
         return natives
 
     def _is_gate_calibrated(self, gate, compiler) -> bool:
         """Helper method to check if a gate is calibrated."""
         try:
-            compiler[gate.__class__](gate, self.platform)
+            compiler[type(gate)](gate, self.platform)
             return True
         except ValueError:
             return False

From cdf87052c7c37cb3840795c268803b9a8bcc34dd Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Thu, 24 Oct 2024 11:28:40 +0400
Subject: [PATCH 45/70] fix: natives() return any available gate

---
 src/qibolab/backends.py | 28 +++++++++++++++++++++++-----
 tests/test_backends.py  |  1 +
 2 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index 09e9847465..823e22b737 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -62,6 +62,20 @@ def connectivity(self) -> list[tuple[Union[str, int], Union[str, int]]]:
         """Returns the list of connected qubits."""
         return list(self.platform.pairs)
 
+    # @property
+    # def natives(self) -> list[str]:
+    #     """Returns the list of native gates supported by the platform."""
+    #     compiler = Compiler.default()
+    #     natives = [g.__name__ for g in list(compiler.rules)]
+
+    #     check_2q = ["CZ", "CNOT"]
+    #     for gate in check_2q:
+    #         if gate in natives and any(
+    #             not self._is_gate_calibrated(getattr(gates, gate)(*pair), compiler)
+    #             for pair in self.connectivity
+    #         ):
+    #             natives.remove(gate)
+    #     return natives
     @property
     def natives(self) -> list[str]:
         """Returns the list of native gates supported by the platform."""
@@ -70,11 +84,15 @@ def natives(self) -> list[str]:
 
         check_2q = ["CZ", "CNOT"]
         for gate in check_2q:
-            if gate in natives and any(
-                not self._is_gate_calibrated(getattr(gates, gate)(*pair), compiler)
-                for pair in self.connectivity
-            ):
-                natives.remove(gate)
+            if gate in natives:
+                for pair in self.connectivity:
+                    logical_pair = [list(self.platform.qubits).index(q) for q in pair]
+                    if self._is_gate_calibrated(
+                        getattr(gates, gate)(*logical_pair), compiler
+                    ):
+                        break
+                else:
+                    natives.remove(gate)
         return natives
 
     def _is_gate_calibrated(self, gate, compiler) -> bool:
diff --git a/tests/test_backends.py b/tests/test_backends.py
index 94a01887a3..d3effec884 100644
--- a/tests/test_backends.py
+++ b/tests/test_backends.py
@@ -53,6 +53,7 @@ def test_natives():
         "RZ",
         "U3",
         "CZ",
+        "CNOT",
         "GPI2",
         "GPI",
         "M",

From 92022c410df591051282cfa85c6969a6ca7258f9 Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Thu, 24 Oct 2024 11:29:42 +0400
Subject: [PATCH 46/70] fix: remove dead code

---
 src/qibolab/backends.py | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index 823e22b737..ca595242cb 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -62,20 +62,6 @@ def connectivity(self) -> list[tuple[Union[str, int], Union[str, int]]]:
         """Returns the list of connected qubits."""
         return list(self.platform.pairs)
 
-    # @property
-    # def natives(self) -> list[str]:
-    #     """Returns the list of native gates supported by the platform."""
-    #     compiler = Compiler.default()
-    #     natives = [g.__name__ for g in list(compiler.rules)]
-
-    #     check_2q = ["CZ", "CNOT"]
-    #     for gate in check_2q:
-    #         if gate in natives and any(
-    #             not self._is_gate_calibrated(getattr(gates, gate)(*pair), compiler)
-    #             for pair in self.connectivity
-    #         ):
-    #             natives.remove(gate)
-    #     return natives
     @property
     def natives(self) -> list[str]:
         """Returns the list of native gates supported by the platform."""

From a15cd83eb20ca51ab5bb82c360feec0767b4c2a9 Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Fri, 25 Oct 2024 10:21:05 +0400
Subject: [PATCH 47/70] fix: natives() use QubitPair.native_gates

---
 src/qibolab/backends.py | 25 +++++++------------------
 1 file changed, 7 insertions(+), 18 deletions(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index ca595242cb..d752c5cb4a 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -3,7 +3,6 @@
 
 import numpy as np
 from qibo import __version__ as qibo_version
-from qibo import gates
 from qibo.backends import NumpyBackend
 from qibo.config import raise_error
 from qibo.models import Circuit
@@ -67,27 +66,17 @@ def natives(self) -> list[str]:
         """Returns the list of native gates supported by the platform."""
         compiler = Compiler.default()
         natives = [g.__name__ for g in list(compiler.rules)]
+        calibrated = self.platform.pairs
 
         check_2q = ["CZ", "CNOT"]
         for gate in check_2q:
-            if gate in natives:
-                for pair in self.connectivity:
-                    logical_pair = [list(self.platform.qubits).index(q) for q in pair]
-                    if self._is_gate_calibrated(
-                        getattr(gates, gate)(*logical_pair), compiler
-                    ):
-                        break
-                else:
-                    natives.remove(gate)
-        return natives
+            if gate in natives and all(
+                getattr(calibrated[p].native_gates, gate) is None
+                for p in self.connectivity
+            ):
+                natives.remove(gate)
 
-    def _is_gate_calibrated(self, gate, compiler) -> bool:
-        """Helper method to check if a gate is calibrated."""
-        try:
-            compiler[type(gate)](gate, self.platform)
-            return True
-        except ValueError:
-            return False
+        return natives
 
     def apply_gate(self, gate, state, nqubits):  # pragma: no cover
         raise_error(NotImplementedError, "Qibolab cannot apply gates directly.")

From 2a19f003fd66f7fe4a7514b7cc200a27dcd60d3f Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Fri, 25 Oct 2024 11:53:39 +0400
Subject: [PATCH 48/70] fix: add test_natives_no_cz_cnot

---
 tests/test_backends.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/tests/test_backends.py b/tests/test_backends.py
index d3effec884..da0676269e 100644
--- a/tests/test_backends.py
+++ b/tests/test_backends.py
@@ -60,6 +60,24 @@ def test_natives():
     }
 
 
+def test_natives_no_cz_cnot():
+    platform = create_platform("dummy")
+    for p in platform.pairs:
+        platform.pairs[p].native_gates.CZ = None
+        platform.pairs[p].native_gates.CNOT = None
+
+    backend = QibolabBackend(platform)
+    assert set(backend.natives) == {
+        "I",
+        "Z",
+        "RZ",
+        "U3",
+        "GPI2",
+        "GPI",
+        "M",
+    }
+
+
 def test_execute_circuit_initial_state():
     backend = QibolabBackend("dummy")
     circuit = Circuit(1)

From 82526b70391913cee719c8b6b25e8ad295685036 Mon Sep 17 00:00:00 2001
From: Changsoo Kim <57739683+csookim@users.noreply.github.com>
Date: Fri, 25 Oct 2024 13:45:48 +0400
Subject: [PATCH 49/70] Update tests/test_backends.py

Co-authored-by: Alessandro Candido <candido.ale@gmail.com>
---
 tests/test_backends.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/tests/test_backends.py b/tests/test_backends.py
index da0676269e..3ce064e8fb 100644
--- a/tests/test_backends.py
+++ b/tests/test_backends.py
@@ -62,10 +62,6 @@ def test_natives():
 
 def test_natives_no_cz_cnot():
     platform = create_platform("dummy")
-    for p in platform.pairs:
-        platform.pairs[p].native_gates.CZ = None
-        platform.pairs[p].native_gates.CNOT = None
-
     backend = QibolabBackend(platform)
     assert set(backend.natives) == {
         "I",
@@ -75,7 +71,14 @@ def test_natives_no_cz_cnot():
         "GPI2",
         "GPI",
         "M",
+        "CZ",
+        "CNOT"
     }
+    
+    for gate in ["CZ", "CNOT"]:
+        for p in platform.pairs:
+            setattr(platform.pairs[p].native_gates, gate, None)
+        assert gate not in set(backend.natives)
 
 
 def test_execute_circuit_initial_state():

From b96e3b483c337c7ea755bacfc6a4c12f447f51b9 Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Mon, 28 Oct 2024 16:28:46 +0400
Subject: [PATCH 50/70] fix: use QubitId, QubitPairId

---
 src/qibolab/backends.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index d752c5cb4a..44cdb06c00 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -13,6 +13,7 @@
 from qibolab.platform import Platform, create_platform
 from qibolab.platform.load import available_platforms
 from qibolab.version import __version__ as qibolab_version
+from qibolab.qubits import QubitId, QubitPairId
 
 
 def execute_qasm(circuit: str, platform, initial_state=None, nshots=1000):
@@ -52,12 +53,12 @@ def __init__(self, platform):
         self.compiler = Compiler.default()
 
     @property
-    def qubits(self) -> list[Union[str, int]]:
+    def qubits(self) -> list[QubitId]:
         """Returns the qubits in the platform."""
         return list(self.platform.qubits)
 
     @property
-    def connectivity(self) -> list[tuple[Union[str, int], Union[str, int]]]:
+    def connectivity(self) -> list[QubitPairId]:
         """Returns the list of connected qubits."""
         return list(self.platform.pairs)
 

From a30c55264e0d0348aa2763debe9605d134a01340 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 28 Oct 2024 13:50:21 +0000
Subject: [PATCH 51/70] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/qibolab/backends.py | 3 +--
 tests/test_backends.py  | 4 ++--
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index 44cdb06c00..53f2bcaa9f 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -1,5 +1,4 @@
 from collections import deque
-from typing import Union
 
 import numpy as np
 from qibo import __version__ as qibo_version
@@ -12,8 +11,8 @@
 from qibolab.execution_parameters import ExecutionParameters
 from qibolab.platform import Platform, create_platform
 from qibolab.platform.load import available_platforms
-from qibolab.version import __version__ as qibolab_version
 from qibolab.qubits import QubitId, QubitPairId
+from qibolab.version import __version__ as qibolab_version
 
 
 def execute_qasm(circuit: str, platform, initial_state=None, nshots=1000):
diff --git a/tests/test_backends.py b/tests/test_backends.py
index 3ce064e8fb..5b189bfbb3 100644
--- a/tests/test_backends.py
+++ b/tests/test_backends.py
@@ -72,9 +72,9 @@ def test_natives_no_cz_cnot():
         "GPI",
         "M",
         "CZ",
-        "CNOT"
+        "CNOT",
     }
-    
+
     for gate in ["CZ", "CNOT"]:
         for p in platform.pairs:
             setattr(platform.pairs[p].native_gates, gate, None)

From 54dca9e5bb6cc59fd6016704a383bf73ddfe397e Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Thu, 24 Oct 2024 16:56:33 +0400
Subject: [PATCH 52/70] feat: use qibo.Circuit.wire_names to specify hw qubit

---
 src/qibolab/compilers/default.py | 17 ++++++++++-------
 tests/test_backends.py           | 15 +++++++++++++--
 2 files changed, 23 insertions(+), 9 deletions(-)

diff --git a/src/qibolab/compilers/default.py b/src/qibolab/compilers/default.py
index b178eefe92..e69f1779a2 100644
--- a/src/qibolab/compilers/default.py
+++ b/src/qibolab/compilers/default.py
@@ -15,19 +15,19 @@ def identity_rule(gate, platform):
 
 def z_rule(gate, platform):
     """Z gate applied virtually."""
-    qubit = list(platform.qubits)[gate.target_qubits[0]]
+    qubit = platform.get_qubit(gate.target_qubits[0])
     return PulseSequence(), {qubit: math.pi}
 
 
 def rz_rule(gate, platform):
     """RZ gate applied virtually."""
-    qubit = list(platform.qubits)[gate.target_qubits[0]]
+    qubit = platform.get_qubit(gate.target_qubits[0])
     return PulseSequence(), {qubit: -gate.parameters[0]}
 
 
 def gpi2_rule(gate, platform):
     """Rule for GPI2."""
-    qubit = list(platform.qubits)[gate.target_qubits[0]]
+    qubit = platform.get_qubit(gate.target_qubits[0])
     theta = gate.parameters[0]
     sequence = PulseSequence()
     pulse = platform.create_RX90_pulse(qubit, start=0, relative_phase=theta)
@@ -37,7 +37,7 @@ def gpi2_rule(gate, platform):
 
 def gpi_rule(gate, platform):
     """Rule for GPI."""
-    qubit = list(platform.qubits)[gate.target_qubits[0]]
+    qubit = platform.get_qubit(gate.target_qubits[0])
     theta = gate.parameters[0]
     sequence = PulseSequence()
     # the following definition has a global phase difference compare to
@@ -51,7 +51,7 @@ def gpi_rule(gate, platform):
 
 def u3_rule(gate, platform):
     """U3 applied as RZ-RX90-RZ-RX90-RZ."""
-    qubit = list(platform.qubits)[gate.target_qubits[0]]
+    qubit = platform.get_qubit(gate.target_qubits[0])
     # Transform gate to U3 and add pi/2-pulses
     theta, phi, lam = gate.parameters
     # apply RZ(lam)
@@ -85,18 +85,21 @@ def cz_rule(gate, platform):
     Applying the CZ gate may involve sending pulses on qubits that the
     gate is not directly acting on.
     """
-    return platform.create_CZ_pulse_sequence(gate.qubits)
+    qubits = tuple(platform.get_qubit(q) for q in gate.qubits)
+    return platform.create_CZ_pulse_sequence(qubits)
 
 
 def cnot_rule(gate, platform):
     """CNOT applied as defined in the platform runcard."""
-    return platform.create_CNOT_pulse_sequence(gate.qubits)
+    qubits = tuple(platform.get_qubit(q) for q in gate.qubits)
+    return platform.create_CNOT_pulse_sequence(qubits)
 
 
 def measurement_rule(gate, platform):
     """Measurement gate applied using the platform readout pulse."""
     sequence = PulseSequence()
     for qubit in gate.target_qubits:
+        qubit = platform.get_qubit(qubit)
         MZ_pulse = platform.create_MZ_pulse(qubit, start=0)
         sequence.add(MZ_pulse)
     return sequence, {}
diff --git a/tests/test_backends.py b/tests/test_backends.py
index 5b189bfbb3..bf5065723e 100644
--- a/tests/test_backends.py
+++ b/tests/test_backends.py
@@ -11,10 +11,11 @@
 from qibolab.backends import QibolabBackend
 
 
-def generate_circuit_with_gate(nqubits, gate, **kwargs):
+def generate_circuit_with_gate(nqubits, gate, names, **kwargs):
     circuit = Circuit(nqubits)
     circuit.add(gate(qubit, **kwargs) for qubit in range(nqubits))
     circuit.add(gates.M(*range(nqubits)))
+    circuit._wire_names = names
     return circuit
 
 
@@ -86,6 +87,7 @@ def test_execute_circuit_initial_state():
     circuit = Circuit(1)
     circuit.add(gates.GPI2(0, phi=0))
     circuit.add(gates.M(0))
+    circuit._wire_names = [0]
     with pytest.raises(ValueError):
         backend.execute_circuit(circuit, initial_state=np.ones(2))
 
@@ -107,7 +109,7 @@ def test_execute_circuit_initial_state():
 def test_execute_circuit(gate, kwargs):
     backend = QibolabBackend("dummy")
     nqubits = backend.platform.nqubits
-    circuit = generate_circuit_with_gate(nqubits, gate, **kwargs)
+    circuit = generate_circuit_with_gate(nqubits, gate, list(range(nqubits)), **kwargs)
     result = backend.execute_circuit(circuit, nshots=100)
 
 
@@ -117,12 +119,14 @@ def test_measurement_samples():
 
     circuit = Circuit(nqubits)
     circuit.add(gates.M(*range(nqubits)))
+    circuit._wire_names = list(range(nqubits))
     result = backend.execute_circuit(circuit, nshots=100)
     assert result.samples().shape == (100, nqubits)
     assert sum(result.frequencies().values()) == 100
 
     circuit = Circuit(nqubits)
     circuit.add(gates.M(0, 2))
+    circuit._wire_names = list(range(nqubits))
     result = backend.execute_circuit(circuit, nshots=100)
     assert result.samples().shape == (100, 2)
     assert sum(result.frequencies().values()) == 100
@@ -135,6 +139,7 @@ def test_execute_circuits():
     circuit = Circuit(3)
     circuit.add(gates.GPI2(i, phi=np.pi / 2) for i in range(3))
     circuit.add(gates.M(0, 1, 2))
+    circuit._wire_names = list(range(3))
 
     results = backend.execute_circuits(
         5 * [circuit], initial_states=initial_state_circuit, nshots=100
@@ -151,6 +156,7 @@ def test_multiple_measurements():
     circuit = Circuit(4)
     circuit.add(gates.GPI2(i, phi=np.pi / 2) for i in range(2))
     circuit.add(gates.CZ(1, 2))
+    circuit._wire_names = list(range(4))
     res0 = circuit.add(gates.M(0))
     res1 = circuit.add(gates.M(3))
     res2 = circuit.add(gates.M(1))
@@ -171,6 +177,7 @@ def dummy_string_qubit_names():
     platform.pairs = {
         (f"A{q0}", f"A{q1}"): pair for (q0, q1), pair in platform.pairs.items()
     }
+    platform.wire_names = [f"A{q}" for q in range(platform.nqubits)]
     return platform
 
 
@@ -182,6 +189,7 @@ def test_execute_circuit_str_qubit_names():
     circuit.add(gates.GPI2(i, phi=np.pi / 2) for i in range(2))
     circuit.add(gates.CZ(1, 2))
     circuit.add(gates.M(0, 1))
+    circuit._wire_names = ["A0", "A1", "A2"]
     result = backend.execute_circuit(circuit, nshots=20)
     assert result.samples().shape == (20, 2)
 
@@ -195,6 +203,7 @@ def test_ground_state_probabilities_circuit(connected_backend):
     nqubits = connected_backend.platform.nqubits
     circuit = Circuit(nqubits)
     circuit.add(gates.M(*range(nqubits)))
+    circuit._wire_names = list(range(nqubits))
     result = connected_backend.execute_circuit(circuit, nshots=nshots)
     freqs = result.frequencies(binary=False)
     probs = [freqs[i] / nshots for i in range(2**nqubits)]
@@ -214,6 +223,7 @@ def test_excited_state_probabilities_circuit(connected_backend):
     circuit = Circuit(nqubits)
     circuit.add(gates.X(q) for q in range(nqubits))
     circuit.add(gates.M(*range(nqubits)))
+    circuit._wire_names = list(range(nqubits))
     result = connected_backend.execute_circuit(circuit, nshots=nshots)
     freqs = result.frequencies(binary=False)
     probs = [freqs[i] / nshots for i in range(2**nqubits)]
@@ -237,6 +247,7 @@ def test_superposition_for_all_qubits(connected_backend):
         circuit = Circuit(nqubits)
         circuit.add(gates.GPI2(q=q, phi=np.pi / 2))
         circuit.add(gates.M(q))
+        circuit._wire_names = list(range(nqubits))
         freqs = connected_backend.execute_circuit(circuit, nshots=nshots).frequencies(
             binary=False
         )

From 5945732e8a7b85ca22dcf03e3f2d95e19c61d0d6 Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Fri, 25 Oct 2024 13:14:40 +0400
Subject: [PATCH 53/70] fix: revert cz/cnot/measurement_rule

---
 src/qibolab/compilers/default.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/src/qibolab/compilers/default.py b/src/qibolab/compilers/default.py
index e69f1779a2..2c91b211c1 100644
--- a/src/qibolab/compilers/default.py
+++ b/src/qibolab/compilers/default.py
@@ -85,21 +85,18 @@ def cz_rule(gate, platform):
     Applying the CZ gate may involve sending pulses on qubits that the
     gate is not directly acting on.
     """
-    qubits = tuple(platform.get_qubit(q) for q in gate.qubits)
-    return platform.create_CZ_pulse_sequence(qubits)
+    return platform.create_CZ_pulse_sequence(gate.qubits)
 
 
 def cnot_rule(gate, platform):
     """CNOT applied as defined in the platform runcard."""
-    qubits = tuple(platform.get_qubit(q) for q in gate.qubits)
-    return platform.create_CNOT_pulse_sequence(qubits)
+    return platform.create_CNOT_pulse_sequence(gate.qubits)
 
 
 def measurement_rule(gate, platform):
     """Measurement gate applied using the platform readout pulse."""
     sequence = PulseSequence()
     for qubit in gate.target_qubits:
-        qubit = platform.get_qubit(qubit)
         MZ_pulse = platform.create_MZ_pulse(qubit, start=0)
         sequence.add(MZ_pulse)
     return sequence, {}

From 801dced7c51ae42085987f8b251b5e553eb82e37 Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Mon, 28 Oct 2024 17:25:32 +0400
Subject: [PATCH 54/70] fix: remove platform.wire_names

---
 src/qibolab/backends.py | 12 ++++++++++++
 tests/test_backends.py  | 11 ++++-------
 2 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index 53f2bcaa9f..ea80aebffb 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -125,6 +125,18 @@ def execute_circuit(self, circuit, initial_state=None, nshots=1000):
                 "Hardware backend only supports circuits as initial states.",
             )
 
+        if not all(q in circuit.wire_names for q in self.platform.qubits):
+            # This should be done in qibo side
+            # raise_error(
+            #     ValueError,
+            #     "Circuit qubits do not match the platform qubits.",
+            # )
+
+            # Temporary fix: overwrite the wire names
+            circuit._wire_names = self.qubits
+
+        self.platform.wire_names = circuit.wire_names
+
         sequence, measurement_map = self.compiler.compile(circuit, self.platform)
 
         if not self.platform.is_connected:
diff --git a/tests/test_backends.py b/tests/test_backends.py
index bf5065723e..232106764c 100644
--- a/tests/test_backends.py
+++ b/tests/test_backends.py
@@ -63,6 +63,10 @@ def test_natives():
 
 def test_natives_no_cz_cnot():
     platform = create_platform("dummy")
+    for p in platform.pairs:
+        platform.pairs[p].native_gates.CZ = None
+        platform.pairs[p].native_gates.CNOT = None
+
     backend = QibolabBackend(platform)
     assert set(backend.natives) == {
         "I",
@@ -72,15 +76,8 @@ def test_natives_no_cz_cnot():
         "GPI2",
         "GPI",
         "M",
-        "CZ",
-        "CNOT",
     }
 
-    for gate in ["CZ", "CNOT"]:
-        for p in platform.pairs:
-            setattr(platform.pairs[p].native_gates, gate, None)
-        assert gate not in set(backend.natives)
-
 
 def test_execute_circuit_initial_state():
     backend = QibolabBackend("dummy")

From 17a778040bdebdc9e6caf9d622254ace1cd28dd3 Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Mon, 28 Oct 2024 18:44:53 +0400
Subject: [PATCH 55/70] fix: update compiler/rules to use circuit.wire_names

---
 src/qibolab/backends.py           | 15 +++++-----
 src/qibolab/compilers/compiler.py | 24 ++++++++++++++--
 src/qibolab/compilers/default.py  | 46 +++++++++++++++----------------
 tests/test_compilers_default.py   |  2 ++
 4 files changed, 53 insertions(+), 34 deletions(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index ea80aebffb..4c1c31a3a8 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -125,14 +125,9 @@ def execute_circuit(self, circuit, initial_state=None, nshots=1000):
                 "Hardware backend only supports circuits as initial states.",
             )
 
+        # This should be done in qibo side
+        # Temporary fix: overwrite the wire names
         if not all(q in circuit.wire_names for q in self.platform.qubits):
-            # This should be done in qibo side
-            # raise_error(
-            #     ValueError,
-            #     "Circuit qubits do not match the platform qubits.",
-            # )
-
-            # Temporary fix: overwrite the wire names
             circuit._wire_names = self.qubits
 
         self.platform.wire_names = circuit.wire_names
@@ -179,6 +174,12 @@ def execute_circuits(self, circuits, initial_states=None, nshots=1000):
                 "Hardware backend only supports circuits as initial states.",
             )
 
+        # This should be done in qibo side
+        # Temporary fix: overwrite the wire names
+        for circuit in circuits:
+            if not all(q in circuit.wire_names for q in self.platform.qubits):
+                circuit._wire_names = self.qubits
+
         # TODO: Maybe these loops can be parallelized
         sequences, measurement_maps = zip(
             *(self.compiler.compile(circuit, self.platform) for circuit in circuits)
diff --git a/src/qibolab/compilers/compiler.py b/src/qibolab/compilers/compiler.py
index 316fde2586..38fb9c7628 100644
--- a/src/qibolab/compilers/compiler.py
+++ b/src/qibolab/compilers/compiler.py
@@ -99,12 +99,24 @@ def inner(func):
         return inner
 
     def _compile_gate(
-        self, gate, platform, sequence, virtual_z_phases, moment_start, delays
+        self,
+        gate,
+        platform,
+        sequence,
+        virtual_z_phases,
+        moment_start,
+        delays,
+        wire_names,
     ):
         """Adds a single gate to the pulse sequence."""
         rule = self[gate.__class__]
+
         # get local sequence and phases for the current gate
-        gate_sequence, gate_phases = rule(gate, platform)
+        qubits_ids = (
+            [wire_names[qubit] for qubit in gate.control_qubits],
+            [wire_names[qubit] for qubit in gate.target_qubits],
+        )
+        gate_sequence, gate_phases = rule(qubits_ids, platform, gate.parameters)
 
         # update global pulse sequence
         # determine the right start time based on the availability of the qubits involved
@@ -154,7 +166,13 @@ def compile(self, circuit, platform):
                         delays[qubit] += gate.delay
                     continue
                 gate_sequence, gate_phases = self._compile_gate(
-                    gate, platform, sequence, virtual_z_phases, moment_start, delays
+                    gate,
+                    platform,
+                    sequence,
+                    virtual_z_phases,
+                    moment_start,
+                    delays,
+                    circuit.wire_names,
                 )
                 for qubit in gate.qubits:
                     delays[qubit] = 0
diff --git a/src/qibolab/compilers/default.py b/src/qibolab/compilers/default.py
index 2c91b211c1..317a22ac32 100644
--- a/src/qibolab/compilers/default.py
+++ b/src/qibolab/compilers/default.py
@@ -8,52 +8,48 @@
 from qibolab.pulses import PulseSequence
 
 
-def identity_rule(gate, platform):
+def identity_rule(qubits_ids, platform, parameters=None):
     """Identity gate skipped."""
     return PulseSequence(), {}
 
 
-def z_rule(gate, platform):
+def z_rule(qubits_ids, platform, parameters=None):
     """Z gate applied virtually."""
-    qubit = platform.get_qubit(gate.target_qubits[0])
-    return PulseSequence(), {qubit: math.pi}
+    return PulseSequence(), {qubits_ids[1][0]: math.pi}
 
 
-def rz_rule(gate, platform):
+def rz_rule(qubits_ids, platform, parameters=None):
     """RZ gate applied virtually."""
-    qubit = platform.get_qubit(gate.target_qubits[0])
-    return PulseSequence(), {qubit: -gate.parameters[0]}
+    return PulseSequence(), {qubits_ids[1][0]: -parameters[0]}
 
 
-def gpi2_rule(gate, platform):
+def gpi2_rule(qubits_ids, platform, parameters=None):
     """Rule for GPI2."""
-    qubit = platform.get_qubit(gate.target_qubits[0])
-    theta = gate.parameters[0]
+    theta = parameters[0]
     sequence = PulseSequence()
-    pulse = platform.create_RX90_pulse(qubit, start=0, relative_phase=theta)
+    pulse = platform.create_RX90_pulse(qubits_ids[1][0], start=0, relative_phase=theta)
     sequence.add(pulse)
     return sequence, {}
 
 
-def gpi_rule(gate, platform):
+def gpi_rule(qubits_ids, platform, parameters=None):
     """Rule for GPI."""
-    qubit = platform.get_qubit(gate.target_qubits[0])
-    theta = gate.parameters[0]
+    theta = parameters[0]
     sequence = PulseSequence()
     # the following definition has a global phase difference compare to
     # to the matrix representation. See
     # https://github.com/qiboteam/qibolab/pull/804#pullrequestreview-1890205509
     # for more detail.
-    pulse = platform.create_RX_pulse(qubit, start=0, relative_phase=theta)
+    pulse = platform.create_RX_pulse(qubits_ids[1][0], start=0, relative_phase=theta)
     sequence.add(pulse)
     return sequence, {}
 
 
-def u3_rule(gate, platform):
+def u3_rule(qubits_ids, platform, parameters=None):
     """U3 applied as RZ-RX90-RZ-RX90-RZ."""
-    qubit = platform.get_qubit(gate.target_qubits[0])
+    qubit = qubits_ids[1][0]
     # Transform gate to U3 and add pi/2-pulses
-    theta, phi, lam = gate.parameters
+    theta, phi, lam = parameters
     # apply RZ(lam)
     virtual_z_phases = {qubit: lam}
     sequence = PulseSequence()
@@ -79,24 +75,26 @@ def u3_rule(gate, platform):
     return sequence, virtual_z_phases
 
 
-def cz_rule(gate, platform):
+def cz_rule(qubits_ids, platform, parameters=None):
     """CZ applied as defined in the platform runcard.
 
     Applying the CZ gate may involve sending pulses on qubits that the
     gate is not directly acting on.
     """
-    return platform.create_CZ_pulse_sequence(gate.qubits)
+    qubits = qubits_ids[0] + qubits_ids[1]
+    return platform.create_CZ_pulse_sequence(qubits)
 
 
-def cnot_rule(gate, platform):
+def cnot_rule(qubits_ids, platform, parameters=None):
     """CNOT applied as defined in the platform runcard."""
-    return platform.create_CNOT_pulse_sequence(gate.qubits)
+    qubits = qubits_ids[0] + qubits_ids[1]
+    return platform.create_CNOT_pulse_sequence(qubits)
 
 
-def measurement_rule(gate, platform):
+def measurement_rule(qubits_ids, platform, parameters=None):
     """Measurement gate applied using the platform readout pulse."""
     sequence = PulseSequence()
-    for qubit in gate.target_qubits:
+    for qubit in qubits_ids[1]:
         MZ_pulse = platform.create_MZ_pulse(qubit, start=0)
         sequence.add(MZ_pulse)
     return sequence, {}
diff --git a/tests/test_compilers_default.py b/tests/test_compilers_default.py
index a1a85c3667..fdadbef49c 100644
--- a/tests/test_compilers_default.py
+++ b/tests/test_compilers_default.py
@@ -32,6 +32,8 @@ def test_u3_sim_agreement():
 def compile_circuit(circuit, platform):
     """Compile a circuit to a pulse sequence."""
     compiler = Compiler.default()
+    # Temporary fix: overwrite the wire names
+    circuit._wire_names = list(platform.qubits)
     sequence, _ = compiler.compile(circuit, platform)
     return sequence
 

From fd1a9f603b8d8c2ad60ae904e2593a4962159739 Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Mon, 28 Oct 2024 18:56:43 +0400
Subject: [PATCH 56/70] fix: update documentation compiler.rst

---
 doc/source/tutorials/compiler.rst | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/doc/source/tutorials/compiler.rst b/doc/source/tutorials/compiler.rst
index a445e8e7f1..b6ae145d0a 100644
--- a/doc/source/tutorials/compiler.rst
+++ b/doc/source/tutorials/compiler.rst
@@ -80,11 +80,10 @@ The following example shows how to modify the compiler in order to execute a cir
 
 
     # define a compiler rule that translates X to the pi-pulse
-    def x_rule(gate, platform):
+    def x_rule(qubits_ids, platform, parameters=None):
         """X gate applied with a single pi-pulse."""
-        qubit = gate.target_qubits[0]
         sequence = PulseSequence()
-        sequence.add(platform.create_RX_pulse(qubit, start=0))
+        sequence.add(platform.create_RX_pulse(qubits_ids[1][0], start=0))
         return sequence, {}
 
 

From 1b3f5f8b2ebf39494d75ace88bd402d4837ead9b Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Mon, 28 Oct 2024 19:41:34 +0400
Subject: [PATCH 57/70] fix: remove dead code

---
 src/qibolab/backends.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index 4c1c31a3a8..42eeeb03da 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -130,8 +130,6 @@ def execute_circuit(self, circuit, initial_state=None, nshots=1000):
         if not all(q in circuit.wire_names for q in self.platform.qubits):
             circuit._wire_names = self.qubits
 
-        self.platform.wire_names = circuit.wire_names
-
         sequence, measurement_map = self.compiler.compile(circuit, self.platform)
 
         if not self.platform.is_connected:

From eac4e141eaa9d9bdb8338283a0cd286417b08e5a Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Tue, 29 Oct 2024 09:37:05 +0400
Subject: [PATCH 58/70] fix: resolve diff

---
 tests/test_backends.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/tests/test_backends.py b/tests/test_backends.py
index 232106764c..bf5065723e 100644
--- a/tests/test_backends.py
+++ b/tests/test_backends.py
@@ -63,10 +63,6 @@ def test_natives():
 
 def test_natives_no_cz_cnot():
     platform = create_platform("dummy")
-    for p in platform.pairs:
-        platform.pairs[p].native_gates.CZ = None
-        platform.pairs[p].native_gates.CNOT = None
-
     backend = QibolabBackend(platform)
     assert set(backend.natives) == {
         "I",
@@ -76,8 +72,15 @@ def test_natives_no_cz_cnot():
         "GPI2",
         "GPI",
         "M",
+        "CZ",
+        "CNOT",
     }
 
+    for gate in ["CZ", "CNOT"]:
+        for p in platform.pairs:
+            setattr(platform.pairs[p].native_gates, gate, None)
+        assert gate not in set(backend.natives)
+
 
 def test_execute_circuit_initial_state():
     backend = QibolabBackend("dummy")

From 9e9d625c2fefbc8409c4e200898812884bbba803 Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Tue, 29 Oct 2024 10:53:45 +0400
Subject: [PATCH 59/70] fix: temp fix minor update

---
 src/qibolab/backends.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index 42eeeb03da..229b2c015c 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -127,7 +127,7 @@ def execute_circuit(self, circuit, initial_state=None, nshots=1000):
 
         # This should be done in qibo side
         # Temporary fix: overwrite the wire names
-        if not all(q in circuit.wire_names for q in self.platform.qubits):
+        if not all(q in circuit.wire_names for q in self.qubits):
             circuit._wire_names = self.qubits
 
         sequence, measurement_map = self.compiler.compile(circuit, self.platform)
@@ -175,7 +175,7 @@ def execute_circuits(self, circuits, initial_states=None, nshots=1000):
         # This should be done in qibo side
         # Temporary fix: overwrite the wire names
         for circuit in circuits:
-            if not all(q in circuit.wire_names for q in self.platform.qubits):
+            if not all(q in circuit.wire_names for q in self.qubits):
                 circuit._wire_names = self.qubits
 
         # TODO: Maybe these loops can be parallelized

From 923fe93c209f3263d918bc586955ae6d99f7ffea Mon Sep 17 00:00:00 2001
From: Edoardo-Pedicillo <edoardo.pedicillo@gmail.com>
Date: Wed, 30 Oct 2024 20:14:00 +0400
Subject: [PATCH 60/70] fix: change qubit targets in dummy virtual z
 corrections

---
 src/qibolab/dummy/parameters.json | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/qibolab/dummy/parameters.json b/src/qibolab/dummy/parameters.json
index 498ab97d58..1ea6198ea0 100644
--- a/src/qibolab/dummy/parameters.json
+++ b/src/qibolab/dummy/parameters.json
@@ -280,7 +280,7 @@
                     {
                         "type": "virtual_z",
                         "phase": 0.0,
-                        "qubit": 1
+                        "qubit": 0
                     },
                     {
                         "type": "virtual_z",
@@ -396,7 +396,7 @@
                     {
                         "type": "virtual_z",
                         "phase": 0.0,
-                        "qubit": 1
+                        "qubit": 3
                     },
                     {
                         "type": "virtual_z",
@@ -426,7 +426,7 @@
                     {
                         "type": "virtual_z",
                         "phase": 0.0,
-                        "qubit": 1
+                        "qubit": 3
                     },
                     {
                         "type": "virtual_z",
@@ -476,7 +476,7 @@
                     {
                         "type": "virtual_z",
                         "phase": 0.0,
-                        "qubit": 1
+                        "qubit": 4
                     },
                     {
                         "type": "virtual_z",

From 134efd252649a5af93bc8a3a2cd75f7d55ce021a Mon Sep 17 00:00:00 2001
From: changsookim <>
Date: Thu, 31 Oct 2024 14:20:04 +0400
Subject: [PATCH 61/70] fix: update condition in temp fix

---
 src/qibolab/backends.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/qibolab/backends.py b/src/qibolab/backends.py
index 229b2c015c..b2207505c3 100644
--- a/src/qibolab/backends.py
+++ b/src/qibolab/backends.py
@@ -127,8 +127,8 @@ def execute_circuit(self, circuit, initial_state=None, nshots=1000):
 
         # This should be done in qibo side
         # Temporary fix: overwrite the wire names
-        if not all(q in circuit.wire_names for q in self.qubits):
-            circuit._wire_names = self.qubits
+        if not all(q in self.qubits for q in circuit.wire_names):
+            circuit._wire_names = self.qubits[: circuit.nqubits]
 
         sequence, measurement_map = self.compiler.compile(circuit, self.platform)
 
@@ -175,8 +175,8 @@ def execute_circuits(self, circuits, initial_states=None, nshots=1000):
         # This should be done in qibo side
         # Temporary fix: overwrite the wire names
         for circuit in circuits:
-            if not all(q in circuit.wire_names for q in self.qubits):
-                circuit._wire_names = self.qubits
+            if not all(q in self.qubits for q in circuit.wire_names):
+                circuit._wire_names = self.qubits[: circuit.nqubits]
 
         # TODO: Maybe these loops can be parallelized
         sequences, measurement_maps = zip(

From 49b6572aee42f7ab38961e964042246ecac389fc Mon Sep 17 00:00:00 2001
From: Stefano Carrazza <scarrazza@users.noreply.github.com>
Date: Fri, 1 Nov 2024 21:43:12 +0400
Subject: [PATCH 62/70] Update pyproject.toml

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index ff0656b367..06fa87e18c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "qibolab"
-version = "0.1.10"
+version = "0.1.11"
 description = "Quantum hardware module and drivers for Qibo"
 authors = ["The Qibo team"]
 license = "Apache License 2.0"

From a6784132e8e00a38bfc3f4d6cc5172452c6426a5 Mon Sep 17 00:00:00 2001
From: Stavros Efthymiou <35475381+stavros11@users.noreply.github.com>
Date: Wed, 13 Nov 2024 18:20:01 +0400
Subject: [PATCH 63/70] fix: drop compiler phase from flux pulses

---
 src/qibolab/compilers/compiler.py |  4 ++--
 src/qibolab/dummy/parameters.json |  4 ++--
 tests/test_compilers_default.py   | 15 +++++++++++++++
 tests/test_dummy.py               |  2 +-
 4 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/src/qibolab/compilers/compiler.py b/src/qibolab/compilers/compiler.py
index 38fb9c7628..dcc7c2a784 100644
--- a/src/qibolab/compilers/compiler.py
+++ b/src/qibolab/compilers/compiler.py
@@ -15,7 +15,7 @@
     u3_rule,
     z_rule,
 )
-from qibolab.pulses import PulseSequence, ReadoutPulse
+from qibolab.pulses import DrivePulse, PulseSequence
 
 
 @dataclass
@@ -131,7 +131,7 @@ def _compile_gate(
         # shift start time and phase according to the global sequence
         for pulse in gate_sequence:
             pulse.start += start
-            if not isinstance(pulse, ReadoutPulse):
+            if isinstance(pulse, DrivePulse):
                 pulse.relative_phase += virtual_z_phases[pulse.qubit]
             sequence.add(pulse)
 
diff --git a/src/qibolab/dummy/parameters.json b/src/qibolab/dummy/parameters.json
index 1ea6198ea0..fb4632ff47 100644
--- a/src/qibolab/dummy/parameters.json
+++ b/src/qibolab/dummy/parameters.json
@@ -309,12 +309,12 @@
                     },
                     {
                         "type": "virtual_z",
-                        "phase": 0.0,
+                        "phase": 0.1,
                         "qubit": 1
                     },
                     {
                         "type": "virtual_z",
-                        "phase": 0.0,
+                        "phase": 0.2,
                         "qubit": 2
                     },
                     {
diff --git a/tests/test_compilers_default.py b/tests/test_compilers_default.py
index fdadbef49c..5ba3d95f18 100644
--- a/tests/test_compilers_default.py
+++ b/tests/test_compilers_default.py
@@ -185,6 +185,21 @@ def test_cz_to_sequence(platform):
     assert sequence == test_sequence
 
 
+def test_twocz_to_sequence(platform):
+    if (1, 2) not in platform.pairs:
+        pytest.skip(
+            f"Skipping CZ test for {platform} because pair (1, 2) is not available."
+        )
+
+    circuit = Circuit(3)
+    circuit.add(gates.CZ(1, 2))
+    circuit.add(gates.CZ(1, 2))
+
+    sequence = compile_circuit(circuit, platform)
+    assert sequence[0].relative_phase == 0
+    assert sequence[1].relative_phase == 0
+
+
 def test_cnot_to_sequence():
     platform = create_platform("dummy")
     circuit = Circuit(4)
diff --git a/tests/test_dummy.py b/tests/test_dummy.py
index 42f454f252..145e9a74d6 100644
--- a/tests/test_dummy.py
+++ b/tests/test_dummy.py
@@ -88,7 +88,7 @@ def test_dummy_execute_pulse_sequence_couplers():
     result = platform.execute_pulse_sequence(sequence, options)
 
     test_pulses = "PulseSequence\nFluxPulse(0, 30, 0.05, GaussianSquare(5, 0.75), flux-2, 2)\nCouplerFluxPulse(0, 30, 0.05, GaussianSquare(5, 0.75), flux_coupler-1, 1)"
-    test_phases = {1: 0.0, 2: 0.0}
+    test_phases = {1: 0.1, 2: 0.2}
 
     assert test_pulses == cz.serial
     assert test_phases == cz_phases

From 97595fbc4b91ae8986670c3f18f8d6e0a80068ee Mon Sep 17 00:00:00 2001
From: Stavros Efthymiou <35475381+stavros11@users.noreply.github.com>
Date: Sat, 23 Nov 2024 18:00:01 +0400
Subject: [PATCH 64/70] build: update qm-qua version to 1.2.1

---
 poetry.lock    | 101 +++++++++++++++++++------------------------------
 pyproject.toml |   2 +-
 2 files changed, 40 insertions(+), 63 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 44aadec062..33d033bb9e 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -193,39 +193,23 @@ lxml = ["lxml"]
 
 [[package]]
 name = "betterproto"
-version = "2.0.0b5"
+version = "2.0.0b7"
 description = "A better Protobuf / gRPC generator & library"
 optional = false
-python-versions = ">=3.6.2,<4.0"
+python-versions = "<4.0,>=3.7"
 files = [
-    {file = "betterproto-2.0.0b5-py3-none-any.whl", hash = "sha256:d3e6115c7d5136f1d5974e565b7560273f66b43065e74218e472321ee1258f4c"},
-    {file = "betterproto-2.0.0b5.tar.gz", hash = "sha256:00a301c70a2db4d3cdd2b261522ae1d34972fb04b655a154d67daaaf4131102e"},
+    {file = "betterproto-2.0.0b7-py3-none-any.whl", hash = "sha256:401ab8055e2f814e77b9c88a74d0e1ae3d1e8a969cced6aeb1b59f71ad63fbd2"},
+    {file = "betterproto-2.0.0b7.tar.gz", hash = "sha256:1b1458ca5278d519bcd62556a4c236f998a91d503f0f71c67b0b954747052af2"},
 ]
 
 [package.dependencies]
 grpclib = ">=0.4.1,<0.5.0"
 python-dateutil = ">=2.8,<3.0"
+typing-extensions = ">=4.7.1,<5.0.0"
 
 [package.extras]
-compiler = ["black (>=19.3b0)", "isort (>=5.10.1,<6.0.0)", "jinja2 (>=3.0.3)"]
-
-[[package]]
-name = "betterproto"
-version = "2.0.0b6"
-description = "A better Protobuf / gRPC generator & library"
-optional = false
-python-versions = ">=3.7,<4.0"
-files = [
-    {file = "betterproto-2.0.0b6-py3-none-any.whl", hash = "sha256:a0839ec165d110a69d0d116f4d0e2bec8d186af4db826257931f0831dab73fcf"},
-    {file = "betterproto-2.0.0b6.tar.gz", hash = "sha256:720ae92697000f6fcf049c69267d957f0871654c8b0d7458906607685daee784"},
-]
-
-[package.dependencies]
-grpclib = ">=0.4.1,<0.5.0"
-python-dateutil = ">=2.8,<3.0"
-
-[package.extras]
-compiler = ["black (>=19.3b0)", "isort (>=5.11.5,<6.0.0)", "jinja2 (>=3.0.3)"]
+compiler = ["black (>=23.1.0)", "isort (>=5.11.5,<6.0.0)", "jinja2 (>=3.0.3)"]
+rust-codec = ["betterproto-rust-codec (==0.1.1)"]
 
 [[package]]
 name = "bleach"
@@ -2199,20 +2183,22 @@ files = [
 
 [[package]]
 name = "marshmallow"
-version = "3.0.0"
+version = "3.23.1"
 description = "A lightweight library for converting complex datatypes to and from native Python datatypes."
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.9"
 files = [
-    {file = "marshmallow-3.0.0-py2.py3-none-any.whl", hash = "sha256:e5e9fd0c2e919b4ece915eb30808206349a49a45df72e99ed20e27a9053d574b"},
-    {file = "marshmallow-3.0.0.tar.gz", hash = "sha256:fa2d8a4b61d09b0e161a14acc5ad8ab7aaaf1477f3dd52819ddd6c6c8275733a"},
+    {file = "marshmallow-3.23.1-py3-none-any.whl", hash = "sha256:fece2eb2c941180ea1b7fcbd4a83c51bfdd50093fdd3ad2585ee5e1df2508491"},
+    {file = "marshmallow-3.23.1.tar.gz", hash = "sha256:3a8dfda6edd8dcdbf216c0ede1d1e78d230a6dc9c5a088f58c4083b974a0d468"},
 ]
 
+[package.dependencies]
+packaging = ">=17.0"
+
 [package.extras]
-dev = ["flake8 (==3.7.8)", "flake8-bugbear (==19.8.0)", "pre-commit (>=1.17,<2.0)", "pytest", "pytz", "simplejson", "tox"]
-docs = ["alabaster (==0.7.12)", "sphinx (==2.1.2)", "sphinx-issues (==1.2.0)", "sphinx-version-warning (==1.1.2)"]
-lint = ["flake8 (==3.7.8)", "flake8-bugbear (==19.8.0)", "pre-commit (>=1.17,<2.0)"]
-tests = ["pytest", "pytz", "simplejson"]
+dev = ["marshmallow[tests]", "pre-commit (>=3.5,<5.0)", "tox"]
+docs = ["alabaster (==1.0.0)", "autodocsumm (==0.2.14)", "sphinx (==8.1.3)", "sphinx-issues (==5.0.0)", "sphinx-version-warning (==1.1.2)"]
+tests = ["pytest", "simplejson"]
 
 [[package]]
 name = "marshmallow-polyfield"
@@ -2825,6 +2811,7 @@ optional = false
 python-versions = ">=3.9"
 files = [
     {file = "pandas-2.2.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:90c6fca2acf139569e74e8781709dccb6fe25940488755716d1d354d6bc58bce"},
+    {file = "pandas-2.2.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:c7adfc142dac335d8c1e0dcbd37eb8617eac386596eb9e1a1b77791cf2498238"},
     {file = "pandas-2.2.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:4abfe0be0d7221be4f12552995e58723c7422c80a659da13ca382697de830c08"},
     {file = "pandas-2.2.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8635c16bf3d99040fdf3ca3db669a7250ddf49c55dc4aa8fe0ae0fa8d6dcc1f0"},
     {file = "pandas-2.2.2-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:40ae1dffb3967a52203105a077415a86044a2bea011b5f321c6aa64b379a3f51"},
@@ -2838,12 +2825,14 @@ files = [
     {file = "pandas-2.2.2-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:0cace394b6ea70c01ca1595f839cf193df35d1575986e484ad35c4aeae7266c1"},
     {file = "pandas-2.2.2-cp311-cp311-win_amd64.whl", hash = "sha256:873d13d177501a28b2756375d59816c365e42ed8417b41665f346289adc68d24"},
     {file = "pandas-2.2.2-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:9dfde2a0ddef507a631dc9dc4af6a9489d5e2e740e226ad426a05cabfbd7c8ef"},
+    {file = "pandas-2.2.2-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:e9b79011ff7a0f4b1d6da6a61aa1aa604fb312d6647de5bad20013682d1429ce"},
     {file = "pandas-2.2.2-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1cb51fe389360f3b5a4d57dbd2848a5f033350336ca3b340d1c53a1fad33bcad"},
     {file = "pandas-2.2.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:eee3a87076c0756de40b05c5e9a6069c035ba43e8dd71c379e68cab2c20f16ad"},
     {file = "pandas-2.2.2-cp312-cp312-musllinux_1_1_aarch64.whl", hash = "sha256:3e374f59e440d4ab45ca2fffde54b81ac3834cf5ae2cdfa69c90bc03bde04d76"},
     {file = "pandas-2.2.2-cp312-cp312-musllinux_1_1_x86_64.whl", hash = "sha256:43498c0bdb43d55cb162cdc8c06fac328ccb5d2eabe3cadeb3529ae6f0517c32"},
     {file = "pandas-2.2.2-cp312-cp312-win_amd64.whl", hash = "sha256:d187d355ecec3629624fccb01d104da7d7f391db0311145817525281e2804d23"},
     {file = "pandas-2.2.2-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:0ca6377b8fca51815f382bd0b697a0814c8bda55115678cbc94c30aacbb6eff2"},
+    {file = "pandas-2.2.2-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:9057e6aa78a584bc93a13f0a9bf7e753a5e9770a30b4d758b8d5f2a62a9433cd"},
     {file = "pandas-2.2.2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:001910ad31abc7bf06f49dcc903755d2f7f3a9186c0c040b827e522e9cef0863"},
     {file = "pandas-2.2.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:66b479b0bd07204e37583c191535505410daa8df638fd8e75ae1b383851fe921"},
     {file = "pandas-2.2.2-cp39-cp39-musllinux_1_1_aarch64.whl", hash = "sha256:a77e9d1c386196879aa5eb712e77461aaee433e54c68cf253053a73b7e49c33a"},
@@ -4313,64 +4302,52 @@ full = ["pyro4"]
 
 [[package]]
 name = "qm-octave"
-version = "2.0.1"
+version = "2.1.3"
 description = "SDK to control an Octave with QUA"
 optional = false
-python-versions = ">=3.7,<3.12"
+python-versions = "<3.13,>=3.8"
 files = [
-    {file = "qm_octave-2.0.1-py3-none-any.whl", hash = "sha256:ef2607101b978beb306f30bfc56656f087fe7764133ba22e3ce5739a409c4edb"},
-    {file = "qm_octave-2.0.1.tar.gz", hash = "sha256:f20844d98e493a253bedb72f86fcb665bc7461a46d502de3cc7c91f3d54416d6"},
+    {file = "qm_octave-2.1.3-py3-none-any.whl", hash = "sha256:1957eadaa6d8e3150c57bb8b378d3d9fbcd9dc66163ace3a317ecb94685e606a"},
+    {file = "qm_octave-2.1.3.tar.gz", hash = "sha256:f7981b73dc51276f306e553f9906e40119024067ce7cab79c19f07b53778cc7b"},
 ]
 
 [package.dependencies]
-betterproto = [
-    {version = "2.0.0b5", markers = "python_version >= \"3.7\" and python_version < \"3.11\""},
-    {version = "2.0.0b6", markers = "python_version >= \"3.11\" and python_version < \"4.0\""},
-]
+betterproto = "2.0.0b7"
 grpcio = ">=1.59.2,<2.0.0"
 grpclib = {version = ">=0.4.3rc3,<0.5.0", markers = "python_version >= \"3.10\" and python_version < \"4.0\""}
 protobuf = [
-    {version = ">=3.17.3,<4.0.0", markers = "python_version >= \"3.7\" and python_version < \"3.11\""},
+    {version = ">=3.17.3,<4.0.0", markers = "python_version >= \"3.8\" and python_version < \"3.11\""},
     {version = ">=4.24,<5.0", markers = "python_version >= \"3.11\""},
 ]
 
 [[package]]
 name = "qm-qua"
-version = "1.1.6"
+version = "1.2.1"
 description = "QUA language SDK to control a Quantum Computer"
 optional = false
-python-versions = ">=3.7,<3.12"
+python-versions = "<3.13,>=3.8"
 files = [
-    {file = "qm_qua-1.1.6-py3-none-any.whl", hash = "sha256:69f8159805889fe9389b1acb4e94afacc37d68e1455017ec0e58a4fcc238bd8c"},
-    {file = "qm_qua-1.1.6.tar.gz", hash = "sha256:9e09240bf1d9623c0f5b15fb2bc955f7387da15280d0b02c266e42a40818a2b1"},
+    {file = "qm_qua-1.2.1-py3-none-any.whl", hash = "sha256:3315379d16929468b058adbe489f6ac3979d1a5fcae102d4fc498bb7ac2feded"},
+    {file = "qm_qua-1.2.1.tar.gz", hash = "sha256:9a6af3cbab527bd95948c78a640d84d4ec8487ab1e146afd9e38f0ce9f939701"},
 ]
 
 [package.dependencies]
-betterproto = [
-    {version = "2.0.0b5", markers = "python_version >= \"3.7\" and python_version < \"3.11\""},
-    {version = "2.0.0b6", markers = "python_version == \"3.11\""},
-]
+betterproto = "2.0.0b7"
 datadog-api-client = ">=2.6.0,<3.0.0"
 dependency_injector = ">=4.41.0,<5.0.0"
 deprecation = ">=2.1.0,<3.0.0"
 grpcio = [
-    {version = ">=1.39.0,<2.0.0", markers = "python_version >= \"3.7\" and python_version < \"3.11\""},
+    {version = ">=1.39.0,<2.0.0", markers = "python_version >= \"3.8\" and python_version < \"3.11\""},
     {version = ">=1.57,<2.0", markers = "python_version >= \"3.11\""},
 ]
 grpclib = {version = ">=0.4.5,<0.5.0", markers = "python_version >= \"3.10\""}
-httpx = {version = ">=0.23.3,<0.24.0", extras = ["http2"]}
-marshmallow = "3"
+httpx = {version = ">=0.23.3,<1", extras = ["http2"]}
+marshmallow = ">=3.20.1,<4.0.0"
 marshmallow-polyfield = ">=5.7,<6.0"
-numpy = [
-    {version = ">=1.17.0,<2.0.0", markers = "python_version >= \"3.7\" and python_version < \"3.11\""},
-    {version = ">=1.24,<2.0", markers = "python_version >= \"3.11\""},
-]
+numpy = {version = ">=1.17.0,<2", markers = "python_version >= \"3.8\" and python_version < \"3.12\""}
 plotly = ">=5.13.0,<6.0.0"
-protobuf = [
-    {version = ">=3.17.3,<4.0.0", markers = "python_version >= \"3.7\" and python_version < \"3.11\""},
-    {version = ">=4.24,<5.0", markers = "python_version >= \"3.11\""},
-]
-qm-octave = ">=2.0.1,<2.1.0"
+protobuf = ">=3.17.3,<5"
+qm-octave = "2.1.3"
 tinydb = ">=4.6.1,<5.0.0"
 typing-extensions = ">=4.5,<5.0"
 
@@ -5798,4 +5775,4 @@ zh = ["laboneq"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "2e9555b32f971566f63c0505cb15a651f0dabd88ce630a265e96bc27cf250f6e"
+content-hash = "593881ae2ecdab7ce87f556217d8be30ae8cbb0e5e7d61a43f0f839b2060b45e"
diff --git a/pyproject.toml b/pyproject.toml
index 06fa87e18c..7258638f67 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -30,7 +30,7 @@ qblox-instruments = { version = "0.12.0", optional = true }
 qcodes = { version = "^0.37.0", optional = true }
 qcodes_contrib_drivers = { version = "0.18.0", optional = true }
 pyvisa-py = { version = "0.5.3", optional = true }
-qm-qua = { version = "==1.1.6", optional = true }
+qm-qua = { version = "==1.2.1", optional = true }
 qualang-tools = { version = "^0.15.0", optional = true }
 setuptools = { version = ">67.0.0", optional = true }
 laboneq = { version = "==2.25.0", optional = true }

From e11e0d04e60ef22f26221a28bf3457b5bdbda466 Mon Sep 17 00:00:00 2001
From: Stavros Efthymiou <35475381+stavros11@users.noreply.github.com>
Date: Wed, 27 Nov 2024 17:16:00 +0400
Subject: [PATCH 65/70] fix: remove QM manager when disconnecting

---
 src/qibolab/instruments/qm/controller.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/qibolab/instruments/qm/controller.py b/src/qibolab/instruments/qm/controller.py
index e9017bb4b0..abbb6f5d35 100644
--- a/src/qibolab/instruments/qm/controller.py
+++ b/src/qibolab/instruments/qm/controller.py
@@ -258,6 +258,7 @@ def disconnect(self):
         self._reset_temporary_calibration()
         if self.manager is not None:
             self.manager.close_all_quantum_machines()
+            self.manager = None
             self.is_connected = False
 
     def calibrate_mixers(self, qubits):

From e46b12c0a57c593a7932d8a3ae8fe7101f6280ca Mon Sep 17 00:00:00 2001
From: Stavros Efthymiou <35475381+stavros11@users.noreply.github.com>
Date: Wed, 27 Nov 2024 17:22:00 +0400
Subject: [PATCH 66/70] feat: raise error when not connected

---
 src/qibolab/instruments/qm/controller.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/qibolab/instruments/qm/controller.py b/src/qibolab/instruments/qm/controller.py
index abbb6f5d35..c7d7871dea 100644
--- a/src/qibolab/instruments/qm/controller.py
+++ b/src/qibolab/instruments/qm/controller.py
@@ -288,6 +288,10 @@ def execute_program(self, program):
         Args:
             program: QUA program.
         """
+        if self.manager is None:
+            raise RuntimeError(
+                "Quantum Machines are not connected. Please use ``platform.connect()``."
+            )
         machine = self.manager.open_qm(self.config.__dict__)
         return machine.execute(program)
 

From 1ee377827db1b732f2ec85c78438122fc551762f Mon Sep 17 00:00:00 2001
From: Stavros Efthymiou <35475381+stavros11@users.noreply.github.com>
Date: Sun, 1 Dec 2024 17:48:24 +0400
Subject: [PATCH 67/70] feat: disconnect platform when job is interrupted

---
 src/qibolab/platform/platform.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/src/qibolab/platform/platform.py b/src/qibolab/platform/platform.py
index 5178978cbc..706585f3e3 100644
--- a/src/qibolab/platform/platform.py
+++ b/src/qibolab/platform/platform.py
@@ -1,5 +1,6 @@
 """A platform for executing quantum algorithms."""
 
+import signal
 from collections import defaultdict
 from dataclasses import dataclass, field, replace
 from typing import Dict, List, Optional, Tuple
@@ -117,6 +118,10 @@ class Platform:
     """Graph representing the qubit connectivity in the quantum chip."""
 
     def __post_init__(self):
+        signal.signal(signal.SIGTERM, self.termination_handler)
+        signal.signal(signal.SIGINT, self.termination_handler)
+        log.info("signals registered")
+
         log.info("Loading platform %s", self.name)
         if self.resonator_type is None:
             self.resonator_type = "3D" if self.nqubits == 1 else "2D"
@@ -168,6 +173,12 @@ def disconnect(self):
                 instrument.disconnect()
         self.is_connected = False
 
+    def termination_handler(self, signum, frame):
+        self.disconnect()
+        raise RuntimeError(
+            f"Platform {self.name} disconnected because job was cancelled. Signal type: {signum}."
+        )
+
     def _execute(self, sequence, options, **kwargs):
         """Executes sequence on the controllers."""
         result = {}

From 3025a0abe21f958bac533190ab83482d2dbde2cf Mon Sep 17 00:00:00 2001
From: Stavros Efthymiou <35475381+stavros11@users.noreply.github.com>
Date: Sun, 1 Dec 2024 17:55:54 +0400
Subject: [PATCH 68/70] chore: drop log message

---
 src/qibolab/platform/platform.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/qibolab/platform/platform.py b/src/qibolab/platform/platform.py
index 706585f3e3..88f3a310f9 100644
--- a/src/qibolab/platform/platform.py
+++ b/src/qibolab/platform/platform.py
@@ -120,7 +120,6 @@ class Platform:
     def __post_init__(self):
         signal.signal(signal.SIGTERM, self.termination_handler)
         signal.signal(signal.SIGINT, self.termination_handler)
-        log.info("signals registered")
 
         log.info("Loading platform %s", self.name)
         if self.resonator_type is None:

From 74b86173e93daa53ef87a535fe897773bcc7827b Mon Sep 17 00:00:00 2001
From: Stavros Efthymiou <35475381+stavros11@users.noreply.github.com>
Date: Sat, 28 Dec 2024 00:22:23 +0400
Subject: [PATCH 69/70] fix: compilation error when running mixer calibration

---
 src/qibolab/instruments/qm/config.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/qibolab/instruments/qm/config.py b/src/qibolab/instruments/qm/config.py
index 578efc24a5..7915f1b917 100644
--- a/src/qibolab/instruments/qm/config.py
+++ b/src/qibolab/instruments/qm/config.py
@@ -11,7 +11,7 @@
 SAMPLING_RATE = 1
 """Sampling rate of Quantum Machines OPX in GSps."""
 
-DEFAULT_INPUTS = {1: {}, 2: {}}
+DEFAULT_INPUTS = {1: {"offset": 0}, 2: {"offset": 0}}
 """Default controller config section.
 
 Inputs are always registered to avoid issues with automatic mixer
@@ -57,7 +57,7 @@ def register_port(self, port):
                     controllers[port.device] = {"type": "opx1000", "fems": {}}
                 else:
                     controllers[port.device] = {
-                        "analog_inputs": DEFAULT_INPUTS,
+                        "analog_inputs": DEFAULT_INPUTS.copy(),
                         "digital_outputs": {},
                     }
 
@@ -66,7 +66,7 @@ def register_port(self, port):
                 if port.fem_number not in fems:
                     fems[port.fem_number] = {
                         "type": port.fem_type,
-                        "analog_inputs": DEFAULT_INPUTS,
+                        "analog_inputs": DEFAULT_INPUTS.copy(),
                         "digital_outputs": {},
                     }
                 device = fems[port.fem_number]

From 4d9895aca0adc7e2479aa321e86238d195b0f518 Mon Sep 17 00:00:00 2001
From: Stavros Efthymiou <35475381+stavros11@users.noreply.github.com>
Date: Sat, 28 Dec 2024 00:35:15 +0400
Subject: [PATCH 70/70] fix: tests

---
 tests/test_instruments_qm.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_instruments_qm.py b/tests/test_instruments_qm.py
index fee8633709..f018e554e5 100644
--- a/tests/test_instruments_qm.py
+++ b/tests/test_instruments_qm.py
@@ -158,7 +158,7 @@ def test_qm_register_port(qmcontroller, offset):
     controllers = qmcontroller.config.controllers
     assert controllers == {
         "con1": {
-            "analog_inputs": {1: {}, 2: {}},
+            "analog_inputs": {1: {"offset": 0}, 2: {"offset": 0}},
             "analog_outputs": {1: {"offset": offset, "filter": {}}},
             "digital_outputs": {},
         }
@@ -173,7 +173,7 @@ def test_qm_register_port_filter(qmcontroller):
     controllers = qmcontroller.config.controllers
     assert controllers == {
         "con1": {
-            "analog_inputs": {1: {}, 2: {}},
+            "analog_inputs": {1: {"offset": 0}, 2: {"offset": 0}},
             "analog_outputs": {
                 2: {
                     "filter": {"feedback": [0.95], "feedforward": [1, -1]},