From e0bd4574b30231b1d3ca0f257ed903735b4248ea Mon Sep 17 00:00:00 2001
From: Andrea Pasquale <andreapasquale97@gmail.com>
Date: Tue, 22 Oct 2024 09:55:40 +0200
Subject: [PATCH 01/22] feat: Start implementation of calibration platform

---
 src/qibocal/calibration/__init__.py    |  2 +
 src/qibocal/calibration/calibration.py | 96 ++++++++++++++++++++++++++
 src/qibocal/calibration/platform.py    | 43 ++++++++++++
 3 files changed, 141 insertions(+)
 create mode 100644 src/qibocal/calibration/__init__.py
 create mode 100644 src/qibocal/calibration/calibration.py
 create mode 100644 src/qibocal/calibration/platform.py

diff --git a/src/qibocal/calibration/__init__.py b/src/qibocal/calibration/__init__.py
new file mode 100644
index 000000000..3acd14429
--- /dev/null
+++ b/src/qibocal/calibration/__init__.py
@@ -0,0 +1,2 @@
+from .calibration import Calibration
+from .platform import CalibrationPlatform
diff --git a/src/qibocal/calibration/calibration.py b/src/qibocal/calibration/calibration.py
new file mode 100644
index 000000000..1235c9222
--- /dev/null
+++ b/src/qibocal/calibration/calibration.py
@@ -0,0 +1,96 @@
+from pydantic import BaseModel, ConfigDict, Field
+from qibolab._core.identifier import QubitId, QubitPairId
+from qibolab._core.serialize import NdArray
+
+
+class Model(BaseModel):
+    """Global qibolab model, holding common configurations."""
+
+    model_config = ConfigDict(extra="forbid")
+
+
+class Resonator(Model):
+    """Representation of resonator parameters."""
+
+    bare_frequency: float = 0
+    """Bare resonator frequency [Hz]."""
+    dressed_frequency: float = 0
+    """Dressed resonator frequency [Hz]."""
+    depletion_time: int = 0
+    """Depletion time [ns]."""
+
+    # TODO: Add something related to resonator calibration
+
+
+class Qubit(Model):
+    """Representation of Qubit parameters"""
+
+    omega_01: float = 0
+    """"0->1 transition frequency."""
+    omega_12: float = 0
+    """1->2 transition frequency."""
+    asymmetry: float = 0
+    """Junctions asymmetry."""
+    sweetspot: float = 0
+    """Qubit sweetspot [V]."""
+
+
+class Readout(Model):
+    """Readout parameters."""
+
+    assignment_fidelity: float = 0
+    """Assignment fidelity."""
+    readout_fidelity: float = 0
+    """Readout fidelity."""
+    ground_state: list[float] = Field(default_factory=list)
+    """Ground state position in IQ plane."""
+    excited_state: list[float] = Field(default_factory=list)
+    """Excited state position in IQ plane."""
+
+
+class Coherence(Model):
+    """Coherence times of qubit."""
+
+    t1: int = 0
+    """Relaxation time [ns]."""
+    t2: int = 0
+    """T2 of the qubit [ns]."""
+    t2_spin_echo: int = 0
+    """T2 hanh echo [ns]."""
+
+
+class QubitCalibration(Model):
+    """Container for calibration of single qubit."""
+
+    resonator: Resonator
+    """Resonator calibration."""
+    qubit: Qubit
+    """Qubit calibration."""
+    readout: Readout
+    """Readout information."""
+    coherence: Coherence
+    """Coherence times of the qubit."""
+    rb_fidelity: float
+    """Standard rb pulse fidelity."""
+
+
+class TwoQubitCalibration(Model):
+    """Container for calibration of qubit pair."""
+
+    gate_fidelity: float = 0
+    """Two qubit standard rb fidelity."""
+    cz_fidelity: float = 0
+    """CZ interleaved rb fidelity."""
+
+
+class Calibration(Model):
+    """Calibration container."""
+
+    single_qubits: dict[QubitId, QubitCalibration] = Field(default_factory=dict)
+    """Dict with single qubit calibration."""
+    two_qubits: dict[QubitPairId, TwoQubitCalibration] = Field(default_factory=dict)
+    """Dict with qubit pairs calibration."""
+    readout_mitigation_matrix: NdArray = None
+    """Readout mitigation matrix."""
+    flux_crosstalk_matrix: NdArray = None
+    """Crosstalk flux matrix."""
diff --git a/src/qibocal/calibration/platform.py b/src/qibocal/calibration/platform.py
new file mode 100644
index 000000000..2f696015d
--- /dev/null
+++ b/src/qibocal/calibration/platform.py
@@ -0,0 +1,43 @@
+import os
+from dataclasses import dataclass
+from pathlib import Path
+
+from qibolab import Platform, create_platform
+
+from .calibration import Calibration
+
+
+@dataclass
+class CalibrationPlatform:
+    """Qibolab platform with calibration information."""
+
+    platform: Platform = None
+    """Qibolab platforms."""
+    calibration: Calibration = None
+    """Calibration information."""
+
+    @property
+    def natives(self):
+        return self.platform.natives
+
+    @property
+    def parameters(self):
+        return self.platform.parameters
+
+    def execute(self, *args, **kwargs):
+        return self.execute(*args, **kwargs)
+
+    @classmethod
+    def load(cls, name: str):
+
+        platform = create_platform(name)
+        path = Path(os.getenv("QIBOLAB_PLATFORMS")) / name
+        calibration = Calibration.model_validate_json(path.read_text())
+
+        return cls(platform, calibration)
+
+
+# def create_calibration_platform(name: str) -> CalibrationPlatform:
+
+#     platform = create_platform(name)
+#     calibration = Calibration.

From 7edd452dba4e65f75f8583edd75f1a4b162610d7 Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Tue, 22 Oct 2024 15:19:16 +0400
Subject: [PATCH 02/22] feat: Add create_calibration_platform

---
 src/qibocal/calibration/__init__.py    |  3 +-
 src/qibocal/calibration/calibration.py | 40 ++++++++++++++++++--------
 src/qibocal/calibration/platform.py    | 14 +++++++--
 3 files changed, 40 insertions(+), 17 deletions(-)

diff --git a/src/qibocal/calibration/__init__.py b/src/qibocal/calibration/__init__.py
index 3acd14429..45af0be9b 100644
--- a/src/qibocal/calibration/__init__.py
+++ b/src/qibocal/calibration/__init__.py
@@ -1,2 +1 @@
-from .calibration import Calibration
-from .platform import CalibrationPlatform
+from .platform import create_calibration_platform
diff --git a/src/qibocal/calibration/calibration.py b/src/qibocal/calibration/calibration.py
index 1235c9222..026ec6f91 100644
--- a/src/qibocal/calibration/calibration.py
+++ b/src/qibocal/calibration/calibration.py
@@ -1,6 +1,7 @@
 from pydantic import BaseModel, ConfigDict, Field
-from qibolab._core.identifier import QubitId, QubitPairId
-from qibolab._core.serialize import NdArray
+
+# from qibolab._core.identifier import QubitId, QubitPairId
+# from qibolab._core.serialize import NdArray
 
 
 class Model(BaseModel):
@@ -34,6 +35,16 @@ class Qubit(Model):
     sweetspot: float = 0
     """Qubit sweetspot [V]."""
 
+    @property
+    def anharmonicity(self):
+        """Anharmonicity of the qubit in Hz."""
+        return self.omega_12 - self.omega_01
+
+    @property
+    def charging_energy(self):
+        """Charging energy Ec."""
+        return -self.anharmonicity
+
 
 class Readout(Model):
     """Readout parameters."""
@@ -47,6 +58,9 @@ class Readout(Model):
     excited_state: list[float] = Field(default_factory=list)
     """Excited state position in IQ plane."""
 
+    # TODO: drop one of the two between readout and assignment fidelities
+    # TODO: possibly rename one of them fidelity
+
 
 class Coherence(Model):
     """Coherence times of qubit."""
@@ -62,22 +76,22 @@ class Coherence(Model):
 class QubitCalibration(Model):
     """Container for calibration of single qubit."""
 
-    resonator: Resonator
+    resonator: Resonator = Field(default_factory=Resonator)
     """Resonator calibration."""
-    qubit: Qubit
+    qubit: Qubit = Field(default_factory=Qubit)
     """Qubit calibration."""
-    readout: Readout
+    readout: Readout = Field(default_factory=Readout)
     """Readout information."""
-    coherence: Coherence
+    coherence: Coherence = Field(default_factory=Coherence)
     """Coherence times of the qubit."""
-    rb_fidelity: float
+    rb_fidelity: float = 0
     """Standard rb pulse fidelity."""
 
 
 class TwoQubitCalibration(Model):
     """Container for calibration of qubit pair."""
 
-    gate_fidelity: float = 0
+    rb_fidelity: float = 0
     """Two qubit standard rb fidelity."""
     cz_fidelity: float = 0
     """CZ interleaved rb fidelity."""
@@ -86,11 +100,13 @@ class TwoQubitCalibration(Model):
 class Calibration(Model):
     """Calibration container."""
 
-    single_qubits: dict[QubitId, QubitCalibration] = Field(default_factory=dict)
+    single_qubits: dict[str, QubitCalibration] = Field(default_factory=dict)
     """Dict with single qubit calibration."""
-    two_qubits: dict[QubitPairId, TwoQubitCalibration] = Field(default_factory=dict)
+    # TODO: dump pair as str instead of tuple
+    two_qubits: dict[tuple, TwoQubitCalibration] = Field(default_factory=dict)
     """Dict with qubit pairs calibration."""
-    readout_mitigation_matrix: NdArray = None
+    # TODO: fix this as well
+    readout_mitigation_matrix: str = None
     """Readout mitigation matrix."""
-    flux_crosstalk_matrix: NdArray = None
+    flux_crosstalk_matrix: str = None
     """Crosstalk flux matrix."""
diff --git a/src/qibocal/calibration/platform.py b/src/qibocal/calibration/platform.py
index 2f696015d..0e6293458 100644
--- a/src/qibocal/calibration/platform.py
+++ b/src/qibocal/calibration/platform.py
@@ -6,6 +6,9 @@
 
 from .calibration import Calibration
 
+CALIBRATION = "calibration.json"
+"""Calibration file."""
+
 
 @dataclass
 class CalibrationPlatform:
@@ -37,7 +40,12 @@ def load(cls, name: str):
         return cls(platform, calibration)
 
 
-# def create_calibration_platform(name: str) -> CalibrationPlatform:
+def create_calibration_platform(name: str) -> CalibrationPlatform:
+
+    path = Path(os.getenv("QIBOLAB_PLATFORMS"))
+    platform = create_platform(name)
+    calibration = Calibration.model_validate_json(
+        (path / name / CALIBRATION).read_text()
+    )
 
-#     platform = create_platform(name)
-#     calibration = Calibration.
+    return CalibrationPlatform(platform=platform, calibration=calibration)

From 315154740aedabc188e4eff4b5c5ba70b6f737d3 Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Tue, 22 Oct 2024 16:21:35 +0400
Subject: [PATCH 03/22] chore: Working version on hardware

---
 src/qibocal/auto/execute.py            |  16 +--
 src/qibocal/calibration/__init__.py    |   2 +-
 src/qibocal/calibration/calibration.py |   3 +
 src/qibocal/calibration/dummy.json     | 161 +++++++++++++++++++++++++
 src/qibocal/calibration/platform.py    |  27 +++--
 5 files changed, 190 insertions(+), 19 deletions(-)
 create mode 100644 src/qibocal/calibration/dummy.json

diff --git a/src/qibocal/auto/execute.py b/src/qibocal/auto/execute.py
index 120102996..a6784b58b 100644
--- a/src/qibocal/auto/execute.py
+++ b/src/qibocal/auto/execute.py
@@ -11,11 +11,11 @@
 from typing import Optional, Union
 
 from qibo.backends import construct_backend
-from qibolab import Platform, create_platform
 
 from qibocal import protocols
 from qibocal.config import log
 
+from ..calibration import CalibrationPlatform, create_calibration_platform
 from .history import History
 from .mode import AUTOCALIBRATION, ExecutionMode
 from .operation import Routine
@@ -71,7 +71,7 @@ class Executor:
     """The execution history, with results and exit states."""
     targets: Targets
     """Qubits/Qubit Pairs to be calibrated."""
-    platform: Platform
+    platform: CalibrationPlatform
     """Qubits' platform."""
     update: bool = True
     """Runcard update mechanism."""
@@ -98,12 +98,12 @@ def __post_init__(self):
             _register(self.name, self)
 
     @classmethod
-    def create(cls, name: str, platform: Union[Platform, str, None] = None):
+    def create(cls, name: str, platform: Union[CalibrationPlatform, str, None] = None):
         """Load list of protocols."""
         platform = (
             platform
-            if isinstance(platform, Platform)
-            else create_platform(
+            if isinstance(platform, CalibrationPlatform)
+            else create_calibration_platform(
                 platform
                 if platform is not None
                 else os.environ.get("QIBO_PLATFORM", "dummy")
@@ -251,7 +251,7 @@ def init(
         self,
         path: os.PathLike,
         force: bool = False,
-        platform: Union[Platform, str, None] = None,
+        platform: Union[CalibrationPlatform, str, None] = None,
         update: Optional[bool] = None,
         targets: Optional[Targets] = None,
     ):
@@ -261,7 +261,7 @@ def init(
 
         backend = construct_backend(backend="qibolab", platform=platform)
         platform = self.platform = backend.platform
-        assert isinstance(platform, Platform)
+        assert isinstance(platform, CalibrationPlatform)
 
         if update is not None:
             self.update = update
@@ -310,7 +310,7 @@ def open(
         name: str,
         path: os.PathLike,
         force: bool = False,
-        platform: Union[Platform, str, None] = None,
+        platform: Union[CalibrationPlatform, str, None] = None,
         update: Optional[bool] = None,
         targets: Optional[Targets] = None,
     ):
diff --git a/src/qibocal/calibration/__init__.py b/src/qibocal/calibration/__init__.py
index 45af0be9b..fc3d1d777 100644
--- a/src/qibocal/calibration/__init__.py
+++ b/src/qibocal/calibration/__init__.py
@@ -1 +1 @@
-from .platform import create_calibration_platform
+from .platform import CalibrationPlatform, create_calibration_platform
diff --git a/src/qibocal/calibration/calibration.py b/src/qibocal/calibration/calibration.py
index 026ec6f91..21fc5ff31 100644
--- a/src/qibocal/calibration/calibration.py
+++ b/src/qibocal/calibration/calibration.py
@@ -3,6 +3,9 @@
 # from qibolab._core.identifier import QubitId, QubitPairId
 # from qibolab._core.serialize import NdArray
 
+CALIBRATION = "calibration.json"
+"""Calibration file."""
+
 
 class Model(BaseModel):
     """Global qibolab model, holding common configurations."""
diff --git a/src/qibocal/calibration/dummy.json b/src/qibocal/calibration/dummy.json
new file mode 100644
index 000000000..bf648ee64
--- /dev/null
+++ b/src/qibocal/calibration/dummy.json
@@ -0,0 +1,161 @@
+{
+    "single_qubits": {
+        "0": {
+            "resonator": {
+                "bare_frequency": 0.0,
+                "dressed_frequency": 5200000000.0,
+                "depletion_time": 0
+            },
+            "qubit": {
+                "omega_01": 4000000000.0,
+                "omega_12": 4700000000.0,
+                "asymmetry": 0.0,
+                "sweetspot": 0.0
+            },
+            "readout": {
+                "assignment_fidelity": 0.5,
+                "readout_fidelity": 0.0,
+                "ground_state": [
+                    0.0,
+                    1.0
+                ],
+                "excited_state": [
+                    1.0,
+                    0.0
+                ]
+            },
+            "coherence": {
+                "t1": 0.0,
+                "t2": 0.0,
+                "t2_spin_echo": 0
+            },
+            "rb_fidelity": 0.5
+        },
+        "1": {
+            "resonator": {
+                "bare_frequency": 0.0,
+                "dressed_frequency": 4900000000.0,
+                "depletion_time": 0
+            },
+            "qubit": {
+                "omega_01": 4200000000.0,
+                "omega_12": 4855663000.0,
+                "asymmetry": 0.0,
+                "sweetspot": 0.0
+            },
+            "readout": {
+                "assignment_fidelity": 0.5,
+                "readout_fidelity": 0.0,
+                "ground_state": [
+                    0.25,
+                    0.0
+                ],
+                "excited_state": [
+                    0.0,
+                    0.25
+                ]
+            },
+            "coherence": {
+                "t1": 0.0,
+                "t2": 0.0,
+                "t2_spin_echo": 0
+            },
+            "rb_fidelity": 0.5
+        },
+        "2": {
+            "resonator": {
+                "bare_frequency": 0.0,
+                "dressed_frequency": 6100000000.0,
+                "depletion_time": 0
+            },
+            "qubit": {
+                "omega_01": 4500000000.0,
+                "omega_12": 2700000000.0,
+                "asymmetry": 0.0,
+                "sweetspot": 0.0
+            },
+            "readout": {
+                "assignment_fidelity": 0.1,
+                "readout_fidelity": 0.0,
+                "ground_state": [
+                    0.5,
+                    0.0
+                ],
+                "excited_state": [
+                    0.0,
+                    0.5
+                ]
+            },
+            "coherence": {
+                "t1": 0.0,
+                "t2": 0.0,
+                "t2_spin_echo": 0
+            },
+            "rb_fidelity": 0.5
+        },
+        "3": {
+            "resonator": {
+                "bare_frequency": 0.0,
+                "dressed_frequency": 5800000000.0,
+                "depletion_time": 0
+            },
+            "qubit": {
+                "omega_01": 4150000000.0,
+                "omega_12": 5855663000.0,
+                "asymmetry": 0.0,
+                "sweetspot": 0.0
+            },
+            "readout": {
+                "assignment_fidelity": 0.1,
+                "readout_fidelity": 0.0,
+                "ground_state": [
+                    0.75,
+                    0.0
+                ],
+                "excited_state": [
+                    0.0,
+                    0.75
+                ]
+            },
+            "coherence": {
+                "t1": 0.0,
+                "t2": 0.0,
+                "t2_spin_echo": 0
+            },
+            "rb_fidelity": 0.5
+        },
+        "4": {
+            "resonator": {
+                "bare_frequency": 0.0,
+                "dressed_frequency": 5500000000.0,
+                "depletion_time": 0
+            },
+            "qubit": {
+                "omega_01": 4100000000.0,
+                "omega_12": 5855663000.0,
+                "asymmetry": 0.0,
+                "sweetspot": 0.0
+            },
+            "readout": {
+                "assignment_fidelity": 0.1,
+                "readout_fidelity": 0.0,
+                "ground_state": [
+                    1.0,
+                    0.0
+                ],
+                "excited_state": [
+                    0.0,
+                    1.0
+                ]
+            },
+            "coherence": {
+                "t1": 0.0,
+                "t2": 0.0,
+                "t2_spin_echo": 0
+            },
+            "rb_fidelity":0.5
+        }
+    },
+    "two_qubits": {
+    }
+}
diff --git a/src/qibocal/calibration/platform.py b/src/qibocal/calibration/platform.py
index 0e6293458..feeae7521 100644
--- a/src/qibocal/calibration/platform.py
+++ b/src/qibocal/calibration/platform.py
@@ -2,12 +2,9 @@
 from dataclasses import dataclass
 from pathlib import Path
 
-from qibolab import Platform, create_platform
+from qibolab import Platform, create_dummy, create_platform
 
-from .calibration import Calibration
-
-CALIBRATION = "calibration.json"
-"""Calibration file."""
+from .calibration import CALIBRATION, Calibration
 
 
 @dataclass
@@ -23,6 +20,10 @@ class CalibrationPlatform:
     def natives(self):
         return self.platform.natives
 
+    @property
+    def qubits(self):
+        return self.platform.qubits
+
     @property
     def parameters(self):
         return self.platform.parameters
@@ -42,10 +43,16 @@ def load(cls, name: str):
 
 def create_calibration_platform(name: str) -> CalibrationPlatform:
 
-    path = Path(os.getenv("QIBOLAB_PLATFORMS"))
-    platform = create_platform(name)
-    calibration = Calibration.model_validate_json(
-        (path / name / CALIBRATION).read_text()
-    )
+    if name == "dummy":
+        platform = create_dummy()
+        calibration = Calibration.model_validate_json(
+            (Path(__file__).parent / "dummy.json").read_text()
+        )
+    else:
+        path = Path(os.getenv("QIBOLAB_PLATFORMS"))
+        platform = create_platform(name)
+        calibration = Calibration.model_validate_json(
+            (path / name / CALIBRATION).read_text()
+        )
 
     return CalibrationPlatform(platform=platform, calibration=calibration)

From df4530057d4523faf501740b3a13ddce057c61ed Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Tue, 22 Oct 2024 17:15:41 +0400
Subject: [PATCH 04/22] refactor: Calibration platform as inheritance of
 Platform

---
 src/qibocal/auto/output.py             |  8 ++--
 src/qibocal/calibration/calibration.py |  6 +++
 src/qibocal/calibration/platform.py    | 57 +++++++++-----------------
 src/qibocal/cli/acquisition.py         |  3 +-
 src/qibocal/cli/autocalibration.py     |  4 +-
 5 files changed, 34 insertions(+), 44 deletions(-)

diff --git a/src/qibocal/auto/output.py b/src/qibocal/auto/output.py
index 2b8bdf194..3ec65163c 100644
--- a/src/qibocal/auto/output.py
+++ b/src/qibocal/auto/output.py
@@ -7,8 +7,8 @@
 from typing import Optional
 
 from qibo.backends import construct_backend
-from qibolab import Platform
 
+from ..calibration import CalibrationPlatform
 from ..config import log
 from ..version import __version__
 from .history import History
@@ -154,7 +154,7 @@ class Output:
 
     history: History
     meta: Metadata
-    platform: Optional[Platform] = None
+    platform: Optional[CalibrationPlatform] = None
 
     @classmethod
     def load(cls, path: Path):
@@ -201,7 +201,7 @@ def dump(self, path: Path):
             self.update_platform(self.platform, path)
 
     @staticmethod
-    def update_platform(platform: Platform, path: Path):
+    def update_platform(platform: CalibrationPlatform, path: Path):
         """Dump platform used.
 
         If the original one is not defined, use the current one as the
@@ -212,7 +212,7 @@ def update_platform(platform: Platform, path: Path):
             platpath = path / UPDATED_PLATFORM
 
         platpath.mkdir(parents=True, exist_ok=True)
-        # dump_platform(platform, platpath)
+        platform.dump(path)
 
     def _export_stats(self):
         """Export task statistics.
diff --git a/src/qibocal/calibration/calibration.py b/src/qibocal/calibration/calibration.py
index 21fc5ff31..afb054f8b 100644
--- a/src/qibocal/calibration/calibration.py
+++ b/src/qibocal/calibration/calibration.py
@@ -1,3 +1,5 @@
+from pathlib import Path
+
 from pydantic import BaseModel, ConfigDict, Field
 
 # from qibolab._core.identifier import QubitId, QubitPairId
@@ -113,3 +115,7 @@ class Calibration(Model):
     """Readout mitigation matrix."""
     flux_crosstalk_matrix: str = None
     """Crosstalk flux matrix."""
+
+    def dump(self, path: Path):
+        """Dump platform."""
+        (path / CALIBRATION).write_text(self.model_dump_json(indent=4))
diff --git a/src/qibocal/calibration/platform.py b/src/qibocal/calibration/platform.py
index feeae7521..da033fb5e 100644
--- a/src/qibocal/calibration/platform.py
+++ b/src/qibocal/calibration/platform.py
@@ -2,57 +2,38 @@
 from dataclasses import dataclass
 from pathlib import Path
 
-from qibolab import Platform, create_dummy, create_platform
+from qibolab import Platform, create_platform
 
 from .calibration import CALIBRATION, Calibration
 
 
 @dataclass
-class CalibrationPlatform:
+class CalibrationPlatform(Platform):
     """Qibolab platform with calibration information."""
 
-    platform: Platform = None
-    """Qibolab platforms."""
     calibration: Calibration = None
     """Calibration information."""
 
-    @property
-    def natives(self):
-        return self.platform.natives
-
-    @property
-    def qubits(self):
-        return self.platform.qubits
-
-    @property
-    def parameters(self):
-        return self.platform.parameters
-
-    def execute(self, *args, **kwargs):
-        return self.execute(*args, **kwargs)
-
     @classmethod
-    def load(cls, name: str):
+    def from_platform(cls, platform: Platform):
+        name = platform.name
+        if name == "dummy":
+            calibration = Calibration.model_validate_json(
+                (Path(__file__).parent / "dummy.json").read_text()
+            )
+        else:
+            path = Path(os.getenv("QIBOLAB_PLATFORMS")) / name
+            calibration = Calibration.model_validate_json(
+                (path / CALIBRATION).read_text()
+            )
 
-        platform = create_platform(name)
-        path = Path(os.getenv("QIBOLAB_PLATFORMS")) / name
-        calibration = Calibration.model_validate_json(path.read_text())
+        return cls(**vars(platform), calibration=calibration)
 
-        return cls(platform, calibration)
+    def dump(self, path: Path):
+        super().dump(path)
+        self.calibration.dump(path)
 
 
 def create_calibration_platform(name: str) -> CalibrationPlatform:
-
-    if name == "dummy":
-        platform = create_dummy()
-        calibration = Calibration.model_validate_json(
-            (Path(__file__).parent / "dummy.json").read_text()
-        )
-    else:
-        path = Path(os.getenv("QIBOLAB_PLATFORMS"))
-        platform = create_platform(name)
-        calibration = Calibration.model_validate_json(
-            (path / name / CALIBRATION).read_text()
-        )
-
-    return CalibrationPlatform(platform=platform, calibration=calibration)
+    platform = create_platform(name)
+    return CalibrationPlatform.from_platform(platform)
diff --git a/src/qibocal/cli/acquisition.py b/src/qibocal/cli/acquisition.py
index dd8aa9285..956f553c9 100644
--- a/src/qibocal/cli/acquisition.py
+++ b/src/qibocal/cli/acquisition.py
@@ -6,6 +6,7 @@
 from ..auto.mode import ExecutionMode
 from ..auto.output import Metadata, Output
 from ..auto.runcard import Runcard
+from ..calibration import CalibrationPlatform
 
 
 def acquire(runcard: Runcard, folder: Path, force: bool):
@@ -17,7 +18,7 @@ def acquire(runcard: Runcard, folder: Path, force: bool):
     """
     # rename for brevity
     backend = construct_backend(backend=runcard.backend, platform=runcard.platform)
-    platform = backend.platform
+    platform = CalibrationPlatform.from_platform(backend.platform)
     if platform is None:
         raise ValueError("Qibocal requires a Qibolab platform to run.")
 
diff --git a/src/qibocal/cli/autocalibration.py b/src/qibocal/cli/autocalibration.py
index 6e4686369..d3f60464a 100644
--- a/src/qibocal/cli/autocalibration.py
+++ b/src/qibocal/cli/autocalibration.py
@@ -6,6 +6,7 @@
 from ..auto.mode import AUTOCALIBRATION
 from ..auto.output import Metadata, Output
 from ..auto.runcard import Runcard
+from ..calibration import CalibrationPlatform
 from .report import report
 
 
@@ -18,7 +19,8 @@ def autocalibrate(runcard: Runcard, folder: Path, force, update):
     """
     # rename for brevity
     backend = construct_backend(backend=runcard.backend, platform=runcard.platform)
-    platform = backend.platform
+    platform = CalibrationPlatform.from_platform(backend.platform)
+
     if platform is None:
         raise ValueError("Qibocal requires a Qibolab platform to run.")
 

From dd620ba46f266cd2d7fd132cde13621241935efa Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Tue, 22 Oct 2024 17:20:46 +0400
Subject: [PATCH 05/22] fix: dump platform correctly

---
 src/qibocal/auto/output.py | 2 +-
 src/qibocal/update.py      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/qibocal/auto/output.py b/src/qibocal/auto/output.py
index 3ec65163c..62446e6ab 100644
--- a/src/qibocal/auto/output.py
+++ b/src/qibocal/auto/output.py
@@ -212,7 +212,7 @@ def update_platform(platform: CalibrationPlatform, path: Path):
             platpath = path / UPDATED_PLATFORM
 
         platpath.mkdir(parents=True, exist_ok=True)
-        platform.dump(path)
+        platform.dump(platpath)
 
     def _export_stats(self):
         """Export task statistics.
diff --git a/src/qibocal/update.py b/src/qibocal/update.py
index b623dcf47..2d0f40e21 100644
--- a/src/qibocal/update.py
+++ b/src/qibocal/update.py
@@ -35,7 +35,7 @@ def readout_frequency(freq: float, platform: Platform, qubit: QubitId):
 
 def bare_resonator_frequency(freq: float, platform: Platform, qubit: QubitId):
     """Update rbare frequency value in platform for specific qubit."""
-    # platform.qubits[qubit].bare_resonator_frequency = int(freq)
+    platform.calibration.single_qubits[qubit].resonator.bare_frequency = int(freq)
 
 
 def readout_amplitude(amp: float, platform: Platform, qubit: QubitId):

From 99533e60513f778829a87e304ee2ff5c58dc1fde Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Wed, 23 Oct 2024 10:41:48 +0400
Subject: [PATCH 06/22] refactor: Assignment fidelity as derived from ro
 fidelity

---
 src/qibocal/calibration/calibration.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/qibocal/calibration/calibration.py b/src/qibocal/calibration/calibration.py
index afb054f8b..e94da1c56 100644
--- a/src/qibocal/calibration/calibration.py
+++ b/src/qibocal/calibration/calibration.py
@@ -54,17 +54,19 @@ def charging_energy(self):
 class Readout(Model):
     """Readout parameters."""
 
-    assignment_fidelity: float = 0
-    """Assignment fidelity."""
-    readout_fidelity: float = 0
+    fidelity: float = 0
     """Readout fidelity."""
+    effective_temperature: float = 0
+    """Qubit effective temperature."""
     ground_state: list[float] = Field(default_factory=list)
     """Ground state position in IQ plane."""
     excited_state: list[float] = Field(default_factory=list)
     """Excited state position in IQ plane."""
 
-    # TODO: drop one of the two between readout and assignment fidelities
-    # TODO: possibly rename one of them fidelity
+    @property
+    def assignment_fidelity(self):
+        """Assignment fidelity."""
+        return (1 + self.fidelity) / 2
 
 
 class Coherence(Model):

From 25250ecbaf46572d3928772e259ff4b758a41518 Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Wed, 23 Oct 2024 10:56:28 +0400
Subject: [PATCH 07/22] feat: Update for classification and other protocols

---
 src/qibocal/calibration/dummy.json      | 15 +++------
 src/qibocal/protocols/classification.py |  1 -
 src/qibocal/update.py                   | 45 ++++++++++---------------
 3 files changed, 23 insertions(+), 38 deletions(-)

diff --git a/src/qibocal/calibration/dummy.json b/src/qibocal/calibration/dummy.json
index bf648ee64..2d40fe207 100644
--- a/src/qibocal/calibration/dummy.json
+++ b/src/qibocal/calibration/dummy.json
@@ -13,8 +13,7 @@
                 "sweetspot": 0.0
             },
             "readout": {
-                "assignment_fidelity": 0.5,
-                "readout_fidelity": 0.0,
+                "fidelity": 0.0,
                 "ground_state": [
                     0.0,
                     1.0
@@ -44,8 +43,7 @@
                 "sweetspot": 0.0
             },
             "readout": {
-                "assignment_fidelity": 0.5,
-                "readout_fidelity": 0.0,
+                "fidelity": 0.0,
                 "ground_state": [
                     0.25,
                     0.0
@@ -75,8 +73,7 @@
                 "sweetspot": 0.0
             },
             "readout": {
-                "assignment_fidelity": 0.1,
-                "readout_fidelity": 0.0,
+                "fidelity": 0.0,
                 "ground_state": [
                     0.5,
                     0.0
@@ -106,8 +103,7 @@
                 "sweetspot": 0.0
             },
             "readout": {
-                "assignment_fidelity": 0.1,
-                "readout_fidelity": 0.0,
+                "fidelity": 0.0,
                 "ground_state": [
                     0.75,
                     0.0
@@ -137,8 +133,7 @@
                 "sweetspot": 0.0
             },
             "readout": {
-                "assignment_fidelity": 0.1,
-                "readout_fidelity": 0.0,
+                "fidelity": 0.0,
                 "ground_state": [
                     1.0,
                     0.0
diff --git a/src/qibocal/protocols/classification.py b/src/qibocal/protocols/classification.py
index 59eb3dc9a..b01683bca 100644
--- a/src/qibocal/protocols/classification.py
+++ b/src/qibocal/protocols/classification.py
@@ -409,7 +409,6 @@ def _update(
     update.mean_gnd_states(results.mean_gnd_states[target], platform, target)
     update.mean_exc_states(results.mean_exc_states[target], platform, target)
     update.readout_fidelity(results.fidelity[target], platform, target)
-    update.assignment_fidelity(results.assignment_fidelity[target], platform, target)
 
 
 single_shot_classification = Routine(_acquisition, _fit, _plot, _update)
diff --git a/src/qibocal/update.py b/src/qibocal/update.py
index 2d0f40e21..56fa657c8 100644
--- a/src/qibocal/update.py
+++ b/src/qibocal/update.py
@@ -3,7 +3,6 @@
 from collections.abc import Iterable
 from typing import Union
 
-import numpy as np
 from pydantic import BaseModel
 from qibolab import Platform
 
@@ -93,24 +92,19 @@ def threshold(threshold: float, platform: Platform, qubit: QubitId):
     pass
 
 
-def mean_gnd_states(gnd_state: list, platform: Platform, qubit: QubitId):
+def mean_gnd_states(ground_state: list, platform: Platform, qubit: QubitId):
     """Update mean ground state value in platform for specific qubit."""
-    # platform.qubits[qubit].mean_gnd_states = gnd_state
+    platform.calibration.single_qubits[qubit].readout.ground_state = ground_state
 
 
-def mean_exc_states(exc_state: list, platform: Platform, qubit: QubitId):
+def mean_exc_states(excited_state: list, platform: Platform, qubit: QubitId):
     """Update mean excited state value in platform for specific qubit."""
-    # platform.qubits[qubit].mean_exc_states = exc_state
+    platform.calibration.single_qubits[qubit].readout.excited_state = excited_state
 
 
 def readout_fidelity(fidelity: float, platform: Platform, qubit: QubitId):
     """Update fidelity of single shot classification."""
-    # platform.qubits[qubit].readout_fidelity = float(fidelity)
-
-
-def assignment_fidelity(fidelity: float, platform: Platform, qubit: QubitId):
-    """Update fidelity of single shot classification."""
-    # platform.qubits[qubit].assignment_fidelity = float(fidelity)
+    platform.calibration.single_qubits[qubit].readout.fidelity = float(fidelity)
 
 
 def virtual_phases(
@@ -165,25 +159,25 @@ def iSWAP_amplitude(amp: float, platform: Platform, pair: QubitPairId):
 def t1(t1: int, platform: Platform, qubit: QubitId):
     """Update t1 value in platform for specific qubit."""
     if isinstance(t1, Iterable):
-        platform.qubits[qubit].T1 = int(t1[0])
+        platform.calibration.single_qubits[qubit].t1 = int(t1[0])
     else:
-        platform.qubits[qubit].T1 = int(t1)
+        platform.calibration.single_qubits[qubit].t1 = int(t1)
 
 
 def t2(t2: int, platform: Platform, qubit: QubitId):
     """Update t2 value in platform for specific qubit."""
     if isinstance(t2, Iterable):
-        platform.qubits[qubit].T2 = int(t2[0])
+        platform.calibration.single_qubits[qubit].t2 = int(t2[0])
     else:
-        platform.qubits[qubit].T2 = int(t2)
+        platform.calibration.single_qubits[qubit].t2 = int(t2)
 
 
 def t2_spin_echo(t2_spin_echo: float, platform: Platform, qubit: QubitId):
     """Update t2 echo value in platform for specific qubit."""
     if isinstance(t2_spin_echo, Iterable):
-        platform.qubits[qubit].T2_spin_echo = int(t2_spin_echo[0])
+        platform.calibration.single_qubits[qubit].t2_spin_echo = int(t2_spin_echo[0])
     else:
-        platform.qubits[qubit].T2_spin_echo = int(t2_spin_echo)
+        platform.calibration.single_qubits[qubit].t2_spin_echo = int(t2_spin_echo)
 
 
 def drag_pulse_beta(beta: float, platform: Platform, qubit: QubitId):
@@ -196,10 +190,11 @@ def drag_pulse_beta(beta: float, platform: Platform, qubit: QubitId):
 
 def sweetspot(sweetspot: float, platform: Platform, qubit: QubitId):
     """Update sweetspot parameter in platform for specific qubit."""
-    platform.qubits[qubit].sweetspot = float(sweetspot)
+    platform.calibration.single_qubits[qubit].qubit.sweetspot = float(sweetspot)
 
 
 def frequency_12_transition(frequency: int, platform: Platform, qubit: QubitId):
+    platform.calibration.single_qubits[qubit].qubit.omega_12 = int(frequency)
     platform.qubits[qubit].native_gates.RX12.frequency = int(frequency)
 
 
@@ -222,17 +217,13 @@ def twpa_power(power: float, platform: Platform, qubit: QubitId):
     platform.qubits[qubit].twpa.local_oscillator.power = float(power)
 
 
-def anharmonicity(anharmonicity: float, platform: Platform, qubit: QubitId):
-    platform.qubits[qubit].anharmonicity = int(anharmonicity)
-
-
 def asymmetry(asymmetry: float, platform: Platform, qubit: QubitId):
-    platform.qubits[qubit].asymmetry = float(asymmetry)
+    platform.calibration.single_qubits[qubit].asymmetry = float(asymmetry)
 
 
-def coupling(g: float, platform: Platform, qubit: QubitId):
-    platform.qubits[qubit].g = float(g)
+# def coupling(g: float, platform: Platform, qubit: QubitId):
+#     platform.qubits[qubit].g = float(g)
 
 
-def kernel(kernel: np.ndarray, platform: Platform, qubit: QubitId):
-    platform.qubits[qubit].kernel = kernel
+# def kernel(kernel: np.ndarray, platform: Platform, qubit: QubitId):
+#     platform.qubits[qubit].kernel = kernel

From 68313d4d5f6e3a0453db2f3183be7b6f190ed753 Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Fri, 25 Oct 2024 11:34:45 +0400
Subject: [PATCH 08/22] fix: Dump qubit pair as string

---
 src/qibocal/calibration/calibration.py | 36 +++++++++++++-------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/src/qibocal/calibration/calibration.py b/src/qibocal/calibration/calibration.py
index e94da1c56..4276bf99e 100644
--- a/src/qibocal/calibration/calibration.py
+++ b/src/qibocal/calibration/calibration.py
@@ -1,9 +1,9 @@
 from pathlib import Path
+from typing import Optional
 
 from pydantic import BaseModel, ConfigDict, Field
-
-# from qibolab._core.identifier import QubitId, QubitPairId
-# from qibolab._core.serialize import NdArray
+from qibolab._core.identifier import QubitId, QubitPairId
+from qibolab._core.serialize import NdArray
 
 CALIBRATION = "calibration.json"
 """Calibration file."""
@@ -18,9 +18,9 @@ class Model(BaseModel):
 class Resonator(Model):
     """Representation of resonator parameters."""
 
-    bare_frequency: float = 0
+    bare_frequency: Optional[float] = None
     """Bare resonator frequency [Hz]."""
-    dressed_frequency: float = 0
+    dressed_frequency: Optional[float] = None
     """Dressed resonator frequency [Hz]."""
     depletion_time: int = 0
     """Depletion time [ns]."""
@@ -31,13 +31,13 @@ class Resonator(Model):
 class Qubit(Model):
     """Representation of Qubit parameters"""
 
-    omega_01: float = 0
+    omega_01: Optional[float] = None
     """"0->1 transition frequency."""
-    omega_12: float = 0
+    omega_12: Optional[float] = None
     """1->2 transition frequency."""
-    asymmetry: float = 0
+    asymmetry: Optional[float] = None
     """Junctions asymmetry."""
-    sweetspot: float = 0
+    sweetspot: Optional[float] = None
     """Qubit sweetspot [V]."""
 
     @property
@@ -54,9 +54,9 @@ def charging_energy(self):
 class Readout(Model):
     """Readout parameters."""
 
-    fidelity: float = 0
+    fidelity: Optional[float] = None
     """Readout fidelity."""
-    effective_temperature: float = 0
+    effective_temperature: Optional[float] = None
     """Qubit effective temperature."""
     ground_state: list[float] = Field(default_factory=list)
     """Ground state position in IQ plane."""
@@ -91,31 +91,31 @@ class QubitCalibration(Model):
     """Readout information."""
     coherence: Coherence = Field(default_factory=Coherence)
     """Coherence times of the qubit."""
-    rb_fidelity: float = 0
+    rb_fidelity: Optional[float] = None
     """Standard rb pulse fidelity."""
 
 
 class TwoQubitCalibration(Model):
     """Container for calibration of qubit pair."""
 
-    rb_fidelity: float = 0
+    rb_fidelity: Optional[float] = None
     """Two qubit standard rb fidelity."""
-    cz_fidelity: float = 0
+    cz_fidelity: Optional[float] = None
     """CZ interleaved rb fidelity."""
 
 
 class Calibration(Model):
     """Calibration container."""
 
-    single_qubits: dict[str, QubitCalibration] = Field(default_factory=dict)
+    single_qubits: dict[QubitId, QubitCalibration] = Field(default_factory=dict)
     """Dict with single qubit calibration."""
     # TODO: dump pair as str instead of tuple
-    two_qubits: dict[tuple, TwoQubitCalibration] = Field(default_factory=dict)
+    two_qubits: dict[QubitPairId, TwoQubitCalibration] = Field(default_factory=dict)
     """Dict with qubit pairs calibration."""
     # TODO: fix this as well
-    readout_mitigation_matrix: str = None
+    readout_mitigation_matrix: Optional[NdArray] = None
     """Readout mitigation matrix."""
-    flux_crosstalk_matrix: str = None
+    flux_crosstalk_matrix: Optional[NdArray] = None
     """Crosstalk flux matrix."""
 
     def dump(self, path: Path):

From 879c3a1a2fb6bf101585792bb394dd293ee05d8d Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Fri, 25 Oct 2024 11:37:29 +0400
Subject: [PATCH 09/22] build: Update lock file

---
 poetry.lock | 1976 +++++++++++++++++++++++++++++----------------------
 1 file changed, 1127 insertions(+), 849 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 3dcd8947c..3e2f5dbfa 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.2 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"
@@ -11,6 +11,25 @@ files = [
     {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
 ]
 
+[[package]]
+name = "alembic"
+version = "1.13.3"
+description = "A database migration tool for SQLAlchemy."
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "alembic-1.13.3-py3-none-any.whl", hash = "sha256:908e905976d15235fae59c9ac42c4c5b75cfcefe3d27c0fbf7ae15a37715d80e"},
+    {file = "alembic-1.13.3.tar.gz", hash = "sha256:203503117415561e203aa14541740643a611f641517f0209fcae63e9fa09f1a2"},
+]
+
+[package.dependencies]
+Mako = "*"
+SQLAlchemy = ">=1.3.0"
+typing-extensions = ">=4"
+
+[package.extras]
+tz = ["backports.zoneinfo"]
+
 [[package]]
 name = "annotated-types"
 version = "0.7.0"
@@ -137,112 +156,127 @@ files = [
 
 [[package]]
 name = "certifi"
-version = "2024.7.4"
+version = "2024.8.30"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"},
-    {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"},
+    {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
+    {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
 ]
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.2"
+version = "3.4.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:25baf083bf6f6b341f4121c2f3c548875ee6f5339300e08be3f2b2ba1721cdd3"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:06435b539f889b1f6f4ac1758871aae42dc3a8c0e24ac9e60c2384973ad73027"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9063e24fdb1e498ab71cb7419e24622516c4a04476b17a2dab57e8baa30d6e03"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6897af51655e3691ff853668779c7bad41579facacf5fd7253b0133308cf000d"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:1d3193f4a680c64b4b6a9115943538edb896edc190f0b222e73761716519268e"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:cd70574b12bb8a4d2aaa0094515df2463cb429d8536cfb6c7ce983246983e5a6"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8465322196c8b4d7ab6d1e049e4c5cb460d0394da4a27d23cc242fbf0034b6b5"},
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 [[package]]
@@ -259,17 +293,6 @@ files = [
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
-[[package]]
-name = "cloudpickle"
-version = "3.0.0"
-description = "Pickler class to extend the standard pickle.Pickler functionality"
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-
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 version = "3.4.0"
@@ -316,6 +339,23 @@ humanfriendly = ">=9.1"
 [package.extras]
 cron = ["capturer (>=2.4)"]
 
+[[package]]
+name = "colorlog"
+version = "6.8.2"
+description = "Add colours to the output of Python's logging module."
+optional = false
+python-versions = ">=3.6"
+files = [
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+
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+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+
+[package.extras]
+development = ["black", "flake8", "mypy", "pytest", "types-colorama"]
+
 [[package]]
 name = "commonmark"
 version = "0.9.1"
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@@ -497,13 +548,13 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "dash"
-version = "2.17.1"
+version = "2.18.1"
 description = "A Python framework for building reactive web-apps. Developed by Plotly."
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 python-versions = ">=3.8"
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@@ -592,13 +643,13 @@ pygments = ["pygments (>=2.2.0)"]
 
 [[package]]
 name = "dill"
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+version = "0.3.9"
 description = "serialize all of Python"
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 [package.extras]
@@ -632,13 +683,13 @@ test = ["pytest (>=6)"]
 
 [[package]]
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+version = "2.1.0"
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 [package.extras]
@@ -776,13 +833,13 @@ woff = ["brotli (>=1.0.1)", "brotlicffi (>=0.8.0)", "zopfli (>=0.1.4)"]
 
 [[package]]
 name = "fsspec"
-version = "2024.6.1"
+version = "2024.10.0"
 description = "File-system specification"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -831,15 +888,90 @@ sphinx = ">=5.0,<7.0"
 sphinx-basic-ng = "*"
 
 [[package]]
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-version = "1.0.0"
-description = "Clean single-source support for Python 3 and 2"
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 optional = false
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+
+[package.extras]
+docs = ["Sphinx", "furo"]
+test = ["objgraph", "psutil"]
 
 [[package]]
 name = "html5lib"
@@ -864,13 +996,13 @@ lxml = ["lxml"]
 
 [[package]]
 name = "huggingface-hub"
-version = "0.24.6"
+version = "0.26.1"
 description = "Client library to download and publish models, datasets and other repos on the huggingface.co hub"
 optional = false
 python-versions = ">=3.8.0"
 files = [
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 [package.dependencies]
@@ -883,16 +1015,16 @@ tqdm = ">=4.42.1"
 typing-extensions = ">=3.7.4.3"
 
 [package.extras]
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+all = ["InquirerPy (==0.3.4)", "Jinja2", "Pillow", "aiohttp", "fastapi", "gradio (>=4.0.0)", "jedi", "libcst (==1.4.0)", "mypy (==1.5.1)", "numpy", "pytest (>=8.1.1,<8.2.2)", "pytest-asyncio", "pytest-cov", "pytest-env", "pytest-mock", "pytest-rerunfailures", "pytest-vcr", "pytest-xdist", "ruff (>=0.5.0)", "soundfile", "types-PyYAML", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "typing-extensions (>=4.8.0)", "urllib3 (<2.0)"]
 cli = ["InquirerPy (==0.3.4)"]
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-inference = ["aiohttp", "minijinja (>=1.0)"]
-quality = ["mypy (==1.5.1)", "ruff (>=0.5.0)"]
+inference = ["aiohttp"]
+quality = ["libcst (==1.4.0)", "mypy (==1.5.1)", "ruff (>=0.5.0)"]
 tensorflow = ["graphviz", "pydot", "tensorflow"]
 tensorflow-testing = ["keras (<3.0)", "tensorflow"]
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 typing = ["types-PyYAML", "types-requests", "types-simplejson", "types-toml", "types-tqdm", "types-urllib3", "typing-extensions (>=4.8.0)"]
 
@@ -910,44 +1042,20 @@ files = [
 [package.dependencies]
 pyreadline3 = {version = "*", markers = "sys_platform == \"win32\" and python_version >= \"3.8\""}
 
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-numpy = "*"
-py4j = "*"
-scipy = "*"
-six = "*"
-tqdm = "*"
-
-[package.extras]
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-dev = ["black", "nose", "pre-commit", "pytest"]
-mongotrials = ["pymongo"]
-sparktrials = ["pyspark"]
-
 [[package]]
 name = "idna"
-version = "3.8"
+version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
 python-versions = ">=3.6"
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+
 [[package]]
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 version = "1.4.1"
@@ -961,32 +1069,36 @@ files = [
 
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 [package.dependencies]
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+zipp = ">=3.20"
 
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+type = ["pytest-mypy"]
 
 [[package]]
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+version = "6.4.5"
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 [package.dependencies]
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@@ -1444,6 +1566,25 @@ html5 = ["html5lib"]
 htmlsoup = ["BeautifulSoup4"]
 source = ["Cython (>=3.0.11)"]
 
+[[package]]
+name = "mako"
+version = "1.3.6"
+description = "A super-fast templating language that borrows the best ideas from the existing templating languages."
+optional = false
+python-versions = ">=3.8"
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+]
+
+[package.dependencies]
+MarkupSafe = ">=0.9.2"
+
+[package.extras]
+babel = ["Babel"]
+lingua = ["lingua"]
+testing = ["pytest"]
+
 [[package]]
 name = "markdown"
 version = "3.7"
@@ -1464,71 +1605,72 @@ testing = ["coverage", "pyyaml"]
 
 [[package]]
 name = "markupsafe"
-version = "2.1.5"
+version = "3.0.2"
 description = "Safely add untrusted strings to HTML/XML markup."
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 [package.dependencies]
@@ -1832,6 +1974,33 @@ all = ["antlr4-python3-runtime (>=4.7,<4.14)", "importlib-metadata", "pytest (>=
 parser = ["antlr4-python3-runtime (>=4.7,<4.14)", "importlib-metadata"]
 tests = ["pytest (>=6.0)", "pyyaml"]
 
+[[package]]
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+version = "4.0.0"
+description = "A hyperparameter optimization framework"
+optional = false
+python-versions = ">=3.7"
+files = [
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+[package.dependencies]
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+colorlog = "*"
+numpy = "*"
+packaging = ">=20.0"
+PyYAML = "*"
+sqlalchemy = ">=1.3.0"
+tqdm = "*"
+
+[package.extras]
+benchmark = ["asv (>=0.5.0)", "botorch", "cma", "virtualenv"]
+checking = ["black", "blackdoc", "flake8", "isort", "mypy", "mypy-boto3-s3", "types-PyYAML", "types-redis", "types-setuptools", "types-tqdm", "typing-extensions (>=3.10.0.0)"]
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+test = ["coverage", "fakeredis[lua]", "kaleido", "moto", "pytest", "scipy (>=1.9.2)", "torch"]
+
 [[package]]
 name = "packaging"
 version = "24.1"
@@ -1845,40 +2014,53 @@ files = [
 
 [[package]]
 name = "pandas"
-version = "2.2.2"
+version = "2.2.3"
 description = "Powerful data structures for data analysis, time series, and statistics"
 optional = false
 python-versions = ">=3.9"
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 [package.dependencies]
@@ -1969,95 +2151,90 @@ ptyprocess = ">=0.5"
 
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 fpx = ["olefile"]
 mic = ["olefile"]
 tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
@@ -2066,29 +2243,29 @@ xmp = ["defusedxml"]
 
 [[package]]
 name = "platformdirs"
-version = "4.2.2"
+version = "4.3.6"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
 python-versions = ">=3.8"
 files = [
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-type = ["mypy (>=1.8)"]
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+type = ["mypy (>=1.11.2)"]
 
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 name = "plotly"
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 description = "An open-source, interactive data visualization library for Python"
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 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -2112,13 +2289,13 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.47"
+version = "3.0.48"
 description = "Library for building powerful interactive command lines in Python"
 optional = false
 python-versions = ">=3.7.0"
 files = [
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 ]
 
 [package.dependencies]
@@ -2126,22 +2303,22 @@ wcwidth = "*"
 
 [[package]]
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+version = "5.28.3"
 description = ""
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 ]
 
 [[package]]
@@ -2169,17 +2346,6 @@ files = [
 [package.extras]
 tests = ["pytest"]
 
-[[package]]
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-version = "0.10.9.7"
-description = "Enables Python programs to dynamically access arbitrary Java objects"
-optional = false
-python-versions = "*"
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-
 [[package]]
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 version = "0.24.0"
@@ -2216,119 +2382,120 @@ pybtex = ">=0.16"
 
 [[package]]
 name = "pydantic"
-version = "2.8.2"
+version = "2.9.2"
 description = "Data validation using Python type hints"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
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-pydantic-core = "2.20.1"
+annotated-types = ">=0.6.0"
+pydantic-core = "2.23.4"
 typing-extensions = {version = ">=4.6.1", markers = "python_version < \"3.13\""}
 
 [package.extras]
 email = ["email-validator (>=2.0.0)"]
+timezone = ["tzdata"]
 
 [[package]]
 name = "pydantic-core"
-version = "2.20.1"
+version = "2.23.4"
 description = "Core functionality for Pydantic validation and serialization"
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
@@ -2393,13 +2560,13 @@ testutils = ["gitpython (>3)"]
 
 [[package]]
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+version = "3.2.0"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = true
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 ]
 
 [package.extras]
@@ -2417,15 +2584,18 @@ files = [
 
 [[package]]
 name = "pyreadline3"
-version = "3.4.1"
+version = "3.5.4"
 description = "A python implementation of GNU readline."
 optional = true
-python-versions = "*"
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+[package.extras]
+dev = ["build", "flake8", "mypy", "pytest", "twine"]
+
 [[package]]
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 version = "0.9.0"
@@ -2526,13 +2696,13 @@ six = ">=1.5"
 
 [[package]]
 name = "pytz"
-version = "2024.1"
+version = "2024.2"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [[package]]
@@ -2599,24 +2769,23 @@ files = [
 
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-version = "0.2.11"
+version = "0.2.12"
 description = "A framework for quantum computing with hardware acceleration."
 optional = false
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 networkx = ">=3.2.1,<4.0.0"
 numpy = ">=1.26.4,<2.0.0"
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 scipy = ">=1.10.1,<2.0.0"
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 sympy = ">=1.11.1,<2.0.0"
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 ]
 
 [package.dependencies]
@@ -2743,11 +2917,11 @@ threadpoolctl = ">=3.1.0"
 [package.extras]
 benchmark = ["matplotlib (>=3.3.4)", "memory_profiler (>=0.57.0)", "pandas (>=1.1.5)"]
 build = ["cython (>=3.0.10)", "meson-python (>=0.16.0)", "numpy (>=1.19.5)", "scipy (>=1.6.0)"]
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 [[package]]
 name = "scipy"
@@ -2814,18 +2988,23 @@ stats = ["scipy (>=1.3)", "statsmodels (>=0.10)"]
 
 [[package]]
 name = "setuptools"
-version = "70.3.0"
+version = "75.2.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [[package]]
 name = "six"
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 standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
+[[package]]
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+typing-extensions = ">=4.6.0"
+
+[package.extras]
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+aioodbc = ["aioodbc", "greenlet (!=0.4.17)"]
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+mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5,!=1.1.10)"]
+mssql = ["pyodbc"]
+mssql-pymssql = ["pymssql"]
+mssql-pyodbc = ["pyodbc"]
+mypy = ["mypy (>=0.910)"]
+mysql = ["mysqlclient (>=1.4.0)"]
+mysql-connector = ["mysql-connector-python"]
+oracle = ["cx_oracle (>=8)"]
+oracle-oracledb = ["oracledb (>=1.0.1)"]
+postgresql = ["psycopg2 (>=2.7)"]
+postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
+postgresql-pg8000 = ["pg8000 (>=1.29.1)"]
+postgresql-psycopg = ["psycopg (>=3.0.7)"]
+postgresql-psycopg2binary = ["psycopg2-binary"]
+postgresql-psycopg2cffi = ["psycopg2cffi"]
+postgresql-psycopgbinary = ["psycopg[binary] (>=3.0.7)"]
+pymysql = ["pymysql"]
+sqlcipher = ["sqlcipher3_binary"]
+
 [[package]]
 name = "stack-data"
 version = "0.6.3"
@@ -3115,13 +3389,13 @@ tests = ["cython", "littleutils", "pygments", "pytest", "typeguard"]
 
 [[package]]
 name = "sympy"
-version = "1.13.2"
+version = "1.13.3"
 description = "Computer algebra system (CAS) in Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -3172,13 +3446,13 @@ files = [
 
 [[package]]
 name = "tomli"
-version = "2.0.1"
+version = "2.0.2"
 description = "A lil' TOML parser"
 optional = false
-python-versions = ">=3.7"
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 ]
 
 [[package]]
@@ -3240,24 +3514,24 @@ files = [
 
 [[package]]
 name = "tzdata"
-version = "2024.1"
+version = "2024.2"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
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 ]
 
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-version = "2.2.2"
+version = "2.2.3"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -3290,13 +3564,13 @@ files = [
 
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 name = "werkzeug"
-version = "3.0.4"
+version = "3.0.5"
 description = "The comprehensive WSGI web application library."
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.dependencies]
@@ -3403,18 +3677,22 @@ files = [
 
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+version = "3.20.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
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 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+type = ["pytest-mypy"]
 
 [extras]
 classify = ["matplotlib", "onnxruntime", "seaborn", "skl2onnx"]
@@ -3423,4 +3701,4 @@ viz = ["pydot"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "ca3b3838087ba97df70a82e21044f440b01310f7e7a73819449915d1c499f7f2"
+content-hash = "496267548f0e6ad4a7d47e62497ae78facad7555d536d376f2756c5a5c86e7f8"

From 58efd520284917a929246f9ac212142fbfe562c9 Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Fri, 25 Oct 2024 19:10:05 +0400
Subject: [PATCH 10/22] docs: Minor adjustments

---
 src/qibocal/calibration/calibration.py | 23 ++++++++++-------------
 1 file changed, 10 insertions(+), 13 deletions(-)

diff --git a/src/qibocal/calibration/calibration.py b/src/qibocal/calibration/calibration.py
index 4276bf99e..f8cf7fc9e 100644
--- a/src/qibocal/calibration/calibration.py
+++ b/src/qibocal/calibration/calibration.py
@@ -10,7 +10,7 @@
 
 
 class Model(BaseModel):
-    """Global qibolab model, holding common configurations."""
+    """Global model, holding common configurations."""
 
     model_config = ConfigDict(extra="forbid")
 
@@ -22,9 +22,8 @@ class Resonator(Model):
     """Bare resonator frequency [Hz]."""
     dressed_frequency: Optional[float] = None
     """Dressed resonator frequency [Hz]."""
-    depletion_time: int = 0
+    depletion_time: Optional[int] = None
     """Depletion time [ns]."""
-
     # TODO: Add something related to resonator calibration
 
 
@@ -32,9 +31,9 @@ class Qubit(Model):
     """Representation of Qubit parameters"""
 
     omega_01: Optional[float] = None
-    """"0->1 transition frequency."""
+    """"0->1 transition frequency [Hz]."""
     omega_12: Optional[float] = None
-    """1->2 transition frequency."""
+    """1->2 transition frequency [Hz]."""
     asymmetry: Optional[float] = None
     """Junctions asymmetry."""
     sweetspot: Optional[float] = None
@@ -42,12 +41,12 @@ class Qubit(Model):
 
     @property
     def anharmonicity(self):
-        """Anharmonicity of the qubit in Hz."""
+        """Anharmonicity of the qubit [Hz]."""
         return self.omega_12 - self.omega_01
 
     @property
     def charging_energy(self):
-        """Charging energy Ec."""
+        """Charging energy Ec [Hz]."""
         return -self.anharmonicity
 
 
@@ -72,11 +71,11 @@ def assignment_fidelity(self):
 class Coherence(Model):
     """Coherence times of qubit."""
 
-    t1: int = 0
+    t1: Optional[int] = 0
     """Relaxation time [ns]."""
-    t2: int = 0
+    t2: Optional[int] = 0
     """T2 of the qubit [ns]."""
-    t2_spin_echo: int = 0
+    t2_spin_echo: Optional[int] = 0
     """T2 hanh echo [ns]."""
 
 
@@ -109,15 +108,13 @@ class Calibration(Model):
 
     single_qubits: dict[QubitId, QubitCalibration] = Field(default_factory=dict)
     """Dict with single qubit calibration."""
-    # TODO: dump pair as str instead of tuple
     two_qubits: dict[QubitPairId, TwoQubitCalibration] = Field(default_factory=dict)
     """Dict with qubit pairs calibration."""
-    # TODO: fix this as well
     readout_mitigation_matrix: Optional[NdArray] = None
     """Readout mitigation matrix."""
     flux_crosstalk_matrix: Optional[NdArray] = None
     """Crosstalk flux matrix."""
 
     def dump(self, path: Path):
-        """Dump platform."""
+        """Dump calibration model."""
         (path / CALIBRATION).write_text(self.model_dump_json(indent=4))

From 2cbfb87dfd257137408b5fb3de1855f98f0f7fd8 Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Fri, 25 Oct 2024 20:25:18 +0400
Subject: [PATCH 11/22] refactor: Renaming + crosstalk matrix update

---
 src/qibocal/calibration/calibration.py        | 16 ++++++++---
 src/qibocal/calibration/dummy.json            | 20 +++++++-------
 .../protocols/coherence/spin_echo_signal.py   |  4 +--
 src/qibocal/protocols/coherence/t1_signal.py  |  4 +--
 .../flux_dependence/qubit_flux_dependence.py  | 10 ++++---
 src/qibocal/update.py                         | 27 ++++++++++++++-----
 6 files changed, 54 insertions(+), 27 deletions(-)

diff --git a/src/qibocal/calibration/calibration.py b/src/qibocal/calibration/calibration.py
index f8cf7fc9e..eacf15f2b 100644
--- a/src/qibocal/calibration/calibration.py
+++ b/src/qibocal/calibration/calibration.py
@@ -30,10 +30,12 @@ class Resonator(Model):
 class Qubit(Model):
     """Representation of Qubit parameters"""
 
-    omega_01: Optional[float] = None
+    frequency_01: Optional[float] = None
     """"0->1 transition frequency [Hz]."""
-    omega_12: Optional[float] = None
+    frequency_12: Optional[float] = None
     """1->2 transition frequency [Hz]."""
+    maximum_frequency: Optional[float] = None
+    """Maximum transition frequency [Hz]."""
     asymmetry: Optional[float] = None
     """Junctions asymmetry."""
     sweetspot: Optional[float] = None
@@ -42,7 +44,7 @@ class Qubit(Model):
     @property
     def anharmonicity(self):
         """Anharmonicity of the qubit [Hz]."""
-        return self.omega_12 - self.omega_01
+        return self.frequency_12 - self.frequency_01
 
     @property
     def charging_energy(self):
@@ -118,3 +120,11 @@ class Calibration(Model):
     def dump(self, path: Path):
         """Dump calibration model."""
         (path / CALIBRATION).write_text(self.model_dump_json(indent=4))
+
+    @property
+    def qubits(self) -> list:
+        return list(self.single_qubits)
+
+    @property
+    def nqubits(self) -> int:
+        return len(self.qubits)
diff --git a/src/qibocal/calibration/dummy.json b/src/qibocal/calibration/dummy.json
index 2d40fe207..46fc030e6 100644
--- a/src/qibocal/calibration/dummy.json
+++ b/src/qibocal/calibration/dummy.json
@@ -7,8 +7,8 @@
                 "depletion_time": 0
             },
             "qubit": {
-                "omega_01": 4000000000.0,
-                "omega_12": 4700000000.0,
+                "frequency_01": 4000000000.0,
+                "frequency_12": 4700000000.0,
                 "asymmetry": 0.0,
                 "sweetspot": 0.0
             },
@@ -37,8 +37,8 @@
                 "depletion_time": 0
             },
             "qubit": {
-                "omega_01": 4200000000.0,
-                "omega_12": 4855663000.0,
+                "frequency_01": 4200000000.0,
+                "frequency_12": 4855663000.0,
                 "asymmetry": 0.0,
                 "sweetspot": 0.0
             },
@@ -67,8 +67,8 @@
                 "depletion_time": 0
             },
             "qubit": {
-                "omega_01": 4500000000.0,
-                "omega_12": 2700000000.0,
+                "frequency_01": 4500000000.0,
+                "frequency_12": 2700000000.0,
                 "asymmetry": 0.0,
                 "sweetspot": 0.0
             },
@@ -97,8 +97,8 @@
                 "depletion_time": 0
             },
             "qubit": {
-                "omega_01": 4150000000.0,
-                "omega_12": 5855663000.0,
+                "frequency_01": 4150000000.0,
+                "frequency_12": 5855663000.0,
                 "asymmetry": 0.0,
                 "sweetspot": 0.0
             },
@@ -127,8 +127,8 @@
                 "depletion_time": 0
             },
             "qubit": {
-                "omega_01": 4100000000.0,
-                "omega_12": 5855663000.0,
+                "frequency_01": 4100000000.0,
+                "frequency_12": 5855663000.0,
                 "asymmetry": 0.0,
                 "sweetspot": 0.0
             },
diff --git a/src/qibocal/protocols/coherence/spin_echo_signal.py b/src/qibocal/protocols/coherence/spin_echo_signal.py
index 1f13e4a5a..ed1ae762c 100644
--- a/src/qibocal/protocols/coherence/spin_echo_signal.py
+++ b/src/qibocal/protocols/coherence/spin_echo_signal.py
@@ -8,6 +8,7 @@
 from qibocal.auto.operation import Parameters, QubitId, Results, Routine
 from qibocal.result import magnitude, phase
 
+from ... import update
 from ..utils import table_dict, table_html
 from .t1_signal import T1SignalData
 from .utils import CoherenceType, exp_decay, exponential_fit, spin_echo_sequence
@@ -171,8 +172,7 @@ def _plot(data: SpinEchoSignalData, target: QubitId, fit: SpinEchoSignalResults
 
 
 def _update(results: SpinEchoSignalResults, platform: Platform, target: QubitId):
-    pass
-    # update.t2_spin_echo(results.t2_spin_echo[target], platform, target)
+    update.t2_spin_echo(results.t2_spin_echo[target], platform, target)
 
 
 spin_echo_signal = Routine(_acquisition, _fit, _plot, _update)
diff --git a/src/qibocal/protocols/coherence/t1_signal.py b/src/qibocal/protocols/coherence/t1_signal.py
index f730ebcce..9f042a3c6 100644
--- a/src/qibocal/protocols/coherence/t1_signal.py
+++ b/src/qibocal/protocols/coherence/t1_signal.py
@@ -17,6 +17,7 @@
 from qibocal.auto.operation import Data, Parameters, QubitId, Results, Routine
 from qibocal.result import magnitude, phase
 
+from ... import update
 from ..utils import table_dict, table_html
 from . import utils
 
@@ -215,8 +216,7 @@ def _plot(data: T1SignalData, target: QubitId, fit: T1SignalResults = None):
 
 
 def _update(results: T1SignalResults, platform: Platform, target: QubitId):
-    pass
-    # update.t1(results.t1[target], platform, target)
+    update.t1(results.t1[target], platform, target)
 
 
 t1_signal = Routine(_acquisition, _fit, _plot, _update)
diff --git a/src/qibocal/protocols/flux_dependence/qubit_flux_dependence.py b/src/qibocal/protocols/flux_dependence/qubit_flux_dependence.py
index eda8880f9..b1ecd5395 100644
--- a/src/qibocal/protocols/flux_dependence/qubit_flux_dependence.py
+++ b/src/qibocal/protocols/flux_dependence/qubit_flux_dependence.py
@@ -19,6 +19,7 @@
 from qibocal.result import magnitude, phase
 from qibocal.update import replace
 
+from ... import update
 from ..utils import GHZ_TO_HZ, HZ_TO_GHZ, extract_feature, table_dict, table_html
 from . import utils
 from .resonator_flux_dependence import ResonatorFluxParameters
@@ -283,10 +284,13 @@ def _plot(data: QubitFluxData, fit: QubitFluxResults, target: QubitId):
 
 
 def _update(results: QubitFluxResults, platform: Platform, qubit: QubitId):
-    pass
     # update.drive_frequency(results.frequency[qubit], platform, qubit)
-    # update.sweetspot(results.sweetspot[qubit], platform, qubit)
-    # update.crosstalk_matrix(results.matrix_element[qubit], platform, qubit, qubit)
+    # TODO: shall we add also frequency_10 here?
+    update.sweetspot(results.sweetspot[qubit], platform, qubit)
+    platform.calibration.single_qubits[qubit].qubit.maximum_frequency = int(
+        results.frequency[qubit]
+    )
+    update.crosstalk_matrix(results.matrix_element[qubit], platform, qubit, qubit)
 
 
 qubit_flux = Routine(_acquisition, _fit, _plot, _update)
diff --git a/src/qibocal/update.py b/src/qibocal/update.py
index 56fa657c8..eb05fbf96 100644
--- a/src/qibocal/update.py
+++ b/src/qibocal/update.py
@@ -3,6 +3,7 @@
 from collections.abc import Iterable
 from typing import Union
 
+import numpy as np
 from pydantic import BaseModel
 from qibolab import Platform
 
@@ -78,7 +79,15 @@ def crosstalk_matrix(
     matrix_element: float, platform: Platform, qubit: QubitId, flux_qubit: QubitId
 ):
     """Update crosstalk_matrix element."""
-    platform.qubits[qubit].crosstalk_matrix[flux_qubit] = float(matrix_element)
+    if platform.calibration.flux_crosstalk_matrix is None:
+        platform.calibration.flux_crosstalk_matrix = np.zeros(
+            (platform.calibration.nqubits, platform.calibration.nqubits)
+        )
+
+    a, b = platform.calibration.qubits.index(qubit), platform.calibration.qubits.index(
+        flux_qubit
+    )
+    platform.calibration.flux_crosstalk_matrix[a, b] = float(matrix_element)
 
 
 def iq_angle(angle: float, platform: Platform, qubit: QubitId):
@@ -159,25 +168,29 @@ def iSWAP_amplitude(amp: float, platform: Platform, pair: QubitPairId):
 def t1(t1: int, platform: Platform, qubit: QubitId):
     """Update t1 value in platform for specific qubit."""
     if isinstance(t1, Iterable):
-        platform.calibration.single_qubits[qubit].t1 = int(t1[0])
+        platform.calibration.single_qubits[qubit].coherence.t1 = int(t1[0])
     else:
-        platform.calibration.single_qubits[qubit].t1 = int(t1)
+        platform.calibration.single_qubits[qubit].coherence.t1 = int(t1)
 
 
 def t2(t2: int, platform: Platform, qubit: QubitId):
     """Update t2 value in platform for specific qubit."""
     if isinstance(t2, Iterable):
-        platform.calibration.single_qubits[qubit].t2 = int(t2[0])
+        platform.calibration.single_qubits[qubit].coherence.t2 = int(t2[0])
     else:
-        platform.calibration.single_qubits[qubit].t2 = int(t2)
+        platform.calibration.single_qubits[qubit].coherence.t2 = int(t2)
 
 
 def t2_spin_echo(t2_spin_echo: float, platform: Platform, qubit: QubitId):
     """Update t2 echo value in platform for specific qubit."""
     if isinstance(t2_spin_echo, Iterable):
-        platform.calibration.single_qubits[qubit].t2_spin_echo = int(t2_spin_echo[0])
+        platform.calibration.single_qubits[qubit].coherence.t2_spin_echo = int(
+            t2_spin_echo[0]
+        )
     else:
-        platform.calibration.single_qubits[qubit].t2_spin_echo = int(t2_spin_echo)
+        platform.calibration.single_qubits[qubit].coherence.t2_spin_echo = int(
+            t2_spin_echo
+        )
 
 
 def drag_pulse_beta(beta: float, platform: Platform, qubit: QubitId):

From 2a07e1d8bd5056231888e52f1da7d05af9fde58f Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Fri, 25 Oct 2024 20:56:30 +0400
Subject: [PATCH 12/22] refactor: resonator flux with new calibration model

---
 src/qibocal/calibration/calibration.py              |  9 +++++++++
 .../flux_dependence/resonator_flux_dependence.py    | 13 ++++++++-----
 src/qibocal/update.py                               |  6 +-----
 3 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/src/qibocal/calibration/calibration.py b/src/qibocal/calibration/calibration.py
index eacf15f2b..b095d37f4 100644
--- a/src/qibocal/calibration/calibration.py
+++ b/src/qibocal/calibration/calibration.py
@@ -128,3 +128,12 @@ def qubits(self) -> list:
     @property
     def nqubits(self) -> int:
         return len(self.qubits)
+
+    # TODO: add crosstalk object where I can do this
+    def get_crosstalk_element(self, qubit1: QubitId, qubit2: QubitId):
+        a, b = self.qubits.index(qubit1), self.qubits.index(qubit2)
+        return self.flux_crosstalk_matrix[a, b]
+
+    def set_crosstalk_element(self, qubit1: QubitId, qubit2: QubitId, value: float):
+        a, b = self.qubits.index(qubit1), self.qubits.index(qubit2)
+        self.flux_crosstalk_matrix[a, b] = value
diff --git a/src/qibocal/protocols/flux_dependence/resonator_flux_dependence.py b/src/qibocal/protocols/flux_dependence/resonator_flux_dependence.py
index df548f2c6..cd0d473e3 100644
--- a/src/qibocal/protocols/flux_dependence/resonator_flux_dependence.py
+++ b/src/qibocal/protocols/flux_dependence/resonator_flux_dependence.py
@@ -17,6 +17,7 @@
 from qibocal.config import log
 from qibocal.result import magnitude, phase
 
+from ... import update
 from ..utils import GHZ_TO_HZ, HZ_TO_GHZ, extract_feature, table_dict, table_html
 from . import utils
 
@@ -130,10 +131,12 @@ def _acquisition(
         )
 
         qubit_frequency[q] = platform.config(qubit.drive).frequency
-        bare_resonator_frequency[q] = 0  # qubit.bare_resonator_frequency
-        matrix_element[q] = 1  # qubit.crosstalk_matrix[q]
+        bare_resonator_frequency[q] = platform.calibration.single_qubits[
+            q
+        ].resonator.bare_frequency
+        matrix_element[q] = platform.calibration.get_crosstalk_element(q, q)
         offset[q] = -offset0 * matrix_element[q]
-        charging_energy[q] = 0  # -qubit.anharmonicity
+        charging_energy[q] = platform.calibration.single_qubits[q].qubit.charging_energy
 
     data = ResonatorFluxData(
         resonator_type=platform.resonator_type,
@@ -274,9 +277,9 @@ def _plot(data: ResonatorFluxData, fit: ResonatorFluxResults, target: QubitId):
 
 
 def _update(results: ResonatorFluxResults, platform: Platform, qubit: QubitId):
-    pass
-    # update.bare_resonator_frequency(results.bare_resonator_freq[qubit], platform, qubit)
+    update.bare_resonator_frequency(results.bare_resonator_freq[qubit], platform, qubit)
     # update.readout_frequency(results.resonator_freq[qubit], platform, qubit)
+    # TODO: add coupling somewhere
     # update.coupling(results.coupling[qubit], platform, qubit)
 
 
diff --git a/src/qibocal/update.py b/src/qibocal/update.py
index eb05fbf96..7ec366000 100644
--- a/src/qibocal/update.py
+++ b/src/qibocal/update.py
@@ -83,11 +83,7 @@ def crosstalk_matrix(
         platform.calibration.flux_crosstalk_matrix = np.zeros(
             (platform.calibration.nqubits, platform.calibration.nqubits)
         )
-
-    a, b = platform.calibration.qubits.index(qubit), platform.calibration.qubits.index(
-        flux_qubit
-    )
-    platform.calibration.flux_crosstalk_matrix[a, b] = float(matrix_element)
+    platform.calibration.set_crosstalk_element(qubit, flux_qubit, matrix_element)
 
 
 def iq_angle(angle: float, platform: Platform, qubit: QubitId):

From 1d7b990abbe1e4edfd6747bd2d2889b5a8f163f8 Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Fri, 25 Oct 2024 21:19:27 +0400
Subject: [PATCH 13/22] fix:  Fixing #1018

---
 src/qibocal/protocols/qubit_spectroscopy.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/qibocal/protocols/qubit_spectroscopy.py b/src/qibocal/protocols/qubit_spectroscopy.py
index 5c8aeccb4..0b6314f09 100644
--- a/src/qibocal/protocols/qubit_spectroscopy.py
+++ b/src/qibocal/protocols/qubit_spectroscopy.py
@@ -117,7 +117,7 @@ def _acquisition(
             error_phase = np.std(_phase, axis=0, ddof=1) / np.sqrt(_phase.shape[0])
             _phase = np.mean(_phase, axis=0)
         else:
-            error_signal, error_phase = 0, 0
+            error_signal, error_phase = None, None
         data.register_qubit(
             ResSpecType,
             (qubit),
@@ -170,7 +170,9 @@ def _plot(data: QubitSpectroscopyData, target: QubitId, fit: QubitSpectroscopyRe
 
 
 def _update(results: QubitSpectroscopyResults, platform: Platform, target: QubitId):
-    pass
+    platform.calibration.single_qubits[target].qubit.frequency_01 = results.frequency[
+        target
+    ]
     # update.drive_frequency(results.frequency[target], platform, target)
 
 

From 1fced97a56ee275c87b25d38fe121467c1aea906 Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Fri, 25 Oct 2024 21:28:31 +0400
Subject: [PATCH 14/22] feat: Restoring update in ramsey

---
 src/qibocal/protocols/ramsey/ramsey_signal.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/qibocal/protocols/ramsey/ramsey_signal.py b/src/qibocal/protocols/ramsey/ramsey_signal.py
index 0f6a13da2..71dbee130 100644
--- a/src/qibocal/protocols/ramsey/ramsey_signal.py
+++ b/src/qibocal/protocols/ramsey/ramsey_signal.py
@@ -10,6 +10,7 @@
 from qibocal.config import log
 from qibocal.result import magnitude
 
+from ... import update
 from ..utils import table_dict, table_html
 from .utils import fitting, process_fit, ramsey_fit, ramsey_sequence
 
@@ -283,11 +284,10 @@ def _plot(data: RamseySignalData, target: QubitId, fit: RamseySignalResults = No
 
 
 def _update(results: RamseySignalResults, platform: Platform, target: QubitId):
-    pass
     # if results.detuning is not None:
     #    update.drive_frequency(results.frequency[target][0], platform, target)
     # else:
-    #    update.t2(results.t2[target][0], platform, target)
+    update.t2(results.t2[target][0], platform, target)
 
 
 ramsey_signal = Routine(_acquisition, _fit, _plot, _update)

From 24a6ff218227de73903ea3b1949617fd25bf8675 Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Fri, 25 Oct 2024 21:37:52 +0400
Subject: [PATCH 15/22] refactor: Restoring update for punchout

---
 src/qibocal/protocols/resonator_punchout.py | 7 +++++--
 src/qibocal/update.py                       | 5 +++++
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/qibocal/protocols/resonator_punchout.py b/src/qibocal/protocols/resonator_punchout.py
index 7ffe367ee..bc5bbe988 100644
--- a/src/qibocal/protocols/resonator_punchout.py
+++ b/src/qibocal/protocols/resonator_punchout.py
@@ -14,6 +14,7 @@
     Sweeper,
 )
 
+from qibocal import update
 from qibocal.auto.operation import Data, Parameters, QubitId, Results, Routine
 from qibocal.result import magnitude, phase
 
@@ -256,9 +257,11 @@ def _plot(
 
 
 def _update(results: ResonatorPunchoutResults, platform: Platform, target: QubitId):
-    pass
     # update.readout_frequency(results.readout_frequency[target], platform, target)
-    # update.bare_resonator_frequency(results.bare_frequency[target], platform, target)
+    update.bare_resonator_frequency(results.bare_frequency[target], platform, target)
+    update.dressed_resonator_frequency(
+        results.readout_frequency[target], platform, target
+    )
     # update.readout_amplitude(results.readout_amplitude[target], platform, target)
 
 
diff --git a/src/qibocal/update.py b/src/qibocal/update.py
index 7ec366000..07a3478b5 100644
--- a/src/qibocal/update.py
+++ b/src/qibocal/update.py
@@ -38,6 +38,11 @@ def bare_resonator_frequency(freq: float, platform: Platform, qubit: QubitId):
     platform.calibration.single_qubits[qubit].resonator.bare_frequency = int(freq)
 
 
+def dressed_resonator_frequency(freq: float, platform: Platform, qubit: QubitId):
+    """Update rbare frequency value in platform for specific qubit."""
+    platform.calibration.single_qubits[qubit].resonator.dressed_frequency = int(freq)
+
+
 def readout_amplitude(amp: float, platform: Platform, qubit: QubitId):
     """Update readout amplitude value in platform for specific qubit."""
     # platform.natives.single_qubit[qubit].MZ.amplitude = float(amp)

From e844acf4c0493908f5c066f9a2a8dc0a722cfb0b Mon Sep 17 00:00:00 2001
From: Andrea Pasquale <andreapasquale97@gmail.com>
Date: Sun, 27 Oct 2024 10:48:40 +0100
Subject: [PATCH 16/22] refactor: get PLATFORMS from qibolab

---
 src/qibocal/calibration/platform.py | 3 ++-
 src/qibocal/cli/update.py           | 4 +++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/qibocal/calibration/platform.py b/src/qibocal/calibration/platform.py
index da033fb5e..67b03a83c 100644
--- a/src/qibocal/calibration/platform.py
+++ b/src/qibocal/calibration/platform.py
@@ -3,6 +3,7 @@
 from pathlib import Path
 
 from qibolab import Platform, create_platform
+from qibolab._core.platform.load import PLATFORMS
 
 from .calibration import CALIBRATION, Calibration
 
@@ -22,7 +23,7 @@ def from_platform(cls, platform: Platform):
                 (Path(__file__).parent / "dummy.json").read_text()
             )
         else:
-            path = Path(os.getenv("QIBOLAB_PLATFORMS")) / name
+            path = Path(os.getenv(PLATFORMS)) / name
             calibration = Calibration.model_validate_json(
                 (path / CALIBRATION).read_text()
             )
diff --git a/src/qibocal/cli/update.py b/src/qibocal/cli/update.py
index 9d57929fe..ef95e6bac 100644
--- a/src/qibocal/cli/update.py
+++ b/src/qibocal/cli/update.py
@@ -3,6 +3,8 @@
 import pathlib
 import shutil
 
+from qibolab._core.platform.load import PLATFORMS
+
 from ..auto.output import META, UPDATED_PLATFORM
 from ..config import log, raise_error
 
@@ -18,7 +20,7 @@ def update(path: pathlib.Path):
         raise_error(FileNotFoundError, f"No updated runcard platform found in {path}.")
 
     platform_name = json.loads((path / META).read_text())["platform"]
-    platform_path = pathlib.Path(os.getenv("QIBOLAB_PLATFORMS")) / platform_name
+    platform_path = pathlib.Path(os.getenv(PLATFORMS)) / platform_name
 
     for filename in os.listdir(new_platform_path):
         shutil.copy(

From 124c01b9a486fd16c77ad3b0eff1a6ac47f43c17 Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Mon, 28 Oct 2024 14:09:30 +0400
Subject: [PATCH 17/22] feat: Use locate_platform

---
 src/qibocal/calibration/platform.py | 6 ++----
 src/qibocal/cli/update.py           | 4 ++--
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/src/qibocal/calibration/platform.py b/src/qibocal/calibration/platform.py
index 67b03a83c..73c3be870 100644
--- a/src/qibocal/calibration/platform.py
+++ b/src/qibocal/calibration/platform.py
@@ -1,9 +1,7 @@
-import os
 from dataclasses import dataclass
 from pathlib import Path
 
-from qibolab import Platform, create_platform
-from qibolab._core.platform.load import PLATFORMS
+from qibolab import Platform, create_platform, locate_platform
 
 from .calibration import CALIBRATION, Calibration
 
@@ -23,7 +21,7 @@ def from_platform(cls, platform: Platform):
                 (Path(__file__).parent / "dummy.json").read_text()
             )
         else:
-            path = Path(os.getenv(PLATFORMS)) / name
+            path = locate_platform(name)
             calibration = Calibration.model_validate_json(
                 (path / CALIBRATION).read_text()
             )
diff --git a/src/qibocal/cli/update.py b/src/qibocal/cli/update.py
index ef95e6bac..f4ccd3124 100644
--- a/src/qibocal/cli/update.py
+++ b/src/qibocal/cli/update.py
@@ -3,7 +3,7 @@
 import pathlib
 import shutil
 
-from qibolab._core.platform.load import PLATFORMS
+from qibolab import locate_platform
 
 from ..auto.output import META, UPDATED_PLATFORM
 from ..config import log, raise_error
@@ -20,7 +20,7 @@ def update(path: pathlib.Path):
         raise_error(FileNotFoundError, f"No updated runcard platform found in {path}.")
 
     platform_name = json.loads((path / META).read_text())["platform"]
-    platform_path = pathlib.Path(os.getenv(PLATFORMS)) / platform_name
+    platform_path = locate_platform(platform_name)
 
     for filename in os.listdir(new_platform_path):
         shutil.copy(

From 3ee58881d8a32433c134c036c60151ad1b3b1b93 Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Tue, 29 Oct 2024 13:53:15 +0400
Subject: [PATCH 18/22] feat: Add errors to coherence values

---
 src/qibocal/calibration/calibration.py        | 44 +++++++++++--------
 src/qibocal/calibration/dummy.json            | 35 +++------------
 src/qibocal/protocols/ramsey/ramsey.py        |  2 +-
 src/qibocal/protocols/ramsey/ramsey_signal.py |  4 +-
 src/qibocal/update.py                         | 19 ++------
 5 files changed, 37 insertions(+), 67 deletions(-)

diff --git a/src/qibocal/calibration/calibration.py b/src/qibocal/calibration/calibration.py
index b095d37f4..bb9e71ba3 100644
--- a/src/qibocal/calibration/calibration.py
+++ b/src/qibocal/calibration/calibration.py
@@ -1,13 +1,21 @@
 from pathlib import Path
-from typing import Optional
+from typing import Annotated, Optional
 
-from pydantic import BaseModel, ConfigDict, Field
+from pydantic import BaseModel, BeforeValidator, ConfigDict, Field, PlainSerializer
 from qibolab._core.identifier import QubitId, QubitPairId
 from qibolab._core.serialize import NdArray
 
 CALIBRATION = "calibration.json"
 """Calibration file."""
 
+# TODO: convert to int if used only for coherence values
+Measure = Annotated[
+    tuple[float, Optional[float]],
+    BeforeValidator(lambda p: tuple(p.split("+/-")) if isinstance(p, str) else p),
+    PlainSerializer(lambda p: f"{p[0]}+/-{p[1]}"),
+]
+"""Measure serialized in runcard."""
+
 
 class Model(BaseModel):
     """Global model, holding common configurations."""
@@ -51,6 +59,11 @@ def charging_energy(self):
         """Charging energy Ec [Hz]."""
         return -self.anharmonicity
 
+    @property
+    def josephson_energy(self):
+        """Josephson energy [Hz]."""
+        # TODO: Add josephson energy
+
 
 class Readout(Model):
     """Readout parameters."""
@@ -70,17 +83,6 @@ def assignment_fidelity(self):
         return (1 + self.fidelity) / 2
 
 
-class Coherence(Model):
-    """Coherence times of qubit."""
-
-    t1: Optional[int] = 0
-    """Relaxation time [ns]."""
-    t2: Optional[int] = 0
-    """T2 of the qubit [ns]."""
-    t2_spin_echo: Optional[int] = 0
-    """T2 hanh echo [ns]."""
-
-
 class QubitCalibration(Model):
     """Container for calibration of single qubit."""
 
@@ -90,18 +92,22 @@ class QubitCalibration(Model):
     """Qubit calibration."""
     readout: Readout = Field(default_factory=Readout)
     """Readout information."""
-    coherence: Coherence = Field(default_factory=Coherence)
-    """Coherence times of the qubit."""
-    rb_fidelity: Optional[float] = None
+    t1: Optional[Measure] = None
+    """Relaxation time [ns]."""
+    t2: Optional[Measure] = None
+    """T2 of the qubit [ns]."""
+    t2_spin_echo: Optional[Measure] = None
+    """T2 hanh echo [ns]."""
+    rb_fidelity: Optional[Measure] = None
     """Standard rb pulse fidelity."""
 
 
 class TwoQubitCalibration(Model):
     """Container for calibration of qubit pair."""
 
-    rb_fidelity: Optional[float] = None
+    rb_fidelity: Optional[Measure] = None
     """Two qubit standard rb fidelity."""
-    cz_fidelity: Optional[float] = None
+    cz_fidelity: Optional[Measure] = None
     """CZ interleaved rb fidelity."""
 
 
@@ -123,10 +129,12 @@ def dump(self, path: Path):
 
     @property
     def qubits(self) -> list:
+        """List of qubits available in the model."""
         return list(self.single_qubits)
 
     @property
     def nqubits(self) -> int:
+        """Number of qubits available."""
         return len(self.qubits)
 
     # TODO: add crosstalk object where I can do this
diff --git a/src/qibocal/calibration/dummy.json b/src/qibocal/calibration/dummy.json
index 46fc030e6..c23cc43fe 100644
--- a/src/qibocal/calibration/dummy.json
+++ b/src/qibocal/calibration/dummy.json
@@ -23,12 +23,7 @@
                     0.0
                 ]
             },
-            "coherence": {
-                "t1": 0.0,
-                "t2": 0.0,
-                "t2_spin_echo": 0
-            },
-            "rb_fidelity": 0.5
+            "rb_fidelity": null
         },
         "1": {
             "resonator": {
@@ -53,12 +48,7 @@
                     0.25
                 ]
             },
-            "coherence": {
-                "t1": 0.0,
-                "t2": 0.0,
-                "t2_spin_echo": 0
-            },
-            "rb_fidelity": 0.5
+            "rb_fidelity": null
         },
         "2": {
             "resonator": {
@@ -83,12 +73,7 @@
                     0.5
                 ]
             },
-            "coherence": {
-                "t1": 0.0,
-                "t2": 0.0,
-                "t2_spin_echo": 0
-            },
-            "rb_fidelity": 0.5
+            "rb_fidelity": null
         },
         "3": {
             "resonator": {
@@ -113,12 +98,7 @@
                     0.75
                 ]
             },
-            "coherence": {
-                "t1": 0.0,
-                "t2": 0.0,
-                "t2_spin_echo": 0
-            },
-            "rb_fidelity": 0.5
+            "rb_fidelity": null
         },
         "4": {
             "resonator": {
@@ -143,12 +123,7 @@
                     1.0
                 ]
             },
-            "coherence": {
-                "t1": 0.0,
-                "t2": 0.0,
-                "t2_spin_echo": 0
-            },
-            "rb_fidelity":0.5
+            "rb_fidelity": null
         }
     },
     "two_qubits": {
diff --git a/src/qibocal/protocols/ramsey/ramsey.py b/src/qibocal/protocols/ramsey/ramsey.py
index 40a99695e..ebb2e84a9 100644
--- a/src/qibocal/protocols/ramsey/ramsey.py
+++ b/src/qibocal/protocols/ramsey/ramsey.py
@@ -90,7 +90,7 @@ def _acquisition(
     )
 
     updates = []
-    if params.detuning != 0:
+    if params.detuning is not None:
         for qubit in targets:
             channel = platform.qubits[qubit].drive
             f0 = platform.config(channel).frequency
diff --git a/src/qibocal/protocols/ramsey/ramsey_signal.py b/src/qibocal/protocols/ramsey/ramsey_signal.py
index 71dbee130..f7a1ec682 100644
--- a/src/qibocal/protocols/ramsey/ramsey_signal.py
+++ b/src/qibocal/protocols/ramsey/ramsey_signal.py
@@ -102,7 +102,7 @@ def _acquisition(
     )
 
     updates = []
-    if params.detuning != 0:
+    if params.detuning is not None:
         for qubit in targets:
             channel = platform.qubits[qubit].drive
             f0 = platform.config(channel).frequency
@@ -287,7 +287,7 @@ def _update(results: RamseySignalResults, platform: Platform, target: QubitId):
     # if results.detuning is not None:
     #    update.drive_frequency(results.frequency[target][0], platform, target)
     # else:
-    update.t2(results.t2[target][0], platform, target)
+    update.t2(results.t2[target], platform, target)
 
 
 ramsey_signal = Routine(_acquisition, _fit, _plot, _update)
diff --git a/src/qibocal/update.py b/src/qibocal/update.py
index 07a3478b5..bd43e9f44 100644
--- a/src/qibocal/update.py
+++ b/src/qibocal/update.py
@@ -168,30 +168,17 @@ def iSWAP_amplitude(amp: float, platform: Platform, pair: QubitPairId):
 
 def t1(t1: int, platform: Platform, qubit: QubitId):
     """Update t1 value in platform for specific qubit."""
-    if isinstance(t1, Iterable):
-        platform.calibration.single_qubits[qubit].coherence.t1 = int(t1[0])
-    else:
-        platform.calibration.single_qubits[qubit].coherence.t1 = int(t1)
+    platform.calibration.single_qubits[qubit].t1 = t1
 
 
 def t2(t2: int, platform: Platform, qubit: QubitId):
     """Update t2 value in platform for specific qubit."""
-    if isinstance(t2, Iterable):
-        platform.calibration.single_qubits[qubit].coherence.t2 = int(t2[0])
-    else:
-        platform.calibration.single_qubits[qubit].coherence.t2 = int(t2)
+    platform.calibration.single_qubits[qubit].t2 = t2
 
 
 def t2_spin_echo(t2_spin_echo: float, platform: Platform, qubit: QubitId):
     """Update t2 echo value in platform for specific qubit."""
-    if isinstance(t2_spin_echo, Iterable):
-        platform.calibration.single_qubits[qubit].coherence.t2_spin_echo = int(
-            t2_spin_echo[0]
-        )
-    else:
-        platform.calibration.single_qubits[qubit].coherence.t2_spin_echo = int(
-            t2_spin_echo
-        )
+    platform.calibration.single_qubits[qubit].t2_spin_echo = t2_spin_echo
 
 
 def drag_pulse_beta(beta: float, platform: Platform, qubit: QubitId):

From 6b4ec48a0b266e50758141102ab505a752cc2874 Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Tue, 29 Oct 2024 16:03:08 +0400
Subject: [PATCH 19/22] refactor: Convert measure to list to ease json
 serialization

---
 src/qibocal/auto/operation.py          |  4 +--
 src/qibocal/calibration/calibration.py | 39 ++++++++++++++++++--------
 2 files changed, 29 insertions(+), 14 deletions(-)

diff --git a/src/qibocal/auto/operation.py b/src/qibocal/auto/operation.py
index b00eb6003..51aa98cec 100644
--- a/src/qibocal/auto/operation.py
+++ b/src/qibocal/auto/operation.py
@@ -13,11 +13,9 @@
 
 from qibocal.config import log
 
+from ..calibration.calibration import QubitId, QubitPairId
 from .serialize import deserialize, load, serialize
 
-QubitId = Union[str, int]
-QubitPairId = tuple[QubitId, QubitId]
-
 OperationId = NewType("OperationId", str)
 """Identifier for a calibration routine."""
 ParameterValue = Union[float, int]
diff --git a/src/qibocal/calibration/calibration.py b/src/qibocal/calibration/calibration.py
index bb9e71ba3..f7d476346 100644
--- a/src/qibocal/calibration/calibration.py
+++ b/src/qibocal/calibration/calibration.py
@@ -1,20 +1,24 @@
 from pathlib import Path
-from typing import Annotated, Optional
+from typing import Annotated, Optional, Union
 
 from pydantic import BaseModel, BeforeValidator, ConfigDict, Field, PlainSerializer
-from qibolab._core.identifier import QubitId, QubitPairId
 from qibolab._core.serialize import NdArray
 
+QubitId = Annotated[Union[int, str], Field(union_mode="left_to_right")]
+"""Qubit name."""
+
+QubitPairId = Annotated[
+    tuple[QubitId, QubitId],
+    BeforeValidator(lambda p: tuple(p.split("-")) if isinstance(p, str) else p),
+    PlainSerializer(lambda p: f"{p[0]}-{p[1]}"),
+]
+"""Qubit pair name."""
+
 CALIBRATION = "calibration.json"
 """Calibration file."""
 
-# TODO: convert to int if used only for coherence values
-Measure = Annotated[
-    tuple[float, Optional[float]],
-    BeforeValidator(lambda p: tuple(p.split("+/-")) if isinstance(p, str) else p),
-    PlainSerializer(lambda p: f"{p[0]}+/-{p[1]}"),
-]
-"""Measure serialized in runcard."""
+Measure = list[float]
+"""Measured is represented as two values: mean and error."""
 
 
 class Model(BaseModel):
@@ -61,8 +65,17 @@ def charging_energy(self):
 
     @property
     def josephson_energy(self):
-        """Josephson energy [Hz]."""
-        # TODO: Add josephson energy
+        """Josephson energy [Hz].
+
+        The following formula is the inversion of the maximum frequency
+        obtained from the flux dependence protoco.
+
+        """
+        return (
+            (self.maximum_frequency + self.charging_energy) ** 2
+            / 8
+            / self.charging_energy
+        )
 
 
 class Readout(Model):
@@ -70,6 +83,8 @@ class Readout(Model):
 
     fidelity: Optional[float] = None
     """Readout fidelity."""
+    coupling: Optional[float] = None
+    """Readout coupling [Hz]."""
     effective_temperature: Optional[float] = None
     """Qubit effective temperature."""
     ground_state: list[float] = Field(default_factory=list)
@@ -109,6 +124,8 @@ class TwoQubitCalibration(Model):
     """Two qubit standard rb fidelity."""
     cz_fidelity: Optional[Measure] = None
     """CZ interleaved rb fidelity."""
+    coupling: Optional[float] = None
+    """Qubit-qubit coupling."""
 
 
 class Calibration(Model):

From e3c96e3883e8ae11145e649a94feced81c1e3a64 Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Tue, 29 Oct 2024 18:40:24 +0400
Subject: [PATCH 20/22] test: Adding test for calibration

---
 src/qibocal/update.py     |  4 +--
 tests/test_calibration.py | 66 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 68 insertions(+), 2 deletions(-)
 create mode 100644 tests/test_calibration.py

diff --git a/src/qibocal/update.py b/src/qibocal/update.py
index bd43e9f44..82fe1a831 100644
--- a/src/qibocal/update.py
+++ b/src/qibocal/update.py
@@ -222,8 +222,8 @@ def asymmetry(asymmetry: float, platform: Platform, qubit: QubitId):
     platform.calibration.single_qubits[qubit].asymmetry = float(asymmetry)
 
 
-# def coupling(g: float, platform: Platform, qubit: QubitId):
-#     platform.qubits[qubit].g = float(g)
+def coupling(g: float, platform: Platform, qubit: QubitId):
+    platform.calibration.single_qubits[qubit].readout.coupling = float(g)
 
 
 # def kernel(kernel: np.ndarray, platform: Platform, qubit: QubitId):
diff --git a/tests/test_calibration.py b/tests/test_calibration.py
new file mode 100644
index 000000000..d1aea221c
--- /dev/null
+++ b/tests/test_calibration.py
@@ -0,0 +1,66 @@
+import numpy as np
+
+from qibocal.calibration.calibration import (
+    CALIBRATION,
+    QubitCalibration,
+    TwoQubitCalibration,
+)
+from qibocal.calibration.platform import Calibration
+
+
+def test_serialization_single_qubits(tmp_path):
+    """Testing serialization forn single qubits."""
+
+    cal = Calibration()
+
+    for i in range(2):
+        cal.single_qubits[i] = QubitCalibration()
+
+        cal.single_qubits[i].qubit.frequency_01 = 5e9
+        cal.single_qubits[i].qubit.frequency_12 = 4.8e9
+        cal.single_qubits[i].qubit.maximum_frequency = cal.single_qubits[
+            0
+        ].qubit.frequency_01
+        cal.single_qubits[i].t1 = [10e6, 1e6]
+
+        assert cal.single_qubits[i].qubit.anharmonicity == -0.2e9
+        assert cal.single_qubits[i].qubit.charging_energy == 0.2e9
+
+    assert cal.nqubits == 2
+    assert cal.qubits == list(range(2))
+
+    cal.dump(tmp_path)
+    new_cal = cal.model_validate_json((tmp_path / CALIBRATION).read_text())
+
+    assert new_cal == cal
+
+
+def test_serialization_qubit_pairs(tmp_path):
+    """Testing serialization for qubit pairs."""
+
+    cal = Calibration()
+    cal.two_qubits[0, 1] = TwoQubitCalibration(rb_fidelity=[0.99, 0.1], coupling=0.5)
+    cal.dump(tmp_path)
+    new_cal = cal.model_validate_json((tmp_path / CALIBRATION).read_text())
+    assert new_cal == cal
+
+
+def test_serialization_crosstalk_matrix(tmp_path):
+    """Testing serialization from crosstalk matrix."""
+
+    cal = Calibration()
+    for i in range(5):
+        cal.single_qubits[f"A{i}"] = QubitCalibration()
+
+    nqubits = cal.nqubits
+    cal.flux_crosstalk_matrix = np.random.rand(nqubits, nqubits)
+    assert cal.get_crosstalk_element("A0", "A1") == cal.flux_crosstalk_matrix[0, 1]
+
+    cal.set_crosstalk_element("A3", "A4", 99)
+
+    cal.dump(tmp_path)
+    new_cal = cal.model_validate_json((tmp_path / CALIBRATION).read_text())
+    assert cal.get_crosstalk_element("A3", "A4") == 99
+    np.testing.assert_allclose(
+        new_cal.flux_crosstalk_matrix, new_cal.flux_crosstalk_matrix
+    )

From e5a49cdf51c500b4288f1c927b60664a8373d848 Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Wed, 30 Oct 2024 11:38:00 +0400
Subject: [PATCH 21/22] chore: Add TODO

---
 src/qibocal/calibration/platform.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/qibocal/calibration/platform.py b/src/qibocal/calibration/platform.py
index 73c3be870..3e45ff4db 100644
--- a/src/qibocal/calibration/platform.py
+++ b/src/qibocal/calibration/platform.py
@@ -25,7 +25,7 @@ def from_platform(cls, platform: Platform):
             calibration = Calibration.model_validate_json(
                 (path / CALIBRATION).read_text()
             )
-
+        # TODO: this is loading twice a platform
         return cls(**vars(platform), calibration=calibration)
 
     def dump(self, path: Path):

From f4b7049d6e0974750c7599466c128acdd4cc4c4c Mon Sep 17 00:00:00 2001
From: Andrea <andreapasquale97@gmail.com>
Date: Wed, 30 Oct 2024 20:37:17 +0400
Subject: [PATCH 22/22] feat: Adding dispersive shift

---
 src/qibocal/calibration/calibration.py | 7 +++++++
 src/qibocal/update.py                  | 2 +-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/qibocal/calibration/calibration.py b/src/qibocal/calibration/calibration.py
index f7d476346..e68e19bc8 100644
--- a/src/qibocal/calibration/calibration.py
+++ b/src/qibocal/calibration/calibration.py
@@ -36,6 +36,13 @@ class Resonator(Model):
     """Dressed resonator frequency [Hz]."""
     depletion_time: Optional[int] = None
     """Depletion time [ns]."""
+
+    @property
+    def dispersive_shift(self):
+        """Dispersive shift."""
+        return self.bare_frequency - self.dressed_frequency
+
+    # TODO: Add setter for dispersive shift as well
     # TODO: Add something related to resonator calibration
 
 
diff --git a/src/qibocal/update.py b/src/qibocal/update.py
index 82fe1a831..746dd9f32 100644
--- a/src/qibocal/update.py
+++ b/src/qibocal/update.py
@@ -195,7 +195,7 @@ def sweetspot(sweetspot: float, platform: Platform, qubit: QubitId):
 
 
 def frequency_12_transition(frequency: int, platform: Platform, qubit: QubitId):
-    platform.calibration.single_qubits[qubit].qubit.omega_12 = int(frequency)
+    platform.calibration.single_qubits[qubit].qubit.frequency_12 = int(frequency)
     platform.qubits[qubit].native_gates.RX12.frequency = int(frequency)