diff --git a/poetry.lock b/poetry.lock
index 31f2f4e48..4791e8462 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 1.6.1 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -80,13 +80,13 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p
 
 [[package]]
 name = "babel"
-version = "2.14.0"
+version = "2.15.0"
 description = "Internationalization utilities"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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-    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
+    {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"},
+    {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"},
 ]
 
 [package.extras]
@@ -115,13 +115,13 @@ lxml = ["lxml"]
 
 [[package]]
 name = "blinker"
-version = "1.7.0"
+version = "1.8.1"
 description = "Fast, simple object-to-object and broadcast signaling"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "blinker-1.7.0.tar.gz", hash = "sha256:e6820ff6fa4e4d1d8e2747c2283749c3f547e4fee112b98555cdcdae32996182"},
+    {file = "blinker-1.8.1-py3-none-any.whl", hash = "sha256:5f1cdeff423b77c31b89de0565cd03e5275a03028f44b2b15f912632a58cced6"},
+    {file = "blinker-1.8.1.tar.gz", hash = "sha256:da44ec748222dcd0105ef975eed946da197d5bdf8bafb6aa92f5bc89da63fa25"},
 ]
 
 [[package]]
@@ -384,63 +384,63 @@ test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"]
 
 [[package]]
 name = "coverage"
-version = "7.4.4"
+version = "7.5.1"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
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 [package.dependencies]
@@ -466,13 +466,13 @@ tests = ["pytest", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "dash"
-version = "2.16.1"
+version = "2.17.0"
 description = "A Python framework for building reactive web-apps. Developed by Plotly."
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 python-versions = ">=3.8"
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 [package.dependencies]
@@ -491,7 +491,7 @@ Werkzeug = "<3.1"
 
 [package.extras]
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 diskcache = ["diskcache (>=5.2.1)", "multiprocess (>=0.70.12)", "psutil (>=5.8.0)"]
@@ -587,13 +587,13 @@ files = [
 
 [[package]]
 name = "exceptiongroup"
-version = "1.2.0"
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 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
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 [[package]]
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+version = "3.14.0"
 description = "A platform independent file lock."
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@@ -646,13 +646,13 @@ typing = ["typing-extensions (>=4.8)"]
 
 [[package]]
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+version = "3.0.3"
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 python-versions = ">=3.8"
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 [package.extras]
@@ -808,13 +808,13 @@ files = [
 
 [[package]]
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-version = "0.22.2"
+version = "0.23.0"
 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]
@@ -827,16 +827,16 @@ tqdm = ">=4.42.1"
 typing-extensions = ">=3.7.4.3"
 
 [package.extras]
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 [[package]]
@@ -1051,13 +1051,13 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
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-version = "1.3.2"
+version = "1.4.2"
 description = "Lightweight pipelining with Python functions"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
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 [[package]]
@@ -1368,13 +1368,13 @@ python-dateutil = ">=2.7"
 
 [[package]]
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 [package.dependencies]
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 python-versions = "*"
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 ]
 
 [package.dependencies]
@@ -1680,18 +1680,18 @@ test = ["hypothesis (>=5.5.3)", "pytest (>=6.0)", "pytest-xdist (>=1.31)"]
 
 [[package]]
 name = "parso"
-version = "0.8.3"
+version = "0.8.4"
 description = "A Python Parser"
 optional = false
 python-versions = ">=3.6"
 files = [
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 ]
 
 [package.extras]
-qa = ["flake8 (==3.8.3)", "mypy (==0.782)"]
-testing = ["docopt", "pytest (<6.0.0)"]
+qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
+testing = ["docopt", "pytest"]
 
 [[package]]
 name = "pdbpp"
@@ -1815,28 +1815,29 @@ xmp = ["defusedxml"]
 
 [[package]]
 name = "platformdirs"
-version = "4.2.0"
-description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+version = "4.2.1"
+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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 ]
 
 [package.extras]
 docs = ["furo (>=2023.9.10)", "proselint (>=0.13)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
 test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)"]
+type = ["mypy (>=1.8)"]
 
 [[package]]
 name = "plotly"
-version = "5.20.0"
+version = "5.22.0"
 description = "An open-source, interactive data visualization library for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -1845,13 +1846,13 @@ tenacity = ">=6.2.0"
 
 [[package]]
 name = "pluggy"
-version = "1.4.0"
+version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -2030,17 +2031,16 @@ pyparsing = ">=2.1.4"
 
 [[package]]
 name = "pygments"
-version = "2.17.2"
+version = "2.18.0"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
-plugins = ["importlib-metadata"]
 windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
@@ -2224,7 +2224,6 @@ files = [
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@@ -2261,13 +2260,13 @@ files = [
 
 [[package]]
 name = "qibo"
-version = "0.2.6"
+version = "0.2.7"
 description = "A framework for quantum computing with hardware acceleration."
 optional = false
-python-versions = ">=3.9,<3.12"
+python-versions = "<3.12,>=3.9"
 files = [
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-    {file = "qibo-0.2.6.tar.gz", hash = "sha256:145f2ab3137100746c132ee5f9e8f5c8746908e6ee025484202022172e3ec5a3"},
+    {file = "qibo-0.2.7-py3-none-any.whl", hash = "sha256:20e42ad27f7a9795f84565ab5645e3b24d4af62a0a8c6de5110b5ae6894b35a2"},
+    {file = "qibo-0.2.7.tar.gz", hash = "sha256:a57e98a3eccfc3c43c4a697448a4618c9a158f72645d5c93b0b2bdd3ace882ef"},
 ]
 
 [package.dependencies]
@@ -2284,32 +2283,36 @@ tabulate = ">=0.9.0,<0.10.0"
 [package.extras]
 qinfo = ["cvxpy (>=1.4.2,<2.0.0)"]
 tensorflow = ["tensorflow (>=2.14.1,<2.16)"]
+torch = ["torch (>=2.1.1,<3.0.0)"]
 
 [[package]]
 name = "qibolab"
 version = "0.1.6"
 description = "Quantum hardware module and drivers for Qibo"
 optional = false
-python-versions = "<3.12,>=3.9"
-files = [
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-    {file = "qibolab-0.1.6.tar.gz", hash = "sha256:bf8a0f8463c7574c512b3401b4fa26401b5adc2e9ddd0bc3da97d641ffe1efd6"},
-]
+python-versions = ">=3.9,<3.12"
+files = []
+develop = false
 
 [package.dependencies]
-more-itertools = ">=9.1.0,<10.0.0"
-networkx = ">=3.0,<4.0"
-numpy = ">=1.26.4,<2.0.0"
+more-itertools = "^9.1.0"
+networkx = "^3.0"
+numpy = "^1.26.4"
 qibo = ">=0.2.6"
-setuptools = ">67.0.0"
 
 [package.extras]
 los = ["pyvisa-py (==0.5.3)", "qcodes (>=0.37.0,<0.38.0)", "qcodes_contrib_drivers (==0.18.0)"]
-qblox = ["pyvisa-py (==0.5.3)", "qblox-instruments (==0.11.0)", "qcodes (>=0.37.0,<0.38.0)", "qcodes_contrib_drivers (==0.18.0)"]
+qblox = ["pyvisa-py (==0.5.3)", "qblox-instruments (==0.12.0)", "qcodes (>=0.37.0,<0.38.0)", "qcodes_contrib_drivers (==0.18.0)"]
 qm = ["qm-qua (==1.1.6)", "qualang-tools (>=0.15.0,<0.16.0)"]
-rfsoc = ["qibosoq (>=0.0.4,<0.2)"]
+rfsoc = ["qibosoq (>=0.1.2,<0.2)"]
 zh = ["laboneq (==2.25.0)"]
 
+[package.source]
+type = "git"
+url = "https://github.com/qiboteam/qibolab.git"
+reference = "HEAD"
+resolved_reference = "41fcafde38801179cbd5a39b72bfbb00b52e4c07"
+
 [[package]]
 name = "recommonmark"
 version = "0.7.1"
@@ -2363,37 +2366,37 @@ six = ">=1.7.0"
 
 [[package]]
 name = "scikit-learn"
-version = "1.4.1.post1"
+version = "1.4.2"
 description = "A set of python modules for machine learning and data mining"
 optional = false
 python-versions = ">=3.9"
 files = [
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+    {file = "scikit_learn-1.4.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d36d0bc983336bbc1be22f9b686b50c964f593c8a9a913a792442af9bf4f5e68"},
+    {file = "scikit_learn-1.4.2-cp312-cp312-win_amd64.whl", hash = "sha256:d762070980c17ba3e9a4a1e043ba0518ce4c55152032f1af0ca6f39b376b5928"},
+    {file = "scikit_learn-1.4.2-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:d9993d5e78a8148b1d0fdf5b15ed92452af5581734129998c26f481c46586d68"},
+    {file = "scikit_learn-1.4.2-cp39-cp39-macosx_12_0_arm64.whl", hash = "sha256:426d258fddac674fdf33f3cb2d54d26f49406e2599dbf9a32b4d1696091d4256"},
+    {file = "scikit_learn-1.4.2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:5460a1a5b043ae5ae4596b3126a4ec33ccba1b51e7ca2c5d36dac2169f62ab1d"},
+    {file = "scikit_learn-1.4.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:49d64ef6cb8c093d883e5a36c4766548d974898d378e395ba41a806d0e824db8"},
+    {file = "scikit_learn-1.4.2-cp39-cp39-win_amd64.whl", hash = "sha256:c97a50b05c194be9146d61fe87dbf8eac62b203d9e87a3ccc6ae9aed2dfaf361"},
 ]
 
 [package.dependencies]
 joblib = ">=1.2.0"
-numpy = ">=1.19.5,<2.0"
+numpy = ">=1.19.5"
 scipy = ">=1.6.0"
 threadpoolctl = ">=2.0.0"
 
@@ -2468,19 +2471,19 @@ stats = ["scipy (>=1.3)", "statsmodels (>=0.10)"]
 
 [[package]]
 name = "setuptools"
-version = "67.8.0"
+version = "69.5.1"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "setuptools-67.8.0-py3-none-any.whl", hash = "sha256:5df61bf30bb10c6f756eb19e7c9f3b473051f48db77fddbe06ff2ca307df9a6f"},
-    {file = "setuptools-67.8.0.tar.gz", hash = "sha256:62642358adc77ffa87233bc4d2354c4b2682d214048f500964dbe760ccedf102"},
+    {file = "setuptools-69.5.1-py3-none-any.whl", hash = "sha256:c636ac361bc47580504644275c9ad802c50415c7522212252c033bd15f301f32"},
+    {file = "setuptools-69.5.1.tar.gz", hash = "sha256:6c1fccdac05a97e598fb0ae3bbed5904ccb317337a51139dcd51453611bbb987"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mypy (==1.9)", "packaging (>=23.2)", "pip (>=19.1)", "pytest (>=6,!=8.1.1)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.2)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "six"
@@ -2812,13 +2815,13 @@ doc = ["reno", "sphinx", "tornado (>=4.5)"]
 
 [[package]]
 name = "threadpoolctl"
-version = "3.4.0"
+version = "3.5.0"
 description = "threadpoolctl"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "threadpoolctl-3.4.0-py3-none-any.whl", hash = "sha256:8f4c689a65b23e5ed825c8436a92b818aac005e0f3715f6a1664d7c7ee29d262"},
-    {file = "threadpoolctl-3.4.0.tar.gz", hash = "sha256:f11b491a03661d6dd7ef692dd422ab34185d982466c49c8f98c8f716b5c93196"},
+    {file = "threadpoolctl-3.5.0-py3-none-any.whl", hash = "sha256:56c1e26c150397e58c4926da8eeee87533b1e32bef131bd4bf6a2f45f3185467"},
+    {file = "threadpoolctl-3.5.0.tar.gz", hash = "sha256:082433502dd922bf738de0d8bcc4fdcbf0979ff44c42bd40f5af8a282f6fa107"},
 ]
 
 [[package]]
@@ -2845,13 +2848,13 @@ files = [
 
 [[package]]
 name = "tqdm"
-version = "4.66.3"
+version = "4.66.4"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "tqdm-4.66.3-py3-none-any.whl", hash = "sha256:4f41d54107ff9a223dca80b53efe4fb654c67efaba7f47bada3ee9d50e05bd53"},
-    {file = "tqdm-4.66.3.tar.gz", hash = "sha256:23097a41eba115ba99ecae40d06444c15d1c0c698d527a01c6c8bd1c5d0647e5"},
+    {file = "tqdm-4.66.4-py3-none-any.whl", hash = "sha256:b75ca56b413b030bc3f00af51fd2c1a1a5eac6a0c1cca83cbb37a5c52abce644"},
+    {file = "tqdm-4.66.4.tar.gz", hash = "sha256:e4d936c9de8727928f3be6079590e97d9abfe8d39a590be678eb5919ffc186bb"},
 ]
 
 [package.dependencies]
@@ -2865,28 +2868,28 @@ telegram = ["requests"]
 
 [[package]]
 name = "traitlets"
-version = "5.14.2"
+version = "5.14.3"
 description = "Traitlets Python configuration system"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "traitlets-5.14.2-py3-none-any.whl", hash = "sha256:fcdf85684a772ddeba87db2f398ce00b40ff550d1528c03c14dbf6a02003cd80"},
-    {file = "traitlets-5.14.2.tar.gz", hash = "sha256:8cdd83c040dab7d1dee822678e5f5d100b514f7b72b01615b26fc5718916fdf9"},
+    {file = "traitlets-5.14.3-py3-none-any.whl", hash = "sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f"},
+    {file = "traitlets-5.14.3.tar.gz", hash = "sha256:9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7"},
 ]
 
 [package.extras]
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
-test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.1)", "pytest-mock", "pytest-mypy-testing"]
+test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.2)", "pytest-mock", "pytest-mypy-testing"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.10.0"
+version = "4.11.0"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "typing_extensions-4.10.0-py3-none-any.whl", hash = "sha256:69b1a937c3a517342112fb4c6df7e72fc39a38e7891a5730ed4985b5214b5475"},
-    {file = "typing_extensions-4.10.0.tar.gz", hash = "sha256:b0abd7c89e8fb96f98db18d86106ff1d90ab692004eb746cf6eda2682f91b3cb"},
+    {file = "typing_extensions-4.11.0-py3-none-any.whl", hash = "sha256:c1f94d72897edaf4ce775bb7558d5b79d8126906a14ea5ed1635921406c0387a"},
+    {file = "typing_extensions-4.11.0.tar.gz", hash = "sha256:83f085bd5ca59c80295fc2a82ab5dac679cbe02b9f33f7d83af68e241bea51b0"},
 ]
 
 [[package]]
@@ -3052,4 +3055,4 @@ viz = ["pydot"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<3.12"
-content-hash = "b962c665a140a54bf691a0c09ebd7474cd6b709835bcfbcce063645682cc52b2"
+content-hash = "6655c1ee3820666edaed7cca4e7662a58d89669cc9a0d81ddf4ea93839c9aec0"
diff --git a/pyproject.toml b/pyproject.toml
index d3c8f2036..0728815ac 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -17,8 +17,8 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
-qibolab = "^0.1.6"
-qibo ="^0.2.6"
+qibolab = { git = "https://github.com/qiboteam/qibolab.git"}
+qibo = "^0.2.7"
 numpy = "^1.26.4"
 scipy = "^1.10.1"
 pandas = "^1.4.3"
@@ -30,7 +30,7 @@ dash = "^2.6.0"
 skops = "^0.6.0"
 scikit-learn = "^1.2.1"
 # Explicit dependency required to cope for dash: https://github.com/plotly/dash/issues/2557
-setuptools = "^67.8.0"
+setuptools = "^69.0.0"
 matplotlib = { version = "^3.7.0", optional = true }
 seaborn = { version = "^0.12.2", optional = true }
 pydot = { version = "^1.4.2", optional = true }
diff --git a/src/qibocal/auto/runcard.py b/src/qibocal/auto/runcard.py
index 2115b44da..117c1e76c 100644
--- a/src/qibocal/auto/runcard.py
+++ b/src/qibocal/auto/runcard.py
@@ -5,7 +5,6 @@
 
 from pydantic.dataclasses import dataclass
 from qibo.backends import Backend, GlobalBackend
-from qibo.transpiler.pipeline import Passes
 from qibolab.platform import Platform
 from qibolab.qubits import QubitId, QubitPairId
 
@@ -61,11 +60,7 @@ def __post_init__(self):
     def backend_obj(self) -> Backend:
         """Allocate backend."""
         GlobalBackend.set_backend(self.backend, platform=self.platform)
-        backend = GlobalBackend()
-        if backend.platform is not None:
-            backend.transpiler = Passes(connectivity=backend.platform.topology)
-            backend.transpiler.passes = backend.transpiler.passes[-1:]
-        return backend
+        return GlobalBackend()
 
     @property
     def platform_obj(self) -> Platform:
diff --git a/src/qibocal/auto/transpile.py b/src/qibocal/auto/transpile.py
new file mode 100644
index 000000000..b8327730d
--- /dev/null
+++ b/src/qibocal/auto/transpile.py
@@ -0,0 +1,87 @@
+from typing import Optional
+
+from qibo import Circuit
+from qibo.backends import Backend
+from qibo.transpiler.pipeline import Passes
+from qibo.transpiler.unroller import NativeGates, Unroller
+
+
+def execute_transpiled_circuits(
+    circuits: list[Circuit],
+    qubit_maps: list[list[int]],
+    backend: Backend,
+    initial_states=None,
+    nshots=1000,
+    transpiler: Optional[Passes] = None,
+):
+    """
+    If the `qibolab` backend is used, this function pads the `circuits` in new
+    ones with a number of qubits equal to the one provided by the platform.
+    At the end, the circuits are transpiled, executed and the results returned.
+    The input `transpiler` is optional, but it should be provided if the backend
+    is `qibolab`.
+    For the qubit map look :func:`dummy_transpiler`.
+    This function returns the list of transpiled circuits and the execution results.
+    """
+    new_circuits = []
+    if backend.name == "qibolab":
+        platform_nqubits = backend.platform.nqubits
+        for circuit, qubit_map in zip(circuits, qubit_maps):
+            new_circuit = pad_circuit(platform_nqubits, circuit, qubit_map)
+            transpiled_circ, _ = transpiler(new_circuit)
+            new_circuits.append(transpiled_circ)
+    else:
+        new_circuits = circuits
+    return new_circuits, backend.execute_circuits(
+        new_circuits, initial_states=initial_states, nshots=nshots
+    )
+
+
+def execute_transpiled_circuit(
+    circuit: Circuit,
+    qubit_map: list[int],
+    backend: Backend,
+    initial_state=None,
+    nshots=1000,
+    transpiler: Optional[Passes] = None,
+):
+    """
+    If the `qibolab` backend is used, this function pads the `circuit` in new a
+    one with a number of qubits equal to the one provided by the platform.
+    At the end, the circuit is transpiled, executed and the results returned.
+    The input `transpiler` is optional, but it should be provided if the backend
+    is `qibolab`.
+    For the qubit map look :func:`dummy_transpiler`.
+    This function returns the transpiled circuit and the execution results.
+    """
+    if backend.name == "qibolab":
+        platform_nqubits = backend.platform.nqubits
+        new_circuit = pad_circuit(platform_nqubits, circuit, qubit_map)
+        transpiled_circ, _ = transpiler(new_circuit)
+    else:
+        transpiled_circ = circuit
+    return transpiled_circ, backend.execute_circuit(
+        transpiled_circ, initial_state=initial_state, nshots=nshots
+    )
+
+
+def dummy_transpiler(backend) -> Optional[Passes]:
+    """
+    If the backend is `qibolab`, a transpiler with just an unroller is returned,
+    otherwise None.
+    """
+    if backend.name == "qibolab":
+        unroller = Unroller(NativeGates.default())
+        return Passes(connectivity=backend.platform.topology, passes=[unroller])
+    return None
+
+
+def pad_circuit(nqubits, circuit: Circuit, qubit_map: list[int]) -> Circuit:
+    """
+    Pad `circuit` in a new one with `nqubits` qubits, according to `qubit_map`.
+    `qubit_map` is a list `[i, j, k, ...]`, where the i-th physical qubit is mapped
+    into the 0th logical qubit and so on.
+    """
+    new_circuit = Circuit(nqubits)
+    new_circuit.add(circuit.on_qubits(*qubit_map))
+    return new_circuit
diff --git a/src/qibocal/protocols/characterization/allxy/allxy.py b/src/qibocal/protocols/characterization/allxy/allxy.py
index 76d9f1a38..4a87e68f4 100644
--- a/src/qibocal/protocols/characterization/allxy/allxy.py
+++ b/src/qibocal/protocols/characterization/allxy/allxy.py
@@ -144,11 +144,9 @@ def add_gate_pair_pulses_to_sequence(
 
     for gate in gates:
         if gate == "I":
-            # print("Transforming to sequence I gate")
             pass
 
         if gate == "Xp":
-            # print("Transforming to sequence Xp gate")
             if beta_param == None:
                 RX_pulse = platform.create_RX_pulse(
                     qubit,
@@ -163,7 +161,6 @@ def add_gate_pair_pulses_to_sequence(
             sequence.add(RX_pulse)
 
         if gate == "X9":
-            # print("Transforming to sequence X9 gate")
             if beta_param == None:
                 RX90_pulse = platform.create_RX90_pulse(
                     qubit,
@@ -178,7 +175,6 @@ def add_gate_pair_pulses_to_sequence(
             sequence.add(RX90_pulse)
 
         if gate == "Yp":
-            # print("Transforming to sequence Yp gate")
             if beta_param == None:
                 RY_pulse = platform.create_RX_pulse(
                     qubit,
@@ -195,7 +191,6 @@ def add_gate_pair_pulses_to_sequence(
             sequence.add(RY_pulse)
 
         if gate == "Y9":
-            # print("Transforming to sequence Y9 gate")
             if beta_param == None:
                 RY90_pulse = platform.create_RX90_pulse(
                     qubit,
diff --git a/src/qibocal/protocols/characterization/randomized_benchmarking/circuit_tools.py b/src/qibocal/protocols/characterization/randomized_benchmarking/circuit_tools.py
index 4fd019542..978affc91 100644
--- a/src/qibocal/protocols/characterization/randomized_benchmarking/circuit_tools.py
+++ b/src/qibocal/protocols/characterization/randomized_benchmarking/circuit_tools.py
@@ -30,7 +30,7 @@ def layer_circuit(rb_gen: Callable, depth: int, qubit) -> tuple[Circuit, dict]:
         new_layer, random_index = rb_gen.layer_gen()
         # Ensure new_layer is a circuit
         if isinstance(new_layer, Gate):
-            new_circuit = Circuit(1, wire_names=qubits_str)
+            new_circuit = Circuit(1)
             new_circuit.add(new_layer)
             random_indexes.append(random_index)
 
@@ -48,7 +48,7 @@ def layer_circuit(rb_gen: Callable, depth: int, qubit) -> tuple[Circuit, dict]:
                 f"layer_gen must return type Circuit or Gate, but it is type {type(new_layer)}.",
             )
         if full_circuit is None:  # instantiate in first loop
-            full_circuit = Circuit(new_circuit.nqubits, wire_names=qubits_str)
+            full_circuit = Circuit(new_circuit.nqubits)
         full_circuit = full_circuit + new_circuit
     return full_circuit, random_indexes
 
diff --git a/src/qibocal/protocols/characterization/randomized_benchmarking/standard_rb.py b/src/qibocal/protocols/characterization/randomized_benchmarking/standard_rb.py
index a75fc79ed..e3eb1e1aa 100644
--- a/src/qibocal/protocols/characterization/randomized_benchmarking/standard_rb.py
+++ b/src/qibocal/protocols/characterization/randomized_benchmarking/standard_rb.py
@@ -10,6 +10,11 @@
 from qibolab.qubits import QubitId
 
 from qibocal.auto.operation import Data, Parameters, Results, Routine
+from qibocal.auto.transpile import (
+    dummy_transpiler,
+    execute_transpiled_circuit,
+    execute_transpiled_circuits,
+)
 from qibocal.config import raise_error
 from qibocal.protocols.characterization.randomized_benchmarking import noisemodels
 
@@ -240,19 +245,32 @@ def _acquisition(
         circuits.extend(circuits_depth)
         for qubit in random_indexes.keys():
             indexes[(qubit, depth)] = random_indexes[qubit]
+    transpiler = dummy_transpiler(backend)
+    qubit_maps = [[i] for i in targets] * (len(params.depths) * params.niter)
     # Execute the circuits
     if params.unrolling:
-        executed_circuits = backend.execute_circuits(circuits, nshots=params.nshots)
+        _, executed_circuits = execute_transpiled_circuits(
+            circuits,
+            qubit_maps=qubit_maps,
+            backend=backend,
+            nshots=params.nshots,
+            transpiler=transpiler,
+        )
     else:
         executed_circuits = [
-            backend.execute_circuit(circuit, nshots=params.nshots)
-            for circuit in circuits
+            execute_transpiled_circuit(
+                circuit,
+                qubit_map=qubit_map,
+                backend=backend,
+                nshots=params.nshots,
+                transpiler=transpiler,
+            )[1]
+            for circuit, qubit_map in zip(circuits, qubit_maps)
         ]
 
     for circ in executed_circuits:
         samples.extend(circ.samples())
     samples = np.reshape(samples, (-1, nqubits, params.nshots))
-
     for i, depth in enumerate(params.depths):
         index = (i * params.niter, (i + 1) * params.niter)
         for nqubit, qubit_id in enumerate(targets):
diff --git a/src/qibocal/protocols/characterization/readout_mitigation_matrix.py b/src/qibocal/protocols/characterization/readout_mitigation_matrix.py
index 70d40dfbd..f6612e678 100644
--- a/src/qibocal/protocols/characterization/readout_mitigation_matrix.py
+++ b/src/qibocal/protocols/characterization/readout_mitigation_matrix.py
@@ -5,6 +5,7 @@
 import numpy.typing as npt
 import plotly.express as px
 from qibo import gates
+from qibo.backends import GlobalBackend
 from qibo.models import Circuit
 from qibolab import ExecutionParameters
 from qibolab.platform import Platform
@@ -12,6 +13,7 @@
 from qibolab.qubits import QubitId
 
 from qibocal.auto.operation import Data, Parameters, Results, Routine
+from qibocal.auto.transpile import dummy_transpiler, execute_transpiled_circuit
 from qibocal.config import log
 
 from .utils import calculate_frequencies
@@ -95,6 +97,9 @@ def _acquisition(
     data = ReadoutMitigationMatrixData(
         nshots=params.nshots, qubit_list=[list(qq) for qq in targets]
     )
+    backend = GlobalBackend()
+    transpiler = dummy_transpiler(backend)
+    qubit_map = [i for i in range(platform.nqubits)]
     for qubits in targets:
         nqubits = len(qubits)
         for i in range(2**nqubits):
@@ -121,13 +126,17 @@ def _acquisition(
                     tuple(qubits), state, calculate_frequencies(results, tuple(qubits))
                 )
             else:
-                c = Circuit(platform.nqubits)
+                c = Circuit(
+                    platform.nqubits,
+                    wire_names=[str(i) for i in range(platform.nqubits)],
+                )
                 for q, bit in enumerate(state):
                     if bit == "1":
                         c.add(gates.X(qubits[q]))
                     c.add(gates.M(qubits[q]))
-                results = c(nshots=params.nshots)
-
+                _, results = execute_transpiled_circuit(
+                    c, qubit_map, backend, nshots=params.nshots, transpiler=transpiler
+                )
                 data.add(tuple(qubits), state, dict(results.frequencies()))
     return data
 
diff --git a/src/qibocal/protocols/characterization/two_qubit_interaction/chsh/protocol.py b/src/qibocal/protocols/characterization/two_qubit_interaction/chsh/protocol.py
index 48f48f1ea..d612d4699 100644
--- a/src/qibocal/protocols/characterization/two_qubit_interaction/chsh/protocol.py
+++ b/src/qibocal/protocols/characterization/two_qubit_interaction/chsh/protocol.py
@@ -8,11 +8,13 @@
 import numpy as np
 import numpy.typing as npt
 import plotly.graph_objects as go
+from qibo.backends import GlobalBackend
 from qibolab import ExecutionParameters
 from qibolab.platform import Platform
 from qibolab.qubits import QubitId, QubitPairId
 
 from qibocal.auto.operation import Data, Parameters, Results, Routine
+from qibocal.auto.transpile import dummy_transpiler, execute_transpiled_circuit
 
 from ...readout_mitigation_matrix import (
     ReadoutMitigationMatrixParameters as mitigation_params,
@@ -211,7 +213,9 @@ def _acquisition_circuits(
         bell_states=params.bell_states,
         thetas=thetas.tolist(),
     )
-
+    backend = GlobalBackend()
+    transpiler = dummy_transpiler(backend)
+    qubit_map = [i for i in range(platform.nqubits)]
     if params.apply_error_mitigation:
         mitigation_data = mitigation_acquisition(
             mitigation_params(pulses=False, nshots=params.nshots), platform, targets
@@ -232,7 +236,13 @@ def _acquisition_circuits(
                     native=params.native,
                 )
                 for basis, circuit in chsh_circuits.items():
-                    result = circuit(nshots=params.nshots)
+                    _, result = execute_transpiled_circuit(
+                        circuit,
+                        nshots=params.nshots,
+                        transpiler=transpiler,
+                        backend=backend,
+                        qubit_map=qubit_map,
+                    )
                     frequencies = result.frequencies()
                     data.register_basis(pair, bell_state, basis, frequencies)
 
diff --git a/tests/test_transpile.py b/tests/test_transpile.py
new file mode 100644
index 000000000..499ac9d28
--- /dev/null
+++ b/tests/test_transpile.py
@@ -0,0 +1,67 @@
+import numpy as np
+from qibo import Circuit, gates, set_backend
+from qibo.backends import GlobalBackend
+
+from qibocal.auto.transpile import (
+    dummy_transpiler,
+    execute_transpiled_circuit,
+    execute_transpiled_circuits,
+    pad_circuit,
+)
+
+
+def test_padd_circuit():
+    small_circuit = Circuit(2)
+    small_circuit.add(gates.X(0))
+    small_circuit.add(gates.X(1))
+    qubit_map = [1, 2]
+    big_circuit = pad_circuit(4, small_circuit, qubit_map)
+
+    true_circ = Circuit(4)
+    true_circ.add(gates.X(1))
+    true_circ.add(gates.X(2))
+    assert np.all(true_circ.unitary() == big_circuit.unitary())
+
+
+def test_execute_transpiled_circuit():
+
+    circuit = Circuit(2)
+    circuit.add(gates.X(0))
+    circuit.add(gates.X(1))
+    qubit_map = [1, 2]
+    set_backend("qibolab", platform="dummy")
+    backend = GlobalBackend()
+    transpiler = dummy_transpiler(backend)
+    transpiled_circuit, _ = execute_transpiled_circuit(
+        circuit, qubit_map, backend, transpiler=transpiler
+    )
+    true_circuit = Circuit(5)
+    true_circuit.add(gates.GPI2(1, np.pi / 2))
+    true_circuit.add(gates.GPI2(1, np.pi / 2))
+    true_circuit.add(gates.GPI2(2, np.pi / 2))
+    true_circuit.add(gates.GPI2(2, np.pi / 2))
+    true_circuit.add(gates.Z(1))
+    true_circuit.add(gates.Z(2))
+    assert np.all(true_circuit.unitary() == transpiled_circuit.unitary())
+
+
+def test_execute_transpiled_circuits():
+
+    circuit = Circuit(2)
+    circuit.add(gates.X(0))
+    circuit.add(gates.X(1))
+    qubit_map = [1, 2]
+    set_backend("qibolab", platform="dummy")
+    backend = GlobalBackend()
+    transpiler = dummy_transpiler(backend)
+    transpiled_circuits, _ = execute_transpiled_circuits(
+        [circuit], [qubit_map], backend, transpiler=transpiler
+    )
+    true_circuit = Circuit(5)
+    true_circuit.add(gates.GPI2(1, np.pi / 2))
+    true_circuit.add(gates.GPI2(1, np.pi / 2))
+    true_circuit.add(gates.GPI2(2, np.pi / 2))
+    true_circuit.add(gates.GPI2(2, np.pi / 2))
+    true_circuit.add(gates.Z(1))
+    true_circuit.add(gates.Z(2))
+    assert np.all(true_circuit.unitary() == transpiled_circuits[0].unitary())