diff --git a/README.md b/README.md
index 4454b239b..745ceba8d 100644
--- a/README.md
+++ b/README.md
@@ -29,6 +29,7 @@ Its design facilitates research and accelerates prototyping in the intersection
 - Provides all the quantities included in the Euler-Poincarè formulation of the equations of motion.
 - Supports body-fixed, inertial-fixed, and mixed [velocity representations][notation].
 - Exposes all the necessary quantities to develop controllers in centroidal coordinates.
+- Supports running open-loop and full closed-loop control architectures on hardware accelerators.
 
 ### JaxSim for robot learning
 
@@ -82,7 +83,7 @@ You can install the project using [`pypa/pip`][pip], preferably in a [virtual en
 pip install jaxsim
 ```
 
-Check [`setup.cfg`](setup.cfg) for the complete list of optional dependencies.
+Check [`pyproject.toml`](pyproject.toml) for the complete list of optional dependencies.
 You can obtain a full installation using `jaxsim[all]`.
 
 If you need GPU support, follow the official [installation instructions][jax_gpu] of JAX.
@@ -112,6 +113,71 @@ pip install --no-deps -e .
 [venv]: https://docs.python.org/3/tutorial/venv.html
 [jax_gpu]: https://github.com/google/jax/#installation
 
+## Overview
+
+<details>
+<summary>Structure of the Python package</summary>
+
+```
+# tree -L 2 -I "__pycache__" -I "__init__*" -I "__main__*" src/jaxsim
+
+src/jaxsim
+|-- api..........................# Package containing the main functional APIs.
+|   |-- com.py...................# |-- APIs for computing quantities related to the center of mass.
+|   |-- common.py................# |-- Common utilities used in the current package.
+|   |-- contact.py...............# |-- APIs for computing quantities related to the collidable points.
+|   |-- data.py..................# |-- Class storing the data of a simulated model.
+|   |-- frame.py.................# |-- APIs for computing quantities related to additional frames.
+|   |-- joint.py.................# |-- APIs for computing quantities related to the joints.
+|   |-- kin_dyn_parameters.py....# |-- Class storing kinematic and dynamic parameters of a model.
+|   |-- link.py..................# |-- APIs for computing quantities related to the links.
+|   |-- model.py.................# |-- Class defining a simulated model and APIs for computing related quantities.
+|   |-- ode.py...................# |-- APIs for computing quantities related to the system dynamics.
+|   |-- ode_data.py..............# |-- Set of classes to store the data of the system dynamics.
+|   `-- references.py............# `-- Helper class to create references (link forces and joint torques).
+|-- exceptions.py................# Module containing functions to raise exceptions from JIT-compiled functions.
+|-- integrators..................# Package containing the integrators used to simulate the system dynamics.
+|   |-- common.py................# |-- Common utilities used in the current package.
+|   |-- fixed_step.py............# |-- Fixed-step integrators (explicit Runge-Kutta schemes).
+|   `-- variable_step.py.........# `-- Variable-step integrators (embedded Runge-Kutta schemes).
+|-- logging.py...................# Module containing logging utilities.
+|-- math.........................# Package containing mathematical utilities.
+|   |-- adjoint.py...............# |-- APIs for creating and manipulating 6D transformations.
+|   |-- cross.py.................# |-- APIs for computing cross products of 6D quantities.
+|   |-- inertia.py...............# |-- APIs for creating and manipulating 6D inertia matrices.
+|   |-- joint_model.py...........# |-- APIs defining the supported joint model and the corresponding transformations.
+|   |-- quaternion.py............# |-- APIs for creating and manipulating quaternions.
+|   |-- rotation.py..............# |-- APIs for creating and manipulating rotation matrices.
+|   |-- skew.py..................# |-- APIs for creating and manipulating skew-symmetric matrices.
+|   `-- transform.py.............# `-- APIs for creating and manipulating homogeneous transformations.
+|-- mujoco.......................# Package containing utilities to interact with the Mujoco passive viewer.
+|   |-- loaders.py...............# |-- Utilities for converting JaxSim models to Mujoco models.
+|   |-- model.py.................# |-- Class providing high-level methods to compute quantities using Mujoco.
+|   `-- visualizer.py............# `-- Class that simplifies opening the passive viewer and recording videos.
+|-- parsers......................# Package containing utilities to parse model descriptions (SDF and URDF models).
+|   |-- descriptions/............# |-- Package containing the intermediate representation of a model description.
+|   |-- kinematic_graph.py.......# |-- Definition of the kinematic graph associated with a parsed model description.
+|   `-- rod/.....................# `-- Package to create the intermediate representation from model descriptions using ROD.
+|-- rbda.........................# Package containing the low-level rigid body dynamics algorithms.
+|   |-- aba.py...................# |-- The Articulated Body Algorithm.
+|   |-- collidable_points.py.....# |-- Kinematics of collidable points.
+|   |-- contacts/................# |-- Package containing the supported contact models.
+|   |-- crba.py..................# |-- The Composite Rigid Body Algorithm.
+|   |-- forward_kinematics.py....# |-- Forward kinematics of the model.
+|   |-- jacobian.py..............# |-- Full Jacobian and full Jacobian derivative.
+|   |-- rnea.py..................# |-- The Recursive Newton-Euler Algorithm.
+|   `-- utils.py.................# `-- Common utilities used in the current package.
+|-- terrain......................# Package containing resources to specify the terrain.
+|   `-- terrain.py...............# `-- Classes defining the supported terrains.
+|-- typing.py....................# Module containing type hints.
+`-- utils........................# Package of common utilities.
+    |-- jaxsim_dataclass.py......# |-- Utilities to operate on pytree dataclasses.
+    |-- tracing.py...............# |-- Utilities to use when JAX is tracing functions.
+    `-- wrappers.py..............# `-- Utilities to wrap objects for specific use cases on pytree dataclass attributes.
+```
+
+</details>
+
 ## Credits
 
 The RBDAs are based on the theory of the [Rigid Body Dynamics Algorithms][RBDA]
@@ -157,6 +223,19 @@ Please read the [contributing guide](./CONTRIBUTING.md) to get started.
 }
 ```
 
+Theoretical aspects of JaxSim are based on Chapters 7 and 8 of the following Ph.D. thesis:
+
+```bibtex
+@phdthesis{ferigo_phd_thesis_2022,
+  title = {Simulation Architectures for Reinforcement Learning applied to Robotics},
+  author = {Diego Ferigo},
+  school = {University of Manchester},
+  type = {PhD Thesis},
+  month = {July},
+  year = {2022},
+}
+```
+
 ## People
 
 | Author | Maintainers |
diff --git a/pyproject.toml b/pyproject.toml
index 266a1e053..e3abd4ba4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,19 +1,112 @@
 [project]
-dynamic = ["version", "dependencies", "optional-dependencies", "urls", "classifiers", "keywords", "authors", "requires-python", "license", "readme"]
 name = "jaxsim"
+dynamic = ["version"]
+requires-python = ">= 3.10"
+description = "A differentiable physics engine and multibody dynamics library for control and robot learning."
+authors = [
+    { name = "Diego Ferigo", email = "dgferigo@gmail.com" },
+]
+maintainers = [
+    { name = "Diego Ferigo", email = "dgferigo@gmail.com" },
+    { name = "Filippo Luca Ferretti", email = "filippo.ferretti@iit.it" },
+]
+license.file = "LICENSE"
+keywords = [
+    "physics",
+    "physics engine",
+    "jax",
+    "rigid body dynamics",
+    "featherstone",
+    "reinforcement learning",
+    "robot",
+    "robotics",
+    "sdf",
+    "urdf",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Framework :: Robot Framework",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS",
+    "Operating System :: Microsoft",
+    "Programming Language :: Python :: 3 :: Only",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Topic :: Games/Entertainment :: Simulation",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Software Development",
+]
+dependencies = [
+    "coloredlogs",
+    "jax >= 0.4.13",
+    "jaxlib >= 0.4.13",
+    "jaxlie >= 1.3.0",
+    "jax_dataclasses >= 1.4.0",
+    "pptree",
+    "rod >= 0.3.0",
+    "typing_extensions ; python_version < '3.12'",
+]
+
+[project.optional-dependencies]
+style = [
+    "black[jupyter] ~= 24.0",
+    "isort",
+    "pre-commit",
+]
+testing = [
+    "idyntree >= 12.2.1",
+    "pytest >=6.0",
+    "pytest-icdiff",
+    "robot-descriptions",
+]
+viz = [
+    "lxml",
+    "mediapy",
+    "mujoco >= 3.0.0",
+]
+all = [
+    "jaxsim[style,testing,viz]",
+]
+
+[project.readme]
+file = "README.md"
+content-type = "text/markdown"
+
+[project.urls]
+Changelog = "https://github.com/ami-iit/jaxsim/releases"
+Documentation = "https://jaxsim.readthedocs.io"
+Source = "https://github.com/ami-iit/jaxsim"
+Tracker = "https://github.com/ami-iit/jaxsim/issues"
+
+# ===========
+# Build tools
+# ===========
 
 [build-system]
 build-backend = "setuptools.build_meta"
 requires = [
-  "wheel",
-  "setuptools>=64",
-  "setuptools_scm[toml]>=8",
+    "setuptools>=64",
+    "setuptools-scm[toml]>=8",
+    "wheel",
 ]
 
+[tool.setuptools]
+package-dir = { "" = "src" }
+
 [tool.setuptools_scm]
 local_scheme = "dirty-tag"
 version_file = "src/jaxsim/_version.py"
 
+# =================
+# Style and testing
+# =================
+
 [tool.black]
 line-length = 88
 
@@ -25,42 +118,46 @@ profile = "black"
 addopts = "-rsxX -v --strict-markers"
 minversion = "6.0"
 testpaths = [
-  "tests",
+    "tests",
 ]
 
+# ==================
+# Ruff configuration
+# ==================
+
 [tool.ruff]
 exclude = [
-  ".git",
-  ".pytest_cache",
-  ".ruff_cache",
-  ".vscode",
-  ".devcontainer",
-  "__pycache__",
+    ".git",
+    ".pytest_cache",
+    ".ruff_cache",
+    ".vscode",
+    ".devcontainer",
+    "__pycache__",
 ]
 preview = true
 
 [tool.ruff.lint]
 # https://docs.astral.sh/ruff/rules/
 select = [
-  "B",
-  "E",
-  "F",
-  "I",
-  "W",
-  "RUF",
-  "YTT",
+    "B",
+    "E",
+    "F",
+    "I",
+    "W",
+    "RUF",
+    "YTT",
 ]
 
 ignore = [
-  "B008", # Function call in default argument
-  "B024", # Abstract base class without abstract methods
-  "E402", # Module level import not at top of file
-  "E501", # Line too long
-  "E731", # Do not assign a `lambda` expression, use a `def`
-  "E741", # Ambiguous variable name
-  "F841", # Local variable is assigned to but never used
-  "I001", # Import block is unsorted or unformatted
-  "RUF003", # Ambigous unicode character in comment
+    "B008", # Function call in default argument
+    "B024", # Abstract base class without abstract methods
+    "E402", # Module level import not at top of file
+    "E501", # Line too long
+    "E731", # Do not assign a `lambda` expression, use a `def`
+    "E741", # Ambiguous variable name
+    "F841", # Local variable is assigned to but never used
+    "I001", # Import block is unsorted or unformatted
+    "RUF003", # Ambigous unicode character in comment
 ]
 
 [tool.ruff.lint.per-file-ignores]
@@ -70,6 +167,10 @@ ignore = [
 "__init__.py" = ["F401"]
 "docs/conf.py" = ["F401"]
 
+# ==================
+# Pixi configuration
+# ==================
+
 [tool.pixi.project]
 channels = ["conda-forge"]
 platforms = ["linux-64", "osx-arm64", "osx-64"]
@@ -90,9 +191,9 @@ sdformat14 = "*"
 typing_extensions = "*"
 
 [tool.pixi.feature.test.tasks]
-examples = {cmd = "jupyter notebook ./examples"}
+examples = { cmd = "jupyter notebook ./examples" }
 pipcheck = "pip check"
-test = {cmd = "pytest", depends_on = ["pipcheck"]}
+test = { cmd = "pytest", depends_on = ["pipcheck"] }
 
 [tool.pixi.feature.test.dependencies]
 black = "24.*"
@@ -105,15 +206,15 @@ pytest-icdiff = "*"
 robot_descriptions = "*"
 
 [tool.pixi.feature.gpu]
-dependencies = {cuda-version = "12.*", cuda-cupti = "*", jaxlib = "**cuda*"}
+dependencies = { cuda-version = "12.*", cuda-cupti = "*", jaxlib = "**cuda*" }
 platforms = ["linux-64"]
-system-requirements = {cuda = "12.1"}
+system-requirements = { cuda = "12.1" }
 
 [tool.pixi.pypi-dependencies]
-jaxsim = {path = "./", editable = true}
+jaxsim = { path = "./", editable = true }
 
 [tool.pixi.environments]
-default = {solve-group = "cpugroup"}
-gpu = {features = ["gpu"], solve-group = "gpugroup"}
-test-cpu = {features = ["test"], solve-group = "cpugroup"}
-test-gpu = {features = ["test", "gpu"], solve-group = "gpugroup"}
+default = { solve-group = "cpugroup" }
+gpu = { features = ["gpu"], solve-group = "gpugroup" }
+test-cpu = { features = ["test"], solve-group = "cpugroup" }
+test-gpu = { features = ["test", "gpu"], solve-group = "gpugroup" }
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 0061982ed..000000000
--- a/setup.cfg
+++ /dev/null
@@ -1,87 +0,0 @@
-[metadata]
-name = jaxsim
-description = A differentiable physics engine and multibody dynamics library for control and robot learning.
-long_description = file: README.md
-long_description_content_type = text/markdown
-author = Diego Ferigo
-author_email = diego.ferigo@iit.it
-license = BSD
-license_files = LICENSE
-platforms = any
-url = https://github.com/ami-iit/jaxsim
-
-project_urls =
-    Changelog = https://github.com/ami-iit/jaxsim/releases
-    Documentation = https://jaxsim.readthedocs.io
-    Source = https://github.com/ami-iit/jaxsim
-    Tracker = https://github.com/ami-iit/jaxsim/issues
-
-keywords =
-    physics
-    physics engine
-    jax
-    rigid body dynamics
-    featherstone
-    reinforcement learning
-    robot
-    robotics
-    sdf
-    urdf
-
-classifiers =
-    Development Status :: 4 - Beta
-    Framework :: Robot Framework
-    Intended Audience :: Developers
-    Intended Audience :: Science/Research
-    License :: OSI Approved :: BSD License
-    Operating System :: POSIX :: Linux
-    Operating System :: MacOS
-    Operating System :: Microsoft
-    Programming Language :: Python :: 3.10
-    Programming Language :: Python :: 3.11
-    Programming Language :: Python :: 3.12
-    Programming Language :: Python :: 3 :: Only
-    Programming Language :: Python :: Implementation :: CPython
-    Topic :: Games/Entertainment :: Simulation
-    Topic :: Scientific/Engineering :: Artificial Intelligence
-    Topic :: Scientific/Engineering :: Physics
-    Topic :: Software Development
-
-[options]
-zip_safe = False
-packages = find:
-package_dir =
-    =src
-python_requires = >=3.10
-install_requires =
-    coloredlogs
-    jax >= 0.4.13
-    jaxlib >= 0.4.13
-    jaxlie >= 1.3.0
-    jax_dataclasses >= 1.4.0
-    pptree
-    rod >= 0.3.0
-    typing_extensions ; python_version < '3.12'
-
-[options.packages.find]
-where = src
-
-[options.extras_require]
-style =
-    # Note: keep the black version in sync with style.yml and environment.yml.
-    black[jupyter] ~= 24.0
-    isort
-    pre-commit
-testing =
-    idyntree >= 12.2.1
-    pytest >=6.0
-    pytest-icdiff
-    robot-descriptions
-viz =
-    lxml
-    mediapy
-    mujoco >= 3.0.0
-all =
-    %(style)s
-    %(testing)s
-    %(viz)s
diff --git a/src/jaxsim/mujoco/model.py b/src/jaxsim/mujoco/model.py
index 6b61177ff..bb11d6399 100644
--- a/src/jaxsim/mujoco/model.py
+++ b/src/jaxsim/mujoco/model.py
@@ -378,7 +378,7 @@ def _mask_qpos(self, joint_names: tuple[str, ...]) -> npt.NDArray:
                             for i in range(self.joint_dofs(joint_name=joint_name))
                         ]
                     )
-                    for idx, joint_name in zip(idxs, joint_names)
+                    for idx, joint_name in zip(idxs, joint_names, strict=True)
                 ]
             ).squeeze()
         )
diff --git a/src/jaxsim/parsers/kinematic_graph.py b/src/jaxsim/parsers/kinematic_graph.py
index 9edf811b4..5073894f1 100644
--- a/src/jaxsim/parsers/kinematic_graph.py
+++ b/src/jaxsim/parsers/kinematic_graph.py
@@ -797,7 +797,7 @@ def initial_joint_positions(
         self._transform_cache.clear()
 
         # Update initial joint positions.
-        for joint_name, position in zip(joint_names, s):
+        for joint_name, position in zip(joint_names, s, strict=True):
             self._initial_joint_positions[joint_name] = position
 
     def transform(self, name: str) -> npt.NDArray:
diff --git a/tests/test_api_frame.py b/tests/test_api_frame.py
index f721c80fa..7d2e6322d 100644
--- a/tests/test_api_frame.py
+++ b/tests/test_api_frame.py
@@ -163,7 +163,7 @@ def test_frame_jacobians(
 
     assert len(frame_indices) == len(frame_names)
 
-    for frame_name, frame_index in zip(frame_names, frame_indices):
+    for frame_name, frame_index in zip(frame_names, frame_indices, strict=True):
 
         J_WL_js = js.frame.jacobian(model=model, data=data, frame_index=frame_index)
         J_WL_idt = kin_dyn.jacobian_frame(frame_name=frame_name)
diff --git a/tests/test_api_link.py b/tests/test_api_link.py
index 1e808687d..418f78a99 100644
--- a/tests/test_api_link.py
+++ b/tests/test_api_link.py
@@ -75,6 +75,7 @@ def test_link_inertial_properties(
     for link_name, link_idx in zip(
         model.link_names(),
         js.link.names_to_idxs(model=model, link_names=model.link_names()),
+        strict=True,
     ):
         if link_name == model.base_link():
             continue
@@ -118,7 +119,7 @@ def test_link_transforms(
 
     assert W_H_LL_model == pytest.approx(W_H_LL_links)
 
-    for W_H_L, link_name in zip(W_H_LL_links, model.link_names()):
+    for W_H_L, link_name in zip(W_H_LL_links, model.link_names(), strict=True):
 
         assert W_H_L == pytest.approx(
             kin_dyn.frame_transform(frame_name=link_name)
@@ -152,7 +153,7 @@ def test_link_jacobians(
         lambda idx: js.link.jacobian(model=model, data=data, link_index=idx)
     )(jnp.arange(model.number_of_links()))
 
-    for J_WL, link_name in zip(J_WL_links, model.link_names()):
+    for J_WL, link_name in zip(J_WL_links, model.link_names(), strict=True):
         assert J_WL == pytest.approx(
             kin_dyn.jacobian_frame(frame_name=link_name), abs=1e-9
         ), link_name
@@ -164,6 +165,7 @@ def test_link_jacobians(
     for link_name, link_idx in zip(
         model.link_names(),
         js.link.names_to_idxs(model=model, link_names=model.link_names()),
+        strict=True,
     ):
         v_WL_idt = kin_dyn.frame_velocity(frame_name=link_name)
         v_WL_js = js.link.velocity(model=model, data=data, link_index=link_idx)
@@ -184,6 +186,7 @@ def test_link_jacobians(
         for link_name, link_idx in zip(
             model.link_names(),
             js.link.names_to_idxs(model=model, link_names=model.link_names()),
+            strict=True,
         ):
             v_WL_idt = kin_dyn_other_repr.frame_velocity(frame_name=link_name)
             v_WL_js = js.link.velocity(
@@ -218,6 +221,7 @@ def test_link_bias_acceleration(
     for name, index in zip(
         model.link_names(),
         js.link.names_to_idxs(model=model, link_names=model.link_names()),
+        strict=True,
     ):
         Jν_idt = kin_dyn.frame_bias_acc(frame_name=name)
         Jν_js = js.link.bias_acceleration(model=model, data=data, link_index=index)
diff --git a/tests/test_api_model.py b/tests/test_api_model.py
index 24654f726..a0fe49db5 100644
--- a/tests/test_api_model.py
+++ b/tests/test_api_model.py
@@ -84,6 +84,7 @@ def test_model_creation_and_reduction(
                 data_full.joint_positions(
                     model=model_full, joint_names=model_full.joint_names()
                 ).tolist(),
+                strict=True,
             )
         ),
     )
diff --git a/tests/utils_idyntree.py b/tests/utils_idyntree.py
index 3dc0df833..5376a82ef 100644
--- a/tests/utils_idyntree.py
+++ b/tests/utils_idyntree.py
@@ -64,6 +64,7 @@ def build_kindyncomputations_from_jaxsim_model(
             zip(
                 model.joint_names(),
                 data.joint_positions(model=model, joint_names=model.joint_names()),
+                strict=True,
             )
         )
     )