diff --git a/MANIFEST.in b/MANIFEST.in
index 6abcd1e3b..c373117d0 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,3 +1,14 @@
-include pyproject.toml
+graft src
+
 include LICENSE
-include VERSION
+include README.md
+
+prune docs
+prune tests
+prune .github
+prune .tox
+
+exclude .gitignore
+exclude tox.ini
+
+global-exclude *.py[cod] __pycache__/* *.so *.dylib
diff --git a/VERSION b/VERSION
deleted file mode 100644
index 6e8bf73aa..000000000
--- a/VERSION
+++ /dev/null
@@ -1 +0,0 @@
-0.1.0
diff --git a/metatensor_models/__init__.py b/bin/__init__.py
similarity index 100%
rename from metatensor_models/__init__.py
rename to bin/__init__.py
diff --git a/bin/eval-metatensor-model.py b/bin/eval-metatensor-model.py
new file mode 100644
index 000000000..eacb83ed3
--- /dev/null
+++ b/bin/eval-metatensor-model.py
@@ -0,0 +1 @@
+print("eval")
diff --git a/bin/export-metatensor-model.py b/bin/export-metatensor-model.py
new file mode 100644
index 000000000..ed7570b13
--- /dev/null
+++ b/bin/export-metatensor-model.py
@@ -0,0 +1 @@
+print("export")
diff --git a/bin/train-metatensor-model.py b/bin/train-metatensor-model.py
new file mode 100644
index 000000000..c859094af
--- /dev/null
+++ b/bin/train-metatensor-model.py
@@ -0,0 +1 @@
+print("train")
diff --git a/metatensor_models/kernel/__init__.py b/metatensor_models/kernel/__init__.py
deleted file mode 100644
index e69de29bb..000000000
diff --git a/metatensor_models/kernel/example/__init__.py b/metatensor_models/kernel/example/__init__.py
deleted file mode 100644
index 8a0ea15fc..000000000
--- a/metatensor_models/kernel/example/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-from .example import Example  # noqa: F401
diff --git a/metatensor_models/kernel/example/example.py b/metatensor_models/kernel/example/example.py
deleted file mode 100644
index 7caf4c566..000000000
--- a/metatensor_models/kernel/example/example.py
+++ /dev/null
@@ -1,16 +0,0 @@
-from typing import Dict, List, Tuple
-
-from metatensor.torch import TensorMap
-
-from ..kernel import KernelModel
-
-
-class Example(KernelModel):
-    def __init__(self, equivariant_selection: List[Tuple[int, int]], hypers: Dict):
-        super(Example, self).__init__(equivariant_selection, hypers)
-
-    def forward(self, systems: TensorMap):
-        return systems
-
-    def compute_kernels(self, systems: TensorMap):
-        return systems
diff --git a/metatensor_models/kernel/example/train_example.py b/metatensor_models/kernel/example/train_example.py
deleted file mode 100644
index e69de29bb..000000000
diff --git a/metatensor_models/kernel/kernel.py b/metatensor_models/kernel/kernel.py
deleted file mode 100644
index bcd60461e..000000000
--- a/metatensor_models/kernel/kernel.py
+++ /dev/null
@@ -1,31 +0,0 @@
-import abc
-from typing import Dict, List, Tuple
-
-import torch
-from metatensor.torch import TensorMap  # , System
-
-
-class KernelModel(torch.nn.Module, abc.ABC):
-    def __init__(self, equivariant_selection: List[Tuple[int, int]], hypers: Dict):
-        """
-        The initialization function. This takes as arguments `equivariant_selection`,
-        i.e. a list of (lambda, sigma) tuples that indicate the symmetry of the
-        targets with respect to rotation and inversion, as well as the hypers of the
-        model as a dictionary. These hypers are model-specific.
-        """
-        super(KernelModel, self).__init__()
-        self.regression_coefficients = torch.empty(())
-
-    @abc.abstractmethod
-    def forward(self, systems: TensorMap) -> TensorMap:
-        """
-        The forward function of the linear model.
-        """
-        pass
-
-    @abc.abstractmethod
-    def compute_kernels(self, systems: TensorMap) -> TensorMap:
-        """
-        A function that computes the kernels of the model.
-        """
-        pass
diff --git a/metatensor_models/linear/__init__.py b/metatensor_models/linear/__init__.py
deleted file mode 100644
index e69de29bb..000000000
diff --git a/metatensor_models/linear/example/__init__.py b/metatensor_models/linear/example/__init__.py
deleted file mode 100644
index 8a0ea15fc..000000000
--- a/metatensor_models/linear/example/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-from .example import Example  # noqa: F401
diff --git a/metatensor_models/linear/example/example.py b/metatensor_models/linear/example/example.py
deleted file mode 100644
index 738805a68..000000000
--- a/metatensor_models/linear/example/example.py
+++ /dev/null
@@ -1,16 +0,0 @@
-from typing import Dict, List, Tuple
-
-from metatensor.torch import TensorMap
-
-from ..linear import LinearModel
-
-
-class Example(LinearModel):
-    def __init__(self, equivariant_selection: List[Tuple[int, int]], hypers: Dict):
-        super(Example, self).__init__(equivariant_selection, hypers)
-
-    def forward(self, systems: TensorMap):
-        return systems
-
-    def compute_features(self, systems: TensorMap):
-        return systems
diff --git a/metatensor_models/linear/example/train_example.py b/metatensor_models/linear/example/train_example.py
deleted file mode 100644
index e69de29bb..000000000
diff --git a/metatensor_models/linear/linear.py b/metatensor_models/linear/linear.py
deleted file mode 100644
index 1a7aa336d..000000000
--- a/metatensor_models/linear/linear.py
+++ /dev/null
@@ -1,31 +0,0 @@
-import abc
-from typing import Dict, List, Tuple
-
-import torch
-from metatensor.torch import TensorMap  # , System
-
-
-class LinearModel(torch.nn.Module, abc.ABC):
-    def __init__(self, equivariant_selection: List[Tuple[int, int]], hypers: Dict):
-        """
-        The initialization function. This takes as arguments `equivariant_selection`,
-        i.e. a list of (lambda, sigma) tuples that indicate the symmetry of the
-        targets with respect to rotation and inversion, as well as the hypers of the
-        model as a dictionary. These hypers are model-specific.
-        """
-        super(LinearModel, self).__init__()
-        self.regression_coefficients = torch.empty(())
-
-    @abc.abstractmethod
-    def forward(self, systems: TensorMap) -> TensorMap:
-        """
-        The forward function of the linear model.
-        """
-        pass
-
-    @abc.abstractmethod
-    def compute_features(self, TensorMap) -> TensorMap:
-        """
-        A function that computes the features of the linear model.
-        """
-        pass
diff --git a/metatensor_models/nn/__init__.py b/metatensor_models/nn/__init__.py
deleted file mode 100644
index e69de29bb..000000000
diff --git a/metatensor_models/nn/example/__init__.py b/metatensor_models/nn/example/__init__.py
deleted file mode 100644
index 8a0ea15fc..000000000
--- a/metatensor_models/nn/example/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-from .example import Example  # noqa: F401
diff --git a/metatensor_models/nn/example/example.py b/metatensor_models/nn/example/example.py
deleted file mode 100644
index 77b2de7f1..000000000
--- a/metatensor_models/nn/example/example.py
+++ /dev/null
@@ -1,16 +0,0 @@
-from typing import Dict, List, Tuple
-
-from metatensor.torch import TensorMap
-
-from ..nn import NNModel
-
-
-class Example(NNModel):
-    def __init__(self, equivariant_selection: List[Tuple[int, int]], hypers: Dict):
-        super(Example, self).__init__(equivariant_selection, hypers)
-
-    def forward(self, systems: TensorMap):
-        return systems
-
-    def compute_kernels(self, systems: TensorMap):
-        return systems
diff --git a/metatensor_models/nn/example/train_example.py b/metatensor_models/nn/example/train_example.py
deleted file mode 100644
index e69de29bb..000000000
diff --git a/metatensor_models/nn/nn.py b/metatensor_models/nn/nn.py
deleted file mode 100644
index 1e4ec6b0c..000000000
--- a/metatensor_models/nn/nn.py
+++ /dev/null
@@ -1,23 +0,0 @@
-import abc
-from typing import Dict, List, Tuple
-
-import torch
-from metatensor.torch import TensorMap  # , System
-
-
-class NNModel(torch.nn.Module, abc.ABC):
-    def __init__(self, equivariant_selection: List[Tuple[int, int]], hypers: Dict):
-        """
-        The initialization function. This takes as arguments `equivariant_selection`,
-        i.e. a list of (lambda, sigma) tuples that indicate the symmetry of the
-        targets with respect to rotation and inversion, as well as the hypers of the
-        model as a dictionary. These hypers are model-specific.
-        """
-        super(NNModel, self).__init__()
-
-    @abc.abstractmethod
-    def forward(self, systems: TensorMap) -> TensorMap:
-        """
-        The forward function of the NN model, which computes its predictions.
-        """
-        pass
diff --git a/pyproject.toml b/pyproject.toml
index 3ca9dff38..ca20272f1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [project]
-name = "metatensor-models"
+name = "metatensor_models"
 dynamic = ["version"]
 requires-python = ">=3.7"
 
@@ -11,6 +11,7 @@ authors = [
 ]
 
 dependencies = [
+    "ase",
     "torch",
     "metatensor-core",
     "metatensor-torch"
@@ -40,15 +41,46 @@ classifiers = [
 repository = "https://github.com/lab-cosmo/metatensor-models"
 # changelog = "TODO"
 
+[project.scripts]
+maicos = "maicos.__main__:main"
+
 ### ======================================================================== ###
 
 [build-system]
 requires = [
-    "setuptools >=68",
+    "setuptools >= 68",
+    "wheel",
 ]
 build-backend = "setuptools.build_meta"
 
-### ======================================================================== ###
+[project.optional-dependencies]
+soap-bpnn = [
+    "rascaline-torch @ git+https://github.com/luthaf/rascaline#subdirectory=python/rascaline-torch",
+]
+
+[tool.setuptools.packages.find]
+where = ["src", "bin"]
+
+[tool.setuptools.dynamic]
+version = {attr = "metatensor_models.__version__"}
+
+[tool.coverage.report]
+include = [
+    "src/metatensor_models/*"
+]
+
+[tool.coverage.xml]
+output = 'tests/coverage.xml'
+
 [tool.pytest.ini_options]
 python_files = ["*.py"]
 testpaths = ["tests"]
+
+[tool.isort]
+skip = "__init__.py"
+profile = "black"
+line_length = 88
+indent = 4
+include_trailing_comma = true
+lines_after_imports = 2
+known_first_party = "metatensor_models"
diff --git a/setup.py b/setup.py
deleted file mode 100644
index eca11a646..000000000
--- a/setup.py
+++ /dev/null
@@ -1,12 +0,0 @@
-import os
-
-from setuptools import find_packages, setup
-
-ROOT = os.path.realpath(os.path.dirname(__file__))
-
-
-if __name__ == "__main__":
-    with open(os.path.join(ROOT, "VERSION")) as fd:
-        version = fd.read().strip()
-
-    setup(version=version, packages=find_packages())
diff --git a/src/metatensor_models/__init__.py b/src/metatensor_models/__init__.py
new file mode 100644
index 000000000..e728ace74
--- /dev/null
+++ b/src/metatensor_models/__init__.py
@@ -0,0 +1 @@
+__version__ = "0.0.0-dev"
diff --git a/tests/init.py b/tests/init.py
new file mode 100644
index 000000000..e4a2c3cc2
--- /dev/null
+++ b/tests/init.py
@@ -0,0 +1,5 @@
+import metatensor_models
+
+
+def test_version_exists():
+    metatensor_models.__version__
diff --git a/tests/test_kernel.py b/tests/test_kernel.py
deleted file mode 100644
index 83600e829..000000000
--- a/tests/test_kernel.py
+++ /dev/null
@@ -1,18 +0,0 @@
-import torch
-from metatensor.torch import Labels, TensorBlock, TensorMap
-from metatensor_models.kernel.example import Example
-
-
-def test_output():
-    tensor_map = TensorMap(
-        Labels.empty("_"),
-        []
-    )
-    example = Example(equivariant_selection=[(0, 1)], hypers={})
-    output = example(tensor_map)
-    assert isinstance(output, torch.ScriptObject)
-
-
-def test_jit_script():
-    example = Example(equivariant_selection=[(0, 1)], hypers={})
-    torch.jit.script(example)
diff --git a/tests/test_linear.py b/tests/test_linear.py
deleted file mode 100644
index 88c193239..000000000
--- a/tests/test_linear.py
+++ /dev/null
@@ -1,18 +0,0 @@
-import torch
-from metatensor.torch import Labels, TensorBlock, TensorMap
-from metatensor_models.linear.example import Example
-
-
-def test_output():
-    tensor_map = TensorMap(
-        Labels.empty("_"),
-        []
-    )
-    example = Example(equivariant_selection=[(0, 1)], hypers={})
-    output = example(tensor_map)
-    assert isinstance(output, torch.ScriptObject)
-
-
-def test_jit_script():
-    example = Example(equivariant_selection=[(0, 1)], hypers={})
-    torch.jit.script(example)
diff --git a/tests/test_nn.py b/tests/test_nn.py
deleted file mode 100644
index 7f4015ff3..000000000
--- a/tests/test_nn.py
+++ /dev/null
@@ -1,18 +0,0 @@
-import torch
-from metatensor.torch import Labels, TensorBlock, TensorMap
-from metatensor_models.nn.example import Example
-
-
-def test_output():
-    tensor_map = TensorMap(
-        Labels.empty("_"),
-        []
-    )
-    example = Example(equivariant_selection=[(0, 1)], hypers={})
-    output = example(tensor_map)
-    assert isinstance(output, torch.ScriptObject)
-
-
-def test_example():
-    example = Example(equivariant_selection=[(0, 1)], hypers={})
-    torch.jit.script(example)
diff --git a/tox.ini b/tox.ini
index 65ab3e450..8bbd6cd36 100644
--- a/tox.ini
+++ b/tox.ini
@@ -4,11 +4,12 @@ min_version = 4.0
 # execute `tox` in the command-line without anything else
 envlist =
     lint
-    python-tests
+    build
+    tests
 
 [testenv]
 passenv = *
-lint_folders = "{toxinidir}/metatensor_models" "{toxinidir}/setup.py"
+lint_folders = "{toxinidir}/src"
 
 [testenv:lint]
 # this environement lints the Python code with flake8 (code linter), black (code
@@ -41,7 +42,8 @@ commands =
     black {[testenv]lint_folders}
     blackdoc {[testenv]lint_folders}
 
-[testenv:python-tests]
+[testenv:tests]
+description = Run basic package tests with pytest (not the architectures)
 passenv = *
 deps =
     pytest
@@ -49,6 +51,14 @@ deps =
 commands =
     pytest --import-mode=append {posargs}
 
+[testenv:soap-bpnn]
+passenv = *
+deps =
+    pytest
+
+commands =
+    echo "success"
+
 [testenv:build-python]
 # this environement makes sure one can build sdist and wheels for Python
 deps =
@@ -56,19 +66,19 @@ deps =
     wheel
     cmake
     twine
+    build
 
 allowlist_externals =
     bash
 
 commands =
     # check building sdist and wheels from a checkout
-    python setup.py sdist
-    python setup.py bdist_wheel
+    python -m build
     twine check dist/*.tar.gz
     twine check dist/*.whl
 
     # check building wheels from the sdist
-    bash -c "python -m pip wheel --verbose dist/metatensor-models-*.tar.gz -w dist/test"
+    bash -c "python -m pip wheel --verbose dist/metatensor_models-*.tar.gz -w dist/test"
 
 [flake8]
 # longer lines for compatibility with other linters