Fix and clean docs (build)

.gitignore

@@ -155,9 +155,9 @@ celerybeat.pid
 
 # Environments
 .env
-.venv
+.venv*
 env/
-venv/
+venv*/
 ENV/
 env.bak/
 venv.bak/
@@ -189,6 +189,13 @@ cython_debug/
 # tensorboard
 *.pt.trace.json
 
+# AI tools
+.benchmarks/
+.codegraph/
+.pi/
+.pi-subagents/
+.scratch/
+
 # data
 ./*.json
 ./*.csv

docs/requirements.txt

@@ -1,10 +1,11 @@
 numpy<2
 pydantic>=2.0.0
 scipy
-tad-dftd3==0.5.0
-tad-dftd4==0.7.0
-tad-mctc==0.5.3
-tad-multicharge==0.3.3
+tad-mctc==0.7.0
+tad-dftd3==0.6.0
+tad-multicharge==0.5.0
+tad-dftd4==0.8.0
+tad-libcint==0.3.0
 tomli
 tomli-w
 torch>=2.10.0

docs/source/02_indepth/calculators_types.rst

@@ -14,6 +14,6 @@ Types of Calculators
    GFN2 Calculator <../_autosummary/dxtb.calculators.GFN2Calculator>
 
 .. automodule:: dxtb._src.calculators.types
-   :members:
+   :no-index:
    :undoc-members:
    :show-inheritance:

docs/source/02_indepth/integrals_drivers_libcint.rst

@@ -9,20 +9,12 @@ Libcint
 Drivers
 -------
 
-.. automodule:: dxtb._src.integral.driver.libcint.base_driver
-   :members:
-   :show-inheritance:
-
 .. automodule:: dxtb._src.integral.driver.libcint.driver
    :members:
    :show-inheritance:
 
 Implementations
-----------------
-
-.. automodule:: dxtb._src.integral.driver.libcint.base_implementation
-   :members:
-   :show-inheritance:
+---------------
 
 .. automodule:: dxtb._src.integral.driver.libcint.overlap
    :members:

docs/source/02_indepth/integrals_drivers_pytorch.rst

@@ -9,21 +9,13 @@ PyTorch
 Drivers
 -------
 
-.. automodule:: dxtb._src.integral.driver.pytorch.base_driver
-   :members:
-   :show-inheritance:
-
 .. automodule:: dxtb._src.integral.driver.pytorch.driver
    :members:
    :show-inheritance:
 
 Implementations
 ---------------
 
-.. automodule:: dxtb._src.integral.driver.pytorch.base_implementation
-   :members:
-   :show-inheritance:
-
 .. automodule:: dxtb._src.integral.driver.pytorch.overlap
    :members:
    :show-inheritance:

docs/source/02_indepth/integrals_types.rst

@@ -6,11 +6,10 @@ Integral Types
 .. toctree::
    :maxdepth: 1
 
-   HCore <../_autosummary/dxtb.integrals.types.HCore>
-   Overlap <../_autosummary/dxtb.integrals.types.Overlap>
-   Dipole <../_autosummary/dxtb.integrals.types.Dipole>
-   Quadrupole <../_autosummary/dxtb.integrals.types.Quadrupole>
+   Overlap <../_autosummary/dxtb.integrals.types.OverlapIntegral>
+   Dipole <../_autosummary/dxtb.integrals.types.DipoleIntegral>
+   Quadrupole <../_autosummary/dxtb.integrals.types.QuadrupoleIntegral>
 
-.. automodule:: dxtb._src.integral.types.base
-   :members:
+.. automodule:: dxtb._src.integral.types
+   :no-index:
    :show-inheritance:

docs/source/02_indepth/parametrizations.rst

@@ -8,6 +8,7 @@ Parametrizations
 
    BaseModel <parametrizations_base>
    Components <parametrizations_components>
+   Param <../_autosummary/dxtb.Param>
    Predefinded <parametrizations_predefined>
 
 .. automodule:: dxtb._src.param

docs/source/02_indepth/parametrizations_components.rst

@@ -49,7 +49,3 @@ Misc
 .. automodule:: dxtb._src.param.meta
    :members:
    :show-inheritance:
-
-.. automodule:: dxtb._src.param.utils
-   :members:
-   :show-inheritance:

docs/source/conf.py

@@ -33,16 +33,14 @@
 extensions = [
     "sphinx_design",
     "sphinx_copybutton",
-    "sphinx_design",
     "sphinx_togglebutton",
+    "sphinx.ext.napoleon",
     "sphinx.ext.autodoc",
-    "sphinx_autodoc_typehints",  # after autodoc
     "sphinx.ext.viewcode",
     "sphinx.ext.mathjax",
     "sphinx.ext.autosummary",
     "sphinx.ext.intersphinx",
     "sphinx.ext.viewcode",
-    "sphinx.ext.napoleon",
 ]
 
 html_theme = "sphinx_book_theme"
@@ -77,7 +75,7 @@
 intersphinx_mapping = {
     "numpy": ("https://numpy.org/doc/stable/", None),
     "pandas": ("https://pandas.pydata.org/docs/", None),
-    "pydantic": ("https://docs.pydantic.dev/latest/", None),
+    "pydantic": ("https://pydantic.dev/docs/validation/latest/", None),
     "python": ("https://docs.python.org/3", None),
     "tad_dftd3": ("https://tad-dftd3.readthedocs.io/en/latest/", None),
     "tad_dftd4": ("https://tad-dftd4.readthedocs.io/en/latest/", None),
@@ -87,16 +85,17 @@
         "https://tad-multicharge.readthedocs.io/en/latest/",
         None,
     ),
-    "torch": ("https://pytorch.org/docs/stable/", None),
+    "torch": ("https://docs.pytorch.org/docs/stable/", None),
 }
 
 
 # Configuration for sphinx-copybutton
 copybutton_prompt_text = ">>> |... "
 copybutton_prompt_is_regexp = True
 
-napoleon_google_docstring = False
-napoleon_use_param = False
+napoleon_google_docstring = True
+napoleon_numpy_docstring = True
+napoleon_use_param = True
 napoleon_use_ivar = True
 napoleon_use_rtype = True
 

src/dxtb/_src/calculators/gfn1.py

@@ -40,7 +40,7 @@ class GFN1Calculator(Calculator):
     Calculator for the GFN1-xTB method.
 
     This is a simple wrapper around the :class:`~dxtb.Calculator` class with
-    the :data:`GFN1-xTB <dxtb.GFN1_XTB>` parameters passed in as defaults.
+    the :data:`~dxtb.GFN1_XTB` parameters passed in as defaults.
     """
 
     def __init__(

src/dxtb/_src/calculators/gfn2.py

@@ -36,11 +36,10 @@
 
 
 class GFN2Calculator(Calculator):
-    """
-    Calculator for the GFN2-xTB method.
+    """Calculator for the GFN2-xTB method.
 
-    This is a simple wrapper around the :class:`dxtb.Calculator` class with the
-    :data:`GFN2-xTB <dxtb.GFN2_XTB>` parameters passed in as defaults.
+    This is a simple wrapper around the :class:`~dxtb.Calculator` class with the
+    :data:`~dxtb.GFN2_XTB` parameters passed in as defaults.
     """
 
     def __init__(

src/dxtb/_src/calculators/types/abc.py

@@ -131,11 +131,11 @@ def get_forces(
         :mod:`torch.func`'s function transforms (e.g.,
         :func:`torch.func.jacrev`).
 
-        Note
-        ----
-        Using :mod:`torch.func`'s function transforms can apparently be only
-        used once. Hence, for example, the Hessian and the dipole derivatives
-        cannot be both calculated with functorch.
+        .. note::
+
+            Using :mod:`torch.func`'s function transforms can apparently be only
+            used once. Hence, for example, the Hessian and the dipole
+            derivatives cannot be both calculated with functorch.
 
         Parameters
         ----------

src/dxtb/_src/calculators/types/analytical.py

@@ -79,11 +79,11 @@ def forces_analytical(
         :mod:`torch.func`'s function transforms (e.g.,
         :func:`torch.func.jacrev`).
 
-        Note
-        ----
-        Using :mod:`torch.func`'s function transforms can apparently be only
-        used once. Hence, for example, the Hessian and the dipole derivatives
-        cannot be both calculated with functorch.
+        .. note::
+
+            Using :mod:`torch.func`'s function transforms can apparently be only
+            used once. Hence, for example, the Hessian and the dipole
+            derivatives cannot be both calculated with functorch.
 
         Parameters
         ----------
@@ -242,11 +242,11 @@ def _forces_analytical(
         :mod:`torch.func`'s function transforms (e.g.,
         :func:`torch.func.jacrev`).
 
-        Note
-        ----
-        Using :mod:`torch.func`'s function transforms can apparently be only
-        used once. Hence, for example, the Hessian and the dipole derivatives
-        cannot be both calculated with functorch.
+        .. note::
+
+            Using :mod:`torch.func`'s function transforms can apparently be only
+            used once. Hence, for example, the Hessian and the dipole derivatives
+            cannot be both calculated with functorch.
 
         Parameters
         ----------
@@ -506,6 +506,7 @@ def dipole_analytical(
         r"""
         Analytically calculate the electric dipole moment :math:`\mu`.
 
+
         .. math::
 
             \mu = \dfrac{\partial E}{\partial F}

src/dxtb/_src/calculators/types/autograd.py

@@ -56,6 +56,7 @@ class AutogradCalculator(EnergyCalculator):
     This class provides properties via automatic differentiation.
     """
 
+    # Names of implemented methods of the Calculator.
     implemented_properties = EnergyCalculator.implemented_properties + [
         "forces",
         "hessian",
@@ -100,11 +101,11 @@ def forces(
         :mod:`torch.func`'s function transforms (e.g.,
         :func:`torch.func.jacrev`).
 
-        Note
-        ----
-        Using :mod:`torch.func`'s function transforms can apparently be only
-        used once. Hence, for example, the Hessian and the dipole derivatives
-        cannot be both calculated with functorch.
+        .. note::
+
+            Using :mod:`torch.func`'s function transforms can apparently be only
+            used once. Hence, for example, the Hessian and the dipole
+            derivatives cannot be both calculated with functorch.
 
         Parameters
         ----------
@@ -353,11 +354,11 @@ def vibration(
         :mod:`torch.func`'s function transforms (e.g.,
         :func:`torch.func.jacrev`).
 
-        Note
-        ----
-        Using :mod:`torch.func`'s function transforms can apparently be only
-        used once. Hence, for example, the Hessian and the dipole derivatives
-        cannot be both calculated with functorch.
+        .. note::
+
+            Using :mod:`torch.func`'s function transforms can apparently be only
+            used once. Hence, for example, the Hessian and the dipole
+            derivatives cannot be both calculated with functorch.
 
         Parameters
         ----------
@@ -421,11 +422,11 @@ def dipole(
         :mod:`torch.func`'s function transforms (e.g.,
         :func:`torch.func.jacrev`).
 
-        Note
-        ----
-        Using :mod:`torch.func`'s function transforms can apparently be only
-        used once. Hence, for example, the Hessian and the dipole derivatives
-        cannot be both calculated with functorch.
+        .. note::
+
+            Using :mod:`torch.func`'s function transforms can apparently be only
+            used once. Hence, for example, the Hessian and the dipole
+            derivatives cannot be both calculated with functorch.
 
         Parameters
         ----------
@@ -496,11 +497,11 @@ def dipole_deriv(
         :mod:`torch.func`'s function transforms (e.g.,
         :func:`torch.func.jacrev`).
 
-        Note
-        ----
-        Using :mod:`torch.func`'s function transforms can apparently be only
-        used once. Hence, for example, the Hessian and the dipole derivatives
-        cannot be both calculated with functorch.
+        .. note::
+
+            Using :mod:`torch.func`'s function transforms can apparently be only
+            used once. Hence, for example, the Hessian and the dipole
+            derivatives cannot be both calculated with functorch.
 
         Parameters
         ----------
@@ -578,11 +579,11 @@ def polarizability(
         :mod:`torch.func`'s function transforms (e.g.,
         :func:`torch.func.jacrev`).
 
-        Note
-        ----
-        Using :mod:`torch.func`'s function transforms can apparently be only
-        used once. Hence, for example, the Hessian and the dipole derivatives
-        cannot be both calculated with functorch.
+        .. note::
+
+            Using :mod:`torch.func`'s function transforms can apparently be only
+            used once. Hence, for example, the Hessian and the dipole
+            derivatives cannot be both calculated with functorch.
 
         Parameters
         ----------
@@ -686,11 +687,11 @@ def pol_deriv(
         :mod:`torch.func`'s function transforms (e.g.,
         :func:`torch.func.jacrev`).
 
-        Note
-        ----
-        Using :mod:`torch.func`'s function transforms can apparently be only
-        used once. Hence, for example, the Hessian and the dipole derivatives
-        cannot be both calculated with functorch.
+        .. note::
+
+            Using :mod:`torch.func`'s function transforms can apparently be only
+            used once. Hence, for example, the Hessian and the dipole
+            derivatives cannot be both calculated with functorch.
 
         Parameters
         ----------
@@ -779,11 +780,11 @@ def hyperpolarizability(
         :mod:`torch.func`'s function transforms (e.g.,
         :func:`torch.func.jacrev`).
 
-        Note
-        ----
-        Using :mod:`torch.func`'s function transforms can apparently be only
-        used once. Hence, for example, the Hessian and the dipole derivatives
-        cannot be both calculated with functorch.
+        .. note::
+
+            Using :mod:`torch.func`'s function transforms can apparently be only
+            used once. Hence, for example, the Hessian and the dipole
+            derivatives cannot be both calculated with functorch.
 
         Parameters
         ----------

src/dxtb/_src/calculators/types/base.py

@@ -489,12 +489,14 @@ def __init__(
             inferred.
         kwargs : Any
             Additional keyword arguments.
+
             - ``auto_int_level``: Automatically set the integral level based on
               the parametrization. Defaults to ``True``. This should only be
               turned off for testing purposes.
             - ``timer``: Enable the timer. Defaults to ``False``. The global
               timer can also be enabled by setting the environment variable
               ``DXTB_TIMER`` to ``1``.
+
         """
         if not timer.enabled and kwargs.pop("timer", False):
             timer.enable()