Some docs improvements

docs/src/conf.py

@@ -48,6 +48,19 @@
     "reference_url": {"meshlode": None},
     "prefer_full_module": ["meshlode"],
 }
+
+autoclass_content = "both"
+autodoc_member_order = "bysource"
+autodoc_typehints = "both"
+autodoc_typehints_format = "short"
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "torch": ("https://pytorch.org/docs/stable/", None),
+    "metatensor": ("https://lab-cosmo.github.io/metatensor/latest/", None),
+}
+
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for

docs/src/references/index.rst

@@ -14,3 +14,4 @@ functions toegther you might take a look at the :ref:`userdoc-how-to` section.
     calculators/index
     fourier_convolution
     mesh_interpolator
+    system

docs/src/references/system.rst

@@ -0,0 +1,4 @@
+.. automodule:: meshlode.system
+    :members:
+    :undoc-members:
+    :show-inheritance:

docs/src/sg_execution_times.rst

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:00.001** total execution time for 1 file **from all galleries**:
+**00:00.000** total execution time for 1 file **from all galleries**:
 
 .. container::
 
@@ -33,5 +33,5 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_examples_madelung.py` (``../../examples/madelung.py``)
-     - 00:00.001
+     - 00:00.000
      - 0.0

src/meshlode/calculators.py

@@ -36,7 +36,7 @@ class MeshPotential(torch.nn.Module):
         that will be used along each axis.
     :param interpolation_order: Interpolation order for mapping onto the grid, where an
         interpolation order of p corresponds to interpolation by a polynomial of degree
-        p-1 (e.g. p=4 for cubic interpolation).
+        ``p-1`` (e.g. ``p=4`` for cubic interpolation).
     :param subtract_self: bool. If set to true, subtract from the features of an atom
         the contributions to the potential arising from that atom itself (but not the
         periodic images).
@@ -47,19 +47,35 @@ class MeshPotential(torch.nn.Module):
     >>> import torch
     >>> from meshlode import MeshPotential, System
 
-    >>> # Define simple example structure having the CsCl structure
+    Define simple example structure having the CsCl structure
+
     >>> positions = torch.tensor([[0, 0, 0], [0.5, 0.5, 0.5]])
     >>> atomic_numbers = torch.tensor([55, 17])  # Cs and Cl
     >>> frame = System(species=atomic_numbers, positions=positions, cell=torch.eye(3))
 
-    >>> # Compute features
+    Compute features
+
     >>> MP = MeshPotential(
     ...     atomic_gaussian_width=0.2, mesh_spacing=0.1, interpolation_order=4
     ... )
     >>> features = MP.compute(frame)
-    >>> keys = features.keys  # print to see all species combinations
+
+    All species combinations
+
+    >>> features.keys
+    Labels(
+        species_center  species_neighbor
+              17               17
+              17               55
+              55               17
+              55               55
+    )
     >>> block_ClCl = features.block({"species_center": 17, "species_neighbor": 17})
-    >>> values = block_ClCl.values  # the Cl-potential at the position of the Cl atom
+
+    The Cl-potential at the position of the Cl atom
+
+    >>> block_ClCl.values
+    tensor([[1.3755]])
 
     """
 
@@ -91,7 +107,6 @@ def forward(
         return res
         # return 0.
 
-    # @torch.jit.export
     def compute(
         self,
         frames: Union[List[System], System],