final cleaning

docs/api/index.rst

@@ -25,6 +25,7 @@ All methods and submodules are listed  :ref:`here <genindex>` and
    default_geom
    physics
    mixing
+   viz/index
    unit_constant
    utilities
 
@@ -38,5 +39,4 @@ All methods and submodules are listed  :ref:`here <genindex>` and
    :caption: Advanced usage
 
    nodes
-   viz/index
 

docs/api/viz/index.rst

@@ -4,12 +4,37 @@
 Visualization
 =============
 
-.. currentmodule:: sisl.viz
+.. module:: sisl.viz
 
-Visualizations of `sisl` objects and data.
+The visualization module contains tools to plot common visualizations, as well
+as to create custom visualizations that support multiple plotting backends
+automatically.
 
+Plot classes
+-----------------
+
+Plot classes are workflow classes that implement some specific plotting.
+
+.. autosummary::
+    :toctree: generated/
+
+    Plot
+    BandsPlot
+    FatbandsPlot
+    GeometryPlot
+    SitesPlot
+    GridPlot
+    WavefunctionPlot
+    PdosPlot
+
+Utilities
+---------
+
+Utilities to build custom plots
 
 .. autosummary::
-   :toctree: generated/
-   :recursive:
+    :toctree: generated/
 
+    get_figure
+    merge_plots
+    Figure

docs/toolbox/siesta/generated/sisl_toolbox.siesta.atom.AtomInput.rst

@@ -0,0 +1,50 @@
+sisl\_toolbox.siesta.atom.AtomInput
+===================================
+
+.. currentmodule:: sisl_toolbox.siesta.atom
+
+.. autoclass:: AtomInput
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+
+
+
+           ~AtomInput.ae
+
+
+           ~AtomInput.excite
+
+
+           ~AtomInput.from_input
+
+
+           ~AtomInput.from_yaml
+
+
+           ~AtomInput.pg
+
+
+           ~AtomInput.plot
+
+
+           ~AtomInput.write_all_electron
+
+
+           ~AtomInput.write_generation
+
+
+           ~AtomInput.write_header
+
+
+           ~AtomInput.write_test
+
+
+
+
+
+
+

docs/toolbox/transiesta/generated/sisl_toolbox.transiesta.poisson.solve_poisson.rst

@@ -0,0 +1,6 @@
+solve_poisson
+=============================================
+
+.. currentmodule:: sisl_toolbox.transiesta.poisson
+
+.. autofunction:: solve_poisson

docs/visualization/viz_module/index.rst

@@ -35,6 +35,7 @@ The following notebooks will help you develop a deeper understanding of what eac
     :name: viz-plotly-showcase-gallery
 
     showcase/GeometryPlot.ipynb
+    showcase/SitesPlot.ipynb
     showcase/GridPlot.ipynb
     showcase/BandsPlot.ipynb
     showcase/FatbandsPlot.ipynb

docs/visualization/viz_module/showcase/FatbandsPlot.ipynb

@@ -119,7 +119,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fatbands.split_groups(on=\"species\")"
+    "fatbands.split_orbs(on=\"species\", name=\"$species\")"
    ]
   },
   {

docs/visualization/viz_module/showcase/SitesPlot.ipynb

@@ -0,0 +1,160 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "tags": [
+     "notebook-header"
+    ]
+   },
+   "source": [
+    "[![GitHub issues by-label](https://img.shields.io/github/issues-raw/pfebrer/sisl/SitesPlot?style=for-the-badge)](https://github.com/pfebrer/sisl/labels/SitesPlot)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "    \n",
+    "    \n",
+    "SitesPlot\n",
+    "=========\n",
+    "\n",
+    "The `SitesPlot` is simply an adaptation of `GeometryPlot`'s machinery to any class that can be represented as sites in space. The main difference is that it doesn't show bonds, and also inputs with the word `atoms` are renamed to `sites`. Therefore, see `GeometryPlot`'s showcase notebook to understand the full customization possibilities.\n",
+    "\n",
+    "We are just going to show how you can plot the k points of a `BrillouinZone` object with it."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sisl\n",
+    "import sisl.viz\n",
+    "import numpy as np"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Let's create a circle of K points:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "g = sisl.geom.graphene()\n",
+    "\n",
+    "# Create the circle\n",
+    "bz = sisl.BrillouinZone.param_circle(\n",
+    "    g,\n",
+    "    kR=0.0085,\n",
+    "    origin= [0.0, 0.0, 0.0],\n",
+    "    normal= [0.0, 0.0, 1.0],\n",
+    "    N_or_dk=25,\n",
+    "    loop=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "And then generate some fake vectorial data for it:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data = np.zeros((len(bz), 3))\n",
+    "\n",
+    "data[:, 0] = - bz.k[:, 1]\n",
+    "data[:, 1] = bz.k[:, 0]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "And now plot the k points, showing the vectorial data as arrows:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Plot k points as sites\n",
+    "bz.plot.sites(\n",
+    "    axes=\"xy\", drawing_mode=\"line\", sites_style={\"color\": \"black\", \"size\": 2},\n",
+    "    arrows={\"data\": data, \"color\": \"red\", \"width\": 3, \"name\": \"Force\"}\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "-----\n",
+    "This next cell is just to create the thumbnail for the notebook in the docs "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "nbsphinx-thumbnail"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "thumbnail_plot = _\n",
+    "\n",
+    "if thumbnail_plot:\n",
+    "    thumbnail_plot.show(\"png\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "tags": [
+     "notebook-footer"
+    ]
+   },
+   "source": [
+    "-------------"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.15"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

src/sisl/nodes/node.py

@@ -76,7 +76,7 @@ class Node(NDArrayOperatorsMixin):
     _prev_evaluated_inputs: Dict[str, Any]
 
     # Current output value of the node
-    _output: Any
+    _output: Any = _blank
 
     # Nodes that are connected to this node's inputs
     _input_nodes: Dict[str, Node]
@@ -116,7 +116,7 @@ def __call__(self, *args, **kwargs):
     def setup(self, *args, **kwargs):
         """Sets up the node based on its initial inputs."""
         # Parse inputs into arguments.
-        bound_params = self.__class__.__signature__.bind_partial(*args, **kwargs)
+        bound_params = inspect.signature(self.function).bind_partial(*args, **kwargs)
         bound_params.apply_defaults()
 
         self._inputs = bound_params.arguments
@@ -192,7 +192,6 @@ def __init_subclass__(cls):
                 if parameter.kind == parameter.VAR_KEYWORD:
                     cls._kwargs_inputs_key = key
 
-            cls.__init__.__signature__ = init_sig
             cls.__signature__ = no_self_sig
 
         return super().__init_subclass__()
@@ -401,7 +400,7 @@ def get_tree(self):
 
     @property
     def default_inputs(self):
-        params = self.__class__.__signature__.bind_partial()
+        params = inspect.signature(self.function).bind_partial()
         params.apply_defaults()
         return params.arguments
 
@@ -486,7 +485,7 @@ def update_inputs(self, **inputs):
             explicit_kwargs = inputs.pop(self._kwargs_inputs_key, None)
 
         # Parse the inputs. We do this to separate the kwargs from the rest of the inputs.
-        bound = self.__class__.__signature__.bind_partial(**inputs)
+        bound = inspect.signature(self.function).bind_partial(**inputs)
         inputs = bound.arguments
 
         # Now that we have parsed the inputs, put back the args key (if any).

src/sisl/nodes/workflow.py

@@ -737,6 +737,7 @@ def function(*args, **kwargs):
         )
 
     def setup(self, *args, **kwargs):
+        self.nodes = self.dryrun_nodes
         super().setup(*args, **kwargs)
 
         self.nodes = self.dryrun_nodes.copy(inputs=self._inputs)

src/sisl/viz/__init__.py

@@ -5,13 +5,6 @@
 Visualization utilities
 =======================
 
-Various visualization modules are described here.
-
-
-Plotly
-======
-
-The plotly backend.
 """
 
 import os

src/sisl/viz/_plotables.py

@@ -182,7 +182,11 @@ def register_plotable(plotable, plot_cls=None, setting_key=None, plotting_func=N
     # Register the function in the plot_handler
     plot_handler.register(name, plot_dispatch, default=default, **kwargs)
 
-def register_data_source(data_source_cls, plot_cls, setting_key, name=None, default: Sequence[Type] = [], plot_handler_attr='plot', **kwargs):
+def register_data_source(
+    data_source_cls, plot_cls, setting_key, name=None, default: Sequence[Type] = [], plot_handler_attr='plot', 
+    data_source_init_kwargs: dict = {},
+    **kwargs
+):
 
     plot_cls_params = {
         name: param.replace(kind=inspect.Parameter.KEYWORD_ONLY) 
@@ -195,6 +199,15 @@ def register_data_source(data_source_cls, plot_cls, setting_key, name=None, defa
 
         signature = inspect.signature(func)
 
+        register_this = True
+        for k in data_source_init_kwargs.keys():
+            if k not in signature.parameters:
+                register_this = False
+                break
+
+        if not register_this:
+            continue
+
         new_parameters = []
         data_args = []
         replaced_data_args = {}
@@ -241,6 +254,10 @@ def _plot(obj, *args, __params_info=params_info, __signature=signature, **kwargs
                         data_kwargs[data_key] = bound.arguments.pop(k)
             except Exception as e:
                 raise TypeError(f"Error while parsing arguments to create the {data_source_cls.__name__}")
+
+            for k, v in data_source_init_kwargs.items():
+                if k not in data_kwargs:
+                    data_kwargs[k] = v
 
             data = data_source_cls.new(obj, *args, **data_kwargs)