Merge pull request #753 from zerothi/removeplot

removed sisl.plot from the code base

CHANGELOG.md

@@ -77,6 +77,7 @@ we hit release version 1.0.0.
   be done for assigning matrix elements (it fills with 0's).
 
 ### Removed
+- `sisl.plot` is removed (`sisl.viz` is replacing it!)
 - `cell` argument for `Geometry.translate/move` (it never worked)
 - removed `Selector` and `TimeSelector`, they were never used internally
 

src/sisl/__init__.py

@@ -87,9 +87,6 @@
 # import the common options used
 from ._common import *
 
-# Import plot routine
-from ._plot import plot as plot
-
 # Import warning classes
 # We currently do not import warn and info
 # as they are too generic names in case one does from sisl import *

src/sisl/_core/geometry.py

@@ -34,7 +34,6 @@
 )
 
 import sisl._array as _a
-import sisl._plot as plt
 from sisl._category import Category, GenericCategory
 from sisl._dispatch_class import _Dispatchs
 from sisl._dispatcher import AbstractDispatch, ClassDispatcher, TypeDispatcher
@@ -3112,81 +3111,6 @@ def o2sc(self, orbitals: OrbitalsIndex) -> ndarray:
         """
         return self.lattice.offset(self.o2isc(orbitals))
 
-    def __plot__(
-        self,
-        axis=None,
-        lattice: bool = True,
-        axes=False,
-        atom_indices: bool = False,
-        *args,
-        **kwargs,
-    ):
-        """Plot the geometry in a specified ``matplotlib.Axes`` object.
-
-        Parameters
-        ----------
-        axis : array_like, optional
-           only plot a subset of the axis, defaults to all axis
-        lattice : bool, optional
-           If `True` also plot the lattice structure
-        atom_indices : bool, optional
-           if true, also add atomic numbering in the plot (0-based)
-        axes : bool or matplotlib.Axes, optional
-           the figure axes to plot in (if ``matplotlib.Axes`` object).
-           If `True` it will create a new figure to plot in.
-           If `False` it will try and grap the current figure and the current axes.
-        """
-        # Default dictionary for passing to newly created figures
-        d = dict()
-
-        colors = np.linspace(0, 1, num=self.atoms.nspecies, endpoint=False)
-        colors = colors[self.atoms.species]
-        if "s" in kwargs:
-            area = kwargs.pop("s")
-        else:
-            area = _a.arrayd(self.atoms.Z)
-            area[:] *= 20 * np.pi / area.min()
-
-        if axis is None:
-            axis = [0, 1, 2]
-
-        # Ensure we have a new 3D Axes3D
-        if len(axis) == 3:
-            d["projection"] = "3d"
-
-        # The Geometry determines the axes, then we pass it to supercell.
-        axes = plt.get_axes(axes, **d)
-
-        # Start by plotting the supercell
-        if lattice:
-            axes = self.lattice.__plot__(axis, axes=axes, *args, **kwargs)
-
-        # Create short-hand
-        xyz = self.xyz
-
-        if axes.__class__.__name__.startswith("Axes3D"):
-            # We should plot in 3D plots
-            axes.scatter(xyz[:, 0], xyz[:, 1], xyz[:, 2], s=area, c=colors, alpha=0.8)
-            axes.set_zlabel("Ang")
-            if atom_indices:
-                for i, loc in enumerate(xyz):
-                    axes.text(
-                        loc[0], loc[1], loc[2], str(i), verticalalignment="bottom"
-                    )
-
-        else:
-            axes.scatter(xyz[:, axis[0]], xyz[:, axis[1]], s=area, c=colors, alpha=0.8)
-            if atom_indices:
-                for i, loc in enumerate(xyz):
-                    axes.text(
-                        loc[axis[0]], loc[axis[1]], str(i), verticalalignment="bottom"
-                    )
-
-        axes.set_xlabel("Ang")
-        axes.set_ylabel("Ang")
-
-        return axes
-
     def equal(self, other: GeometryLike, R: bool = True, tol: float = 1e-4) -> bool:
         """Whether two geometries are the same (optional not check of the orbital radius)
 

src/sisl/_core/lattice.py

@@ -18,7 +18,6 @@
 from numpy import dot, ndarray
 
 import sisl._array as _a
-import sisl._plot as plt
 from sisl._dispatch_class import _Dispatchs
 from sisl._dispatcher import AbstractDispatch, ClassDispatcher, TypeDispatcher
 from sisl._internal import set_module
@@ -1062,72 +1061,6 @@ def __setstate__(self, d):
         self.__init__(d["cell"], d["nsc"], d["origin"])
         self.sc_off = d["sc_off"]
 
-    def __plot__(self, axis=None, axes=False, *args, **kwargs):
-        """Plot the supercell in a specified ``matplotlib.Axes`` object.
-
-        Parameters
-        ----------
-        axis : array_like, optional
-           only plot a subset of the axis, defaults to all axis
-        axes : bool or matplotlib.Axes, optional
-           the figure axes to plot in (if ``matplotlib.Axes`` object).
-           If ``True`` it will create a new figure to plot in.
-           If ``False`` it will try and grap the current figure and the current axes.
-        """
-        # Default dictionary for passing to newly created figures
-        d = dict()
-
-        # Try and default the color and alpha
-        if "color" not in kwargs and len(args) == 0:
-            kwargs["color"] = "k"
-        if "alpha" not in kwargs:
-            kwargs["alpha"] = 0.5
-
-        if axis is None:
-            axis = [0, 1, 2]
-
-        # Ensure we have a new 3D Axes3D
-        if len(axis) == 3:
-            d["projection"] = "3d"
-
-        axes = plt.get_axes(axes, **d)
-
-        # Create vector objects
-        o = self.origin
-        v = []
-        for a in axis:
-            v.append(np.vstack((o[axis], o[axis] + self.cell[a, axis])))
-        v = np.array(v)
-
-        if axes.__class__.__name__.startswith("Axes3D"):
-            # We should plot in 3D plots
-            for vv in v:
-                axes.plot(vv[:, 0], vv[:, 1], vv[:, 2], *args, **kwargs)
-
-            v0, v1 = v[0], v[1] - o
-            axes.plot(
-                v0[1, 0] + v1[:, 0],
-                v0[1, 1] + v1[:, 1],
-                v0[1, 2] + v1[:, 2],
-                *args,
-                **kwargs,
-            )
-
-            axes.set_zlabel("Ang")
-
-        else:
-            for vv in v:
-                axes.plot(vv[:, 0], vv[:, 1], *args, **kwargs)
-
-            v0, v1 = v[0], v[1] - o[axis]
-            axes.plot(v0[1, 0] + v1[:, 0], v0[1, 1] + v1[:, 1], *args, **kwargs)
-            axes.plot(v1[1, 0] + v0[:, 0], v1[1, 1] + v0[:, 1], *args, **kwargs)
-
-        axes.set_xlabel("Ang")
-        axes.set_ylabel("Ang")
-
-        return axes
-
 
 new_dispatch = Lattice.new
 to_dispatch = Lattice.to

src/sisl/_core/orbital.py

@@ -25,7 +25,6 @@
 from scipy.interpolate import UnivariateSpline
 
 import sisl._array as _a
-import sisl._plot as plt
 from sisl._internal import set_module
 from sisl.constant import a0
 from sisl.messages import warn
@@ -279,52 +278,6 @@ def equal(self, other, psi: bool = False, radial: bool = False):
     def __eq__(self, other):
         return self.equal(other)
 
-    def __plot__(self, harmonics: bool = False, axes=False, *args, **kwargs):
-        """Plot the orbital radial/spherical harmonics
-
-        Parameters
-        ----------
-        harmonics : bool, optional
-           if `True` the spherical harmonics will be plotted in a 3D only plot a subset of the axis, defaults to all axis
-        axes : bool or matplotlib.Axes, optional
-           the figure axes to plot in (if ``matplotlib.Axes`` object).
-           If ``True`` it will create a new figure to plot in.
-           If ``False`` it will try and grap the current figure and the current axes.
-        """
-        d = dict()
-
-        if harmonics:
-            # We are plotting the harmonic part
-            d["projection"] = "polar"
-
-        axes = plt.get_axes(axes, **d)
-
-        # Add plots
-        if harmonics:
-            # Calculate the spherical harmonics
-            theta, phi = np.meshgrid(np.arange(360), np.arange(180) - 90)
-            s = self.spher(np.radians(theta), np.radians(phi))
-
-            # Plot data
-            cax = axes.contourf(theta, phi, s, *args, **kwargs)
-            cax.set_clim(s.min(), s.max())
-            axes.get_figure().colorbar(cax)
-            axes.set_title(r"${}$".format(self.name(True)))
-            # I don't know how exactly to handle this...
-            # axes.set_xlabel(r"Azimuthal angle $\theta$")
-            # axes.set_ylabel(r"Polar angle $\phi$")
-
-        else:
-            # Plot the radial function and 5% above 0 value
-            r = np.linspace(0, self.R * 1.05, 1000)
-            f = self.radial(r)
-            axes.plot(r, f, *args, **kwargs)
-            axes.set_xlim(left=0)
-            axes.set_xlabel("Radius [Ang]")
-            axes.set_ylabel(r"$f(r)$ [1/Ang$^{3/2}$]")
-
-        return axes
-
     def toGrid(
         self, precision: float = 0.05, c: float = 1.0, R=None, dtype=np.float64, atom=1
     ):