Deprecations (#977)

* fixed mailmap for contributors

* mnt: removed reshape calls on ndarrays

In later versions of numpy array.reshape will
be removed.
This commit fixes all that.

* moved orphan

Author: zerothi

.mailmap

@@ -9,17 +9,24 @@
 # gives no duplicates.
 
 A.H. Kole <a.h.kole@uu.nl>
+A.H. Kole <a.h.kole@uu.nl> <35299166+ahkole@users.noreply.github.com>
 Jonas Lundholm Bertelsen <drixi.b@gmail.com>
 Jonas Lundholm Bertelsen <drixi.b@gmail.com> Jonas L. B
 Jonas Lundholm Bertelsen <drixi.b@gmail.com> Jonas Lundholm Bertelsen <jolub@nanotech.dtu.dk>
+Gaetano Calogero <tanocalogero92@gmail.com>
+Gaetano Calogero <tanocalogero92@gmail.com> tanocalogero
+Isaac Alcon <ialcon8@gmail.com>
+Isaac Alcon <ialcon8@gmail.com> <160740748+ialcon@users.noreply.github.com>
 Nick Papior <nickpapior@gmail.com>
 Nick Papior <nickpapior@gmail.com> Nick Papior Andersen
 Nick Papior <nickpapior@gmail.com> Nick R. Papior
+Nils Wittemeier <nils.wittemeier@gmail.com>
+Nils Wittemeier <nils.wittemeier@gmail.com> <39985259+nils-wittemeier@users.noreply.github.com>
 Pol Febrer Calabozo <pfebrer96@gmail.com>
-Pol Febrer Calabozo <pfebrer96@gmail.com> pfebrer <42074085+pfebrer@users.noreply.github.com>
-Pol Febrer Calabozo <pfebrer96@gmail.com> pfebrer96 <42074085+pfebrer96@users.noreply.github.com>
+Pol Febrer Calabozo <pfebrer96@gmail.com> <42074085+pfebrer@users.noreply.github.com>
+Pol Febrer Calabozo <pfebrer96@gmail.com> <42074085+pfebrer96@users.noreply.github.com>
 Pol Febrer Calabozo <pfebrer96@gmail.com> Pol
 Pol Febrer Calabozo <pfebrer96@gmail.com> Pol Febrer
 Sofia Sanz Wuhl <sofiasw2@gmail.com>
-Sofia Sanz Wuhl <sofiasw2@gmail.com> Sofia Sanz <sofiasw2@gmail.com>
+Sofia Sanz Wuhl <sofiasw2@gmail.com> Sofia Sanz
 Thomas Frederiksen <thomas_frederiksen@ehu.eus>

changes/orphan.6.fix.rst

@@ -0,0 +1 @@
+Fixed reshape calls, removed from ndarray in later versions

src/sisl/_core/_ufuncs_geometry.py

@@ -815,14 +815,12 @@ def tile(geometry: Geometry, reps: int, axis: CellAxis) -> Geometry:
 
     # Our first repetition *must* be with
     # the former coordinate
-    xyz = np.tile(geometry.xyz, (reps, 1))
+    xyz = np.tile(geometry.xyz, (reps, 1)).reshape(reps, geometry.na, 3)
     # We may use broadcasting rules instead of repeating stuff
-    xyz.shape = (reps, geometry.na, 3)
-    nr = _a.arangei(reps)
-    nr.shape = (reps, 1, 1)
+    nr = _a.arangei(reps).reshape(reps, 1, 1)
     # Correct the unit-cell offsets
     xyz += nr * geometry.cell[axis, :]
-    xyz.shape = (-1, 3)
+    xyz = xyz.reshape(-1, 3)
 
     # Create the geometry and return it (note the smaller atoms array
     # will also expand via tiling)
@@ -977,15 +975,13 @@ def repeat(geometry: Geometry, reps: int, axis: CellAxis) -> Geometry:
 
     # Our first repetition *must* be with
     # the former coordinate
-    xyz = np.repeat(geometry.xyz, reps, axis=0)
+    xyz = np.repeat(geometry.xyz, reps, axis=0).reshape(geometry.na, reps, 3)
     # We may use broadcasting rules instead of repeating stuff
-    xyz.shape = (geometry.na, reps, 3)
-    nr = _a.arangei(reps)
-    nr.shape = (1, reps)
+    nr = _a.arangei(reps).reshape(1, reps)
     for i in range(3):
         # Correct the unit-cell offsets along `i`
         xyz[:, :, i] += nr * geometry.cell[axis, i]
-    xyz.shape = (-1, 3)
+    xyz = xyz.reshape(-1, 3)
 
     # Create the geometry and return it
     return geometry.__class__(xyz, atoms=geometry.atoms.repeat(reps), lattice=lattice)

src/sisl/_core/_ufuncs_sparse_geometry.py

@@ -110,8 +110,7 @@ def tile(SA: SparseAtom, reps: int, axis: int) -> SparseAtom:
 
     # Create new indptr, indices and D
     indptr = _ncol_to_indptr(np.tile(csr.ncol, reps))
-    indices = _a.emptyi([indptr[-1]])
-    indices.shape = (reps, -1)
+    indices = _a.emptyi([indptr[-1]]).reshape(reps, -1)
 
     # Now we should fill the data
     isc = geom.a2isc(col)
@@ -265,8 +264,7 @@ def tile(SO: SparseOrbital, reps: int, axis: int) -> SparseOrbital:
 
     # Create new indptr, indices and D
     indptr = _ncol_to_indptr(np.tile(ncol, reps))
-    indices = _a.emptyi([indptr[-1]])
-    indices.shape = (reps, -1)
+    indices = _a.emptyi([indptr[-1]]).reshape(reps, -1)
 
     # Now we should fill the data
     isc = geom.o2isc(col)
@@ -428,9 +426,9 @@ def sub(SA: SparseAtom, atoms: AtomsIndex) -> SparseAtom:
 
     idx = np.tile(atoms, SA.n_s)
     # Use broadcasting rules
-    idx.shape = (SA.n_s, -1)
+    idx = idx.reshape(SA.n_s, -1)
     idx += (_a.arangei(SA.n_s) * SA.na).reshape(-1, 1)
-    idx.shape = (-1,)
+    idx = idx.ravel()
 
     # Now create the new sparse orbital class
     S = SA.__class__(geom, SA.dim, SA.dtype, 1, **SA._cls_kwargs())
@@ -470,9 +468,9 @@ def sub(SO: SparseOrbital, atoms: AtomsIndex) -> SparseOrbital:
 
     idx = np.tile(orbs, SO.n_s)
     # Use broadcasting rules
-    idx.shape = (SO.n_s, -1)
+    idx = idx.reshape(SO.n_s, -1)
     idx += (_a.arangei(SO.n_s) * SO.no).reshape(-1, 1)
-    idx.shape = (-1,)
+    idx = idx.ravel()
 
     # Now create the new sparse orbital class
     S = SO.__class__(geom, SO.dim, SO.dtype, 1, **SO._cls_kwargs())

src/sisl/_core/grid.py

@@ -632,7 +632,7 @@ def index_truncate(self, index):
         index = _a.asarrayi(index)
         ndim = index.ndim
 
-        index.shape = (-1, 3)
+        index = index.reshape(-1, 3)
         log_and_reduce = np.logical_and.reduce
         index = index[log_and_reduce(0 <= index, axis=1), :]
         s = _a.asarrayi(self.shape).reshape(1, 3)
@@ -679,7 +679,7 @@ def _index_shape(self, shape):
         i[:, :, :, 1] = iy.reshape(1, -1, 1)
         i[:, :, :, 2] = iz.reshape(1, 1, -1)
         del ix, iy, iz
-        i.shape = (-1, 3)
+        i = i.reshape(-1, 3)
         i = take(i, idx, axis=0)
         del idx
 
@@ -723,7 +723,7 @@ def plane(v1, v2):
         i += sa * sc
         rxyz[:, i : i + sb * sc, :] += plane(b, c)
         del a, b, c, sa, sb, sc
-        rxyz.shape = (-1, 3)
+        rxyz = rxyz.reshape(-1, 3)
 
         # Get all indices of the cuboid planes
         return self.index(rxyz)

src/sisl/_core/orbital.py

@@ -726,8 +726,7 @@ def psi(self, r, m: int = 0):
             p[idx] = self.psi_spher(r, theta, phi, m, cos_phi=True)
             # Reduce memory immediately
             del idx, r, theta, phi
-        p.shape = s
-        return p
+        return p.reshape(s)
 
     def psi_spher(self, r, theta, phi, m: int = 0, cos_phi: bool = False):
         r"""Calculate :math:`\phi(|\mathbf r|, \theta, \phi)` at a given point (in spherical coordinates)
@@ -1588,8 +1587,7 @@ def psi(self, r):
             p[idx] = self.psi_spher(r, theta, phi, cos_phi=True)
             # Reduce memory immediately
             del idx, r, theta, phi
-        p.shape = s
-        return p
+        return p.reshape(s)
 
     def spher(self, theta, phi, cos_phi: bool = False):
         r"""Calculate the spherical harmonics of this orbital at a given point (in spherical coordinates)

src/sisl/_core/sparse.py

@@ -1371,12 +1371,12 @@ def __setitem__(self, key, data):
             ij = broadcast(i, j)
             if data.ndim == 0:
                 # enables checking for shape values
-                data.shape = (1,)
+                data = data.reshape(1)
             elif data.ndim == 1:
                 # this corresponds to:
                 #  [:, :, :] = data.reshape(1, 1, -1)
                 if ij.ndim == 2:
-                    data.shape = (1, -1)
+                    data = data.reshape(1, -1)
                 # if ij.ndim == 1 we shouldn't need
                 # to reshape data since it should correspond to each value
             elif data.ndim == 2:
@@ -1400,7 +1400,7 @@ def __setitem__(self, key, data):
                                 )
                             )
                     # flatten data
-                    data.shape = (-1,)
+                    data = data.ravel()
                 # ij.ndim == 1
                 # this should correspond to the diagonal specification case
                 # and we don't need to do anything
@@ -1410,7 +1410,7 @@ def __setitem__(self, key, data):
                     raise ValueError(
                         "could not broadcast input array from 3 dimensions into 2"
                     )
-                data.shape = (-1, data.shape[2])
+                data = data.reshape(-1, data.shape[2])
 
             # Now we need to figure out the final dimension and how to
             # assign elements.
@@ -1419,7 +1419,7 @@ def __setitem__(self, key, data):
                 k = atleast_1d(key[2])
 
                 if len(k) == 1 and data.ndim == 2:
-                    data.shape = (-1,)
+                    data = data.ravel()
 
                 if data.shape[0] == ij.size:
                     for (i, j), d in zip(ij, data):
@@ -1447,9 +1447,9 @@ def __setitem__(self, key, data):
         else:
             # Ensure correct shape
             if data.size == 1:
-                data.shape = (1, 1)
+                data = data.reshape(1, 1)
             else:
-                data.shape = (-1, self.shape[2])
+                data = data.reshape(-1, self.shape[2])
 
             # Now there are two cases
             if data.shape[0] == 1:

src/sisl/_core/sparse_geometry.py

@@ -823,7 +823,7 @@ def untile(
         # division operations.
         lsc = tile(self.geometry.lattice.sc_off, (1, reps)).reshape(-1, reps, 3)
         lsc[:, :, axis] = lsc[:, :, axis] * reps + _a.arangei(reps) - segment
-        lsc.shape = (-1, 3)
+        lsc = lsc.reshape(-1, 3)
 
         # now we have the *correct* lsc that corresponds to the
         # sc_off in the cut structure.
@@ -2949,9 +2949,9 @@ def toSparseAtom(self, dim: Optional[int] = None, dtype=None):
 
         # Create a conversion vector
         orb2atom = tile(geom.o2a(_a.arangei(geom.no)), geom.n_s)
-        orb2atom.shape = (-1, geom.no)
+        orb2atom = orb2atom.reshape(-1, geom.no)
         orb2atom += _a.arangei(geom.n_s).reshape(-1, 1) * geom.na
-        orb2atom.shape = (-1,)
+        orb2atom = orb2atom.ravel()
 
         # First convert all rows to the same
         csr = self._csr

src/sisl/_core/tests/test_lattice.py

@@ -310,8 +310,8 @@ def test_creation_rotate(self, setup):
 
         lattice = Lattice(param)
 
-        param.shape = (2, 3)
-        parama.shape = (2, 3)
+        param = param.reshape(2, 3)
+        parama = parama.reshape(2, 3)
 
         assert np.allclose(param, np.array(lattice.parameters()))
         assert np.allclose(parama, np.array(lattice.parameters(True)))

src/sisl/_core/tests/test_orbital.py

@@ -39,9 +39,9 @@ def test_spherical():
     xyz = spher2cart(r, theta, phi)
     s = xyz.shape[:-1]
     r1, theta1, phi1 = cart2spher(xyz)
-    r1.shape = s
-    theta1.shape = s
-    phi1.shape = s
+    r1 = r1.reshape(s)
+    theta1 = theta1.reshape(s)
+    phi1 = phi1.reshape(s)
     assert np.allclose(r, r1)
     assert np.allclose(theta, theta1[1:2, :, 1:2])
     assert np.allclose(phi, phi1[0:1, 0:1, :])