fixed remaining old calls

Author: zerothi

src/sisl/geom/bilayer.py

@@ -132,7 +132,7 @@ def bilayer(
             top.tile(rep, axis=0)
             .tile(rep, axis=1)
             .move(align_vec)
-            .rotate(theta, "z", rad=True, what="abc+xyz")
+            .rotate([theta, "z"], rad=True, what="abc+xyz")
         )
 
         inside_idx = cell_box.within_index(top.xyz)
@@ -166,7 +166,7 @@ def bilayer(
         vec = bilayer.cell[0] + bilayer.cell[1]
         vec_costh = vec[0] / vec.dot(vec) ** 0.5
         vec_th = -acos(vec_costh)
-        bilayer = bilayer.move(-offset).rotate(vec_th, "z", rad=True, what="xyz+abc")
+        bilayer = bilayer.move(-offset).rotate([vec_th, "z"], rad=True, what="xyz+abc")
 
     # Sanity check
     assert len(bilayer) == natoms

src/sisl/geom/nanoribbon.py

@@ -125,7 +125,7 @@ def nanoribbon(
                 x.dot([1, 0, 0]) / x.dot(x) ** 0.5
             )  # angle of vectors, x and b=[1, 0, 0]
             ribbon = ribbon.rotate(
-                -angle, "z", origin=ribbon.xyz[0], rad=True, what="abc+xyz"
+                (-angle, "z"), origin=ribbon.xyz[0], rad=True, what="abc+xyz"
             )
             # first lattice vector strictly along x
             ribbon.cell[0, 1] = 0

src/sisl/io/siesta/tests/test_grid.py

@@ -38,7 +38,7 @@ def test_si_pdos_kgrid_grid_fdf(sisl_files):
 
 def test_grid_read_write(sisl_tmp):
     path = sisl_tmp("grid.bin")
-    lat = sisl.Lattice(1).rotate(45, "z").rotate(45, "x")
+    lat = sisl.Lattice(1).rotate((45, "z")).rotate((45, "x"))
     grid = sisl.Grid([4, 5, 6], lattice=lat)
     grid.grid = np.random.rand(*grid.shape)
     gridSile = sisl.io.siesta.gridSileSiesta

src/sisl/io/tests/test_object.py

@@ -264,7 +264,7 @@ def test_write(self, sisl_tmp, sisl_system, sile):
         if issubclass(sile, SileCDF):
             pytest.importorskip("netCDF4")
 
-        G = sisl_system.g.rotate(-30, sisl_system.g.cell[2, :], what="xyz+abc")
+        G = sisl_system.g.rotate([-30, sisl_system.g.cell[2]], what="xyz+abc")
         G.set_nsc([1, 1, 1])
         f = sisl_tmp("test_write")
 
@@ -275,7 +275,7 @@ def test_read_write_lattice(self, sisl_tmp, sisl_system, sile):
         if issubclass(sile, SileCDF):
             pytest.importorskip("netCDF4")
 
-        L = sisl_system.g.rotate(-30, sisl_system.g.cell[2, :], what="xyz+abc").lattice
+        L = sisl_system.g.rotate([-30, sisl_system.g.cell[2]], what="xyz+abc").lattice
         L.set_nsc([1, 1, 1])
         f = sisl_tmp("test_read_write_geom.win")
 
@@ -307,7 +307,7 @@ def test_read_write_lattice(self, sisl_tmp, sisl_system, sile):
         if issubclass(sile, SileCDF):
             pytest.importorskip("netCDF4")
 
-        L = sisl_system.g.rotate(-30, sisl_system.g.cell[2, :], what="xyz+abc").lattice
+        L = sisl_system.g.rotate((-30, sisl_system.g.cell[2]), what="xyz+abc").lattice
         L.set_nsc([1, 1, 1])
         f = sisl_tmp("test_read_write_geom.win")
 
@@ -333,7 +333,7 @@ def test_read_write_geometry(self, sisl_tmp, sisl_system, sile):
         if issubclass(sile, SileCDF):
             pytest.importorskip("netCDF4")
 
-        G = sisl_system.g.rotate(-30, sisl_system.g.cell[2, :], what="xyz+abc")
+        G = sisl_system.g.rotate((-30, sisl_system.g.cell[2]), what="xyz+abc")
         G.set_nsc([1, 1, 1])
         f = sisl_tmp("test_read_write_geom.win")
 
@@ -380,7 +380,7 @@ def test_read_write_hamiltonian(self, sisl_tmp, sisl_system, sile):
         if issubclass(sile, _gfSileSiesta):
             pytest.skip("gfSileSiesta handles writing Hamiltonians in a special way")
 
-        G = sisl_system.g.rotate(-30, sisl_system.g.cell[2, :], what="xyz+abc")
+        G = sisl_system.g.rotate([-30, sisl_system.g.cell[2]], what="xyz+abc")
         H = Hamiltonian(G)
         H.construct([[0.1, 1.45], [0.1, -2.7]])
         f = sisl_tmp("test_read_write_hamiltonian.win")
@@ -409,7 +409,7 @@ def test_read_write_density_matrix(self, sisl_tmp, sisl_system, sile):
         if issubclass(sile, SileCDF):
             pytest.importorskip("netCDF4")
 
-        G = sisl_system.g.rotate(-30, sisl_system.g.cell[2, :], what="xyz+abc")
+        G = sisl_system.g.rotate((-30, sisl_system.g.cell[2]), what="xyz+abc")
         DM = DensityMatrix(G, orthogonal=True)
         DM.construct([[0.1, 1.45], [0.1, -2.7]])
 
@@ -440,7 +440,7 @@ def test_read_write_energy_density_matrix(self, sisl_tmp, sisl_system, sile):
         if issubclass(sile, SileCDF):
             pytest.importorskip("netCDF4")
 
-        G = sisl_system.g.rotate(-30, sisl_system.g.cell[2, :], what="xyz+abc")
+        G = sisl_system.g.rotate((-30, sisl_system.g.cell[2]), what="xyz+abc")
         EDM = EnergyDensityMatrix(G, orthogonal=True)
         EDM.construct([[0.1, 1.45], [0.1, -2.7]])
 
@@ -473,7 +473,7 @@ def test_read_write_hamiltonian_overlap(self, sisl_tmp, sisl_system, sile):
         if issubclass(sile, _gfSileSiesta):
             pytest.skip("gfSileSiesta handles writing Hamiltonians in a special way")
 
-        G = sisl_system.g.rotate(-30, sisl_system.g.cell[2, :], what="xyz+abc")
+        G = sisl_system.g.rotate((-30, sisl_system.g.cell[2]), what="xyz+abc")
         H = Hamiltonian(G, orthogonal=False)
         H.construct([[0.1, 1.45], [(0.1, 1), (-2.7, 0.1)]])
 
@@ -504,7 +504,7 @@ def test_read_write_grid(self, sisl_tmp, sisl_system, sile):
         if issubclass(sile, SileCDF):
             pytest.importorskip("netCDF4")
 
-        g = sisl_system.g.rotate(-30, sisl_system.g.cell[2, :], what="xyz+abc")
+        g = sisl_system.g.rotate((-30, sisl_system.g.cell[2]), what="xyz+abc")
         G = Grid([10, 11, 12])
         G[:, :, :] = np.random.rand(10, 11, 12)