Update environment

.github/workflows/tests.yml

@@ -18,13 +18,16 @@ jobs:
       matrix:
         os: ["ubuntu-latest"]
         python-version: ["3.10"]
-        test-file: [
+        test_file: [
           "tests/test_dcip.py",
           "tests/test_em.py",
           "tests/test_gpr.py tests/test_seismic.py",
           "tests/test_inversion.py",
           "tests/test_gravity.py tests/test_mag.py"
         ]
+    env:
+      PYTEST_DISABLE_PLUGIN_AUTOLOAD: "1"
+      MPLBACKEND: Agg        # avoid GUI backends import cost
 
     steps:
       - uses: actions/checkout@v4

environment-dev.yml

@@ -7,9 +7,9 @@ dependencies:
   - deepdish
   - discretize
   - empymod
-  - ipywidgets>=0.6.0
+  - ipywidgets
   - jupyter
-  - matplotlib=3.4.3
+  - matplotlib
   - Pillow
   - pip
   - pymatsolver

environment.yml

@@ -6,13 +6,13 @@ dependencies:
   - cvxopt
   - deepdish
   - discretize
-  - ipywidgets>=0.6.0
+  - ipywidgets
   - jupyter
-  - matplotlib<3.5
+  - matplotlib
   - Pillow
   - pip
   - pymatsolver
-  - python=3.10
+  - python=3.11
   - requests
   - simpeg
   - pip:

geoscilabs/dcip/DCIP_overburden_PseudoSection.py

@@ -397,7 +397,7 @@ def DC2Dsimulation(mtrue, flag="PoleDipole", nmax=8):
     for i in range(ntx):
         if flag == "PoleDipole":
             A = np.r_[xr[i], zloc]
-            B = np.r_[mesh.vectorCCx.min(), zloc]
+            B = np.r_[mesh.cell_centers_x.min(), zloc]
             if i < ntx - nmax + 1:
                 Mx = xr[i + 1 : i + 1 + nmax]
                 _, Mz = get_Surface(mtrue, Mx)
@@ -421,7 +421,7 @@ def DC2Dsimulation(mtrue, flag="PoleDipole", nmax=8):
             if i < ntx - nmax + 1:
                 Mx = xr[i + 2 : i + 2 + nmax]
                 _, Mz = get_Surface(mtrue, Mx)
-                Nx = np.ones(nmax) * mesh.vectorCCx.max()
+                Nx = np.ones(nmax) * mesh.cell_centers_x.max()
                 _, Nz = get_Surface(mtrue, Nx)
 
                 M = np.c_[Mx, Mz]
@@ -430,7 +430,7 @@ def DC2Dsimulation(mtrue, flag="PoleDipole", nmax=8):
             else:
                 Mx = xr[i + 2 : ntx + 2]
                 _, Mz = get_Surface(mtrue, Mx)
-                Nx = np.ones(ntx - i) * mesh.vectorCCx.max()
+                Nx = np.ones(ntx - i) * mesh.cell_centers_x.max()
                 _, Nz = get_Surface(mtrue, Nx)
                 M = np.c_[Mx, Mz]
                 N = np.c_[Nx, Nz]
@@ -483,7 +483,7 @@ def IP2Dsimulation(miptrue, sigmadc, flag="PoleDipole", nmax=8):
     for i in range(ntx):
         if flag == "PoleDipole":
             A = np.r_[xr[i], zloc]
-            B = np.r_[mesh.vectorCCx.min(), zloc]
+            B = np.r_[mesh.cell_centers_x.min(), zloc]
             if i < ntx - nmax + 1:
                 Mx = xr[i + 1 : i + 1 + nmax]
                 _, Mz = get_Surface(miptrue, Mx)
@@ -507,7 +507,7 @@ def IP2Dsimulation(miptrue, sigmadc, flag="PoleDipole", nmax=8):
             if i < ntx - nmax + 1:
                 Mx = xr[i + 2 : i + 2 + nmax]
                 _, Mz = get_Surface(miptrue, Mx)
-                Nx = np.ones(nmax) * mesh.vectorCCx.max()
+                Nx = np.ones(nmax) * mesh.cell_centers_x.max()
                 _, Nz = get_Surface(miptrue, Nx)
 
                 M = np.c_[Mx, Mz]
@@ -516,7 +516,7 @@ def IP2Dsimulation(miptrue, sigmadc, flag="PoleDipole", nmax=8):
             else:
                 Mx = xr[i + 2 : ntx + 2]
                 _, Mz = get_Surface(miptrue, Mx)
-                Nx = np.ones(ntx - i) * mesh.vectorCCx.max()
+                Nx = np.ones(ntx - i) * mesh.cell_centers_x.max()
                 _, Nz = get_Surface(miptrue, Nx)
                 M = np.c_[Mx, Mz]
                 N = np.c_[Nx, Nz]
@@ -862,7 +862,7 @@ def DCIP2Dfwdfun(
         ax=ax1,
         clim=(u.min(), u.max()),
         grid=True,
-        gridOpts={"color": "k", "alpha": 0.5},
+        grid_opts={"color": "k", "alpha": 0.5},
     )
 
     if which == "IP":

geoscilabs/dcip/DCWidgetPlate2_5D.py

@@ -1,21 +1,18 @@
 import numpy as np
 
-from scipy.constants import epsilon_0
-from scipy.ndimage.measurements import center_of_mass
-
 from ipywidgets import IntSlider, FloatSlider, FloatText, ToggleButtons
 
 import matplotlib
 import matplotlib.pyplot as plt
-import matplotlib.pylab as pylab
 from matplotlib.ticker import LogFormatter
 from matplotlib.path import Path
 import matplotlib.patches as patches
 
 from simpeg.utils.solver_utils import get_default_solver
 
 from discretize import TensorMesh
-from simpeg import maps, SolverLU, utils
+from discretize.utils import closest_points_index
+from simpeg import maps, utils
 from simpeg.utils import extract_core_mesh
 from simpeg.electromagnetics.static import resistivity as DC
 from ..base import widgetify
@@ -196,7 +193,7 @@ def get_Surface_Potentials(survey, src, field_obj):
     phiScale = 0.0
 
     if survey == "Pole-Dipole" or survey == "Pole-Pole":
-        refInd = utils.closestPoints(mesh, [xmax + 60.0, 0.0], gridLoc="CC")
+        refInd = closest_points_index(mesh, [xmax + 60.0, 0.0], grid_loc="CC")
         # refPoint =  CCLoc[refInd]
         # refSurfaceInd = np.where(xSurface == refPoint[0])
         # phiScale = np.median(phiSurface)
@@ -648,7 +645,7 @@ def PLOT(
         view=view,
         stream_opts=streamOpts,
         pcolor_opts=pcolorOpts,
-    )  # gridOpts={'color':'k', 'alpha':0.5}
+    )  # grid_opts={'color':'k', 'alpha':0.5}
 
     # Get plate corners
     plateCorners = getPlateCorners(xc, zc, dx, dz, rotAng)

geoscilabs/dcip/DCWidgetPlate_2D.py

@@ -1,20 +1,18 @@
 import numpy as np
 
-from scipy.constants import epsilon_0
-from scipy.ndimage.measurements import center_of_mass
-
-from ipywidgets import IntSlider, FloatSlider, FloatText, ToggleButtons
+from ipywidgets import FloatSlider, FloatText, ToggleButtons
 
 import matplotlib
 import matplotlib.pyplot as plt
-import matplotlib.pylab as pylab
 from matplotlib.ticker import LogFormatter
 from matplotlib.path import Path
 import matplotlib.patches as patches
 from simpeg.utils.solver_utils import get_default_solver
 
 from discretize import TensorMesh
-from simpeg import maps, SolverLU, utils
+from discretize.utils import closest_points_index
+
+from simpeg import maps, utils
 from simpeg.utils import extract_core_mesh
 from simpeg.electromagnetics.static import resistivity as DC
 
@@ -200,7 +198,7 @@ def get_Surface_Potentials(survey, src, field_obj):
     phiScale = 0.0
 
     if survey == "Pole-Dipole" or survey == "Pole-Pole":
-        refInd = utils.closestPoints(mesh, [xmax + 60.0, 0.0], gridLoc="CC")
+        refInd = closest_points_index(mesh, [xmax + 60.0, 0.0], grid_loc="CC")
         # refPoint =  CCLoc[refInd]
         # refSurfaceInd = np.where(xSurface == refPoint[0])
         # phiScale = np.median(phiSurface)
@@ -649,7 +647,7 @@ def plot_Surface_Potentials(
         view=view,
         stream_opts=streamOpts,
         pcolor_opts=pcolorOpts,
-    )  # gridOpts={'color':'k', 'alpha':0.5}
+    )  # grid_opts={'color':'k', 'alpha':0.5}
 
     # Get plate corners
     if dx >= 80.0:

geoscilabs/dcip/DCWidgetResLayer2D.py

@@ -3,6 +3,7 @@
 from simpeg.utils import extract_core_mesh
 import numpy as np
 from simpeg.electromagnetics.static import resistivity as DC
+from discretize.utils import closest_points_index
 import matplotlib
 import matplotlib.pyplot as plt
 import matplotlib.pylab as pylab
@@ -263,7 +264,7 @@ def get_Surface_Potentials(survey, src, field_obj):
     phiScale = 0.0
 
     if survey == "Pole-Dipole" or survey == "Pole-Pole":
-        refInd = utils.closestPoints(mesh, [xmax + 60.0, 0.0], gridLoc="CC")
+        refInd = closest_points_index(mesh, [xmax + 60.0, 0.0], grid_loc="CC")
         # refPoint =  CCLoc[refInd]
         # refSurfaceInd = np.where(xSurface == refPoint[0])
         # phiScale = np.median(phiSurface)
@@ -678,7 +679,7 @@ def plot_Surface_Potentials(
         view=view,
         stream_opts=streamOpts,
         pcolor_opts=pcolorOpts,
-    )  # gridOpts={'color':'k', 'alpha':0.5}
+    )  # grid_opts={'color':'k', 'alpha':0.5}
 
     # Get cylinder outline
     cylinderPoints = getCylinderPoints(xc, zc, r)

geoscilabs/dcip/DCWidgetResLayer2_5D.py

@@ -10,12 +10,13 @@
 from matplotlib.path import Path
 import matplotlib.patches as patches
 
-from simpeg import maps, SolverLU, utils
+from simpeg import maps, utils
 from simpeg.utils import extract_core_mesh
 from simpeg.electromagnetics.static import resistivity as DC
 from simpeg.utils.solver_utils import get_default_solver
 
 from discretize import TensorMesh
+from discretize.utils import closest_points_index
 
 from ipywidgets import interact, IntSlider, FloatSlider, FloatText, ToggleButtons
 
@@ -266,7 +267,7 @@ def get_Surface_Potentials(survey, src, field_obj):
     phiScale = 0.0
 
     if survey == "Pole-Dipole" or survey == "Pole-Pole":
-        refInd = utils.closestPoints(mesh, [xmax + 60.0, 0.0], gridLoc="CC")
+        refInd = closest_points_index(mesh, [xmax + 60.0, 0.0], grid_loc="CC")
         # refPoint =  CCLoc[refInd]
         # refSurfaceInd = np.where(xSurface == refPoint[0])
         # phiScale = np.median(phiSurface)
@@ -684,7 +685,7 @@ def PLOT(
         view=view,
         stream_opts=streamOpts,
         pcolor_opts=pcolorOpts,
-    )  # gridOpts={'color':'k', 'alpha':0.5}
+    )  # grid_opts={'color':'k', 'alpha':0.5}
 
     # Get cylinder outline
     cylinderPoints = getCylinderPoints(xc, zc, r)

geoscilabs/dcip/DCWidget_Overburden_2_5D.py

@@ -10,17 +10,15 @@
 import matplotlib.patches as patches
 
 from ipywidgets import (
-    interact,
-    interact_manual,
-    IntSlider,
     FloatSlider,
     FloatText,
     ToggleButtons,
     fixed,
-    Widget,
 )
 
 from discretize import TensorMesh
+from discretize.utils import closest_points_index
+
 from simpeg import maps, utils
 from simpeg.utils import extract_core_mesh
 from simpeg.electromagnetics.static import resistivity as DC
@@ -216,7 +214,7 @@ def get_Surface_Potentials(mtrue, survey, src, field_obj):
     phiScale = 0.0
 
     if survey == "Pole-Dipole" or survey == "Pole-Pole":
-        refInd = utils.closestPoints(mesh, [xmax + 60.0, 0.0], gridLoc="CC")
+        refInd = closest_points_index(mesh, [xmax + 60.0, 0.0], grid_loc="CC")
         # refPoint =  CCLoc[refInd]
         # refSurfaceInd = np.where(xSurface == refPoint[0])
         # phiScale = np.median(phiSurface)
@@ -689,7 +687,7 @@ def PLOT(
         view=view,
         stream_opts=streamOpts,
         pcolor_opts=pcolorOpts,
-    )  # gridOpts ={'color':'k', 'alpha':0.5}
+    )  # grid_opts ={'color':'k', 'alpha':0.5}
 
     # Get cylinder outline
     cylinderPoints = getCylinderPoints(xc, zc, ellips_a, ellips_b)

geoscilabs/dcip/DC_Pseudosections.py

@@ -542,7 +542,7 @@ def DC2Dfwdfun(
             ax=ax1,
             clim=(1, 3),
             grid=True,
-            gridOpts={"color": "k", "alpha": 0.5},
+            grid_opts={"color": "k", "alpha": 0.5},
         )
         cb1ticks = [1.0, 2.0, 3.0]
         cb1 = plt.colorbar(dat1[0], ax=ax1, ticks=cb1ticks)
@@ -582,7 +582,7 @@ def DC2Dfwdfun(
             ax=ax1,
             clim=(1, 3),
             grid=True,
-            gridOpts={"color": "k", "alpha": 0.5},
+            grid_opts={"color": "k", "alpha": 0.5},
         )
         cb1ticks = [1.0, 2.0, 3.0]
         cb1 = plt.colorbar(dat1[0], ax=ax1, ticks=cb1ticks)

geoscilabs/dcip/DC_cylinder.py

@@ -9,6 +9,7 @@
 
 from simpeg.utils.solver_utils import get_default_solver
 from discretize import TensorMesh
+from discretize.utils import closest_points_index
 
 from simpeg import maps, utils
 from simpeg.utils import extract_core_mesh, mkvc
@@ -139,7 +140,7 @@ def get_Surface_Potentials(survey, src, field_obj):
     phiScale = 0.0
 
     if survey == "Pole-Dipole" or survey == "Pole-Pole":
-        refInd = utils.closestPoints(mesh, [xmax + 60.0, 0.0], gridLoc="CC")
+        refInd = closest_points_index(mesh, [xmax + 60.0, 0.0], grid_loc="CC")
         phiScale = phi[refInd]
         phiSurface = phiSurface - phiScale
 
@@ -528,7 +529,7 @@ def plot_Surface_Potentials(
         view=view,
         stream_opts=streamOpts,
         pcolor_opts=pcolorOpts,
-    )  # gridOpts={'color':'k', 'alpha':0.5}
+    )  # grid_opts={'color':'k', 'alpha':0.5}
 
     # Get cylinder outline
     cylinderPoints = getCylinderPoints(xc, zc, r)

geoscilabs/em/InductionLoop.py

@@ -156,7 +156,7 @@ def calc_PrimaryRegion(self, X, Z):
         bot = Z ** 2 + (s - a1) ** 2
 
         try:
-            bot[bot==0] = np.NaN
+            bot[bot==0] = np.nan
         except:
             pass
 
@@ -219,7 +219,7 @@ def calc_PrimaryLoop(self):
 
         bot = z ** 2 + (s - a1) ** 2
         try:
-            bot[bot == 0.0] = np.NaN
+            bot[bot == 0.0] = np.nan
         except:
             pass
 
@@ -424,7 +424,7 @@ def plot_PrimaryRegion(self, X, Z, Bpx, Bpz, Babs, ax):
         ax.plot(xRx, zRx, color="black", linewidth=6)
         ax.plot(xRx, zRx, color=((0.4, 0.4, 0.4)), linewidth=4)
         # Cplot = ax.contourf(X,Z,np.log10(Babs),40,cmap='ocean_r')
-        Babs[Babs == 0.0] = np.NaN
+        Babs[Babs == 0.0] = np.nan
         Cplot = ax.contourf(X, Z, np.log10(1e9 * Babs), 40, cmap="viridis")
         cbar = plt.colorbar(Cplot, ax=ax, pad=0.02)
         cbar.set_label(

geoscilabs/em/InductionSphereFEM.py

@@ -262,7 +262,7 @@ def plotAnomalyXYplane(Ax, f, X, Y, Z, H, Comp, Phase):
     H = np.abs(H)
     MAX = np.max(H)
 
-    H[H == 0] = np.NaN
+    H[H == 0] = np.nan
     H = np.log10(tol * H / MAX)
 
     Sign[H < 0] = 0.0