misc: Lint some notebooks

JDBetteridge · JDBetteridge · commit 8d0c3253fcd6 · 2026-01-04T23:27:44.000Z
diff --git a/examples/.ruff.toml b/examples/.ruff.toml
@@ -0,0 +1,6 @@
+# Extend the `pyproject.toml` file in the parent directory
+extend = "../pyproject.toml"
+
+# Use a different line length for examples only
+# TODO: Shorten line lengths in examples
+line-length = 120
diff --git a/examples/cfd/01_convection.ipynb b/examples/cfd/01_convection.ipynb
@@ -109,7 +109,7 @@
     "# Repeat initialisation, so we can re-run the cell\n",
     "init_hat(field=u, dx=dx, dy=dy, value=2.)\n",
     "\n",
-    "for n in range(nt + 1):\n",
+    "for _ in range(nt + 1):\n",
     "    # Copy previous result into a new buffer\n",
     "    un = u.copy()\n",
     "\n",
@@ -122,7 +122,8 @@
     "    u[-1, :] = 1.  # right\n",
     "    u[:, 0] = 1.  # bottom\n",
     "    u[:, -1] = 1.  # top\n",
-    "    # Note that in the above expressions the NumPy index -1 corresponds to the final point of the array along the indexed dimension,\n",
+    "    # Note that in the above expressions the NumPy index -1 corresponds to the\n",
+    "    # final point of the array along the indexed dimension,\n",
     "    #    i.e. here u[-1, :] is equivalent to u[80, :].\n"
    ]
   },
diff --git a/examples/cfd/01_convection_revisited.ipynb b/examples/cfd/01_convection_revisited.ipynb
@@ -103,7 +103,7 @@
     "# Repeat initialisation, so we can re-run the cell\n",
     "init_smooth(field=u, dx=dx, dy=dy)\n",
     "\n",
-    "for n in range(nt + 1):\n",
+    "for _ in range(nt + 1):\n",
     "    # Copy previous result into a new buffer\n",
     "    un = u.copy()\n",
     "\n",
diff --git a/examples/cfd/02_convection_nonlinear.ipynb b/examples/cfd/02_convection_nonlinear.ipynb
@@ -110,7 +110,7 @@
    ],
    "source": [
     "# NBVAL_IGNORE_OUTPUT\n",
-    "for n in range(nt + 1):  # loop across number of time steps\n",
+    "for _ in range(nt + 1):  # loop across number of time steps\n",
     "    un = u.copy()\n",
     "    vn = v.copy()\n",
     "    u[1:, 1:] = (un[1:, 1:] -\n",
diff --git a/examples/cfd/03_diffusion.ipynb b/examples/cfd/03_diffusion.ipynb
@@ -57,7 +57,7 @@
    "outputs": [],
    "source": [
     "def diffuse(u, nt):\n",
-    "    for n in range(nt + 1):\n",
+    "    for _ in range(nt + 1):\n",
     "        un = u.copy()\n",
     "        u[1:-1, 1:-1] = (un[1:-1, 1:-1] +\n",
     "                        nu * dt / dy**2 * (un[1:-1, 2:] - 2 * un[1:-1, 1:-1] + un[1:-1, 0:-2]) +\n",
diff --git a/examples/cfd/03_diffusion_nonuniform.ipynb b/examples/cfd/03_diffusion_nonuniform.ipynb
@@ -80,7 +80,7 @@
    "outputs": [],
    "source": [
     "def diffuse(u, nt, visc):\n",
-    "    for n in range(nt + 1):\n",
+    "    for _ in range(nt + 1):\n",
     "        un = u.copy()\n",
     "        u[1:-1, 1:-1] = (un[1:-1, 1:-1] +\n",
     "                        visc*dt / dy**2 * (un[1:-1, 2:] - 2 * un[1:-1, 1:-1] + un[1:-1, 0:-2]) +\n",
@@ -257,7 +257,6 @@
    ],
    "source": [
     "from devito import Grid, TimeFunction, Eq, solve, Function\n",
-    "from sympy.abc import a\n",
     "\n",
     "# Initialize `u` for space order 2\n",
     "grid = Grid(shape=(nx, ny), extent=(2., 2.))\n",
diff --git a/examples/cfd/06_poisson.ipynb b/examples/cfd/06_poisson.ipynb
@@ -81,7 +81,7 @@
    "source": [
     "%%time\n",
     "# NBVAL_IGNORE_OUTPUT\n",
-    "for it in range(nt):\n",
+    "for _ in range(nt):\n",
     "    pd = p.copy()\n",
     "    p[1:-1, 1:-1] = (((pd[1:-1, 2:] + pd[1:-1, :-2]) * dy**2 +\n",
     "                    (pd[2:, 1:-1] + pd[:-2, 1:-1]) * dx**2 -\n",
diff --git a/examples/cfd/07_cavity_flow.ipynb b/examples/cfd/07_cavity_flow.ipynb
@@ -176,7 +176,7 @@
     "    pn = np.empty_like(p)\n",
     "    pn = p.copy()\n",
     "\n",
-    "    for q in range(nit):\n",
+    "    for _ in range(nit):\n",
     "        pn = p.copy()\n",
     "        p[1:-1, 1:-1] = (((pn[2:, 1:-1] + pn[0:-2, 1:-1]) * dy**2 +\n",
     "                          (pn[1:-1, 2:] + pn[1:-1, 0:-2]) * dx**2) /\n",
@@ -211,7 +211,7 @@
     "    vn = np.empty_like(v)\n",
     "    b = np.zeros((nx, ny))\n",
     "\n",
-    "    for n in range(0, nt):\n",
+    "    for _ in range(0, nt):\n",
     "        un = u.copy()\n",
     "        vn = v.copy()\n",
     "\n",
diff --git a/examples/cfd/08_shallow_water_equation.ipynb b/examples/cfd/08_shallow_water_equation.ipynb
@@ -90,7 +90,7 @@
     "    Operator that solves the equations expressed above.\n",
     "    It computes and returns the discharge fluxes M, N and wave height eta from\n",
     "    the 2D Shallow water equation using the FTCS finite difference method.\n",
-    "    \n",
+    "\n",
     "    Parameters\n",
     "    ----------\n",
     "    eta : TimeFunction\n",
@@ -113,15 +113,18 @@
     "        animations.\n",
     "    \"\"\"\n",
     "\n",
-    "    eps = np.finfo(grid.dtype).eps\n",
+    "    # eps = np.finfo(grid.dtype).eps\n",
     "\n",
     "    # Friction term expresses the loss of amplitude from the friction with the seafloor\n",
     "    frictionTerm = g * alpha**2 * sqrt(M**2 + N**2) / D**(7./3.)\n",
     "\n",
     "    # System of equations\n",
     "    pde_eta = Eq(eta.dt + M.dxc + N.dyc)\n",
     "    pde_M = Eq(M.dt + (M**2/D).dxc + (M*N/D).dyc + g*D*eta.forward.dxc + frictionTerm*M)\n",
-    "    pde_N = Eq(N.dt + (M.forward*N/D).dxc + (N**2/D).dyc + g*D*eta.forward.dyc + g * alpha**2 * sqrt(M.forward**2 + N**2) / D**(7./3.)*N)\n",
+    "    pde_N = Eq(\n",
+    "        N.dt + (M.forward*N/D).dxc + (N**2/D).dyc + g*D*eta.forward.dyc\n",
+    "        + g * alpha**2 * sqrt(M.forward**2 + N**2) / D**(7./3.)*N\n",
+    "    )\n",
     "\n",
     "    stencil_eta = solve(pde_eta, eta.forward)\n",
     "    stencil_M = solve(pde_M, M.forward)\n",
diff --git a/examples/cfd/09_Darcy_flow_equation.ipynb b/examples/cfd/09_Darcy_flow_equation.ipynb
@@ -109,7 +109,7 @@
     "            self.sqrt_eig[0, 0] = 0.0\n",
     "\n",
     "        self.size = []\n",
-    "        for j in range(self.dim):\n",
+    "        for _ in range(self.dim):\n",
     "            self.size.append(size)\n",
     "\n",
     "        self.size = tuple(self.size)\n",
@@ -365,8 +365,8 @@
     "'''\n",
     "Function to generate 'u' from 'a' using Devito\n",
     "\n",
-    "parameters \n",
-    "-----------------\n",
+    "Parameters\n",
+    "----------\n",
     "perm: Array of size (s, s)\n",
     "    This is \"a\"\n",
     "f: Array of size (s, s)\n",
@@ -375,7 +375,6 @@
     "\n",
     "\n",
     "def darcy_flow_2d(perm, f):\n",
-    "\n",
     "    # a(x) is the coefficients\n",
     "    # f is the forcing function\n",
     "    # initialize a, f with inputs permeability and forcing\n",
diff --git a/examples/cfd/example_diffusion.py b/examples/cfd/example_diffusion.py
@@ -51,8 +51,10 @@ def execute_python(ui, spacing=0.01, a=0.5, timesteps=500):
                 uyy = (u[t0, i, j+1] - 2*u[t0, i, j] + u[t0, i, j-1]) / dy2
                 u[t1, i, j] = u[t0, i, j] + dt * a * (uxx + uyy)
     runtime = time.time() - tstart
-    log("Python: Diffusion with dx=%0.4f, dy=%0.4f, executed %d timesteps in %f seconds"
-        % (spacing, spacing, timesteps, runtime))
+    log(
+        f'Python: Diffusion with dx={spacing:0.4f}, dy={spacing:0.4f}, '
+        f'executed {timesteps} timesteps in {runtime} seconds'
+    )
     return u[ti % 2, :, :], runtime
 
 
@@ -73,8 +75,10 @@ def execute_numpy(ui, spacing=0.01, a=0.5, timesteps=500):
         uyy = (u[t0, 1:-1, 2:] - 2*u[t0, 1:-1, 1:-1] + u[t0, 1:-1, :-2]) / dy2
         u[t1, 1:-1, 1:-1] = u[t0, 1:-1, 1:-1] + a * dt * (uxx + uyy)
     runtime = time.time() - tstart
-    log("Numpy: Diffusion with dx=%0.4f, dy=%0.4f, executed %d timesteps in %f seconds"
-        % (spacing, spacing, timesteps, runtime))
+    log(
+        f'Numpy: Diffusion with dx={spacing:0.4f}, dy={spacing:0.4f}, '
+        f'executed {timesteps} timesteps in {runtime} seconds'
+    )
     return u[ti % 2, :, :], runtime
 
 
@@ -108,8 +112,10 @@ def diffusion_stencil():
                                    u[t0, :-2, 1:-1], u[t0, 1:-1, 2:],
                                    u[t0, 1:-1, :-2], dt, spacing)
     runtime = time.time() - tstart
-    log("Lambdify: Diffusion with dx=%0.4f, dy=%0.4f, executed %d timesteps in %f seconds"
-        % (spacing, spacing, timesteps, runtime))
+    log(
+        f'Lambdify: Diffusion with dx={spacing:0.4f}, dy={spacing:0.4f}, '
+        f'executed {timesteps} timesteps in {runtime} seconds'
+    )
     return u[ti % 2, :, :], runtime
 
 
@@ -133,8 +139,10 @@ def execute_devito(ui, spacing=0.01, a=0.5, timesteps=500):
     tstart = time.time()
     op.apply(u=u, t=timesteps, dt=dt)
     runtime = time.time() - tstart
-    log("Devito: Diffusion with dx=%0.4f, dy=%0.4f, executed %d timesteps in %f seconds"
-        % (spacing, spacing, timesteps, runtime))
+    log(
+        f'Devito: Diffusion with dx={spacing:0.4f}, dy={spacing:0.4f}, '
+        f'executed {timesteps} timesteps in {runtime} seconds'
+    )
     return u.data[1, :], runtime
 
 
diff --git a/examples/cfd/tools.py b/examples/cfd/tools.py
@@ -29,9 +29,8 @@ def plot_field(field, xmin=0., xmax=2., ymin=0., ymax=2., zmin=None, zmax=None,
     elif(zmin is None and zmax is not None):
         if np.min(field) >= zmax:
             warning("zmax is less than field's minima. Figure deceptive.")
-    elif(zmin is not None and zmax is None):
-        if np.max(field) <= zmin:
-            warning("zmin is larger than field's maxima. Figure deceptive.")
+    elif(zmin is not None and zmax is None) and np.max(field) <= zmin:
+        warning("zmin is larger than field's maxima. Figure deceptive.")
     x_coord = np.linspace(xmin, xmax, field.shape[0])
     y_coord = np.linspace(ymin, ymax, field.shape[1])
     fig = pyplot.figure(figsize=(11, 7), dpi=100)
diff --git a/examples/finance/bs_ivbp.ipynb b/examples/finance/bs_ivbp.ipynb
@@ -519,8 +519,8 @@
     "\n",
     "endBF = timer.time()\n",
     "\n",
-    "print(\"devito pde    timesteps: %12.6s, %12.6fs runtime\" % (nt-1, endDevito - startDevito))\n",
-    "print(\"call_value_bs timesteps: %12.6s, %12.6fs runtime\" % (len(time), endBF - startBF))\n",
+    "print(f\"devito pde    timesteps: {nt - 1:12.6s}, {endDevito - startDevito:12.6f}s runtime\")\n",
+    "print(f\"call_value_bs timesteps: {len(time):12.6s}, {endBF - startBF:12.6f}s runtime\")\n",
     "\n",
     "s2 = np.linspace(smin, smax, shape[0])\n",
     "plt.figure(figsize=(12, 10))\n",
diff --git a/examples/performance/02_advisor_roofline.ipynb b/examples/performance/02_advisor_roofline.ipynb
@@ -108,8 +108,12 @@
    ],
    "source": [
     "# NBVAL_SKIP\n",
-    "\n",
-    "! python3 $DEVITO_JUPYTER/benchmarks/user/advisor/run_advisor.py --path $DEVITO_JUPYTER/benchmarks/user/benchmark.py --exec-args \"run -P acoustic -d 64 64 64 -so 4 --tn 50 --autotune off\" --output $DEVITO_JUPYTER/examples/performance/profilings --name JupyterProfiling\n"
+    "%%bash\n",
+    "python3 $DEVITO_JUPYTER/benchmarks/user/advisor/run_advisor.py \\\n",
+    "    --path $DEVITO_JUPYTER/benchmarks/user/benchmark.py \\\n",
+    "    --exec-args \"run -P acoustic -d 64 64 64 -so 4 --tn 50 --autotune off\" \\\n",
+    "    --output $DEVITO_JUPYTER/examples/performance/profilings \\\n",
+    "    --name JupyterProfiling"
    ]
   },
   {
@@ -167,8 +171,12 @@
    ],
    "source": [
     "# NBVAL_SKIP\n",
-    "\n",
-    "! python3 $DEVITO_JUPYTER/benchmarks/user/advisor/roofline.py --mode overview --name $DEVITO_JUPYTER/examples/performance/resources/OverviewRoof --project $DEVITO_JUPYTER/examples/performance/profilings/JupyterProfiling\n"
+    "%%bash\n",
+    "python3 $DEVITO_JUPYTER/benchmarks/user/advisor/roofline.py \\\n",
+    "    --mode overview \\\n",
+    "    --name $DEVITO_JUPYTER/examples/performance/resources/OverviewRoof \\\n",
+    "    --project $DEVITO_JUPYTER/examples/performance/profilings/JupyterProfiling \\\n",
+    "    $DEVITO_JUPYTER/benchmarks/user/advisor/run_advisor.py"
    ]
   },
   {
@@ -231,8 +239,11 @@
    ],
    "source": [
     "# NBVAL_SKIP\n",
-    "\n",
-    "! python3 $DEVITO_JUPYTER/benchmarks/user/advisor/roofline.py --mode top-loops --name $DEVITO_JUPYTER/examples/performance/resources/TopLoopsRoof --project $DEVITO_JUPYTER/examples/performance/profilings/JupyterProfiling\n"
+    "%%bash\n",
+    "python3 $DEVITO_JUPYTER/benchmarks/user/advisor/roofline.py \\\n",
+    "    --mode top-loops \\\n",
+    "    --name $DEVITO_JUPYTER/examples/performance/resources/TopLoopsRoof \\\n",
+    "    --project $DEVITO_JUPYTER/examples/performance/profilings/JupyterProfiling \\\n"
    ]
   },
   {
diff --git a/examples/seismic/abc_methods/01_introduction.ipynb b/examples/seismic/abc_methods/01_introduction.ipynb
@@ -357,22 +357,22 @@
    "outputs": [],
    "source": [
     "def graph2dvel(vel):\n",
-    "        plot.figure()\n",
-    "        plot.figure(figsize=(16, 8))\n",
-    "        fscale = 1/10**(3)\n",
-    "        scale = np.amax(vel)\n",
-    "        extent = [fscale*x0, fscale*x1, fscale*z1, fscale*z0]\n",
-    "        fig = plot.imshow(np.transpose(vel), vmin=0., vmax=scale, cmap=cm.seismic, extent=extent)\n",
-    "        plot.gca().xaxis.set_major_formatter(mticker.FormatStrFormatter('%.1f km'))\n",
-    "        plot.gca().yaxis.set_major_formatter(mticker.FormatStrFormatter('%.1f km'))\n",
-    "        plot.title('Velocity Profile')\n",
-    "        plot.grid()\n",
-    "        ax = plot.gca()\n",
-    "        divider = make_axes_locatable(ax)\n",
-    "        cax = divider.append_axes(\"right\", size=\"5%\", pad=0.05)\n",
-    "        cbar = plot.colorbar(fig, cax=cax, format='%.2e')\n",
-    "        cbar.set_label('Velocity [km/s]')\n",
-    "        plot.show()"
+    "    plot.figure()\n",
+    "    plot.figure(figsize=(16, 8))\n",
+    "    fscale = 1/10**(3)\n",
+    "    scale = np.amax(vel)\n",
+    "    extent = [fscale*x0, fscale*x1, fscale*z1, fscale*z0]\n",
+    "    fig = plot.imshow(np.transpose(vel), vmin=0., vmax=scale, cmap=cm.seismic, extent=extent)\n",
+    "    plot.gca().xaxis.set_major_formatter(mticker.FormatStrFormatter('%.1f km'))\n",
+    "    plot.gca().yaxis.set_major_formatter(mticker.FormatStrFormatter('%.1f km'))\n",
+    "    plot.title('Velocity Profile')\n",
+    "    plot.grid()\n",
+    "    ax = plot.gca()\n",
+    "    divider = make_axes_locatable(ax)\n",
+    "    cax = divider.append_axes(\"right\", size=\"5%\", pad=0.05)\n",
+    "    cbar = plot.colorbar(fig, cax=cax, format='%.2e')\n",
+    "    cbar.set_label('Velocity [km/s]')\n",
+    "    plot.show()"
    ]
   },
   {
@@ -561,7 +561,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "src = RickerSource(name='src', grid=grid, f0=f0, npoint=nsource, time_range=time_range, staggered=NODE, dtype=np.float64)\n",
+    "src = RickerSource(\n",
+    "    name='src',\n",
+    "    grid=grid,\n",
+    "    f0=f0,\n",
+    "    npoint=nsource,\n",
+    "    time_range=time_range,\n",
+    "    staggered=NODE,\n",
+    "    dtype=np.float64\n",
+    ")\n",
     "src.coordinates.data[:, 0] = xposf\n",
     "src.coordinates.data[:, 1] = zposf"
    ]
@@ -1026,22 +1034,22 @@
    "outputs": [],
    "source": [
     "def graph2drec(rec):\n",
-    "        plot.figure()\n",
-    "        plot.figure(figsize=(16, 8))\n",
-    "        fscaled = 1/10**(3)\n",
-    "        fscalet = 1/10**(3)\n",
-    "        scale = np.amax(rec)/10.\n",
-    "        extent = [fscaled*x0, fscaled*x1, fscalet*tn, fscalet*t0]\n",
-    "        fig = plot.imshow(rec, vmin=-scale, vmax=scale, cmap=cm.seismic, extent=extent)\n",
-    "        plot.gca().xaxis.set_major_formatter(mticker.FormatStrFormatter('%.1f km'))\n",
-    "        plot.gca().yaxis.set_major_formatter(mticker.FormatStrFormatter('%.1f s'))\n",
-    "        plot.axis('equal')\n",
-    "        plot.title('Receivers Signal Profile - Devito')\n",
-    "        ax = plot.gca()\n",
-    "        divider = make_axes_locatable(ax)\n",
-    "        cax = divider.append_axes(\"right\", size=\"5%\", pad=0.05)\n",
-    "        cbar = plot.colorbar(fig, cax=cax, format='%.2e')\n",
-    "        plot.show()"
+    "    plot.figure()\n",
+    "    plot.figure(figsize=(16, 8))\n",
+    "    fscaled = 1/10**(3)\n",
+    "    fscalet = 1/10**(3)\n",
+    "    scale = np.amax(rec)/10.\n",
+    "    extent = [fscaled*x0, fscaled*x1, fscalet*tn, fscalet*t0]\n",
+    "    fig = plot.imshow(rec, vmin=-scale, vmax=scale, cmap=cm.seismic, extent=extent)\n",
+    "    plot.gca().xaxis.set_major_formatter(mticker.FormatStrFormatter('%.1f km'))\n",
+    "    plot.gca().yaxis.set_major_formatter(mticker.FormatStrFormatter('%.1f s'))\n",
+    "    plot.axis('equal')\n",
+    "    plot.title('Receivers Signal Profile - Devito')\n",
+    "    ax = plot.gca()\n",
+    "    divider = make_axes_locatable(ax)\n",
+    "    cax = divider.append_axes(\"right\", size=\"5%\", pad=0.05)\n",
+    "    _ = plot.colorbar(fig, cax=cax, format='%.2e')\n",
+    "    plot.show()"
    ]
   },
   {
diff --git a/examples/seismic/abc_methods/02_damping.ipynb b/examples/seismic/abc_methods/02_damping.ipynb
diff --git a/examples/seismic/abc_methods/03_pml.ipynb b/examples/seismic/abc_methods/03_pml.ipynb
diff --git a/examples/seismic/abc_methods/04_habc.ipynb b/examples/seismic/abc_methods/04_habc.ipynb
