PMEAL · jgostick · Jul 11, 2025 · Jul 11, 2025 · Jul 11, 2025 · Jul 11, 2025
diff --git a/.github/workflows/examples.yml b/.github/workflows/examples.yml
@@ -24,6 +24,9 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v4
 
+      - name: Install pandoc
+        uses: pandoc/actions/setup@v1
+
       - name: Set up uv
         id: setup-uv
         uses: astral-sh/setup-uv@v6

diff --git a/examples/filters/reference/apply_chords.ipynb b/examples/filters/reference/apply_chords.ipynb
diff --git a/examples/filters/reference/apply_chords_3D.ipynb b/examples/filters/reference/apply_chords_3D.ipynb
diff --git a/examples/filters/reference/apply_padded.ipynb b/examples/filters/reference/apply_padded.ipynb
diff --git a/examples/filters/reference/chunked_func.ipynb b/examples/filters/reference/chunked_func.ipynb
diff --git a/examples/filters/reference/distance_transform_lin.ipynb b/examples/filters/reference/distance_transform_lin.ipynb
diff --git a/examples/filters/reference/fftmorphology.ipynb b/examples/filters/reference/fftmorphology.ipynb
diff --git a/examples/filters/reference/fill_closed_pores.ipynb b/examples/filters/reference/fill_closed_pores.ipynb
diff --git a/examples/filters/reference/find_disconnected_voxels.ipynb b/examples/filters/reference/find_disconnected_voxels.ipynb
diff --git a/examples/filters/reference/find_dt_artifacts.ipynb b/examples/filters/reference/find_dt_artifacts.ipynb
diff --git a/examples/filters/reference/find_peaks.ipynb b/examples/filters/reference/find_peaks.ipynb
diff --git a/examples/filters/reference/find_trapped_clusters.ipynb b/examples/filters/reference/find_trapped_clusters.ipynb
diff --git a/examples/filters/reference/flood.ipynb b/examples/filters/reference/flood.ipynb
diff --git a/examples/filters/reference/flood_func.ipynb b/examples/filters/reference/flood_func.ipynb
diff --git a/examples/filters/reference/hold_peaks.ipynb b/examples/filters/reference/hold_peaks.ipynb
diff --git a/examples/filters/reference/local_thickness.ipynb b/examples/filters/reference/local_thickness.ipynb
diff --git a/examples/filters/reference/nl_means_layered.ipynb b/examples/filters/reference/nl_means_layered.ipynb
diff --git a/examples/filters/reference/nphase_border.ipynb b/examples/filters/reference/nphase_border.ipynb
diff --git a/examples/filters/reference/pc_to_satn.ipynb b/examples/filters/reference/pc_to_satn.ipynb
diff --git a/examples/filters/reference/porosimetry.ipynb b/examples/filters/reference/porosimetry.ipynb
diff --git a/examples/filters/reference/prune_branches.ipynb b/examples/filters/reference/prune_branches.ipynb
diff --git a/examples/filters/reference/reduce_peaks.ipynb b/examples/filters/reference/reduce_peaks.ipynb
diff --git a/examples/filters/reference/region_size.ipynb b/examples/filters/reference/region_size.ipynb
diff --git a/examples/filters/reference/satn_to_seq.ipynb b/examples/filters/reference/satn_to_seq.ipynb
diff --git a/examples/filters/reference/seq_to_satn.ipynb b/examples/filters/reference/seq_to_satn.ipynb
diff --git a/examples/filters/reference/size_to_satn.ipynb b/examples/filters/reference/size_to_satn.ipynb
diff --git a/examples/filters/reference/size_to_seq.ipynb b/examples/filters/reference/size_to_seq.ipynb
diff --git a/examples/filters/reference/snow_partitioning.ipynb b/examples/filters/reference/snow_partitioning.ipynb
diff --git a/examples/filters/reference/snow_partitioning_n.ipynb b/examples/filters/reference/snow_partitioning_n.ipynb
diff --git a/examples/filters/reference/snow_partitioning_parallel.ipynb b/examples/filters/reference/snow_partitioning_parallel.ipynb
diff --git a/examples/filters/reference/trim_disconnected_voxels.ipynb b/examples/filters/reference/trim_disconnected_voxels.ipynb
diff --git a/examples/filters/reference/trim_extrema.ipynb b/examples/filters/reference/trim_extrema.ipynb
diff --git a/examples/filters/reference/trim_floating_solid.ipynb b/examples/filters/reference/trim_floating_solid.ipynb
diff --git a/examples/filters/reference/trim_nearby_peaks.ipynb b/examples/filters/reference/trim_nearby_peaks.ipynb
diff --git a/examples/filters/reference/trim_nonpercolating_paths.ipynb b/examples/filters/reference/trim_nonpercolating_paths.ipynb
diff --git a/examples/filters/reference/trim_saddle_points.ipynb b/examples/filters/reference/trim_saddle_points.ipynb
diff --git a/examples/filters/reference/trim_small_clusters.ipynb b/examples/filters/reference/trim_small_clusters.ipynb
diff --git a/examples/filters/tutorials/adding_chords.ipynb b/examples/filters/tutorials/adding_chords.ipynb
@@ -88,8 +88,8 @@
    ],
    "source": [
     "fig, ax = plt.subplots()\n",
-    "ax.imshow(im, interpolation='none', origin='lower')\n",
-    "ax.axis('off');"
+    "ax.imshow(im, interpolation=\"none\", origin=\"lower\")\n",
+    "ax.axis(\"off\");"
    ]
   },
   {
@@ -131,9 +131,9 @@
     "crds_x = ps.filters.apply_chords(im=im, spacing=4, axis=0)\n",
     "crds_y = ps.filters.apply_chords(im=im, spacing=4, axis=1)\n",
     "fig, ax = plt.subplots(1, 2, figsize=[8, 4])\n",
-    "ax[0].imshow(crds_x, interpolation='none', origin='lower')\n",
+    "ax[0].imshow(crds_x, interpolation=\"none\", origin=\"lower\")\n",
     "ax[0].axis(False)\n",
-    "ax[1].imshow(crds_y, interpolation='none', origin='lower')\n",
+    "ax[1].imshow(crds_y, interpolation=\"none\", origin=\"lower\")\n",
     "ax[1].axis(False);"
    ]
   },
@@ -183,9 +183,9 @@
     "sz_x = ps.filters.region_size(crds_x)\n",
     "sz_y = ps.filters.region_size(crds_y)\n",
     "fig, ax = plt.subplots(1, 2, figsize=[8, 4])\n",
-    "ax[0].imshow(sz_x, interpolation='none', origin='lower')\n",
+    "ax[0].imshow(sz_x, interpolation=\"none\", origin=\"lower\")\n",
     "ax[0].axis(False)\n",
-    "ax[1].imshow(sz_y, interpolation='none', origin='lower')\n",
+    "ax[1].imshow(sz_y, interpolation=\"none\", origin=\"lower\")\n",
     "ax[1].axis(False);"
    ]
   },
@@ -291,8 +291,12 @@
    ],
    "source": [
     "fig, ax = plt.subplots(figsize=(5, 4))\n",
-    "ax.bar(x=data_y.L, height=data_y.cdf, width=data_y.bin_widths, color='b', edgecolor='k', alpha=0.5)\n",
-    "ax.bar(x=data_x.L, height=data_x.cdf, width=data_x.bin_widths, color='r', edgecolor='k', alpha=0.5)\n",
+    "ax.bar(\n",
+    "    x=data_y.L, height=data_y.cdf, width=data_y.bin_widths, color=\"b\", edgecolor=\"k\", alpha=0.5\n",
+    ")\n",
+    "ax.bar(\n",
+    "    x=data_x.L, height=data_x.cdf, width=data_x.bin_widths, color=\"r\", edgecolor=\"k\", alpha=0.5\n",
+    ")\n",
     "ax.set_xlabel(\"Chord length\")\n",
     "ax.set_ylabel(\"Frequency\");"
    ]
@@ -390,7 +394,7 @@
    "source": [
     "crds = ps.filters.apply_chords(im=im, axis=0)\n",
     "fig, ax = plt.subplots()\n",
-    "ax.imshow(crds[:, :, 50], interpolation='none', origin='lower')\n",
+    "ax.imshow(crds[:, :, 50], interpolation=\"none\", origin=\"lower\")\n",
     "ax.axis(False);"
    ]
   },
@@ -425,7 +429,7 @@
    "source": [
     "data = ps.metrics.chord_length_distribution(crds, bins=25)\n",
     "fig, ax = plt.subplots(figsize=(5, 4))\n",
-    "ax.bar(x=data_y.L, height=data.cdf, width=data.bin_widths, color='b', edgecolor='k', alpha=0.5)\n",
+    "ax.bar(x=data_y.L, height=data.cdf, width=data.bin_widths, color=\"b\", edgecolor=\"k\", alpha=0.5)\n",
     "ax.set_xlabel(\"Chord length\")\n",
     "ax.set_ylabel(\"Frequency\");"
    ]

diff --git a/examples/filters/tutorials/finding_and_filling_pores.ipynb b/examples/filters/tutorials/finding_and_filling_pores.ipynb
@@ -118,13 +118,13 @@
     "fig, ax = plt.subplots(1, 3, figsize=[12, 4])\n",
     "ax[0].imshow(im, cmap=cm, vmax=2)\n",
     "ax[0].axis(False)\n",
-    "ax[0].set_title('Original image')\n",
+    "ax[0].set_title(\"Original image\")\n",
     "ax[1].imshow(im_closed, cmap=cm, vmax=2)\n",
     "ax[1].axis(False)\n",
-    "ax[1].set_title('Closed pores')\n",
+    "ax[1].set_title(\"Closed pores\")\n",
     "ax[2].imshow(im_filled, cmap=cm, vmax=2)\n",
     "ax[2].axis(False)\n",
-    "ax[2].set_title('Image without closed pores');"
+    "ax[2].set_title(\"Image without closed pores\");"
    ]
   },
   {
@@ -164,13 +164,13 @@
     "fig, ax = plt.subplots(1, 3, figsize=[12, 4])\n",
     "ax[0].imshow(im, cmap=cm, vmax=2)\n",
     "ax[0].axis(False)\n",
-    "ax[0].set_title('Original image')\n",
+    "ax[0].set_title(\"Original image\")\n",
     "ax[1].imshow(im_surface, cmap=cm, vmax=2)\n",
     "ax[1].axis(False)\n",
-    "ax[1].set_title('Surface pores')\n",
+    "ax[1].set_title(\"Surface pores\")\n",
     "ax[2].imshow(im_filled, cmap=cm, vmax=2)\n",
     "ax[2].axis(False)\n",
-    "ax[2].set_title('Image without closed or surface pores');"
+    "ax[2].set_title(\"Image without closed or surface pores\");"
    ]
   },
   {
@@ -207,13 +207,13 @@
     "fig, ax = plt.subplots(1, 3, figsize=[12, 4])\n",
     "ax[0].imshow(im, cmap=cm, vmax=2)\n",
     "ax[0].axis(False)\n",
-    "ax[0].set_title('Original image')\n",
+    "ax[0].set_title(\"Original image\")\n",
     "ax[1].imshow(im_invalid, cmap=cm, vmax=2)\n",
     "ax[1].axis(False)\n",
-    "ax[1].set_title('Invalid pores')\n",
+    "ax[1].set_title(\"Invalid pores\")\n",
     "ax[2].imshow(im_filled, cmap=cm, vmax=2)\n",
     "ax[2].axis(False)\n",
-    "ax[2].set_title('Image without invalid pores');"
+    "ax[2].set_title(\"Image without invalid pores\");"
    ]
   },
   {
@@ -253,13 +253,13 @@
     "fig, ax = plt.subplots(1, 3, figsize=[12, 4])\n",
     "ax[0].imshow(im, cmap=cm, vmax=2)\n",
     "ax[0].axis(False)\n",
-    "ax[0].set_title('Original image')\n",
+    "ax[0].set_title(\"Original image\")\n",
     "ax[1].imshow(~im_floating, cmap=cm, vmax=2)\n",
     "ax[1].axis(False)\n",
-    "ax[1].set_title('Floating solid')\n",
+    "ax[1].set_title(\"Floating solid\")\n",
     "ax[2].imshow(im_trimmed, cmap=cm, vmax=2)\n",
     "ax[2].axis(False)\n",
-    "ax[2].set_title('Image w no invalid pores or floating solid');"
+    "ax[2].set_title(\"Image w no invalid pores or floating solid\");"
    ]
   },
   {
@@ -299,13 +299,13 @@
     "fig, ax = plt.subplots(1, 3, figsize=[12, 4])\n",
     "ax[0].imshow(im, cmap=cm, vmax=2)\n",
     "ax[0].axis(False)\n",
-    "ax[0].set_title('Original image')\n",
+    "ax[0].set_title(\"Original image\")\n",
     "ax[1].imshow(im_filled_ud, cmap=cm, vmax=2)\n",
     "ax[1].axis(False)\n",
-    "ax[1].set_title('Percolating top to bottom')\n",
+    "ax[1].set_title(\"Percolating top to bottom\")\n",
     "ax[2].imshow(im_filled_lr, cmap=cm, vmax=2)\n",
     "ax[2].axis(False)\n",
-    "ax[2].set_title('Percolating left to right');"
+    "ax[2].set_title(\"Percolating left to right\");"
    ]
   },
   {
@@ -345,13 +345,13 @@
     "fig, ax = plt.subplots(1, 3, figsize=[12, 4])\n",
     "ax[0].imshow(im, cmap=cm, vmax=2)\n",
     "ax[0].axis(False)\n",
-    "ax[0].set_title('Original image')\n",
+    "ax[0].set_title(\"Original image\")\n",
     "ax[1].imshow(im_disconnected, cmap=cm, vmax=2)\n",
     "ax[1].axis(False)\n",
-    "ax[1].set_title('Disconnected from inlets')\n",
+    "ax[1].set_title(\"Disconnected from inlets\")\n",
     "ax[2].imshow(im_filled, cmap=cm, vmax=2)\n",
     "ax[2].axis(False)\n",
-    "ax[2].set_title('After filling');"
+    "ax[2].set_title(\"After filling\");"
    ]
   },
   {

diff --git a/examples/filters/tutorials/local_thickness.ipynb b/examples/filters/tutorials/local_thickness.ipynb
@@ -73,7 +73,7 @@
     "im = ps.generators.random_spheres(im=im, r=15, phi=0.4, smooth=False)\n",
     "im = ps.generators.random_spheres(im=im, r=10, phi=0.6, smooth=False)\n",
     "fig, ax = plt.subplots()\n",
-    "ax.imshow(im, interpolation='none', origin='lower')\n",
+    "ax.imshow(im, interpolation=\"none\", origin=\"lower\")\n",
     "ax.axis(False);"
    ]
   },
@@ -116,7 +116,7 @@
    "source": [
     "thk = ps.filters.local_thickness(im)\n",
     "fig, ax = plt.subplots()\n",
-    "ax.imshow(thk, interpolation='none', origin='lower', cmap=plt.cm.viridis)\n",
+    "ax.imshow(thk, interpolation=\"none\", origin=\"lower\", cmap=plt.cm.viridis)\n",
     "ax.axis(False);"
    ]
   },
@@ -222,9 +222,9 @@
    ],
    "source": [
     "fig, ax = plt.subplots(figsize=(5, 4))\n",
-    "ax.set_xlabel('log(Pore Radius) [voxels]')\n",
-    "ax.set_ylabel('Normalized Volume Fraction')\n",
-    "ax.bar(x=psd.LogR, height=psd.pdf, width=psd.bin_widths, edgecolor='k');"
+    "ax.set_xlabel(\"log(Pore Radius) [voxels]\")\n",
+    "ax.set_ylabel(\"Normalized Volume Fraction\")\n",
+    "ax.bar(x=psd.LogR, height=psd.pdf, width=psd.bin_widths, edgecolor=\"k\");"
    ]
   },
   {
@@ -269,7 +269,7 @@
     "strel = ps.tools.ps_disk(R)\n",
     "im_temp = spim.binary_opening(im, structure=strel)\n",
     "fig, ax = plt.subplots()\n",
-    "ax.imshow(im_temp*2.0, interpolation='none', origin='lower');"
+    "ax.imshow(im_temp * 2.0, interpolation=\"none\", origin=\"lower\");"
    ]
   },
   {
@@ -292,7 +292,7 @@
    },
    "outputs": [],
    "source": [
-    "im_result = im_temp*R"
+    "im_result = im_temp * R"
    ]
   },
   {
@@ -340,7 +340,7 @@
    },
    "outputs": [],
    "source": [
-    "im_result[(im_result == 0)*im_temp] = R"
+    "im_result[(im_result == 0) * im_temp] = R"
    ]
   },
   {
@@ -381,7 +381,7 @@
    ],
    "source": [
     "fig, ax = plt.subplots()\n",
-    "ax.imshow(im_result, interpolation='none', origin='lower');"
+    "ax.imshow(im_result, interpolation=\"none\", origin=\"lower\");"
    ]
   },
   {
@@ -421,7 +421,7 @@
    ],
    "source": [
     "fig, ax = plt.subplots()\n",
-    "ax.imshow(thk, cmap=plt.cm.viridis, interpolation='none', origin='lower');"
+    "ax.imshow(thk, cmap=plt.cm.viridis, interpolation=\"none\", origin=\"lower\");"
    ]
   },
   {

diff --git a/examples/filters/tutorials/snow_partitioning.ipynb b/examples/filters/tutorials/snow_partitioning.ipynb
@@ -473,7 +473,7 @@
    "source": [
     "im = ps.generators.overlapping_spheres([500, 500], r=10, porosity=0.5)\n",
     "fig, ax = plt.subplots()\n",
-    "ax.imshow(im, origin='lower');"
+    "ax.imshow(im, origin=\"lower\");"
    ]
   },
   {
@@ -2193,13 +2193,13 @@
    ],
    "source": [
     "fig, ax = plt.subplots(2, 2, figsize=[8, 8])\n",
-    "ax[0, 0].imshow(snow_out.im, origin='lower')\n",
-    "ax[0, 1].imshow(snow_out.dt, origin='lower')\n",
+    "ax[0, 0].imshow(snow_out.im, origin=\"lower\")\n",
+    "ax[0, 1].imshow(snow_out.dt, origin=\"lower\")\n",
     "dt_peak = snow_out.dt.copy()\n",
     "peaks_dilated = binary_dilation(snow_out.peaks > 0)\n",
     "dt_peak[peaks_dilated > 0] = np.nan\n",
-    "ax[1, 0].imshow(dt_peak, origin='lower')\n",
-    "ax[1, 1].imshow(ps.tools.randomize_colors(snow_out.regions), origin='lower')\n",
+    "ax[1, 0].imshow(dt_peak, origin=\"lower\")\n",
+    "ax[1, 1].imshow(ps.tools.randomize_colors(snow_out.regions), origin=\"lower\")\n",
     "ax[0, 0].set_title(\"Binary image\")\n",
     "ax[0, 1].set_title(\"Distance transform\")\n",
     "ax[1, 0].set_title(\"Distance transform peaks\")\n",

diff --git a/examples/filters/tutorials/snow_partitioning_parallel.ipynb b/examples/filters/tutorials/snow_partitioning_parallel.ipynb
@@ -87,7 +87,7 @@
    "source": [
     "im = ps.generators.overlapping_spheres([1000, 1000], r=10, porosity=0.5)\n",
     "fig, ax = plt.subplots()\n",
-    "ax.imshow(im, origin='lower');"
+    "ax.imshow(im, origin=\"lower\");"
    ]
   },
   {
@@ -117,7 +117,8 @@
    "source": [
     "parallel_kw = {\"divs\": 2}\n",
     "snow_out = ps.filters.snow_partitioning_parallel(\n",
-    "    im=im, parallel_kw=parallel_kw, r_max=5, sigma=0.4)"
+    "    im=im, parallel_kw=parallel_kw, r_max=5, sigma=0.4\n",
+    ")"
    ]
   },
   {
@@ -160,7 +161,7 @@
    "source": [
     "fig, ax = plt.subplots(1, 1, figsize=[6, 6])\n",
     "ax.imshow(randomize_colors(snow_out.regions))\n",
-    "ax.set_title('Segmented Image');"
+    "ax.set_title(\"Segmented Image\");"
    ]
   },
   {