add black_nbconvert to pre-commit hooks (#7)

spatial-model-editor · Aug 24, 2021 · ca0037f · ca0037f
1 parent 2b6622a
commit ca0037f
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Showing 2 changed files with 18 additions and 9 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -12,6 +12,11 @@ repos:
     hooks:
     - id: black
 
+  - repo: https://github.com/dfm/black_nbconvert
+    rev: v0.3.0
+    hooks:
+    - id: black_nbconvert
+
   - repo: https://github.com/kynan/nbstripout
     rev: 0.5.0
     hooks:

diff --git a/docs/notebooks/plot.ipynb b/docs/notebooks/plot.ipynb
@@ -35,12 +35,12 @@
    "outputs": [],
    "source": [
     "model = sme.open_example_model()\n",
-    "fig = plt.figure(figsize=(16,8))\n",
+    "fig = plt.figure(figsize=(16, 8))\n",
     "plt.imshow(model.compartment_image)\n",
     "plt.title(\"Compartment geometry image\")\n",
     "plt.show()\n",
     "results = model.simulate(100, 100)\n",
-    "species = ['B_out', 'B_cell']"
+    "species = [\"B_out\", \"B_cell\"]"
    ]
   },
   {
@@ -63,7 +63,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig = plt.figure(figsize=(16,8))\n",
+    "fig = plt.figure(figsize=(16, 8))\n",
     "smeplot.concentration_heatmap(results[-1], species)\n",
     "plt.show()"
    ]
@@ -81,8 +81,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig = plt.figure(figsize=(16,8))\n",
-    "smeplot.concentration_heatmap(results[-1], species, cmap='flag')\n",
+    "fig = plt.figure(figsize=(16, 8))\n",
+    "smeplot.concentration_heatmap(results[-1], species, cmap=\"flag\")\n",
     "plt.show()"
    ]
   },
@@ -101,7 +101,7 @@
    "source": [
     "# make a black -> green colormap using sme_contrib.plot.colormap:\n",
     "cmap = smeplot.colormap(\"#00ff00\")\n",
-    "fig = plt.figure(figsize=(16,8))\n",
+    "fig = plt.figure(figsize=(16, 8))\n",
     "smeplot.concentration_heatmap(results[-1], species, cmap=cmap)\n",
     "plt.show()"
    ]
@@ -119,9 +119,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fig, (ax_l, ax_r) = plt.subplots(nrows=1, ncols=2, figsize=(16,6))\n",
-    "ax_l, im_l = smeplot.concentration_heatmap(results[-1], ['B_cell'], cmap=smeplot.colormap(\"#00ff00\"), ax=ax_l)\n",
-    "ax_r, im_r = smeplot.concentration_heatmap(results[-1], ['B_out'], cmap=smeplot.colormap(\"#ff00ff\"), ax=ax_r)\n",
+    "fig, (ax_l, ax_r) = plt.subplots(nrows=1, ncols=2, figsize=(16, 6))\n",
+    "ax_l, im_l = smeplot.concentration_heatmap(\n",
+    "    results[-1], [\"B_cell\"], cmap=smeplot.colormap(\"#00ff00\"), ax=ax_l\n",
+    ")\n",
+    "ax_r, im_r = smeplot.concentration_heatmap(\n",
+    "    results[-1], [\"B_out\"], cmap=smeplot.colormap(\"#ff00ff\"), ax=ax_r\n",
+    ")\n",
     "fig.colorbar(im_l, ax=ax_l)\n",
     "fig.colorbar(im_r, ax=ax_r)\n",
     "plt.show()"