infra to ensure notebooks run

.github/workflows/examples.yml

@@ -0,0 +1,39 @@
+name: run-examples
+
+on:
+  pull_request:
+  workflow_call:
+    inputs:
+      job:
+        required: true
+        type: string
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ${{ fromJSON(vars.PYTHON_VERSIONS) }}
+
+    steps:
+    - name: Cancel Previous Runs
+      uses: styfle/[email protected]
+      with:
+        access_token: ${{ github.token }}
+
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+    
+    - name: Ensure notebooks complete without errors with pytest and nbmake
+      run: |
+        pip install '.[tests]'
+        pytest --nbmake examples/*ipynb

examples/customized_meteor_diffmap.ipynb

@@ -149,7 +149,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# 3. TV denoise the map\n",
+    "### 3. TV denoise the map\n",
     "\n",
     "Finally, the main event, the entreé! Let's improve our _k_-weighted map by TV-denoising it."
    ]
@@ -215,12 +215,25 @@
     "plt.show()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 4. Write out the results\n",
+    "\n",
+    "Awesome! Now we have a fancy new diffmap, which we probably want to save so we can do something with it. Like fire up Coot and check it out. If you are curious, the PDB ID corresponding to this dataset is `8a6g`, and you can find a copy of the structure as a PDB file in this repository:\n",
+    "\n",
+    "> `../test/data/8a6g.pdb`"
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 41,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "tv_denosied_map.write_mtz(\"my_denoised_diffmap.mtz\")"
+   ]
   }
  ],
  "metadata": {

pyproject.toml

@@ -32,6 +32,7 @@ tests = [
     "pytest",
     "pytest-cov",
     "pytest-xdist",
+    "nbmake",
 ]
 
 [project.scripts]