add notebook test

.github/workflows/_build-package.yml

@@ -10,6 +10,10 @@ on:
           default: false
           required: false
           type: boolean
+        upload-package:
+          default: false
+          required: false
+          type: boolean
 
 defaults:
   run:
@@ -78,9 +82,19 @@ jobs:
     - name: Cache package
       if: inputs.cache-package
       uses: actions/cache/save@v3
-      id: cache-mols2grid
       with:
         path: |
           dist/mols2grid-*.whl
           dist/mols2grid-*.tar.gz
-        key: mols2grid-${{ runner.os }}-${{ github.sha }}
+        key: mols2grid-${{ runner.os }}-${{ github.sha }}
+
+    - name: Expose package as artifact
+      if: inputs.upload-package
+      uses: actions/upload-artifact@v4
+      with:
+        name: mols2grid-package
+        path: |
+          dist/mols2grid-*.whl
+          dist/mols2grid-*.tar.gz
+        if-no-files-found: error
+        retention-days: 20

.github/workflows/ci.yml

@@ -126,6 +126,7 @@ jobs:
     uses: ./.github/workflows/_build-package.yml
     with:
       cache-package: true
+      upload-package: true
 
   test-build:
     name: Test build
@@ -170,61 +171,90 @@ jobs:
         pip install dist/mols2grid-*.whl \
         && python test_install.py
 
-  # notebook-tests:
-  #   needs: [build]
-  #   name: ${{ matrix.label }}
-  #   runs-on: ubuntu-latest
-  #   strategy:
-  #     matrix:
-  #       include:
-  #         - label: JLab-3-Widgets-7
-  #           extra_dependencies: "'jupyterlab~=3.2' 'ipywidgets~=7.6'"
-  #         - label: JLab-4-Widgets-8
-  #           extra_dependencies: "'jupyterlab~=4.0' 'ipywidgets~=8.1'"
-
-  #   steps:
-  #     - uses: actions/checkout@v3
-
-  #     - name: Retrieve cached package
-  #       uses: actions/cache/restore@v3
-  #       id: cache-mols2grid
-  #       with:
-  #         path: |
-  #           dist/mols2grid-*.whl
-  #           dist/mols2grid-*.tar.gz
-  #         key: mols2grid-${{ runner.os }}-${{ github.sha }}
-
-  #     - name: Cache conda
-  #       uses: actions/cache@v3
-  #       env:
-  #         CACHE_NUMBER: 2
-  #       with:
-  #         path: ~/conda_pkgs_dir
-  #         key:
-  #           conda-${{ matrix.label }}-${{ env.CACHE_NUMBER }}
-
-  #     - name: Setup Conda
-  #       uses: conda-incubator/setup-miniconda@v2
-  #       with:
-  #         python-version: "3.10"
-  #         miniforge-variant: Mambaforge
-  #         miniforge-version: latest
-  #         use-mamba: true
-
-  #     - name: Install remaining conda dependencies
-  #       run: |
-  #         mamba install rdkit pandas ${{ matrix.extra_dependencies }}
-  #         mamba list
-
-  #     - name: Get wheel absolute path
-  #       id: wheel-path
-  #       run: echo "value=$(ls -d $PWD/dist/mols2grid-*.whl)" >> $GITHUB_OUTPUT
-
-  #     - name: Install the extension
-  #       run: |
-  #         pip install 'mols2grid[packaging] @ file://${{ steps.wheel-path.outputs.value }}'
-  #         jupyter labextension list
-
-  #     - name: Run test
-  #       run: |
-  #         echo TODO
+  notebook-tests:
+    needs: [build]
+    name: ${{ matrix.label }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          - label: JLab-3-Widgets-7
+            extra_dependencies: "'jupyterlab~=3.2' 'ipywidgets~=7.6'"
+          - label: JLab-4-Widgets-8
+            extra_dependencies: "'jupyterlab~=4.0' 'ipywidgets~=8.1'"
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Retrieve cached package
+        uses: actions/cache/restore@v3
+        id: cache-mols2grid
+        with:
+          path: |
+            dist/mols2grid-*.whl
+            dist/mols2grid-*.tar.gz
+          key: mols2grid-${{ runner.os }}-${{ github.sha }}
+
+      - name: Cache conda
+        uses: actions/cache@v3
+        env:
+          CACHE_NUMBER: 2
+        with:
+          path: ~/conda_pkgs_dir
+          key:
+            conda-${{ matrix.label }}-${{ env.CACHE_NUMBER }}
+
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: "3.10"
+          miniforge-variant: Mambaforge
+          miniforge-version: latest
+          use-mamba: true
+
+      - name: Install remaining conda dependencies
+        run: |
+          mamba install \
+            rdkit pandas \
+            ${{ matrix.extra_dependencies }}
+          mamba list
+      
+      - name: Install XeLatex
+        run: sudo apt-get install texlive-xetex
+
+      - name: Install the extension
+        run: |
+          pip install dist/mols2grid-*.whl
+          jupyter labextension list
+      
+      - name: Run test notebook and convert to PDF
+        working-directory: tests/notebooks/
+        run: |
+          jupyter nbconvert --to pdf --execute filtering.ipynb
+      
+      - name: Convert to PNG
+        working-directory: tests/notebooks/
+        run: |
+          file=$(ls *.pdf)
+          mv $file ${{ matrix.label }}.pdf
+          ls
+          convert ${{ matrix.label }}.pdf ${{ matrix.label }}.png
+
+      - name: Run diff
+        id: diff-test
+        working-directory: tests/notebooks/
+        run: |
+          delta=$(magick -metric AE -fuzz 10% ref-${{ matrix.label }}.png ${{ matrix.label }}.png null:)
+          echo "Delta: $delta"
+          [[ $delta -eq 0 ]]
+
+      - name: Upload output if fail
+        if: steps.diff-test.outcome.failure
+        uses: actions/upload-artifact@v4
+        with:
+          name: tests/notebooks/notebook-${{ matrix.label }}
+          path: |
+            ${{ matrix.label }}.png
+            ${{ matrix.label }}.pdf
+          if-no-files-found: error
+          retention-days: 5

tests/notebooks/filtering.ipynb

@@ -0,0 +1,76 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from pathlib import Path\n",
+    "from time import sleep\n",
+    "from ipywidgets.widgets import FloatRangeSlider\n",
+    "from ipywidgets import interact\n",
+    "from rdkit import RDConfig\n",
+    "import mols2grid\n",
+    "\n",
+    "assert Path(RDConfig.RDDocsDir).is_dir(), \"Test data not available!\"\n",
+    "\n",
+    "SDF_FILE = f\"{RDConfig.RDDocsDir}/Book/data/solubility.test.sdf\"\n",
+    "df = mols2grid.sdf_to_dataframe(SDF_FILE)\n",
+    "\n",
+    "# setup range slider for the solubility column `SOL`\n",
+    "sol_range = (df[\"SOL\"].min(), df[\"SOL\"].max())\n",
+    "slider = FloatRangeSlider(value=sol_range, min=sol_range[0], max=sol_range[1], step=.5)\n",
+    "\n",
+    "# generate the grid\n",
+    "grid = mols2grid.MolGrid(df, size=(120, 100))\n",
+    "view = grid.display(n_items_per_page=12)\n",
+    "\n",
+    "# add interactive callback that filters the grid on slider interaction\n",
+    "@interact(solubility=slider)\n",
+    "def filter_grid(solubility):\n",
+    "    results = grid.dataframe.query(\n",
+    "        \"@solubility[0] <= SOL <= @solubility[1]\"\n",
+    "    )\n",
+    "    return grid.filter_by_index(results.index)\n",
+    "\n",
+    "# display view\n",
+    "view"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# manually trigger interactive filtering on solubility.\n",
+    "# should display mols at index 68, 86, 115... etc. on the cell above\n",
+    "slider.value = (0, 1)\n",
+    "# give enough time for the callback and RDKit.js to do their thing\n",
+    "sleep(3)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.17"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}