try without sphinx-action

.github/workflows/build.yml

@@ -27,17 +27,16 @@ jobs:
     - name: Install essential
       run: |
         sudo apt update
-        sudo apt install build-essential
+        sudo apt install build-essential pandoc
     - name: Install conda packages
       run: |
         conda install -c anaconda cmake
         conda install rdkit mpi4py h5py pytorch==2.0.0 torchvision==0.15.0 cpuonly -c pytorch -c conda-forge
         conda install -c conda-forge libstdcxx-ng
         conda install -c anaconda gxx_linux-64
-        conda install pandoc
 
     - name: Install the package
-      run: python -m pip install .[test,hpc]
+      run: python -m pip install .[test,hpc,doc]
       env:
         CONDA_PREFIX: /usr/share/miniconda
 
@@ -62,34 +61,13 @@ jobs:
         GITHUB_TOKEN: ${{ secrets.github_token }}
         COVERALLS_FLAG_NAME: python-${{ matrix.version }}
         COVERALLS_PARALLEL: true
-    # Standard drop-in approach that should work for most people.
-    - uses: ammaraskar/sphinx-action@master
-      with:
-        docs-folder: "docs/"
-      env:
-        CONDA_PREFIX: /usr/share/miniconda
-    # Great extra actions to compose with:
-    # Create an artifact of the html output.
-    - uses: actions/upload-artifact@v1
-      with:
-        name: DocumentationHTML
-        path: docs/_build/html/
-
 
-  finish:
-    needs: build
-    runs-on: ubuntu-latest
-    steps:
-      - name: Coveralls Finished
-        uses: coverallsapp/github-action@master
-        with:
-          github-token: ${{ secrets.github_token }}
-          parallel-finished: true
       # Publish built docs to gh-pages branch.
       # ===============================
       - name: Commit documentation changes
         run: |
           git clone https://github.com/NLESC-JCER/QMCTorch.git --branch gh-pages --single-branch gh-pages
+          jupyter nbconvert --to notebook --execute docs/notebooks/sampling.ipynb
           cp -r docs/_build/html/* gh-pages/
           cd gh-pages
           touch .nojekyll
@@ -99,9 +77,23 @@ jobs:
           git commit -m "Update documentation" -a || true
           # The above command will fail if no changes were present, so we ignore
           # that.
+        env:
+          CONDA_PREFIX: /usr/share/miniconda
       - name: Push changes
         uses: ad-m/github-push-action@master
         with:
           branch: gh-pages
           directory: gh-pages
           github_token: ${{ secrets.GITHUB_TOKEN }}
+
+
+  finish:
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+      - name: Coveralls Finished
+        uses: coverallsapp/github-action@master
+        with:
+          github-token: ${{ secrets.github_token }}
+          parallel-finished: true
+

setup.py

@@ -48,7 +48,7 @@
 
     extras_require={
         'hpc': ['horovod==0.27.0'],
-        'doc': ['recommonmark', 'sphinx', 'sphinx_rtd_theme', 'nbsphinx'],
+        'doc': ['recommonmark', 'sphinx', 'sphinx_rtd_theme', 'nbsphinx','nbconvert'],
         'test': ['pytest', 'pytest-runner',
                  'coverage', 'coveralls', 'pycodestyle'],
     }