Fixed Jupyter notebooks (separately for paste and paste2) (#66)

* triggering workflow on PR to main
* cleaned up notebooks to work on CI
* docs extra to contain all documentation-related dependencies

.github/workflows/docs.yml

@@ -3,8 +3,8 @@ name: Docs
 on:
   push:
     branches: [ main ]
-    tags:
-      - '*'
+  pull_request:
+    branches: [ main ]
 
 jobs:
 
@@ -20,19 +20,15 @@ jobs:
         with:
           python-version: ${{ matrix.python }}
 
-      - name: Install Python dependencies
-        run: |
-          pip install sphinx==6.2.1 myst-parser sphinx-autodoc-typehints nbsphinx sphinx-gallery sphinx-rtd-theme sphinx-autodoc-annotation
-
       - uses: actions/checkout@v2
 
-      - name: Install Package
-        run: |
-         pip install .
-
       - name: Install Pandoc
         run: sudo apt-get install -y pandoc
 
+      - name: Install Package with docs extra
+        run: |
+         pip install .[docs]
+
       - name: Setup Envvars
         run: |
             if [[ $GITHUB_REF = "refs/tags/"* ]] ; then echo "PASTE3_VERSION=${GITHUB_REF/refs\/tags\//}" ; else echo "PASTE3_VERSION=" ; fi >> $GITHUB_ENV

docs/source/api.rst

@@ -12,18 +12,6 @@ PASTE Alignment
     paste.pairwise_align
     paste.center_align
 
-PASTE2 Alignment
-~~~~~~~~~~~~~~~~~~
-
-.. autosummary::
-   :toctree: api
-
-    paste2.partial_pairwise_align_given_cost_matrix
-    paste2.partial_pairwise_align_histology
-    paste2.partial_pairwise_align
-    paste2.partial_fused_gromov_wasserstein
-    paste2.gwgrad_partial
-
 Visualization
 ~~~~~~~~~~~~~
 
@@ -33,8 +21,6 @@ Visualization
     visualization.stack_slices_pairwise
     visualization.stack_slices_center
     visualization.plot_slice
-    visualization.partial_stack_slices_pairwise
-    visualization.partial_procrustes_analysis
 
 Model Selection
 ~~~~~~~~~~~~~~~~