Fix acquire-zarr build for docs

Author: melissawm

.github/workflows/deploy_docs.yml

@@ -41,11 +41,11 @@ jobs:
         with:
           path: acquire-python  # place in a named directory
           repository: acquire-project/acquire-python
+          submodules: true
 
       - name: Install acquire-python  # For collecting the API reference
         run: |
           cd acquire-python
-          git submodule update --init --recursive
           python -m pip install -e .
 
       - name: Clone acquire-zarr repo
@@ -54,31 +54,34 @@ jobs:
           path: acquire-zarr  # place in a named directory
           repository: acquire-project/acquire-zarr
 
-      - name: Install acquire-zarr  # For collecting the API reference
+      - name: Install Doxygen
+        run: sudo apt-get install -y doxygen
+
+      - name: Install vcpkg
         run: |
-          cd acquire-zarr
           git clone https://github.com/microsoft/vcpkg.git
           cd vcpkg && ./bootstrap-vcpkg.sh
-          cat >> ~/.bashrc <<EOF
-          export VCPKG_ROOT=${PWD}
-          export PATH=\$VCPKG_ROOT:\$PATH
-          EOF
-          cd ..
+          echo "VCPKG_ROOT=${{github.workspace}}/vcpkg" >> $GITHUB_ENV
+          echo "${{github.workspace}}/vcpkg" >> $GITHUB_PATH
+          ./vcpkg integrate install
+        shell: bash
+
+      - name: Install acquire-zarr  # For collecting the API reference
+        run: |
+          cd acquire-zarr
+          python -m pip install pybind11
           cmake --preset=default -B build -DBUILD_PYTHON=ON .
           cmake --build build
           python -m pip install .
 
-      - name: Install Doxygen
-        run: sudo apt-get install -y doxygen
-
       - name: Build website
         run: |
           cd acquire-docs
           mkdocs build
 
       - name: Replace relative links in Doxygen include
         run: |
-          sed -i 's@acquire_zarr_c_api/acquire_zarr_c_api#@#@g' site/stream_to_zarr/c_api/index.html
+          sed -i 's@acquire_zarr_c_api/acquire_zarr_c_api#@#@g' acquire-docs/site/stream_to_zarr/c_api/index.html
 
       - name: Deploy docs
         uses: peaceiris/actions-gh-pages@v3