try to fix autodoc imports

Author: lily-tomkovic-DWR

.github/workflows/build_sphinx.yml

@@ -33,26 +33,45 @@ jobs:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
 
-      - name: Set up Python 3.10
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libgfortran5
+
+      - name: Set up Python 3.11
         uses: actions/setup-python@v2
         with:
-          python-version: "3.10"
+          python-version: 3.11
+
+      - name: Add conda to system path
+        run: |
+          echo $CONDA/bin >> $GITHUB_PATH
 
-      - name: Install dependencies
+      - name: Conda build env for docs
         run: |
-          python -m pip install --upgrade pip
+          conda env create -f schism_env.yml
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate schism
+          conda install -c conda-forge libgfortran=3
           pip install -r docsrc/requirements.txt
+          pip install -e ./bdschism
 
       - name: Build HTML
         run: |
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate schism
           cd docsrc/
+          # sphinx-apidoc --force -o . ../bdschism
+          make clean
           make html
         
       - name: Run ghp-import
         shell: bash
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
+          source $CONDA/etc/profile.d/conda.sh
+          conda activate schism
           git config http.postBuffer 157286400
           git pull
 

docsrc/requirements.txt

@@ -1,5 +1,6 @@
 # furo==2021.11.16
 sphinx>=7.0
+pillow>=4.0.0
 sphinx-design
 sphinx-argparse  
 sphinxcontrib-bibtex
@@ -9,15 +10,6 @@ ghp-import # for GitHub Pages import
 nbsphinx
 numpydoc
 docutils
-matplotlib # needed for matplotlib.sphinxext.mathmply
-ipython    # neededd for IPython.sphinxext.ipython_directive
-pip
-# baydelta specific stuff
-# needed for many bdschism imports
-suxarray
-vtools
-dms_datastore
-schimpy
-dynaconf
-click
-pyproj
+# matplotlib # removed, already in schism_env.yml
+# ipython    # removed, already in schism_env.yml
+# pip        # removed, already in schism_env.yml