Checkout from main

.github/workflows/github_actions.yml

@@ -1,6 +1,6 @@
 name: AlphaPulldown-github-CI
 
-on: [pull_request, push]
+on: [pull_request,push]
 
 jobs:
   build:
@@ -11,7 +11,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          submodules: recursive
+            submodules: recursive
       - name: Debug List Directory
         run: ls -la -R
       - name: Set up Python ${{ matrix.python-version }}
@@ -35,33 +35,30 @@ jobs:
           conda develop alphapulldown
           conda develop alphapulldown/ColabFold
           conda develop alphafold
+          #conda info
+          #conda list
+          #python -c "import sys; print(sys.path)"
+          #echo "Python path: $PYTHONPATH"
           python -c "import alphafold; import os; print('Alphafold module is located at:', alphafold.__file__); alphafold_dir = os.path.dirname(alphafold.__file__); print('Contents of the Alphafold directory:', os.listdir(alphafold_dir))"
       - name: Install Dependencies
         run: |
           eval "$(conda shell.bash hook)"
           conda activate AlphaPulldown
           conda install -c omnia -c bioconda -c conda-forge openmm==8.0 pdbfixer==1.9 kalign2 cctbx-base importlib_metadata
+          #conda install -c bioconda hmmer hhsuite #this causes conda conflicts
           pip install jax==0.3.25 jaxlib==0.3.25+cuda11.cudnn805 -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
           pip install "absl-py>=0.13.0" dm-haiku "dm-tree>=0.1.6" "h5py>=3.1.0" "ml-collections>=0.1.0" "pandas>=1.3.4" tensorflow "importlib-resources==5.8.0" "nbformat==5.4.0" "py3Dmol==2.0.1" ipython appdirs jupyterlab ipywidgets pytest
       - name: Run Tests
         run: |
           eval "$(conda shell.bash hook)"
           conda activate AlphaPulldown
-          pytest -s test/test_custom_db.py
-          pytest -s test/test_remove_clashes_low_plddt.py
-          #TODO: mock AF dbs and add other tests
-  publish:
-    runs-on: ubuntu-latest
-    if: github.event_name == 'release' && github.event.action == 'published'
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-      - run: python3 -m pip install --upgrade build && python3 -m build
-      - name: Publish package
-        uses: pypa/gh-action-pypi-publish@release/v1
+          pytest test/
+      - name: Build and Push to Docker Hub
+        uses: mr-smithers-excellent/docker-build-push@v5
         with:
-          user: ${{ secrets.PYPI_LOGIN_DIMA }}
-          password: ${{ secrets.PYPI_PASSWORD_DIMA }}
-          repository_url: https://test.pypi.org/legacy/
+          image: dmolodenskiy/AlphaPulldown
+          registry: docker.io
+          dockerfile: docker/Dockerfile
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+          tags: latest