Remove ccp4 and upgrade biopython #1231
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name: AlphaPulldown-CI-CD | |
on: | |
pull_request: | |
push: | |
branches: | |
- main | |
release: | |
types: [published] | |
jobs: | |
build-and-test: | |
runs-on: ubuntu-20.04 | |
strategy: | |
fail-fast: false | |
matrix: | |
python-version: ["3.10", "3.11"] | |
install-type: ['user', 'developer'] | |
steps: | |
- uses: actions/checkout@v4 | |
with: | |
submodules: recursive | |
- run: ls -la -R | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
cache: "pip" | |
- run: python -c "import sys; print(sys.version)" | |
- run: | | |
echo $CONDA/bin >> $GITHUB_PATH | |
echo "$GITHUB_WORKSPACE/alphapulldown" >> $GITHUB_PATH | |
- if: matrix.install-type == 'user' | |
run: | | |
conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 pytest importlib_metadata modelcif | |
eval "$(conda shell.bash hook)" | |
conda activate AlphaPulldown | |
conda install -c bioconda hmmer hhsuite | |
pip install alphapulldown==2.0.0b4 | |
- if: matrix.install-type == 'developer' | |
run: | | |
conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 pytest importlib_metadata modelcif | |
eval "$(conda shell.bash hook)" | |
conda activate AlphaPulldown | |
conda install -c bioconda hmmer hhsuite | |
pip install -e . | |
pip install -e ColabFold --no-deps | |
pip install -e alphafold --no-deps | |
export PYTHONPATH=$PWD/AlphaLink2:$PYTHONPATH | |
# install dependencies for AlphaLink backend | |
# pip install torch==1.13.0+cu117 --extra-index-url https://download.pytorch.org/whl/cu117 | |
# pip install setuptools==69.5.1 # Downgrade setuptools to avoid crashes when installing unicore | |
# git clone https://github.com/dptech-corp/Uni-Core.git | |
# cd Uni-Core | |
# python setup.py install --disable-cuda-ext | |
# cd . | |
python test/test_python_imports.py | |
- if: matrix.install-type == 'developer' | |
run: | | |
eval "$(conda shell.bash hook)" | |
conda activate AlphaPulldown | |
pytest -s test/test_custom_db.py | |
pytest -s test/test_remove_clashes_low_plddt.py | |
pytest -s test/test_modelcif.py | |
pytest -s test/test_features_with_templates.py | |
pytest -s test/test_post_prediction.py | |
export PYTHONPATH=$PWD/alphapulldown/analysis_pipeline:$PYTHONPATH | |
conda install -c bioconda biopandas | |
pip install pyrosetta-installer | |
python -c 'import pyrosetta_installer; pyrosetta_installer.install_pyrosetta()' | |
pytest -s test/test_pdb_analyser.py | |
pytest -s test/test_get_good_inter_pae.py | |
build-fold-container: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout | |
uses: actions/checkout@v4 | |
- name: Free disk space | |
run: | | |
rm -rf /opt/hostedtoolcache | |
- name: Login to Docker Hub | |
uses: docker/login-action@v3 | |
with: | |
username: ${{ secrets.DOCKER_USERNAME }} | |
password: ${{ secrets.DOCKER_PASSWORD }} | |
- name: Set up Docker Buildx | |
uses: docker/setup-buildx-action@v3 | |
- name: Build and push fold container | |
if: github.event_name == 'push' | |
uses: docker/build-push-action@v5 | |
with: | |
context: . | |
file: ./docker/pulldown.dockerfile | |
push: true | |
tags: ${{ secrets.DOCKER_USERNAME }}/fold:latest | |
- name: Build and push fold container with version | |
if: github.event_name == 'release' && github.event.action == 'published' | |
uses: docker/build-push-action@v5 | |
with: | |
context: . | |
file: ./docker/pulldown.dockerfile | |
push: true | |
tags: ${{ secrets.DOCKER_USERNAME }}/fold:${{ github.event.release.tag_name }} | |
build-analysis-container: | |
runs-on: ubuntu-latest | |
steps: | |
- name: Checkout | |
uses: actions/checkout@v4 | |
- name: Free disk space | |
run: | | |
rm -rf /opt/hostedtoolcache | |
- name: Login to Docker Hub | |
uses: docker/login-action@v3 | |
with: | |
username: ${{ secrets.DOCKER_USERNAME }} | |
password: ${{ secrets.DOCKER_PASSWORD }} | |
- name: Set up Docker Buildx | |
uses: docker/setup-buildx-action@v3 | |
- name: Build and push analysis container | |
if: github.event_name == 'push' | |
uses: docker/build-push-action@v5 | |
with: | |
context: . | |
file: ./docker/analysis.dockerfile | |
push: true | |
tags: ${{ secrets.DOCKER_USERNAME }}/fold_analysis:latest | |
- name: Build and push analysis container with version | |
if: github.event_name == 'release' && github.event.action == 'published' | |
uses: docker/build-push-action@v5 | |
with: | |
context: . | |
file: ./docker/analysis.dockerfile | |
push: true | |
tags: ${{ secrets.DOCKER_USERNAME }}/fold_analysis:${{ github.event.release.tag_name }} |