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Remove ccp4 and upgrade biopython #1231

Remove ccp4 and upgrade biopython

Remove ccp4 and upgrade biopython #1231

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 }}