update Docker file #149
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| name: CI | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| push: | |
| branches: | |
| - main | |
| tags: '*' | |
| schedule: | |
| - cron: '00 04 * * 1' # 4am every Monday | |
| workflow_dispatch: | |
| jobs: | |
| test_repo: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: | |
| - 3.9 | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up conda with Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install PyTorch and FAISS | |
| run: conda install pytorch==1.11 faiss-cpu -c pytorch | |
| - name: Install PyTorch Scatter and PyTorch Geometric | |
| run: conda install pytorch-scatter pyg -c pyg | |
| - name: Install STRIDE | |
| run: conda install kimlab::stride | |
| - name: Test install | |
| run: pip install -e . | |
| - name: Test help | |
| run: time python bin/progres -h | |
| - name: Test import | |
| run: time python -c "import progres" | |
| - name: Download structures | |
| run: | | |
| wget https://files.rcsb.org/view/1CRN.pdb | |
| wget https://files.rcsb.org/view/1SSU.cif | |
| wget https://alphafold.ebi.ac.uk/files/AF-P31434-F1-model_v4.pdb | |
| - name: Test search | |
| run: time python bin/progres search -q 1CRN.pdb -t scope95 | |
| - name: Test domain split | |
| run: time python bin/progres search -q AF-P31434-F1-model_v4.pdb -t cath40 -c | |
| - name: Test score | |
| run: time python bin/progres score 1CRN.pdb 1SSU.cif > score.txt | |
| - name: Check score | |
| run: | | |
| sc=$(cat score.txt) | |
| if [ ${sc:0:7} == "0.72652" ]; then echo "Correct score"; else echo "Wrong score, score is $sc"; exit 1; fi | |
| - name: Test database embedding | |
| run: | | |
| cd data | |
| time python ../bin/progres embed -l filepaths.txt -o out.pt | |
| time python ../bin/progres search -q query.pdb -t out.pt | |
| test_pypi: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: | |
| - 3.9 | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up conda with Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install PyTorch and FAISS | |
| run: conda install pytorch==1.11 faiss-cpu -c pytorch | |
| - name: Install PyTorch Scatter and PyTorch Geometric | |
| run: conda install pytorch-scatter pyg -c pyg | |
| - name: Install STRIDE | |
| run: conda install kimlab::stride | |
| - name: Test install | |
| run: pip install progres | |
| - name: Test help | |
| run: time progres -h | |
| - name: Test import | |
| run: time python -c "import progres" | |
| - name: Download structures | |
| run: | | |
| wget https://files.rcsb.org/view/1CRN.pdb | |
| wget https://files.rcsb.org/view/1SSU.cif | |
| wget https://alphafold.ebi.ac.uk/files/AF-P31434-F1-model_v4.pdb | |
| - name: Test search | |
| run: time progres search -q 1CRN.pdb -t scope95 | |
| - name: Test domain split | |
| run: time progres search -q AF-P31434-F1-model_v4.pdb -t cath40 -c | |
| - name: Test score | |
| run: time progres score 1CRN.pdb 1SSU.cif > score.txt | |
| - name: Check score | |
| run: | | |
| sc=$(cat score.txt) | |
| if [ ${sc:0:7} == "0.72652" ]; then echo "Correct score"; else echo "Wrong score, score is $sc"; exit 1; fi | |
| - name: Test database embedding | |
| run: | | |
| cd data | |
| time progres embed -l filepaths.txt -o out.pt | |
| time progres search -q query.pdb -t out.pt |