update vignette with new functions #51
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Run Benchmarks | |
| on: | |
| push: | |
| branches: | |
| - main | |
| paths: | |
| - 'flexynesis/**' | |
| - '.github/workflows/**' | |
| - './spec-file.txt' | |
| - './pyproject.toml' | |
| - './manifest.scm' | |
| - './guix.scm' | |
| jobs: | |
| run_package: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.9' | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: '3.9' | |
| - name: Cache Conda environment | |
| uses: actions/cache@v2 | |
| with: | |
| path: ~/miniconda/envs | |
| key: ${{ runner.os }}-conda-${{ hashFiles('spec-file.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-conda- | |
| - name: Create environment with dependencies | |
| shell: bash -l {0} | |
| run: | | |
| conda create --name my_env --file spec-file.txt | |
| conda activate my_env | |
| - name: Install my package from source | |
| shell: bash -l {0} | |
| run: | | |
| conda activate my_env | |
| pip install -e . | |
| - name: Download dataset1 | |
| run: | | |
| curl -L -o dataset1.tgz https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis-benchmark-datasets/dataset1.tgz | |
| tar -xzvf dataset1.tgz | |
| - name: Download dataset2 | |
| run: | | |
| curl -L -o dataset2.tgz https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis-benchmark-datasets/dataset2.tgz | |
| tar -xzvf dataset2.tgz | |
| - name: Run DirectPred | |
| shell: bash -l {0} | |
| run: | | |
| conda activate my_env | |
| flexynesis --data_path dataset1 --model_class DirectPred --target_variables Erlotinib --batch_variables Crizotinib --fusion_type early --hpo_iter 1 --features_min 500 --features_top_percentile 0.2 --log_transform False --data_types gex,cnv --outdir . --prefix erlotinib_direct | |
| - name: Run supervised_vae | |
| shell: bash -l {0} | |
| run: | | |
| conda activate my_env | |
| flexynesis --data_path dataset1 --model_class supervised_vae --target_variables Erlotinib --batch_variables Crizotinib --fusion_type early --hpo_iter 1 --features_min 500 --features_top_percentile 0.2 --log_transform False --data_types gex,cnv --outdir . --prefix erlotinib_svae | |
| - name: Run MultiTripletNetwork | |
| shell: bash -l {0} | |
| run: | | |
| conda activate my_env | |
| flexynesis --data_path dataset2 --model_class MultiTripletNetwork --target_variables y --fusion_type early --hpo_iter 1 --features_min 500 --features_top_percentile 0.2 --log_transform False --data_types gex,meth --outdir . --prefix msi_triplet | |