updates init template #695
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: tests | |
| on: | |
| push: | |
| schedule: | |
| - cron: "0 0 * * 0" # weekly | |
| env: | |
| CONDA_PKGS_DIRS: /home/runner/pkgs | |
| jobs: | |
| test_models: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Setup conda | |
| uses: s-weigand/setup-conda@678f22c807cb6fde6a290be6f3546877c98ec66f # v1.2.2 | |
| with: | |
| update-conda: true | |
| python-version: 3.7 | |
| conda-channels: anaconda, conda-forge, bioconda | |
| - name: Create environment | |
| run: | | |
| conda install -n base mamba -c conda-forge | |
| conda clean --all -y | |
| mamba env create -f environment.yml | |
| - name: Run tests with pytest | |
| run: | | |
| source activate metamers | |
| pytest tests/test_models.py | |
| test_snakefile: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Setup conda | |
| uses: s-weigand/setup-conda@678f22c807cb6fde6a290be6f3546877c98ec66f # v1.2.2 | |
| with: | |
| update-conda: true | |
| python-version: 3.7 | |
| conda-channels: anaconda, conda-forge, bioconda | |
| - name: Create environment | |
| run: | | |
| conda install -n base mamba | |
| conda clean --all -y | |
| mamba env create -f environment.yml | |
| - name: Setup FFmpeg | |
| uses: FedericoCarboni/[email protected] | |
| - name: Download data | |
| run: | | |
| mkdir -p data/metamers/ref_images/ | |
| curl -O -J -L https://osf.io/4wyg3/download | |
| tar xf textures-subset-for-testing.tar.gz -C data | |
| rm textures-subset-for-testing.tar.gz | |
| - name: modify config.yml | |
| run: | | |
| sed -i 's|DATA_DIR:.*|DATA_DIR: "data/metamers"|g' config.yml | |
| sed -i 's|TEXTURE_DIR:.*|TEXTURE_DIR: "data/textures-subset-for-testing"|g' config.yml | |
| - name: run snakemake test | |
| run: | | |
| source activate metamers | |
| cp extra_packages/data/einstein.pgm data/metamers/ref_images/einstein_size-256,256.png | |
| snakemake -j 5 -prk data/metamers/test_setup/RGC_norm_gaussian_gpu-0/einstein data/metamers/test_setup/V1_norm_s6_gaussian_gpu-0/einstein | |
| run_Freeman_check_notebook: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Setup conda | |
| uses: s-weigand/setup-conda@678f22c807cb6fde6a290be6f3546877c98ec66f # v1.2.2 | |
| with: | |
| update-conda: true | |
| python-version: 3.7 | |
| conda-channels: anaconda, conda-forge, bioconda | |
| - name: Create environment | |
| run: | | |
| conda install -n base mamba | |
| conda clean --all -y | |
| mamba env create -f environment.yml | |
| source activate metamers | |
| mamba install jupyter nbclient>=0.5.5 | |
| - name: modify config.yml | |
| run: | | |
| sed -i 's|DATA_DIR:.*|DATA_DIR: "data/metamers"|g' config.yml | |
| sed -i 's|TEXTURE_DIR:.*|TEXTURE_DIR: "data/textures-subset-for-testing"|g' config.yml | |
| mkdir -p data/metamers | |
| mkdir -p data/textures-subset-for-testing | |
| - name: Download data | |
| run: | | |
| source activate metamers | |
| python download_data.py freeman2011_check_output -s | |
| python download_data.py freeman2011_check_input -s | |
| - name: run nbconvert | |
| run: | | |
| source activate metamers | |
| jupyter execute notebooks/Freeman_Check.ipynb --kernel_name=python3 | |
| test_mcmc: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Setup conda | |
| uses: s-weigand/setup-conda@678f22c807cb6fde6a290be6f3546877c98ec66f # v1.2.2 | |
| with: | |
| update-conda: true | |
| python-version: 3.7 | |
| conda-channels: anaconda, conda-forge, bioconda | |
| - name: Create environment | |
| run: | | |
| conda install -n base mamba | |
| conda clean --all -y | |
| mamba env create -f environment.yml | |
| - name: modify config.yml | |
| run: | | |
| sed -i 's|DATA_DIR:.*|DATA_DIR: "data/metamers"|g' config.yml | |
| sed -i 's|TEXTURE_DIR:.*|TEXTURE_DIR: "data/textures-subset-for-testing"|g' config.yml | |
| mkdir -p data/metamers | |
| mkdir -p data/textures-subset-for-testing | |
| - name: Download data | |
| run: | | |
| source activate metamers | |
| python download_data.py behavioral_data -s | |
| - name: run mcmc test | |
| run: | | |
| source activate metamers | |
| # test one that has a single subject, one with multiple | |
| snakemake -j 5 -prk data/metamers/mcmc/V1_norm_s6_gaussian/task-split_comp-ref/task-split_comp-ref_mcmc_partially-pooled_step-1_prob-.8_depth-10_c-2_d-10_w-10_s-0.nc data/metamers/mcmc/V1_norm_s6_gaussian/task-split_comp-ref-natural/task-split_comp-ref-natural_mcmc_partially-pooled_step-1_prob-.8_depth-10_c-2_d-10_w-10_s-0.nc |