adds ability to toggle physio bars #700
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| 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/setup-ffmpeg@v3.1 | |
| - 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 |