Getting started

A step-by-step guide to getting started with OpenProblems

To get started with contributing to OpenProblems, you’ll need to fork and clone the OpenProblems repository to your local machine.

Step 1: Create a fork

Go to the OpenProblems repository at https://github.com/openproblems-bio/openproblems-v2 and click on the “Fork” button in the top right corner of the page.

This will create a copy of the repository under your GitHub account.

Tip

While you’re at it, why not click the “Star” button as well?

Step 2: Clone the repository

To clone this forked repository to your local machine, copy the URL of the forked repository by clicking the green “Code” button and selecting HTTPS or SSH.

In your terminal or command prompt, navigate to the directory where you want to clone the repository and enter the following command:

git clone <forked repository URL> openproblems-v2
cd openproblems-v2

This will download a copy of the repository to your local machine. You can now make changes to the code, add new functionality, and commit your changes. Please commit your changes to a new branch following the branch naming convention.

Step 3: Download test resources

You will also need to download the test resources by running the following command. These are needed for testing the existing components and can be used for developing new unit tests. From the repository root, run:

viash run src/common/sync_test_resources/config.vsh.yaml

Output

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download: s3://openproblems-data/resources_test/batch_integration/cxg_mouse_pancreas_atlas/state.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/batch_integration/cxg_mouse_pancreas_atlas/state.yaml
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download: s3://openproblems-data/resources_test/batch_integration/cxg_mouse_pancreas_atlas/dataset.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/batch_integration/cxg_mouse_pancreas_atlas/dataset.h5ad
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download: s3://openproblems-data/resources_test/batch_integration/cxg_mouse_pancreas_atlas/solution.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/batch_integration/cxg_mouse_pancreas_atlas/solution.h5ad
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download: s3://openproblems-data/resources_test/batch_integration/pancreas/dataset.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/batch_integration/pancreas/dataset.h5ad
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download: s3://openproblems-data/resources_test/batch_integration/pancreas/state.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/batch_integration/pancreas/state.yaml
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download: s3://openproblems-data/resources_test/batch_integration/cxg_mouse_pancreas_atlas/integrated_graph.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/batch_integration/cxg_mouse_pancreas_atlas/integrated_graph.h5ad
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download: s3://openproblems-data/resources_test/batch_integration/pancreas/solution.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/batch_integration/pancreas/solution.h5ad
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download: s3://openproblems-data/resources_test/batch_integration/cxg_mouse_pancreas_atlas/integrated_embedding.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/batch_integration/cxg_mouse_pancreas_atlas/integrated_embedding.h5ad
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download: s3://openproblems-data/resources_test/batch_integration/pancreas/integrated_graph.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/batch_integration/pancreas/integrated_graph.h5ad
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download: s3://openproblems-data/resources_test/common/cxg_mouse_pancreas_atlas/dataset_metadata.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/cxg_mouse_pancreas_atlas/dataset_metadata.yaml
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download: s3://openproblems-data/resources_test/common/cxg_mouse_pancreas_atlas/state.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/cxg_mouse_pancreas_atlas/state.yaml
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download: s3://openproblems-data/resources_test/batch_integration/pancreas/integrated_embedding.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/batch_integration/pancreas/integrated_embedding.h5ad
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download: s3://openproblems-data/resources_test/batch_integration/pancreas/integrated_feature.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/batch_integration/pancreas/integrated_feature.h5ad
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_metadata_mod2.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_metadata_mod2.yaml
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2021/bmmc_cite/state.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/openproblems_neurips2021/bmmc_cite/state.yaml
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_metadata_mod1.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_metadata_mod1.yaml
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod1.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod1.h5ad
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod2.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod2.h5ad
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2021/bmmc_multiome/dataset_metadata_mod1.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/openproblems_neurips2021/bmmc_multiome/dataset_metadata_mod1.yaml
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download: s3://openproblems-data/resources_test/common/cxg_mouse_pancreas_atlas/dataset.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/cxg_mouse_pancreas_atlas/dataset.h5ad
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2021/bmmc_multiome/dataset_mod1.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/openproblems_neurips2021/bmmc_multiome/dataset_mod1.h5ad
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2021/bmmc_multiome/dataset_metadata_mod2.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/openproblems_neurips2021/bmmc_multiome/dataset_metadata_mod2.yaml
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2021/bmmc_multiome/state.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/openproblems_neurips2021/bmmc_multiome/state.yaml
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download: s3://openproblems-data/resources_test/batch_integration/cxg_mouse_pancreas_atlas/integrated_feature.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/batch_integration/cxg_mouse_pancreas_atlas/integrated_feature.h5ad
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download: s3://openproblems-data/resources_test/common/pancreas/dataset_meta.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/pancreas/dataset_meta.yaml
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download: s3://openproblems-data/resources_test/common/pancreas/hvg.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/pancreas/hvg.h5ad
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download: s3://openproblems-data/resources_test/common/pancreas/dataset.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/pancreas/dataset.h5ad
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download: s3://openproblems-data/resources_test/common/pancreas/normalized.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/pancreas/normalized.h5ad
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download: s3://openproblems-data/resources_test/common/pancreas/state.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/pancreas/state.yaml
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download: s3://openproblems-data/resources_test/common/pancreas/knn.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/pancreas/knn.h5ad
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download: s3://openproblems-data/resources_test/common/scicar_cell_lines/dataset_metadata_mod1.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/scicar_cell_lines/dataset_metadata_mod1.yaml
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download: s3://openproblems-data/resources_test/common/scicar_cell_lines/dataset_metadata_mod2.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/scicar_cell_lines/dataset_metadata_mod2.yaml
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download: s3://openproblems-data/resources_test/common/pancreas/pca.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/pancreas/pca.h5ad
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download: s3://openproblems-data/resources_test/common/pancreas/raw.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/pancreas/raw.h5ad
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download: s3://openproblems-data/resources_test/common/scicar_cell_lines/state.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/scicar_cell_lines/state.yaml
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download: s3://openproblems-data/resources_test/common/scicar_cell_lines/dataset_mod2.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/scicar_cell_lines/dataset_mod2.h5ad
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download: s3://openproblems-data/resources_test/common/task_metadata/input_git_sha.json to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/task_metadata/input_git_sha.json
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2021/bmmc_multiome/dataset_mod2.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/openproblems_neurips2021/bmmc_multiome/dataset_mod2.h5ad
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download: s3://openproblems-data/resources_test/common/task_metadata/method_info.json to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/task_metadata/method_info.json
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download: s3://openproblems-data/resources_test/common/task_metadata/scores.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/task_metadata/scores.yaml
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download: s3://openproblems-data/resources_test/common/task_metadata/method_configs.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/task_metadata/method_configs.yaml
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download: s3://openproblems-data/resources_test/common/scicar_cell_lines/dataset_mod1.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/scicar_cell_lines/dataset_mod1.h5ad
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download: s3://openproblems-data/resources_test/common/task_metadata/state.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/task_metadata/state.yaml
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download: s3://openproblems-data/resources_test/common/task_metadata/trace.txt to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/common/task_metadata/trace.txt
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download: s3://openproblems-data/resources_test/denoising/cxg_mouse_pancreas_atlas/state.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/denoising/cxg_mouse_pancreas_atlas/state.yaml
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download: s3://openproblems-data/resources_test/denoising/cxg_mouse_pancreas_atlas/test.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/denoising/cxg_mouse_pancreas_atlas/test.h5ad
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download: s3://openproblems-data/resources_test/denoising/pancreas/state.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/denoising/pancreas/state.yaml
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download: s3://openproblems-data/resources_test/denoising/pancreas/score.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/denoising/pancreas/score.h5ad
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download: s3://openproblems-data/resources_test/denoising/pancreas/test.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/denoising/pancreas/test.h5ad
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download: s3://openproblems-data/resources_test/denoising/pancreas/train.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/denoising/pancreas/train.h5ad
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download: s3://openproblems-data/resources_test/denoising/pancreas/denoised.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/denoising/pancreas/denoised.h5ad
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download: s3://openproblems-data/resources_test/denoising/cxg_mouse_pancreas_atlas/train.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/denoising/cxg_mouse_pancreas_atlas/train.h5ad
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download: s3://openproblems-data/resources_test/dimensionality_reduction/cxg_mouse_pancreas_atlas/state.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/dimensionality_reduction/cxg_mouse_pancreas_atlas/state.yaml
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download: s3://openproblems-data/resources_test/dimensionality_reduction/pancreas/state.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/dimensionality_reduction/pancreas/state.yaml
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download: s3://openproblems-data/resources_test/dimensionality_reduction/pancreas/embedding.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/dimensionality_reduction/pancreas/embedding.h5ad
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download: s3://openproblems-data/resources_test/dimensionality_reduction/pancreas/score.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/dimensionality_reduction/pancreas/score.h5ad
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download: s3://openproblems-data/resources_test/dimensionality_reduction/cxg_mouse_pancreas_atlas/dataset.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/dimensionality_reduction/cxg_mouse_pancreas_atlas/dataset.h5ad
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download: s3://openproblems-data/resources_test/dimensionality_reduction/pancreas/solution.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/dimensionality_reduction/pancreas/solution.h5ad
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download: s3://openproblems-data/resources_test/dimensionality_reduction/cxg_mouse_pancreas_atlas/solution.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/dimensionality_reduction/cxg_mouse_pancreas_atlas/solution.h5ad
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download: s3://openproblems-data/resources_test/label_projection/cxg_mouse_pancreas_atlas/solution.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/label_projection/cxg_mouse_pancreas_atlas/solution.h5ad
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download: s3://openproblems-data/resources_test/label_projection/cxg_mouse_pancreas_atlas/train.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/label_projection/cxg_mouse_pancreas_atlas/train.h5ad
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download: s3://openproblems-data/resources_test/label_projection/cxg_mouse_pancreas_atlas/test.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/label_projection/cxg_mouse_pancreas_atlas/test.h5ad
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download: s3://openproblems-data/resources_test/label_projection/pancreas/score.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/label_projection/pancreas/score.h5ad
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download: s3://openproblems-data/resources_test/label_projection/cxg_mouse_pancreas_atlas/state.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/label_projection/cxg_mouse_pancreas_atlas/state.yaml
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download: s3://openproblems-data/resources_test/label_projection/pancreas/state.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/label_projection/pancreas/state.yaml
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download: s3://openproblems-data/resources_test/label_projection/pancreas/solution.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/label_projection/pancreas/solution.h5ad
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download: s3://openproblems-data/resources_test/label_projection/pancreas/train.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/label_projection/pancreas/train.h5ad
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download: s3://openproblems-data/resources_test/dimensionality_reduction/pancreas/dataset.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/dimensionality_reduction/pancreas/dataset.h5ad
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download: s3://openproblems-data/resources_test/label_projection/pancreas/prediction.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/label_projection/pancreas/prediction.h5ad
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download: s3://openproblems-data/resources_test/match_modalities/scicar_cell_lines/state.yaml to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/match_modalities/scicar_cell_lines/state.yaml
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download: s3://openproblems-data/resources_test/match_modalities/scicar_cell_lines/dataset_mod2.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/match_modalities/scicar_cell_lines/dataset_mod2.h5ad
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download: s3://openproblems-data/resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/spatial_decomposition/cxg_mouse_pancreas_atlas/single_cell_ref.h5ad
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download: s3://openproblems-data/resources_test/spatial_decomposition/pancreas/single_cell_ref.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/spatial_decomposition/pancreas/single_cell_ref.h5ad
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download: s3://openproblems-data/resources_test/spatial_decomposition/pancreas/dataset_synthetic.h5ad to ../viash_automount/home/runner/work/website/website/_openproblems-v2/resources_test/spatial_decomposition/pancreas/dataset_synthetic.h5ad

The test resources are stored in the resources_test directory.

Ready, set, go!

That’s it! Now you should be able to test whether the existing components work as expected and then start adding functionality to the pipeline. Running an existing component is as simple as running a command in your terminal. Using test data as input, you can try this out immediately.

Run a component

Use the viash run command to run a Viash component. Everything after the -- separator counts as the arguments of the component itself. In this case, the knn component has an --input_train and --input_test argument to which the test resources are passed.

viash run src/tasks/label_projection/methods/knn/config.vsh.yaml -- \
  --input_train resources_test/label_projection/pancreas/train.h5ad \
  --input_test resources_test/label_projection/pancreas/test.h5ad \
  --output output.h5ad

Output

[notice] Checking if Docker image is available at 'ghcr.io/openproblems-bio/label_projection/methods/knn:dev'
[warning] Could not pull from 'ghcr.io/openproblems-bio/label_projection/methods/knn:dev'. Docker image doesn't exist or is not accessible.
[notice] Building container 'ghcr.io/openproblems-bio/label_projection/methods/knn:dev' with Dockerfile
Load input data
Fit to train data
Predict on test data
Write output to file

Testing components

Testing components is an important part of the development process. Each tasks comes with pre-defined unit tests that can be run using the viash test command.

viash test src/tasks/label_projection/methods/knn/config.vsh.yaml

Output

Running tests in temporary directory: '/tmp/viash_test_knn4959427177284732337'
====================================================================
+/tmp/viash_test_knn4959427177284732337/build_executable/knn ---verbosity 6 ---setup cachedbuild
[notice] Building container 'ghcr.io/openproblems-bio/label_projection/methods/knn:test' with Dockerfile
[info] Running 'docker build -t ghcr.io/openproblems-bio/label_projection/methods/knn:test /tmp/viash_test_knn4959427177284732337/build_executable -f /tmp/viash_test_knn4959427177284732337/build_executable/tmp/dockerbuild-knn-BiTVM7/Dockerfile'
#0 building with "default" instance using docker driver

#1 [internal] load .dockerignore
#1 transferring context: 2B done
#1 DONE 0.0s

#2 [internal] load build definition from Dockerfile
#2 transferring dockerfile: 608B done
#2 DONE 0.0s

#3 [internal] load metadata for ghcr.io/openproblems-bio/base_python:1.0.2
#3 DONE 0.1s

#4 [1/2] FROM ghcr.io/openproblems-bio/base_python:1.0.2@sha256:6def76c4092dc79d4c6613e28ca6afaa994ea9563194e6971fdca70362dd70ba
#4 DONE 0.0s

#5 [2/2] RUN pip install --upgrade pip &&   pip install --upgrade --no-cache-dir "scikit-learn" "jsonschema"
#5 CACHED

#6 exporting to image
#6 exporting layers done
#6 writing image sha256:77c1797575e32015a3448b448ba4c9c4f68013be57ef62eb8d74e1cdf48b8771 done
#6 naming to ghcr.io/openproblems-bio/label_projection/methods/knn:test done
#6 DONE 0.0s
====================================================================
+/tmp/viash_test_knn4959427177284732337/test_check_method_config/test_executable
Load config data
Check general fields
Check info fields
Check platform fields
All checks succeeded!
====================================================================
+/tmp/viash_test_knn4959427177284732337/test_run_and_check_adata/test_executable
>> Running test 'run'
>> Checking whether input files exist
>> Running script as test
Load input data
Fit to train data
Predict on test data
Write output to file
>> Checking whether output file exists
>> Reading h5ad files and checking formats
Reading and checking input_train
  AnnData object with n_obs × n_vars = 387 × 1500
    obs: 'label', 'batch'
    var: 'hvg', 'hvg_score'
    uns: 'dataset_id', 'normalization_id'
    obsm: 'X_pca'
    layers: 'counts', 'normalized'
Reading and checking input_test
  AnnData object with n_obs × n_vars = 213 × 1500
    obs: 'batch'
    var: 'hvg', 'hvg_score'
    uns: 'dataset_id', 'normalization_id'
    obsm: 'X_pca'
    layers: 'counts', 'normalized'
Reading and checking output
  AnnData object with n_obs × n_vars = 213 × 1500
    obs: 'batch', 'label_pred'
    var: 'hvg', 'hvg_score'
    uns: 'dataset_id', 'method_id', 'normalization_id'
    obsm: 'X_pca'
    layers: 'counts', 'normalized'
All checks succeeded!
====================================================================
SUCCESS! All 2 out of 2 test scripts succeeded!
Cleaning up temporary directory

If you want to run the unit tests for all of the components of a task, you can use the viash ns test command.

viash ns test --query label_projection --parallel --platform docker

Output

             namespace        functionality             platform            test_name exit_code duration               result
label_projection/methods  logistic_regression               docker                start                                        
label_projection/methods               scanvi               docker                start                                        
label_projection/methods                  knn               docker                start                                        
label_projection/methods                  mlp               docker                start                                        
label_projection/metrics             accuracy               docker                start                                        
label_projection/metrics                   f1               docker                start
label_projection/methods  logistic_regression               docker     build_executable         0        4              SUCCESS
label_projection/methods  logistic_regression               docker      generic_test.py         0        9              SUCCESS
label_projection/metrics                   f1               docker     build_executable         0        7              SUCCESS
label_projection/metrics                   f1               docker      format_check.py         0        8              SUCCESS
label_projection/metrics             accuracy               docker     build_executable         0        8              SUCCESS
label_projection/metrics             accuracy               docker      format_check.py         0        7              SUCCESS
...