Getting started

A step-by-step guide to getting started with contributing to an OpenProblems task

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

Step 1: Create a fork

Go to the OpenProblems organisation at https://github.com/openproblems-bio and search for the task repository you want to start contributing to. Open the repository 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 --recursive <forked repository URL>
cd <repository name>

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.

Note

If somehow there are no files visible in the common submodule after cloning using the above command. Use the following command to update the submodule:

git submodule update --init --recursive

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:

scripts/sync_resources.sh

Output

Syncing 's3://openproblems-data/resources_test/common/' to 'resources_test/common'...
Completed 24 Bytes/~20.5 MiB (57 Bytes/s) with ~55 file(s) remaining (calculating...)
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/.zgroup to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/.zgroup
Completed 24 Bytes/~22.0 MiB (57 Bytes/s) with ~61 file(s) remaining (calculating...)
Completed 8.3 KiB/~22.1 MiB (19.7 KiB/s) with ~64 file(s) remaining (calculating...) 
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/.zattrs to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/.zattrs
Completed 8.3 KiB/~22.6 MiB (19.7 KiB/s) with ~67 file(s) remaining (calculating...)
Completed 8.4 KiB/~49.1 MiB (18.7 KiB/s) with ~144 file(s) remaining (calculating...)
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/.zgroup to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/.zgroup
Completed 8.4 KiB/~49.1 MiB (18.7 KiB/s) with ~145 file(s) remaining (calculating...)
Completed 8.7 KiB/~49.2 MiB (18.7 KiB/s) with ~211 file(s) remaining (calculating...)
Completed 9.1 KiB/~49.2 MiB (19.5 KiB/s) with ~212 file(s) remaining (calculating...)
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/3/.zarray to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/3/.zarray
Completed 9.1 KiB/~49.2 MiB (19.5 KiB/s) with ~216 file(s) remaining (calculating...)
Completed 9.1 KiB/~49.2 MiB (19.4 KiB/s) with ~216 file(s) remaining (calculating...)
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/4/.zarray to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/4/.zarray
Completed 9.1 KiB/~49.2 MiB (19.4 KiB/s) with ~220 file(s) remaining (calculating...)
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/.zgroup to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/.zgroup
Completed 9.1 KiB/~49.2 MiB (19.4 KiB/s) with ~221 file(s) remaining (calculating...)
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Completed 9.9 KiB/~49.3 MiB (20.5 KiB/s) with ~260 file(s) remaining (calculating...)
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/1/.zarray to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/1/.zarray
Completed 9.9 KiB/~49.3 MiB (20.5 KiB/s) with ~264 file(s) remaining (calculating...)
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/0/.zarray to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/0/.zarray
Completed 9.9 KiB/~49.3 MiB (20.5 KiB/s) with ~264 file(s) remaining (calculating...)
Completed 10.3 KiB/~49.8 MiB (19.5 KiB/s) with ~436 file(s) remaining (calculating...)
Completed 18.6 KiB/~49.8 MiB (35.0 KiB/s) with ~440 file(s) remaining (calculating...)
Completed 44.4 KiB/~56.2 MiB (83.3 KiB/s) with ~445 file(s) remaining (calculating...)
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/1/.zarray to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/1/.zarray
Completed 44.4 KiB/~56.2 MiB (83.3 KiB/s) with ~445 file(s) remaining (calculating...)
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/.zattrs to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/.zattrs
Completed 44.4 KiB/~56.3 MiB (83.3 KiB/s) with ~446 file(s) remaining (calculating...)
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/4/0/0/0 to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/4/0/0/0
Completed 44.4 KiB/~56.3 MiB (83.3 KiB/s) with ~446 file(s) remaining (calculating...)
Completed 44.8 KiB/~66.4 MiB (81.2 KiB/s) with ~495 file(s) remaining (calculating...)
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/2/.zarray to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/2/.zarray
Completed 44.8 KiB/~66.4 MiB (81.2 KiB/s) with ~499 file(s) remaining (calculating...)
Completed 139.4 KiB/~66.5 MiB (246.4 KiB/s) with ~546 file(s) remaining (calculating...)
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/3/0/0/0 to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/3/0/0/0
Completed 139.4 KiB/~66.5 MiB (246.4 KiB/s) with ~550 file(s) remaining (calculating...)
Completed 139.4 KiB/~66.5 MiB (244.4 KiB/s) with ~557 file(s) remaining (calculating...)
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/.zgroup to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/.zgroup
Completed 139.4 KiB/~66.5 MiB (244.4 KiB/s) with ~563 file(s) remaining (calculating...)
Completed 395.4 KiB/~716.1 MiB (671.8 KiB/s) with ~613 file(s) remaining (calculating...)
Completed 395.8 KiB/~768.9 MiB (666.0 KiB/s) with ~631 file(s) remaining (calculating...)
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/2/.zarray to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/2/.zarray
Completed 395.8 KiB/~790.4 MiB (666.0 KiB/s) with ~647 file(s) remaining (calculating...)
Completed 651.8 KiB/790.4 MiB (1.1 MiB/s) with 651 file(s) remaining                     
Completed 907.8 KiB/790.4 MiB (1.4 MiB/s) with 651 file(s) remaining                     
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Completed 908.6 KiB/790.4 MiB (1.4 MiB/s) with 651 file(s) remaining                     
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/3/.zarray to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/3/.zarray
Completed 908.6 KiB/790.4 MiB (1.4 MiB/s) with 650 file(s) remaining
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/0/.zarray to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/0/.zarray
Completed 908.6 KiB/790.4 MiB (1.4 MiB/s) with 649 file(s) remaining
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Completed 1.7 MiB/790.4 MiB (2.7 MiB/s) with 649 file(s) remaining  
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/2/0/0/0 to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/2/0/0/0
Completed 1.7 MiB/790.4 MiB (2.7 MiB/s) with 648 file(s) remaining
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Completed 2.0 MiB/790.4 MiB (3.1 MiB/s) with 648 file(s) remaining
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep3_image/.zattrs to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep3_image/.zattrs
Completed 2.0 MiB/790.4 MiB (3.1 MiB/s) with 647 file(s) remaining
Completed 2.2 MiB/790.4 MiB (3.5 MiB/s) with 647 file(s) remaining
Completed 2.3 MiB/790.4 MiB (3.5 MiB/s) with 647 file(s) remaining
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/1/0/0/0 to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/1/0/0/0
Completed 2.3 MiB/790.4 MiB (3.5 MiB/s) with 646 file(s) remaining
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Completed 3.0 MiB/790.4 MiB (4.6 MiB/s) with 646 file(s) remaining
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep3_image/.zgroup to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep3_image/.zgroup
Completed 3.0 MiB/790.4 MiB (4.6 MiB/s) with 645 file(s) remaining
Completed 3.0 MiB/790.4 MiB (4.5 MiB/s) with 645 file(s) remaining
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/4/.zarray to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/4/.zarray
Completed 3.0 MiB/790.4 MiB (4.5 MiB/s) with 644 file(s) remaining
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Completed 4.5 MiB/790.4 MiB (6.6 MiB/s) with 644 file(s) remaining
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/4/0/0/0 to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/4/0/0/0
Completed 4.5 MiB/790.4 MiB (6.6 MiB/s) with 643 file(s) remaining
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep3_image/0/.zarray to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep3_image/0/.zarray
Completed 4.8 MiB/790.4 MiB (6.9 MiB/s) with 642 file(s) remaining
Completed 4.8 MiB/790.4 MiB (6.9 MiB/s) with 642 file(s) remaining
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/1/0/0/0 to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/1/0/0/0
Completed 4.8 MiB/790.4 MiB (6.9 MiB/s) with 641 file(s) remaining
Completed 4.9 MiB/790.4 MiB (7.0 MiB/s) with 641 file(s) remaining
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/2/0/0/0 to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/2/0/0/0
Completed 4.9 MiB/790.4 MiB (7.0 MiB/s) with 640 file(s) remaining
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/3/0/0/0 to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/3/0/0/0
Completed 6.7 MiB/790.4 MiB (9.5 MiB/s) with 639 file(s) remaining
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Completed 7.2 MiB/790.4 MiB (10.1 MiB/s) with 639 file(s) remaining
download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep3_image/1/.zarray to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep3_image/1/.zarray
Completed 7.2 MiB/790.4 MiB (10.1 MiB/s) with 638 file(s) remaining
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep3_image/2/.zarray to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep3_image/2/.zarray
Completed 7.5 MiB/790.4 MiB (10.4 MiB/s) with 637 file(s) remaining
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/0/0/0/0 to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep1_image/0/0/0/0
Completed 10.5 MiB/790.4 MiB (14.4 MiB/s) with 636 file(s) remaining
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep3_image/3/.zarray to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep3_image/3/.zarray
Completed 12.5 MiB/790.4 MiB (16.7 MiB/s) with 635 file(s) remaining
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/.zattrs to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/.zattrs
Completed 12.5 MiB/790.4 MiB (16.7 MiB/s) with 634 file(s) remaining
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/rep1_cell/.zgroup to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/rep1_cell/.zgroup
Completed 12.5 MiB/790.4 MiB (16.6 MiB/s) with 633 file(s) remaining
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep3_image/4/.zarray to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep3_image/4/.zarray
Completed 12.8 MiB/790.4 MiB (16.7 MiB/s) with 632 file(s) remaining
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/0/0/0/0 to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep2_image/0/0/0/0
Completed 13.3 MiB/790.4 MiB (17.3 MiB/s) with 631 file(s) remaining
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/.zgroup to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/.zgroup
Completed 13.3 MiB/790.4 MiB (17.0 MiB/s) with 630 file(s) remaining
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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/_task_template/resources_test/common/cxg_mouse_pancreas_atlas/state.yaml
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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/_task_template/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/dataset.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/cxg_mouse_pancreas_atlas/dataset.h5ad
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download: s3://openproblems-data/resources_test/common/allen_brain_atlas/dataset.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/allen_brain_atlas/dataset.h5ad
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download: s3://openproblems-data/resources_test/common/2023_yao_mouse_brain_scrnaseq_10xv2/dataset.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_yao_mouse_brain_scrnaseq_10xv2/dataset.h5ad
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download: s3://openproblems-data/resources_test/common/cxg_immune_cell_atlas/dataset.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/cxg_immune_cell_atlas/dataset.h5ad
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download: s3://openproblems-data/resources_test/common/mouse_brain_coronal/state.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/mouse_brain_coronal/state.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/_task_template/resources_test/common/openproblems_neurips2021/bmmc_cite/state.yaml
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download: s3://openproblems-data/resources_test/common/neurips2021_bmmc_cite/temp_neurips2021_bmmc_cite.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/neurips2021_bmmc_cite/temp_neurips2021_bmmc_cite.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/_task_template/resources_test/common/openproblems_neurips2021/bmmc_multiome/dataset_metadata_mod1.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/_task_template/resources_test/common/openproblems_neurips2021/bmmc_multiome/state.yaml
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download: s3://openproblems-data/resources_test/common/mouse_brain_coronal/dataset.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/mouse_brain_coronal/dataset.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/_task_template/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_cite/dataset_mod2.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod2.h5ad
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2022/pbmc_cite/dataset_metadata_mod1.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/openproblems_neurips2022/pbmc_cite/dataset_metadata_mod1.yaml
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2022/pbmc_cite/state.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/openproblems_neurips2022/pbmc_cite/state.yaml
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2022/pbmc_cite/dataset_metadata_mod2.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/openproblems_neurips2022/pbmc_cite/dataset_metadata_mod2.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/_task_template/resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod1.h5ad
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2022/pbmc_cite/dataset_mod1.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/openproblems_neurips2022/pbmc_cite/dataset_mod1.h5ad
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2022/pbmc_multiome/dataset_metadata_mod2.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/openproblems_neurips2022/pbmc_multiome/dataset_metadata_mod2.yaml
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download: s3://openproblems-data/resources_test/common/pancreas/dataset_meta.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/pancreas/dataset_meta.yaml
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2022/pbmc_multiome/dataset_metadata_mod1.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/openproblems_neurips2022/pbmc_multiome/dataset_metadata_mod1.yaml
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2022/pbmc_cite/dataset_mod2.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/openproblems_neurips2022/pbmc_cite/dataset_mod2.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/_task_template/resources_test/common/openproblems_neurips2021/bmmc_multiome/dataset_mod1.h5ad
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2022/pbmc_multiome/dataset_mod2.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/openproblems_neurips2022/pbmc_multiome/dataset_mod2.h5ad
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download: s3://openproblems-data/resources_test/common/openproblems_neurips2022/pbmc_multiome/dataset_mod1.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/openproblems_neurips2022/pbmc_multiome/dataset_mod1.h5ad
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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/_task_template/resources_test/common/openproblems_neurips2021/bmmc_multiome/dataset_mod2.h5ad
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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/_task_template/resources_test/common/scicar_cell_lines/dataset_metadata_mod2.yaml
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download: s3://openproblems-data/resources_test/common/pancreas/state.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/pancreas/state.yaml
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download: s3://openproblems-data/resources_test/common/singlecell_broadinstitute_scp2167_human_brain/dataset_meta.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/singlecell_broadinstitute_scp2167_human_brain/dataset_meta.yaml
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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/_task_template/resources_test/common/scicar_cell_lines/dataset_metadata_mod1.yaml
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download: s3://openproblems-data/resources_test/common/scicar_cell_lines/state.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/scicar_cell_lines/state.yaml
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download: s3://openproblems-data/resources_test/common/pancreas/pca.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/pancreas/pca.h5ad
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download: s3://openproblems-data/resources_test/common/singlecell_broadinstitute_scp2167_human_brain/state.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/singlecell_broadinstitute_scp2167_human_brain/state.yaml
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download: s3://openproblems-data/resources_test/common/pancreas/dataset.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/pancreas/dataset.h5ad
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download: s3://openproblems-data/resources_test/common/pancreas/raw.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/pancreas/raw.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/_task_template/resources_test/common/task_metadata/method_info.json
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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/_task_template/resources_test/common/scicar_cell_lines/dataset_mod2.h5ad
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download: s3://openproblems-data/resources_test/common/task_metadata/dataset_info.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/task_metadata/dataset_info.yaml
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download: s3://openproblems-data/resources_test/common/pancreas/knn.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/pancreas/knn.h5ad
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download: s3://openproblems-data/resources_test/common/singlecell_broadinstitute_scp2167_human_brain/dataset.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/singlecell_broadinstitute_scp2167_human_brain/dataset.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/_task_template/resources_test/common/task_metadata/input_git_sha.json
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download: s3://openproblems-data/resources_test/common/task_metadata/task_info.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/task_metadata/task_info.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/_task_template/resources_test/common/task_metadata/method_configs.yaml
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download: s3://openproblems-data/resources_test/common/task_metadata/state.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/task_metadata/state.yaml
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download: s3://openproblems-data/resources_test/common/pancreas/hvg.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/pancreas/hvg.h5ad
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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/_task_template/resources_test/common/scicar_cell_lines/dataset_mod1.h5ad
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download: s3://openproblems-data/resources_test/common/pancreas/normalized.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/pancreas/normalized.h5ad
Syncing 's3://openproblems-data/resources_test/task_template/' to 'resources_test/task_template'...
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download: s3://openproblems-data/resources_test/task_template/cxg_mouse_pancreas_atlas/state.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/task_template/cxg_mouse_pancreas_atlas/state.yaml
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download: s3://openproblems-data/resources_test/task_template/cxg_mouse_pancreas_atlas/score.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/task_template/cxg_mouse_pancreas_atlas/score.h5ad
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download: s3://openproblems-data/resources_test/task_template/cxg_mouse_pancreas_atlas/test.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/task_template/cxg_mouse_pancreas_atlas/test.h5ad
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download: s3://openproblems-data/resources_test/task_template/cxg_mouse_pancreas_atlas/solution.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/task_template/cxg_mouse_pancreas_atlas/solution.h5ad
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download: s3://openproblems-data/resources_test/task_template/cxg_mouse_pancreas_atlas/train.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/task_template/cxg_mouse_pancreas_atlas/train.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 logistic_regression component has an --input_train and --input_test argument to which the test resources are passed.

viash run src/methods/logistic_regression/config.vsh.yaml -- \
  --input_train resources_test/task_template/cxg_mouse_pancreas_atlas/train.h5ad \
  --input_test resources_test/task_template/cxg_mouse_pancreas_atlas/test.h5ad \
  --output output.h5ad

Output

Reading input files
Preprocess data
Train model
Generate predictions
Write output AnnData 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/methods/logistic_regression/config.vsh.yaml

Output

Running tests in temporary directory: '/tmp/viash_test_logistic_regression_11658383382655456536'
====================================================================
+/tmp/viash_test_logistic_regression_11658383382655456536/build_engine_environment/logistic_regression ---verbosity 6 ---setup cachedbuild ---engine docker
[notice] Building container 'ghcr.io/openproblems-bio/task_template/methods/logistic_regression:test' with Dockerfile
[info] docker build -t 'ghcr.io/openproblems-bio/task_template/methods/logistic_regression:test'  '/tmp/viash_test_logistic_regression_11658383382655456536/build_engine_environment' -f '/tmp/viash_test_logistic_regression_11658383382655456536/build_engine_environment/tmp/dockerbuild-logistic_regression-VeYSNw/Dockerfile'
#0 building with "default" instance using docker driver

#1 [internal] load build definition from Dockerfile
#1 transferring dockerfile: 571B done
#1 DONE 0.0s

#2 [internal] load metadata for docker.io/openproblems/base_python:1.0.0
#2 DONE 0.3s

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

#4 [1/2] FROM docker.io/openproblems/base_python:1.0.0@sha256:002c8b57733f22517bd6a83a59756456407059c9691e423288b61414b3d45326
#4 DONE 0.0s

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

#6 exporting to image
#6 exporting layers done
#6 writing image sha256:8d2697268093e105152fdafb09cc46cedf88c652f7885918c92d28fd2fa9ef79 done
#6 naming to ghcr.io/openproblems-bio/task_template/methods/logistic_regression:test done
#6 DONE 0.0s
====================================================================
+/tmp/viash_test_logistic_regression_11658383382655456536/test_run_and_check_output/test_executable
>> Running test 'run'
>> Checking whether input files exist
>> Running script as test
Reading input files
Preprocess data
Train model
Generate predictions
Write output AnnData to file
>> Checking whether output file exists
>> Reading h5ad files and checking formats
Reading and checking output
  AnnData object with n_obs × n_vars = 123 × 0
    obs: 'label_pred'
    uns: 'dataset_id', 'method_id', 'normalization_id'
All checks succeeded!
====================================================================
+/tmp/viash_test_logistic_regression_11658383382655456536/test_check_config/test_executable
Load config data
Check .namespace
Check .info.type
Check component metadata
Check references fields
Checking contents of .info.preferred_normalization
Check Nextflow runner
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 --parallel --engine docker

Output

    namespace                 name               runner               engine            test_name exit_code duration               result
control_methods          true_labels           executable               docker                start                                        
        metrics             accuracy           executable               docker                start                                        
data_processors      process_dataset           executable               docker                start                                        
        methods  logistic_regression           executable               docker                start                                        
data_processors      process_dataset           executable               docker     build_executable         0        2              SUCCESS
data_processors      process_dataset           executable               docker run_and_check_output.py         0        4              SUCCESS
control_methods          true_labels           executable               docker     build_executable         0        2              SUCCESS
control_methods          true_labels           executable               docker run_and_check_output.py         0        4              SUCCESS
control_methods          true_labels           executable               docker      check_config.py         0        3              SUCCESS
        metrics             accuracy           executable               docker     build_executable         0        2              SUCCESS
        metrics             accuracy           executable               docker run_and_check_output.py         0        5              SUCCESS
        metrics             accuracy           executable               docker      check_config.py         0        2              SUCCESS
        methods  logistic_regression           executable               docker     build_executable         0        2              SUCCESS
        methods  logistic_regression           executable               docker run_and_check_output.py         0        5              SUCCESS
        methods  logistic_regression           executable               docker      check_config.py         0        3              SUCCESS

All 11 configs built and tested successfully …