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/~57.3 MiB (43 Bytes/s) with ~470 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 24 Bytes/~58.7 MiB (43 Bytes/s) with ~476 file(s) remaining (calculating...)
Completed 8.3 KiB/~58.8 MiB (15.0 KiB/s) with ~478 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/~58.9 MiB (15.0 KiB/s) with ~484 file(s) remaining (calculating...)
Completed 8.4 KiB/~66.2 MiB (14.8 KiB/s) with ~490 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 8.4 KiB/~66.3 MiB (14.8 KiB/s) with ~494 file(s) remaining (calculating...)
Completed 8.4 KiB/~66.5 MiB (14.2 KiB/s) with ~588 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/~66.5 MiB (14.2 KiB/s) with ~597 file(s) remaining (calculating...)
Completed 8.8 KiB/790.4 MiB (13.6 KiB/s) with 662 file(s) remaining                  
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 8.8 KiB/790.4 MiB (13.6 KiB/s) with 661 file(s) remaining
Completed 9.1 KiB/790.4 MiB (14.0 KiB/s) with 661 file(s) remaining
Completed 9.5 KiB/790.4 MiB (14.5 KiB/s) with 661 file(s) remaining
Completed 9.9 KiB/790.4 MiB (15.1 KiB/s) with 661 file(s) remaining
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/790.4 MiB (15.1 KiB/s) with 660 file(s) remaining
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 9.9 KiB/790.4 MiB (15.1 KiB/s) with 659 file(s) remaining
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 9.9 KiB/790.4 MiB (15.1 KiB/s) with 658 file(s) remaining
Completed 10.3 KiB/790.4 MiB (15.2 KiB/s) with 658 file(s) remaining
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 10.3 KiB/790.4 MiB (15.2 KiB/s) with 657 file(s) remaining
Completed 18.6 KiB/790.4 MiB (27.3 KiB/s) with 657 file(s) remaining
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 18.6 KiB/790.4 MiB (27.3 KiB/s) with 656 file(s) remaining
Completed 18.6 KiB/790.4 MiB (25.5 KiB/s) with 656 file(s) remaining
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 18.6 KiB/790.4 MiB (25.5 KiB/s) with 655 file(s) remaining
Completed 19.0 KiB/790.4 MiB (25.9 KiB/s) with 655 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 19.0 KiB/790.4 MiB (25.9 KiB/s) with 654 file(s) remaining
Completed 113.6 KiB/790.4 MiB (146.4 KiB/s) with 654 file(s) remaining
Completed 114.0 KiB/790.4 MiB (146.7 KiB/s) with 654 file(s) remaining
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 114.0 KiB/790.4 MiB (146.7 KiB/s) with 653 file(s) remaining
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 114.0 KiB/790.4 MiB (146.7 KiB/s) with 652 file(s) remaining
Completed 139.8 KiB/790.4 MiB (178.6 KiB/s) with 652 file(s) remaining
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 139.8 KiB/790.4 MiB (178.6 KiB/s) with 651 file(s) remaining
Completed 140.2 KiB/790.4 MiB (170.2 KiB/s) with 651 file(s) remaining
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 140.2 KiB/790.4 MiB (170.2 KiB/s) with 650 file(s) remaining
Completed 396.2 KiB/790.4 MiB (470.6 KiB/s) with 650 file(s) remaining
Completed 396.6 KiB/790.4 MiB (465.2 KiB/s) with 650 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 396.6 KiB/790.4 MiB (465.2 KiB/s) with 649 file(s) remaining
Completed 397.0 KiB/790.4 MiB (462.9 KiB/s) with 649 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 397.0 KiB/790.4 MiB (462.9 KiB/s) with 648 file(s) remaining
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Completed 909.0 KiB/790.4 MiB (1.0 MiB/s) with 648 file(s) remaining  
Completed 1002.3 KiB/790.4 MiB (1.1 MiB/s) with 648 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 1002.3 KiB/790.4 MiB (1.1 MiB/s) with 647 file(s) remaining
Completed 1002.4 KiB/790.4 MiB (1.1 MiB/s) with 647 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 1002.4 KiB/790.4 MiB (1.1 MiB/s) with 646 file(s) remaining
Completed 1.0 MiB/790.4 MiB (1.1 MiB/s) with 646 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 1.0 MiB/790.4 MiB (1.1 MiB/s) with 645 file(s) remaining
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Completed 1.5 MiB/790.4 MiB (1.6 MiB/s) with 645 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 1.5 MiB/790.4 MiB (1.6 MiB/s) with 644 file(s) remaining
Completed 1.6 MiB/790.4 MiB (1.7 MiB/s) with 644 file(s) remaining
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 1.6 MiB/790.4 MiB (1.7 MiB/s) with 643 file(s) remaining
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Completed 2.1 MiB/790.4 MiB (2.2 MiB/s) with 643 file(s) remaining
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 2.1 MiB/790.4 MiB (2.2 MiB/s) with 642 file(s) remaining
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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 3.6 MiB/790.4 MiB (3.5 MiB/s) with 641 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 3.9 MiB/790.4 MiB (3.7 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/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 5.4 MiB/790.4 MiB (5.1 MiB/s) with 639 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 5.6 MiB/790.4 MiB (5.3 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/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 6.6 MiB/790.4 MiB (6.1 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/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 6.7 MiB/790.4 MiB (6.2 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/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 10.0 MiB/790.4 MiB (8.9 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/.zgroup to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/.zgroup
Completed 10.0 MiB/790.4 MiB (8.9 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/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 10.0 MiB/790.4 MiB (8.8 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/labels/.zattrs to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/.zattrs
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/rep1_cell/.zattrs to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/rep1_cell/.zattrs
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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 12.0 MiB/790.4 MiB (10.1 MiB/s) with 630 file(s) remaining
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep3_image/4/0/0/0 to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/images/rep3_image/4/0/0/0
Completed 12.5 MiB/790.4 MiB (10.4 MiB/s) with 629 file(s) remaining
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/rep1_cell/0/0/0 to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/rep1_cell/0/0/0
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/rep1_nucleus/1/0/0 to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/rep1_nucleus/1/0/0
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/rep2_cell/.zattrs to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/rep2_cell/.zattrs
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/rep1_nucleus/3/0/0 to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/rep1_nucleus/3/0/0
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/rep2_cell/0/0/0 to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/labels/rep2_cell/0/0/0
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium_rep1/dataset.zarr/tables/table/varp/.zattrs to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium_rep1/dataset.zarr/tables/table/varp/.zattrs
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download: s3://openproblems-data/resources_test/common/cxg_immune_cell_atlas/dataset_metadata.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/cxg_immune_cell_atlas/dataset_metadata.yaml
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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/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_immune_cell_atlas/state.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/cxg_immune_cell_atlas/state.yaml
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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/mouse_brain_coronal/dataset_metadata.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/mouse_brain_coronal/dataset_metadata.yaml
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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/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/openproblems_neurips2021/bmmc_cite/dataset_metadata_mod1.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_metadata_mod1.yaml
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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/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/openproblems_neurips2021/bmmc_cite/dataset_metadata_mod2.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_metadata_mod2.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_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/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_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_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/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_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_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_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/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_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/state.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/openproblems_neurips2022/pbmc_multiome/state.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_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/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_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/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/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/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/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/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/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/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/pancreas/normalized.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/pancreas/normalized.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/_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/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/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/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_14831142911939610709'
====================================================================
+/tmp/viash_test_logistic_regression_14831142911939610709/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_14831142911939610709/build_engine_environment' -f '/tmp/viash_test_logistic_regression_14831142911939610709/build_engine_environment/tmp/dockerbuild-logistic_regression-ZWfOmx/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 0.1s

#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@sha256:5ef558717b4c96f14fc8683618c6d43d8c3cf52e9206834aa7fe2e45f746fea0
#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 sha256:269207b558cfa9ab16cef0d9d3a8c5752927aa2cae77fbff9c758a881e6ef92d done
#6 naming to ghcr.io/openproblems-bio/task_template/methods/logistic_regression:test done
#6 DONE 0.0s
====================================================================
+/tmp/viash_test_logistic_regression_14831142911939610709/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_14831142911939610709/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 …