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/task_template/' to 'resources_test/task_template'...
Completed 111 Bytes/6.4 MiB (954 Bytes/s) with 6 file(s) remaining
download: s3://openproblems-data/resources_test/task_template/pancreas/state.yaml to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/task_template/pancreas/state.yaml
Completed 111 Bytes/6.4 MiB (954 Bytes/s) with 5 file(s) remaining
Completed 256.1 KiB/6.4 MiB (1.1 MiB/s) with 5 file(s) remaining  
Completed 512.1 KiB/6.4 MiB (2.1 MiB/s) with 5 file(s) remaining  
Completed 768.1 KiB/6.4 MiB (3.2 MiB/s) with 5 file(s) remaining  
Completed 1.0 MiB/6.4 MiB (4.0 MiB/s) with 5 file(s) remaining    
Completed 1.3 MiB/6.4 MiB (4.9 MiB/s) with 5 file(s) remaining    
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Completed 3.9 MiB/6.4 MiB (13.4 MiB/s) with 5 file(s) remaining   
download: s3://openproblems-data/resources_test/task_template/pancreas/test.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/task_template/pancreas/test.h5ad
Completed 3.9 MiB/6.4 MiB (13.4 MiB/s) with 4 file(s) remaining
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Completed 5.0 MiB/6.4 MiB (16.7 MiB/s) with 4 file(s) remaining
download: s3://openproblems-data/resources_test/task_template/pancreas/train.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/task_template/pancreas/train.h5ad
Completed 5.0 MiB/6.4 MiB (16.7 MiB/s) with 3 file(s) remaining
download: s3://openproblems-data/resources_test/task_template/pancreas/prediction.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/task_template/pancreas/prediction.h5ad
Completed 5.0 MiB/6.4 MiB (16.7 MiB/s) with 2 file(s) remaining
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Completed 5.4 MiB/6.4 MiB (18.1 MiB/s) with 2 file(s) remaining
download: s3://openproblems-data/resources_test/task_template/pancreas/solution.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/task_template/pancreas/solution.h5ad
Completed 5.4 MiB/6.4 MiB (18.1 MiB/s) with 1 file(s) remaining
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Completed 6.4 MiB/6.4 MiB (17.2 MiB/s) with 1 file(s) remaining
download: s3://openproblems-data/resources_test/task_template/pancreas/score.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/task_template/pancreas/score.h5ad
Syncing 's3://openproblems-data/resources_test/common/' to 'resources_test/common'...
Completed 24 Bytes/~49.1 MiB (67 Bytes/s) with ~179 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/~49.1 MiB (67 Bytes/s) with ~185 file(s) remaining (calculating...)
Completed 48 Bytes/~49.2 MiB (126 Bytes/s) with ~263 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 48 Bytes/~49.3 MiB (126 Bytes/s) with ~269 file(s) remaining (calculating...)
Completed 8.4 KiB/~49.4 MiB (21.0 KiB/s) with ~328 file(s) remaining (calculating...)  
Completed 8.4 KiB/~49.4 MiB (21.0 KiB/s) with ~330 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 8.4 KiB/~49.4 MiB (21.0 KiB/s) with ~334 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 8.4 KiB/~49.4 MiB (21.0 KiB/s) with ~334 file(s) remaining (calculating...)
Completed 8.8 KiB/~49.6 MiB (21.1 KiB/s) with ~381 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 8.8 KiB/~49.6 MiB (21.1 KiB/s) with ~391 file(s) remaining (calculating...)
Completed 9.1 KiB/~49.6 MiB (21.4 KiB/s) with ~429 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 9.1 KiB/~49.6 MiB (21.4 KiB/s) with ~433 file(s) remaining (calculating...)
Completed 9.5 KiB/~49.6 MiB (22.1 KiB/s) with ~435 file(s) remaining (calculating...)
Completed 9.9 KiB/~89.5 MiB (23.0 KiB/s) with ~439 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 9.9 KiB/~98.0 MiB (23.0 KiB/s) with ~445 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/~693.8 MiB (23.0 KiB/s) with ~446 file(s) remaining (calculating...)
Completed 18.2 KiB/767.7 MiB (40.0 KiB/s) with 488 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 18.2 KiB/767.7 MiB (40.0 KiB/s) with 487 file(s) remaining
Completed 18.2 KiB/767.7 MiB (39.6 KiB/s) with 487 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 18.2 KiB/767.7 MiB (39.6 KiB/s) with 486 file(s) remaining
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Completed 19.0 KiB/767.7 MiB (39.7 KiB/s) with 486 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 19.0 KiB/767.7 MiB (39.7 KiB/s) with 485 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/767.7 MiB (39.7 KiB/s) with 484 file(s) remaining
Completed 19.4 KiB/767.7 MiB (40.0 KiB/s) with 484 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 19.4 KiB/767.7 MiB (40.0 KiB/s) with 483 file(s) remaining
Completed 114.0 KiB/767.7 MiB (223.0 KiB/s) with 483 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/767.7 MiB (223.0 KiB/s) with 482 file(s) remaining
Completed 139.8 KiB/767.7 MiB (272.7 KiB/s) with 482 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/767.7 MiB (272.7 KiB/s) with 481 file(s) remaining
Completed 395.8 KiB/767.7 MiB (762.7 KiB/s) with 481 file(s) remaining
Completed 489.2 KiB/767.7 MiB (940.8 KiB/s) with 481 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 489.2 KiB/767.7 MiB (940.8 KiB/s) with 480 file(s) remaining
Completed 489.6 KiB/767.7 MiB (915.7 KiB/s) with 480 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 489.6 KiB/767.7 MiB (915.7 KiB/s) with 479 file(s) remaining
Completed 745.6 KiB/767.7 MiB (1.3 MiB/s) with 479 file(s) remaining  
Completed 1001.6 KiB/767.7 MiB (1.8 MiB/s) with 479 file(s) remaining 
Completed 1009.9 KiB/767.7 MiB (1.8 MiB/s) with 479 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 1009.9 KiB/767.7 MiB (1.8 MiB/s) with 478 file(s) remaining
Completed 1010.3 KiB/767.7 MiB (1.7 MiB/s) with 478 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 1010.3 KiB/767.7 MiB (1.7 MiB/s) with 477 file(s) remaining
Completed 1010.3 KiB/767.7 MiB (1.7 MiB/s) with 477 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 1010.3 KiB/767.7 MiB (1.7 MiB/s) with 476 file(s) remaining
Completed 1010.7 KiB/767.7 MiB (1.7 MiB/s) with 476 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 1010.7 KiB/767.7 MiB (1.7 MiB/s) with 475 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 5.8 MiB/767.7 MiB (9.0 MiB/s) with 474 file(s) remaining
Completed 5.8 MiB/767.7 MiB (9.1 MiB/s) with 474 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 5.8 MiB/767.7 MiB (9.1 MiB/s) with 473 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 5.8 MiB/767.7 MiB (9.1 MiB/s) with 472 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 7.3 MiB/767.7 MiB (11.1 MiB/s) with 471 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 7.9 MiB/767.7 MiB (11.6 MiB/s) with 470 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 7.9 MiB/767.7 MiB (11.6 MiB/s) with 469 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 9.0 MiB/767.7 MiB (13.1 MiB/s) with 468 file(s) remaining
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 9.0 MiB/767.7 MiB (13.1 MiB/s) with 467 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 9.0 MiB/767.7 MiB (13.1 MiB/s) with 466 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
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/tables/rep3_cell_table/var/genome/0 to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/tables/rep3_cell_table/var/genome/0
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download: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/tables/rep3_cell_table/varm/.zgroup to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/2023_10x_mouse_brain_xenium/dataset.zarr/tables/rep3_cell_table/varm/.zgroup
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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_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/mouse_brain_coronal_section1/dataset.h5ad to ../viash_automount/home/runner/work/website/website/_task_template/resources_test/common/mouse_brain_coronal_section1/dataset.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/_task_template/resources_test/common/openproblems_neurips2021/bmmc_cite/dataset_mod2.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/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/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/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/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/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_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_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_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_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_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_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_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/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_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_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/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/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/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/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/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/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/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/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

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/pancreas/train.h5ad \
  --input_test resources_test/task_template/pancreas/test.h5ad \
  --output output.h5ad

Output

[notice] Checking if Docker image is available at 'ghcr.io/openproblems-bio/task_template/methods/logistic_regression:dev'
[warning] Could not pull from 'ghcr.io/openproblems-bio/task_template/methods/logistic_regression:dev'. Docker image doesn't exist or is not accessible.
[notice] Building container 'ghcr.io/openproblems-bio/task_template/methods/logistic_regression:dev' with Dockerfile
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_417103042413724771'
====================================================================
+/tmp/viash_test_logistic_regression_417103042413724771/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_417103042413724771/build_engine_environment' -f '/tmp/viash_test_logistic_regression_417103042413724771/build_engine_environment/tmp/dockerbuild-logistic_regression-1Xvb0T/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@sha256:52302746d441804c9eb067b569f8671b68e6ebb3847da83b16e42b9316dcd583
#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 sha256:2eb4f387988176c901225ce1a6546907d602699808fb6aa075796f14ef895ecb done
#6 naming to ghcr.io/openproblems-bio/task_template/methods/logistic_regression:test done
#6 DONE 0.0s
====================================================================
+/tmp/viash_test_logistic_regression_417103042413724771/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 = 213 × 0
    obs: 'label_pred'
    uns: 'dataset_id', 'method_id', 'normalization_id'
All checks succeeded!
====================================================================
+/tmp/viash_test_logistic_regression_417103042413724771/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 …