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Review Guide

This guide explains what steps a project administrator needs to perform when updating a dataset implementation.

Checkout PR

First, checkout the pull-request to obtain a local copy using the GitHub CLI:

gh pr checkout PULL-REQUEST

Basic checks

To ensure the highest possible standard and uniformity of the data set implementations, please check the following dataset requirements.

  • The dataset should be implemented in bigbio/hub/hub_repos/<dataset> and contain (at least) the three default files <dataset>.py, bigbiohub.py and README.md.
  • Check whether all data set meta-data are given in <dataset>.py and README.md. Refer to BC5CDR for an example of a complete set of information.
  • The dataset should not import bigbio but instead use .bigbiohub.

Run unit tests

Run the following command from the top level of the biomedical repo (i.e. the same directory that contains the requirements.txt file). Check if the new or updated dataloader satisfies our unit tests as follows by using this command in the terminal:

python -m tests.test_bigbio_hub <dataset_name> [--data_dir /path/to/local/data] --test_local

Note, you MUST include the --test_local flag to specifically test the script for your PR, otherwise the script will default to downloading a dataloader script from the Hub. Your particular dataset may require use of some of the other command line args in the test script (ex: --data_dir for dataloaders that read local files).
To view full usage instructions you can use the --help command:

python -m tests.test_bigbio --help

This will explain the types of arguments you may need to test for. A brief annotation is as such:

  • dataset_name: Name of the dataset you want to test
  • data_dir: The location of the data for datasets where LOCAL_ = True
  • config_name: Name of the configuration you want to test. By default, the script will test all configs, but if you can use this to debug a specific split, or if your data is prohibitively large.
  • ishub: Use this when unit testing scripts that are not yet uploaded to the hub (this is True for most cases)

If any (severe) errors occur, report these to the PR author.

Update hub dataset

Finally, the data set needs to be updated in the BigBio Huggingface datasets hub.

Note that this step should be performed just before merging the PR, as uploading to the hub might fail due to errors in the README / dataset card that the PR author can still fix.

For this, first create or retrieve an API access token of your huggingface account:

https://huggingface.co/settings/tokens

Note to create a token with write access:

Screenshot HF access token

Run the following command from the top-level of the repository to update the data set in the hub:

HUGGING_FACE_HUB_TOKEN=<ACCESS-TOKEN>  python bigbio/hub/upload.py <dataset>

If the PR is concerned with a completely new data set add the option -c for creating a new data set repo in the hub first:

HUGGING_FACE_HUB_TOKEN=<ACCESS-TOKEN>  python bigbio/hub/upload.py <dataset> -c

Moreover, you can test your upload command by first running a dry-run using option -d:

HUGGING_FACE_HUB_TOKEN=<ACCESS-TOKEN>  python bigbio/hub/upload.py <dataset> -d

After running the command, visit hub webpage of the data set and check if the model card and the data viewer are displayed and the files are updated correctly, e.g. https://huggingface.co/datasets/bigbio/bc5cdr

Merge the PR

If all previous checks could be performed successfully merge the PR into main branch:

gh pr merge PULL-REQUEST