PHI-base 4 pipeline

Python package and command-line application for releasing the PHI-base 4 dataset in Excel and CSV formats, and preparing metadata and files for the Zenodo repository.

Installation

Install the latest release from GitHub:

python -m pip install 'phi4pipeline@git+https://github.com/PHI-base/phi4pipeline.git@1.0.0'

Or install the latest commit on the main branch:

python -m pip install 'phi4pipeline@git+https://github.com/PHI-base/phi4pipeline.git@main'

Usage

Excel release format

To generate a cleaned and validated version of the spreadsheet that contains the PHI-base 4 dataset, use the following command:

python -m phi4pipeline excel -o FILE SPREADSHEET

Explanation of arguments:

• -o, --output: the output path for the processed spreadsheet file.

• SPREADSHEET: the path to the spreadsheet containing the PHI-base 4 dataset.

Zenodo release format

To generate release files to be uploaded to Zenodo, use the following command:

python -m phi4pipeline zenodo --contributors PATH --doi YEAR --fasta PATH -o DIR --year YEAR SPREADSHEET

Explanation of arguments:

• --contributors: the path to the CSV file that contains information about the authors and contributors of the dataset. See the 'Contributors file' section below for more information.

• --doi: the DOI name for the dataset in prefix/suffix form (for example: 10.5281/zenodo.5356870). The DOI name must not be prefixed with 'doi:' or 'https://doi.org/'. The DOI is usually generated when preparing a release on Zenodo.

• --fasta: the path to the FASTA file that accompanies the PHI-base dataset.

• -o, --out_dir: the output directory for the release files that will be uploaded to Zenodo.

• --year: the year of publication of the dataset. This is the first date of publication anywhere online (for example, year of publication on the PHI-base website), not necessarily the year of publication on Zenodo.

• SPREADSHEET: the path to the spreadsheet containing the PHI-base 4 dataset.

Contributors file

The Contributors file is a CSV file that contains information about the people (authors and contributors) related to the dataset. It contains the following columns, in the following order:

• name: the full name of the person.

• orcid: the Open Researcher and Contributor ID (ORCID) for the person, without any URL prefix. For example: 0000-0002-1825-0097

• email: the email address for the person.

• role_readme: the role of the person, as shown in the README file included with the dataset.

• role_frictionless: the role of the author or contributor, as shown in the Frictionless Data Package metadata file (datapackage.json) included with the dataset. The recommended role values can be found in the Data Package specification.

• affiliation: the organization that the author or contributor is affiliated with.

• is_author: TRUE if the person is an author; FALSE if the person is a contributor. Controls which table the person's details appear in the README file.

• is_private: TRUE if the person's personal details should be hidden from the README and datapackage.json files; otherwise FALSE. Defaults to FALSE. This is included to comply with data protection requirements.

License

phi4pipeline is distributed under the terms of the MIT license.

Citation

Please use the following citation for this software:

Seager, J. (2024). PHI-base 4 pipeline (1.0.0). Zenodo. https://doi.org/10.5281/zenodo.13773740

See the CITATION.cff file in this repository for more information.