Zenodo Client

A wrapper for the Zenodo API.

💪 Getting Started

The first example shows how you can set some configuration then never worry about whether it's been uploaded already or not - all baked in with pystow. On the first time this script is run, the new deposition is made, published, and the identifier is stored with the given key in your ~/.config/zenodo.ini. Next time it's run, the deposition will be looked up, and the data will be uploaded. Versioning is given automatically by date, and if multiple versions are uploaded on one day, then a dash and the revision are appended.

from zenodo_client import Creator, Metadata, ensure_zenodo

# Define the metadata that will be used on initial upload
data = Metadata(
    title='Test Upload 3',
    upload_type='dataset',
    description='test description',
    creators=[
        Creator(
            name='Hoyt, Charles Tapley',
            affiliation='Harvard Medical School',
            orcid='0000-0003-4423-4370',
        ),
    ],
)
res = ensure_zenodo(
    key='test3',
    data=data,
    paths='/Users/cthoyt/Desktop/test1.png',
    sandbox=True,
)
from pprint import pprint

pprint(res.json())

A real-world example can be found here: https://github.com/cthoyt/nsockg.

The following example shows how to use the Zenodo uploader if you already know what your deposition identifier is.

from zenodo_client import update_zenodo

# The ID from your deposition
SANDBOX_DEP_ID = '724868'

# Paths to local files. Good to use in combination with resources that are always
# dumped to the same place by a given script
paths = [
    # os.path.join(DATABASE_DIRECTORY, 'alts_sample.tsv')
    '/Users/cthoyt/Desktop/alts_sample.tsv'
]

# Don't forget to set the ZENODO_API_TOKEN environment variable or
# any valid way to get zenodo/api_token from PyStow.
update_zenodo(SANDBOX_DEP_ID, paths)

The following example shows how to look up the latest version of a record.

from zenodo_client import Zenodo

zenodo = Zenodo()
OOH_NA_NA_RECORD = '4020486'
new_record = zenodo.get_latest_record(OOH_NA_NA_RECORD)

Even further, the latest version of names.tsv.gz can be automatically downloaded to the ~/.data/zenodo/<conceptrecid>/<version>/<path> via pystow with:

from zenodo_client import Zenodo

zenodo = Zenodo()
OOH_NA_NA_RECORD = '4020486'
new_record = zenodo.download_latest(OOH_NA_NA_RECORD, 'names.tsv.gz')

A real-world example can be found here where the latest build of the Ooh Na Na nomenclature database is automatically downloaded from Zenodo, even though the PyOBO package only hardcodes the first deposition ID.

Command Line Interface

The zenodo_client command line tool is automatically installed. It can be used from the shell with the --help flag to show all subcommands:

$ zenodo_client --help

It can be run with zenodo_client <deposition ID> <path 1> ... <path N>

⬇️ Installation

The most recent release can be installed from PyPI with:

$ pip install zenodo_client

The most recent code and data can be installed directly from GitHub with:

$ pip install git+https://github.com/cthoyt/zenodo-client.git

To install in development mode, use the following:

$ git clone git+https://github.com/cthoyt/zenodo-client.git
$ cd zenodo-client
$ pip install -e .

⚖️ License

The code in this package is licensed under the MIT License.

🙏 Contributing

Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.rst for more information on getting involved.

🍪 Cookiecutter Acknowledgement

This package was created with @audreyr's cookiecutter package using @cthoyt's cookiecutter-python-package template.

🛠️ Development

The final section of the README is for if you want to get involved by making a code contribution.

❓ Testing

After cloning the repository and installing tox with pip install tox, the unit tests in the tests/ folder can be run reproducibly with:

$ tox

Additionally, these tests are automatically re-run with each commit in a GitHub Action.

📦 Making a Release

After installing the package in development mode and installing tox with pip install tox, the commands for making a new release are contained within the finish environment in tox.ini. Run the following from the shell:

$ tox -e finish

This script does the following:

1. Uses BumpVersion to switch the version number in the setup.cfg and src/zenodo_client/version.py to not have the -dev suffix
2. Packages the code in both a tar archive and a wheel
3. Uploads to PyPI using twine. Be sure to have a .pypirc file configured to avoid the need for manual input at this step
4. Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
5. Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can use tox -e bumpversion minor after.