A wrapper for the Zenodo API.
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', # this is a unique key you pick that will be used to store
# the numeric deposition ID on your local system's cache
data=data,
paths=[
'/Users/cthoyt/Desktop/test1.png',
],
sandbox=True, # remove this when you're ready to upload to real Zenodo
)
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.
The zenodo_client command line tool is automatically installed. It can be used
from the console with the --help flag to show all subcommands:
$ zenodo_client --helpIt can be run with zenodo_client <deposition ID> <path 1> ... <path N>
The most recent release can be installed from PyPI with uv:
$ uv pip install zenodo_clientor with pip:
$ python3 -m pip install zenodo_clientThe most recent code and data can be installed directly from GitHub with uv:
$ uv --preview pip install git+https://github.com/cthoyt/zenodo-client.gitor with pip:
$ UV_PREVIEW=1 python3 -m pip install git+https://github.com/cthoyt/zenodo-client.gitNote that this requires setting UV_PREVIEW mode enabled until the uv build
backend becomes a stable feature.
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.
The code in this package is licensed under the MIT License.
This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.
See developer instructions
The final section of the README is for if you want to get involved by making a code contribution.
To install in development mode, use the following:
$ git clone git+https://github.com/cthoyt/zenodo-client.git
$ cd zenodo-client
$ uv --preview pip install -e .Alternatively, install using pip:
$ UV_PREVIEW=1 python3 -m pip install -e .Note that this requires setting UV_PREVIEW mode enabled until the uv build
backend becomes a stable feature.
This project uses cruft to keep boilerplate (i.e., configuration, contribution
guidelines, documentation configuration) up-to-date with the upstream
cookiecutter package. Install cruft with either uv tool install cruft or
python3 -m pip install cruft then run:
$ cruft updateMore info on Cruft's update command is available here.
After cloning the repository and installing tox with
uv tool install tox --with tox-uv or python3 -m pip install tox tox-uv, the
unit tests in the tests/ folder can be run reproducibly with:
$ tox -e pyAdditionally, these tests are automatically re-run with each commit in a GitHub Action.
The documentation can be built locally using the following:
$ git clone git+https://github.com/cthoyt/zenodo-client.git
$ cd zenodo-client
$ tox -e docs
$ open docs/build/html/index.htmlThe documentation automatically installs the package as well as the docs extra
specified in the pyproject.toml. sphinx plugins like
texext can be added there. Additionally, they need to be added to the
extensions list in docs/source/conf.py.
The documentation can be deployed to ReadTheDocs using
this guide. The
.readthedocs.yml YAML file contains all the configuration
you'll need. You can also set up continuous integration on GitHub to check not
only that Sphinx can build the documentation in an isolated environment (i.e.,
with tox -e docs-test) but also that
ReadTheDocs can build it too.
- Log in to ReadTheDocs with your GitHub account to install the integration at https://readthedocs.org/accounts/login/?next=/dashboard/
- Import your project by navigating to https://readthedocs.org/dashboard/import then clicking the plus icon next to your repository
- You can rename the repository on the next screen using a more stylized name (i.e., with spaces and capital letters)
- Click next, and you're good to go!
Zenodo is a long-term archival system that assigns a DOI to each release of your package.
- Log in to Zenodo via GitHub with this link: https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page that lists all of your organizations and asks you to approve installing the Zenodo app on GitHub. Click "grant" next to any organizations you want to enable the integration for, then click the big green "approve" button. This step only needs to be done once.
- Navigate to https://zenodo.org/account/settings/github/, which lists all of your GitHub repositories (both in your username and any organizations you enabled). Click the on/off toggle for any relevant repositories. When you make a new repository, you'll have to come back to this
After these steps, you're ready to go! After you make "release" on GitHub (steps for this are below), you can navigate to https://zenodo.org/account/settings/github/repository/cthoyt/zenodo-client to see the DOI for the release and link to the Zenodo record for it.
You only have to do the following steps once.
- Register for an account on the Python Package Index (PyPI)
- Navigate to https://pypi.org/manage/account and make sure you have verified your email address. A verification email might not have been sent by default, so you might have to click the "options" dropdown next to your address to get to the "re-send verification email" button
- 2-Factor authentication is required for PyPI since the end of 2023 (see this blog post from PyPI). This means you have to first issue account recovery codes, then set up 2-factor authentication
- Issue an API token from https://pypi.org/manage/account/token
You have to do the following steps once per machine.
$ uv tool install keyring
$ keyring set https://upload.pypi.org/legacy/ __token__
$ keyring set https://test.pypi.org/legacy/ __token__Note that this deprecates previous workflows using .pypirc.
After installing the package in development mode and installing tox with
uv tool install tox --with tox-uv or python3 -m pip install tox tox-uv, run
the following from the console:
$ tox -e finishThis script does the following:
- Uses bump-my-version to
switch the version number in the
pyproject.toml,CITATION.cff,src/zenodo_client/version.py, anddocs/source/conf.pyto not have the-devsuffix - Packages the code in both a tar archive and a wheel using
uv build - Uploads to PyPI using
uv publish. - Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
- 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 -- minorafter.
- Navigate to https://github.com/cthoyt/zenodo-client/releases/new to draft a new release
- Click the "Choose a Tag" dropdown and select the tag corresponding to the release you just made
- Click the "Generate Release Notes" button to get a quick outline of recent changes. Modify the title and description as you see fit
- Click the big green "Publish Release" button
This will trigger Zenodo to assign a DOI to your release as well.