https://github.com/cthoyt/zenodo-client
A tool for automated uploading and version management of scientific data to Zenodo
https://github.com/cthoyt/zenodo-client
Last synced: about 1 month ago
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A tool for automated uploading and version management of scientific data to Zenodo
- Host: GitHub
- URL: https://github.com/cthoyt/zenodo-client
- Owner: cthoyt
- License: mit
- Created: 2021-03-01T18:15:14.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2025-02-21T12:12:50.000Z (3 months ago)
- Last Synced: 2025-03-31T12:05:24.818Z (about 1 month ago)
- Language: Python
- Homepage:
- Size: 112 KB
- Stars: 33
- Watchers: 2
- Forks: 6
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- Contributing: .github/CONTRIBUTING.md
- Funding: .github/FUNDING.yml
- License: LICENSE
- Code of conduct: .github/CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
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`](https://github.com/cthoyt/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.
```python
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.
```python
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.
```python
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///` via `pystow`
with:
```python
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](https://github.com/pyobo/pyobo/blob/master/src/pyobo/resource_utils.py)
where the latest build of the
[Ooh Na Na](https://cthoyt.com/2020/04/18/ooh-na-na.html) 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 console with the `--help` flag to show all subcommands:
```console
$ zenodo_client --help
```
It can be run with `zenodo_client ... `
## 🚀 Installation
The most recent release can be installed from
[PyPI](https://pypi.org/project/zenodo_client/) with uv:
```console
$ uv pip install zenodo_client
```
or with pip:
```console
$ python3 -m pip install zenodo_client
```
The most recent code and data can be installed directly from GitHub with uv:
```console
$ uv --preview pip install git+https://github.com/cthoyt/zenodo-client.git
```
or with pip:
```console
$ UV_PREVIEW=1 python3 -m pip install git+https://github.com/cthoyt/zenodo-client.git
```
Note that this requires setting `UV_PREVIEW` mode enabled until the uv build
backend becomes a stable feature.
## 👐 Contributing
Contributions, whether filing an issue, making a pull request, or forking, are
appreciated. See
[CONTRIBUTING.md](https://github.com/cthoyt/zenodo-client/blob/master/.github/CONTRIBUTING.md)
for more information on getting involved.
## 👋 Attribution
### ⚖️ License
The code in this package is licensed under the MIT License.
### 🍪 Cookiecutter
This package was created with
[@audreyfeldroy](https://github.com/audreyfeldroy)'s
[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using
[@cthoyt](https://github.com/cthoyt)'s
[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack)
template.
## 🛠️ For Developers
See developer instructions
The final section of the README is for if you want to get involved by making a
code contribution.
### Development Installation
To install in development mode, use the following:
```console
$ git clone git+https://github.com/cthoyt/zenodo-client.git
$ cd zenodo-client
$ uv --preview pip install -e .
```
Alternatively, install using pip:
```console
$ 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.
### Updating Package Boilerplate
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:
```console
$ cruft update
```
More info on Cruft's update command is available
[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).
### 🥼 Testing
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:
```console
$ tox -e py
```
Additionally, these tests are automatically re-run with each commit in a
[GitHub Action](https://github.com/cthoyt/zenodo-client/actions?query=workflow%3ATests).
### 📖 Building the Documentation
The documentation can be built locally using the following:
```console
$ git clone git+https://github.com/cthoyt/zenodo-client.git
$ cd zenodo-client
$ tox -e docs
$ open docs/build/html/index.html
```
The documentation automatically installs the package as well as the `docs` extra
specified in the [`pyproject.toml`](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`](docs/source/conf.py).
The documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using
[this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html). The
[`.readthedocs.yml`](.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](https://docs.readthedocs.io/en/stable/pull-requests.html).
#### Configuring ReadTheDocs
1. Log in to ReadTheDocs with your GitHub account to install the integration at
https://readthedocs.org/accounts/login/?next=/dashboard/
2. Import your project by navigating to https://readthedocs.org/dashboard/import
then clicking the plus icon next to your repository
3. You can rename the repository on the next screen using a more stylized name
(i.e., with spaces and capital letters)
4. Click next, and you're good to go!
### 📦 Making a Release
#### Configuring Zenodo
[Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI
to each release of your package.
1. 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.
2. 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.
#### Registering with the Python Package Index (PyPI)
You only have to do the following steps once.
1. Register for an account on the
[Python Package Index (PyPI)](https://pypi.org/account/register)
2. 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
3. 2-Factor authentication is required for PyPI since the end of 2023 (see this
[blog post from PyPI](https://blog.pypi.org/posts/2023-05-25-securing-pypi-with-2fa/)).
This means you have to first issue account recovery codes, then set up
2-factor authentication
4. Issue an API token from https://pypi.org/manage/account/token
#### Configuring your machine's connection to PyPI
You have to do the following steps once per machine.
```console
$ 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`.
#### Uploading to PyPI
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:
```console
$ tox -e finish
```
This script does the following:
1. Uses [bump-my-version](https://github.com/callowayproject/bump-my-version) to
switch the version number in the `pyproject.toml`, `CITATION.cff`,
`src/zenodo_client/version.py`, and
[`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix
2. Packages the code in both a tar archive and a wheel using
[`uv build`](https://docs.astral.sh/uv/guides/publish/#building-your-package)
3. Uploads to PyPI using
[`uv publish`](https://docs.astral.sh/uv/guides/publish/#publishing-your-package).
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.
#### Releasing on GitHub
1. Navigate to https://github.com/cthoyt/zenodo-client/releases/new to draft a
new release
2. Click the "Choose a Tag" dropdown and select the tag corresponding to the
release you just made
3. Click the "Generate Release Notes" button to get a quick outline of recent
changes. Modify the title and description as you see fit
4. Click the big green "Publish Release" button
This will trigger Zenodo to assign a DOI to your release as well.