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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

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    2 of 3 committers (66.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.3%) to scientific vocabulary
Last synced: 7 months ago · JSON representation

Repository

A tool for automated uploading and version management of scientific data to Zenodo

Basic Info
  • Host: GitHub
  • Owner: cthoyt
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 115 KB
Statistics
  • Stars: 38
  • Watchers: 2
  • Forks: 10
  • Open Issues: 7
  • Releases: 15
Created about 5 years ago · Last pushed 11 months ago
Metadata Files
Readme Contributing Funding License Code of conduct

README.md

Zenodo Client

Tests PyPI PyPI - Python Version PyPI - License Documentation Status Codecov status Cookiecutter template from @cthoyt Ruff Contributor Covenant DOI

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.

```python from zenodoclient import Creator, Metadata, ensurezenodo

Define the metadata that will be used on initial upload

data = Metadata( title='Test Upload 3', uploadtype='dataset', description='test description', creators=[ Creator( name='Hoyt, Charles Tapley', affiliation='Harvard Medical School', orcid='0000-0003-4423-4370', ), ], ) res = ensurezenodo( 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 zenodoclient import updatezenodo

The ID from your deposition

SANDBOXDEPID = '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(DATABASEDIRECTORY, 'altssample.tsv') '/Users/cthoyt/Desktop/alts_sample.tsv', ]

Don't forget to set the ZENODOAPITOKEN environment variable or

any valid way to get zenodo/api_token from PyStow.

updatezenodo(SANDBOXDEP_ID, paths) ```

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

```python from zenodo_client import Zenodo

zenodo = Zenodo() OOHNANARECORD = '4020486' newrecord = zenodo.getlatestrecord(OOHNANA_RECORD) ```

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

```python from zenodo_client import Zenodo

zenodo = Zenodo() OOHNANARECORD = '4020486' newrecord = zenodo.downloadlatest(OOHNANARECORD, '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 console with the --help flag to show all subcommands:

console $ 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 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 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's cookiecutter package using @cthoyt's 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.

Owner

  • Name: Charles Tapley Hoyt
  • Login: cthoyt
  • Kind: user
  • Location: Bonn, Germany
  • Company: RWTH Aachen University

GitHub Events

Total
  • Create event: 5
  • Issues event: 2
  • Release event: 1
  • Watch event: 14
  • Delete event: 4
  • Issue comment event: 2
  • Push event: 17
  • Pull request event: 7
  • Fork event: 3
Last Year
  • Create event: 5
  • Issues event: 2
  • Release event: 1
  • Watch event: 14
  • Delete event: 4
  • Issue comment event: 2
  • Push event: 17
  • Pull request event: 7
  • Fork event: 3

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 87
  • Total Committers: 3
  • Avg Commits per committer: 29.0
  • Development Distribution Score (DDS): 0.023
Past Year
  • Commits: 13
  • Committers: 1
  • Avg Commits per committer: 13.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Charles Tapley Hoyt c****t@g****m 85
Eli Chadwick e****k@m****k 1
Daniel Nüst d****t@t****e 1
Committer Domains (Top 20 + Academic)
tu-dresden.de: 1 manchester.ac.uk: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 27
  • Total pull requests: 20
  • Average time to close issues: 3 months
  • Average time to close pull requests: 28 days
  • Total issue authors: 12
  • Total pull request authors: 5
  • Average comments per issue: 2.33
  • Average comments per pull request: 1.9
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 4
Past Year
  • Issues: 1
  • Pull requests: 7
  • Average time to close issues: N/A
  • Average time to close pull requests: 8 days
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.14
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 4
View more stats
Top Authors
Issue Authors
  • sgbaird (7)
  • nuest (5)
  • mberr (2)
  • daviddavo (2)
  • rhigman (2)
  • cthoyt (2)
  • simontaurus (1)
  • wummo (1)
  • mikegerber (1)
  • elichad (1)
  • longavailable (1)
  • bgyori (1)
Pull Request Authors
  • cthoyt (12)
  • nuest (5)
  • github-actions[bot] (4)
  • elichad (2)
  • mberr (1)
Top Labels
Issue Labels
enhancement (3) help wanted (2) good first issue (1) documentation (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 3,777 last-month
  • Total dependent packages: 5
  • Total dependent repositories: 4
  • Total versions: 15
  • Total maintainers: 1
pypi.org: zenodo-client

A wrapper for the Zenodo API.

  • Versions: 15
  • Dependent Packages: 5
  • Dependent Repositories: 4
  • Downloads: 3,777 Last month
  • Docker Downloads: 0
Rankings
Dependent packages count: 1.9%
Docker downloads count: 3.4%
Dependent repos count: 7.5%
Downloads: 9.0%
Average: 9.0%
Stargazers count: 15.2%
Forks count: 16.8%
Maintainers (1)
cthoyt
Last synced: 7 months ago

Dependencies

.github/workflows/tests.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
pyproject.toml pypi