https://github.com/biopragmatics/bioversions
🪝 What's the latest version for each database?
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.0%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
🪝 What's the latest version for each database?
Basic Info
- Host: GitHub
- Owner: biopragmatics
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://biopragmatics.github.io/bioversions
- Size: 5.36 MB
Statistics
- Stars: 27
- Watchers: 2
- Forks: 8
- Open Issues: 8
- Releases: 25
Topics
Metadata Files
README.md
Bioversions
What's the current version for each biological database?
A daily updated static listing of all current versions (that are incorporated) can be found at https://biopragmatics.github.io/bioversions.
💪 Getting Started
```python import bioversions
assert bioversions.get_version('biogrid') == '4.2.192', 'This was true on Dec 5th, 2020!'
If you want more information, use the resolve() function
bioversion = bioversions.resolve('biogrid') assert bioversion.version == '4.2.192' ```
By default, the results are cached and only refreshed once per day with the help
of cachier. The cache is stored in
~/.data/bioversions. The cache location can be overridden by setting the
BIOVERSIONS_HOME environment variable via
pystow.
🌐 Web Application
While https://biopragmatics.github.io/bioversions provides a daily updated static listing of the database, you can run a dynamic version with an API from your shell with:
console
$ bioversions web
Options can be listed with bioversions web --help.
You can navigate to http://localhost:5000 to see all versions as HTML or
programmatically resolve given databases with the
http://localhost:5000/database/<name> endpoint like in the following:
```python import requests
res = requests.get('http://localhost:5000/database/biogrid').json() assert res['success'] assert res['result']['name'] == 'BioGRID' assert res['result']['version'] == '4.2.192', 'This was true on Dec 5th, 2020!' ```
CLI Usage
You can use bioversions get to incorporate the latest versions in your shell
scripts or REPL usage like in:
console
$ wget "https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-$(bioversions get biogrid)/BIOGRID-ALL-$(bioversions get biogrid).mitab.zip"
🚀 Installation
The most recent release can be installed from PyPI with uv:
console
$ uv pip install bioversions
or with pip:
console
$ python3 -m pip install bioversions
The most recent code and data can be installed directly from GitHub with uv:
console
$ uv pip install git+https://github.com/biopragmatics/bioversions.git
or with pip:
console
$ python3 -m pip install git+https://github.com/biopragmatics/bioversions.git
👐 Contributing
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.
To add more databases to the list, you can create a new submodule of
bioversions.sources and extend the bioversions.utils.Getter class to
identify the most recent version for your target database. See
bioversions.sources.biogrid as an example.
👋 Attribution
⚖️ License
The code in this package is licensed under the MIT License.
🎁 Support
The Bioversions service was originally developed by the INDRA Lab, a part of the Laboratory of Systems Pharmacology and the Harvard Program in Therapeutic Science (HiTS) at Harvard Medical School.
💰 Funding
The development of this package was partially funded by the DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).
🍪 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/biopragmatics/bioversions.git $ cd bioversions $ uv pip install -e . ``` Alternatively, install using pip: ```console $ python3 -m pip install -e . ``` ### 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/biopragmatics/bioversions/actions?query=workflow%3ATests). ### 📖 Building the Documentation The documentation can be built locally using the following: ```console $ git clone git+https://github.com/biopragmatics/bioversions.git $ cd bioversions $ 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/biopragmatics/bioversions 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/bioversions/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/biopragmatics/bioversions/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: Biopragmatics Stack
- Login: biopragmatics
- Kind: organization
- Website: https://biopragmatics.github.io
- Twitter: biopragmatics
- Repositories: 9
- Profile: https://github.com/biopragmatics
Software supporting biomedical semantics and pragmatics
GitHub Events
Total
- Create event: 288
- Release event: 3
- Issues event: 10
- Watch event: 3
- Delete event: 26
- Issue comment event: 16
- Push event: 322
- Pull request event: 77
- Fork event: 1
Last Year
- Create event: 288
- Release event: 3
- Issues event: 10
- Watch event: 3
- Delete event: 26
- Issue comment event: 16
- Push event: 322
- Pull request event: 77
- Fork event: 1
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| GitHub Action | a****n@g****m | 2,890 |
| Charles Tapley Hoyt | c****t@g****m | 401 |
| james stevenson | j****n@n****g | 4 |
| Benjamin M. Gyori | b****i@g****m | 3 |
| james stevenson | j****n@g****m | 2 |
| jplfaria | j****a@g****m | 2 |
| kkaris | k****s@g****m | 2 |
| Daniel Himmelstein | d****n@g****m | 1 |
| Egon Willighagen | e****n@g****m | 1 |
| Harshad | h****d@u****m | 1 |
| Marcel Friedrichs | a****s@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 25
- Total pull requests: 87
- Average time to close issues: 11 months
- Average time to close pull requests: about 2 months
- Total issue authors: 7
- Total pull request authors: 10
- Average comments per issue: 1.0
- Average comments per pull request: 0.45
- Merged pull requests: 50
- Bot issues: 0
- Bot pull requests: 27
Past Year
- Issues: 5
- Pull requests: 61
- Average time to close issues: 3 months
- Average time to close pull requests: 11 days
- Issue authors: 4
- Pull request authors: 4
- Average comments per issue: 0.4
- Average comments per pull request: 0.2
- Merged pull requests: 28
- Bot issues: 0
- Bot pull requests: 27
Top Authors
Issue Authors
- cthoyt (12)
- dhimmel (5)
- bgyori (3)
- kkaris (1)
- steppi (1)
- aracnus (1)
- hrshdhgd (1)
Pull Request Authors
- cthoyt (49)
- github-actions[bot] (28)
- jsstevenson (6)
- bgyori (6)
- kkaris (4)
- jplfaria (4)
- egonw (1)
- hrshdhgd (1)
- dhimmel (1)
- AstrorEnales (1)
Top Labels
Issue Labels
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Packages
- Total packages: 1
-
Total downloads:
- pypi 21,928 last-month
- Total dependent packages: 5
- Total dependent repositories: 6
- Total versions: 927
- Total maintainers: 1
pypi.org: bioversions
Get the current version for biological databases
- Homepage: https://github.com/biopragmatics/bioversions
- Documentation: https://bioversions.readthedocs.io
- License: MIT License
-
Latest release: 0.8.129
published 10 months ago
Rankings
Maintainers (1)
Funding
- https://github.com/sponsors/cthoyt
Dependencies
- actions/checkout v2 composite
- actions/setup-python v2 composite
- actions/checkout master composite
- actions/setup-python v2 composite
- ad-m/github-push-action master composite