<p align="center">
<img src="https://github.com/biopragmatics/bioversions/raw/main/docs/source/logo.png" height="150">
</p>
<h1 align="center">
Bioversions
</h1>
<p align="center">
<a href="https://github.com/biopragmatics/bioversions/actions/workflows/tests.yml">
<img alt="Tests" src="https://github.com/biopragmatics/bioversions/actions/workflows/tests.yml/badge.svg" /></a>
<a href="https://pypi.org/project/bioversions">
<img alt="PyPI" src="https://img.shields.io/pypi/v/bioversions" /></a>
<a href="https://pypi.org/project/bioversions">
<img alt="PyPI - Python Version" src="https://img.shields.io/pypi/pyversions/bioversions" /></a>
<a href="https://github.com/biopragmatics/bioversions/blob/main/LICENSE">
<img alt="PyPI - License" src="https://img.shields.io/pypi/l/bioversions" /></a>
<a href='https://bioversions.readthedocs.io/en/latest/?badge=latest'>
<img src='https://readthedocs.org/projects/bioversions/badge/?version=latest' alt='Documentation Status' /></a>
<a href="https://codecov.io/gh/biopragmatics/bioversions/branch/main">
<img src="https://codecov.io/gh/biopragmatics/bioversions/branch/main/graph/badge.svg" alt="Codecov status" /></a>
<a href="https://github.com/cthoyt/cookiecutter-python-package">
<img alt="Cookiecutter template from @cthoyt" src="https://img.shields.io/badge/Cookiecutter-snekpack-blue" /></a>
<a href="https://github.com/astral-sh/ruff">
<img src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" alt="Ruff" style="max-width:100%;"></a>
<a href="https://github.com/biopragmatics/bioversions/blob/main/.github/CODE_OF_CONDUCT.md">
<img src="https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg" alt="Contributor Covenant"/></a>
<a href="https://zenodo.org/badge/latestdoi/318852276">
<img src="https://zenodo.org/badge/318852276.svg" alt="DOI"></a>
<a href="https://github.com/biopragmatics/bioregistry">
<img alt="Powered by the Bioregistry" src="https://img.shields.io/static/v1?label=Powered%20by&message=Bioregistry&color=BA274A&style=flat&logo=image/png;base64,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" /></a>
</p>
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`](https://github.com/shaypal5/cachier). The cache is stored in
`~/.data/bioversions`. The cache location can be overridden by setting the
`BIOVERSIONS_HOME` environment variable via
[`pystow`](https://github.com/cthoyt/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](https://pypi.org/project/bioversions/) 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](https://github.com/biopragmatics/bioversions/blob/master/.github/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.
<!--
### 📖 Citation
Citation goes here!
-->
### 🎁 Support
The Bioversions service was originally developed by the
[INDRA Lab](https://indralab.github.io), a part of the
[Laboratory of Systems Pharmacology](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/about/)
and the
[Harvard Program in Therapeutic Science (HiTS)](https://hits.harvard.edu) at
[Harvard Medical School](https://hms.harvard.edu/).
### 💰 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](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
<details>
<summary>See developer instructions</summary>
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.
</details>
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src='https://readthedocs.org/projects/bioversions/badge/?version=latest' alt='Documentation Status' /></a>\n <a href=\"https://codecov.io/gh/biopragmatics/bioversions/branch/main\">\n <img src=\"https://codecov.io/gh/biopragmatics/bioversions/branch/main/graph/badge.svg\" alt=\"Codecov status\" /></a> \n <a href=\"https://github.com/cthoyt/cookiecutter-python-package\">\n <img alt=\"Cookiecutter template from @cthoyt\" src=\"https://img.shields.io/badge/Cookiecutter-snekpack-blue\" /></a>\n <a href=\"https://github.com/astral-sh/ruff\">\n <img src=\"https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json\" alt=\"Ruff\" style=\"max-width:100%;\"></a>\n <a href=\"https://github.com/biopragmatics/bioversions/blob/main/.github/CODE_OF_CONDUCT.md\">\n <img src=\"https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg\" alt=\"Contributor Covenant\"/></a>\n <a href=\"https://zenodo.org/badge/latestdoi/318852276\">\n <img src=\"https://zenodo.org/badge/318852276.svg\" alt=\"DOI\"></a>\n <a href=\"https://github.com/biopragmatics/bioregistry\">\n <img alt=\"Powered by the Bioregistry\" src=\"https://img.shields.io/static/v1?label=Powered%20by&message=Bioregistry&color=BA274A&style=flat&logo=image/png;base64,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\" /></a>\n</p>\n\nWhat's the current version for each biological database?\n\nA daily updated static listing of all current versions (that are incorporated)\ncan be found at https://biopragmatics.github.io/bioversions.\n\n## \ud83d\udcaa Getting Started\n\n```python\nimport bioversions\n\nassert bioversions.get_version('biogrid') == '4.2.192', 'This was true on Dec 5th, 2020!'\n\n# If you want more information, use the resolve() function\nbioversion = bioversions.resolve('biogrid')\nassert bioversion.version == '4.2.192'\n```\n\nBy default, the results are cached and only refreshed once per day with the help\nof [`cachier`](https://github.com/shaypal5/cachier). The cache is stored in\n`~/.data/bioversions`. The cache location can be overridden by setting the\n`BIOVERSIONS_HOME` environment variable via\n[`pystow`](https://github.com/cthoyt/pystow).\n\n## \ud83c\udf10 Web Application\n\nWhile https://biopragmatics.github.io/bioversions provides a daily updated\nstatic listing of the database, you can run a dynamic version with an API from\nyour shell with:\n\n```console\n$ bioversions web\n```\n\nOptions can be listed with `bioversions web --help`.\n\nYou can navigate to http://localhost:5000 to see all versions as HTML or\nprogrammatically resolve given databases with the\n`http://localhost:5000/database/<name>` endpoint like in the following:\n\n```python\nimport requests\n\nres = requests.get('http://localhost:5000/database/biogrid').json()\nassert res['success']\nassert res['result']['name'] == 'BioGRID'\nassert res['result']['version'] == '4.2.192', 'This was true on Dec 5th, 2020!'\n```\n\n## CLI Usage\n\nYou can use `bioversions get` to incorporate the latest versions in your shell\nscripts or REPL usage like in:\n\n```console\n$ wget \"https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-$(bioversions get biogrid)/BIOGRID-ALL-$(bioversions get biogrid).mitab.zip\"\n```\n\n## \ud83d\ude80 Installation\n\nThe most recent release can be installed from\n[PyPI](https://pypi.org/project/bioversions/) with uv:\n\n```console\n$ uv pip install bioversions\n```\n\nor with pip:\n\n```console\n$ python3 -m pip install bioversions\n```\n\nThe most recent code and data can be installed directly from GitHub with uv:\n\n```console\n$ uv pip install git+https://github.com/biopragmatics/bioversions.git\n```\n\nor with pip:\n\n```console\n$ python3 -m pip install git+https://github.com/biopragmatics/bioversions.git\n```\n\n## \ud83d\udc50 Contributing\n\nContributions, whether filing an issue, making a pull request, or forking, are\nappreciated. See\n[CONTRIBUTING.md](https://github.com/biopragmatics/bioversions/blob/master/.github/CONTRIBUTING.md)\nfor more information on getting involved.\n\nTo add more databases to the list, you can create a new submodule of\n`bioversions.sources` and extend the `bioversions.utils.Getter` class to\nidentify the most recent version for your target database. See\n`bioversions.sources.biogrid` as an example.\n\n## \ud83d\udc4b Attribution\n\n### \u2696\ufe0f License\n\nThe code in this package is licensed under the MIT License.\n\n<!--\n### \ud83d\udcd6 Citation\n\nCitation goes here!\n-->\n\n### \ud83c\udf81 Support\n\nThe Bioversions service was originally developed by the\n[INDRA Lab](https://indralab.github.io), a part of the\n[Laboratory of Systems Pharmacology](https://hits.harvard.edu/the-program/laboratory-of-systems-pharmacology/about/)\nand the\n[Harvard Program in Therapeutic Science (HiTS)](https://hits.harvard.edu) at\n[Harvard Medical School](https://hms.harvard.edu/).\n\n### \ud83d\udcb0 Funding\n\nThe development of this package was partially funded by the DARPA Young Faculty\nAward W911NF2010255 (PI: Benjamin M. Gyori).\n\n### \ud83c\udf6a Cookiecutter\n\nThis package was created with\n[@audreyfeldroy](https://github.com/audreyfeldroy)'s\n[cookiecutter](https://github.com/cookiecutter/cookiecutter) package using\n[@cthoyt](https://github.com/cthoyt)'s\n[cookiecutter-snekpack](https://github.com/cthoyt/cookiecutter-snekpack)\ntemplate.\n\n## \ud83d\udee0\ufe0f For Developers\n\n<details>\n <summary>See developer instructions</summary>\n\nThe final section of the README is for if you want to get involved by making a\ncode contribution.\n\n### Development Installation\n\nTo install in development mode, use the following:\n\n```console\n$ git clone git+https://github.com/biopragmatics/bioversions.git\n$ cd bioversions\n$ uv pip install -e .\n```\n\nAlternatively, install using pip:\n\n```console\n$ python3 -m pip install -e .\n```\n\n### Updating Package Boilerplate\n\nThis project uses `cruft` to keep boilerplate (i.e., configuration, contribution\nguidelines, documentation configuration) up-to-date with the upstream\ncookiecutter package. Install cruft with either `uv tool install cruft` or\n`python3 -m pip install cruft` then run:\n\n```console\n$ cruft update\n```\n\nMore info on Cruft's update command is available\n[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).\n\n### \ud83e\udd7c Testing\n\nAfter cloning the repository and installing `tox` with\n`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, the\nunit tests in the `tests/` folder can be run reproducibly with:\n\n```console\n$ tox -e py\n```\n\nAdditionally, these tests are automatically re-run with each commit in a\n[GitHub Action](https://github.com/biopragmatics/bioversions/actions?query=workflow%3ATests).\n\n### \ud83d\udcd6 Building the Documentation\n\nThe documentation can be built locally using the following:\n\n```console\n$ git clone git+https://github.com/biopragmatics/bioversions.git\n$ cd bioversions\n$ tox -e docs\n$ open docs/build/html/index.html\n```\n\nThe documentation automatically installs the package as well as the `docs` extra\nspecified in the [`pyproject.toml`](pyproject.toml). `sphinx` plugins like\n`texext` can be added there. Additionally, they need to be added to the\n`extensions` list in [`docs/source/conf.py`](docs/source/conf.py).\n\nThe documentation can be deployed to [ReadTheDocs](https://readthedocs.io) using\n[this guide](https://docs.readthedocs.io/en/stable/intro/import-guide.html). The\n[`.readthedocs.yml`](.readthedocs.yml) YAML file contains all the configuration\nyou'll need. You can also set up continuous integration on GitHub to check not\nonly that Sphinx can build the documentation in an isolated environment (i.e.,\nwith `tox -e docs-test`) but also that\n[ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).\n\n#### Configuring ReadTheDocs\n\n1. Log in to ReadTheDocs with your GitHub account to install the integration at\n https://readthedocs.org/accounts/login/?next=/dashboard/\n2. Import your project by navigating to https://readthedocs.org/dashboard/import\n then clicking the plus icon next to your repository\n3. You can rename the repository on the next screen using a more stylized name\n (i.e., with spaces and capital letters)\n4. Click next, and you're good to go!\n\n### \ud83d\udce6 Making a Release\n\n#### Configuring Zenodo\n\n[Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI\nto each release of your package.\n\n1. Log in to Zenodo via GitHub with this link:\n https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page\n that lists all of your organizations and asks you to approve installing the\n Zenodo app on GitHub. Click \"grant\" next to any organizations you want to\n enable the integration for, then click the big green \"approve\" button. This\n step only needs to be done once.\n2. Navigate to https://zenodo.org/account/settings/github/, which lists all of\n your GitHub repositories (both in your username and any organizations you\n enabled). Click the on/off toggle for any relevant repositories. When you\n make a new repository, you'll have to come back to this\n\nAfter these steps, you're ready to go! After you make \"release\" on GitHub (steps\nfor this are below), you can navigate to\nhttps://zenodo.org/account/settings/github/repository/biopragmatics/bioversions\nto see the DOI for the release and link to the Zenodo record for it.\n\n#### Registering with the Python Package Index (PyPI)\n\nYou only have to do the following steps once.\n\n1. Register for an account on the\n [Python Package Index (PyPI)](https://pypi.org/account/register)\n2. Navigate to https://pypi.org/manage/account and make sure you have verified\n your email address. A verification email might not have been sent by default,\n so you might have to click the \"options\" dropdown next to your address to get\n to the \"re-send verification email\" button\n3. 2-Factor authentication is required for PyPI since the end of 2023 (see this\n [blog post from PyPI](https://blog.pypi.org/posts/2023-05-25-securing-pypi-with-2fa/)).\n This means you have to first issue account recovery codes, then set up\n 2-factor authentication\n4. Issue an API token from https://pypi.org/manage/account/token\n\n#### Configuring your machine's connection to PyPI\n\nYou have to do the following steps once per machine.\n\n```console\n$ uv tool install keyring\n$ keyring set https://upload.pypi.org/legacy/ __token__\n$ keyring set https://test.pypi.org/legacy/ __token__\n```\n\nNote that this deprecates previous workflows using `.pypirc`.\n\n#### Uploading to PyPI\n\nAfter installing the package in development mode and installing `tox` with\n`uv tool install tox --with tox-uv` or `python3 -m pip install tox tox-uv`, run\nthe following from the console:\n\n```console\n$ tox -e finish\n```\n\nThis script does the following:\n\n1. Uses [bump-my-version](https://github.com/callowayproject/bump-my-version) to\n switch the version number in the `pyproject.toml`, `CITATION.cff`,\n `src/bioversions/version.py`, and\n [`docs/source/conf.py`](docs/source/conf.py) to not have the `-dev` suffix\n2. Packages the code in both a tar archive and a wheel using\n [`uv build`](https://docs.astral.sh/uv/guides/publish/#building-your-package)\n3. Uploads to PyPI using\n [`uv publish`](https://docs.astral.sh/uv/guides/publish/#publishing-your-package).\n4. Push to GitHub. You'll need to make a release going with the commit where the\n version was bumped.\n5. Bump the version to the next patch. If you made big changes and want to bump\n the version by minor, you can use `tox -e bumpversion -- minor` after.\n\n#### Releasing on GitHub\n\n1. Navigate to https://github.com/biopragmatics/bioversions/releases/new to\n draft a new release\n2. Click the \"Choose a Tag\" dropdown and select the tag corresponding to the\n release you just made\n3. Click the \"Generate Release Notes\" button to get a quick outline of recent\n changes. Modify the title and description as you see fit\n4. Click the big green \"Publish Release\" button\n\nThis will trigger Zenodo to assign a DOI to your release as well.\n\n</details>\n",
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