bioversions 0.5.552__py3-none-any.whl → 0.5.554__py3-none-any.whl

bioversions-0.5.554.dist-info/METADATA

@@ -0,0 +1,382 @@
+Metadata-Version: 2.1
+Name: bioversions
+Version: 0.5.554
+Summary: Get the current version for biological databases
+Author-email: Charles Tapley Hoyt <cthoyt@gmail.com>
+Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2024 Charles Tapley Hoyt
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Bug Tracker, https://github.com/biopragmatics/bioversions/issues
+Project-URL: Homepage, https://github.com/biopragmatics/bioversions
+Project-URL: Repository, https://github.com/biopragmatics/bioversions.git
+Project-URL: Documentation, https://bioversions.readthedocs.io
+Keywords: snekpack,cookiecutter,databases,biological databases,biomedical databases
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Framework :: Pytest
+Classifier: Framework :: tox
+Classifier: Framework :: Sphinx
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3 :: Only
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: requests-ftp
+Requires-Dist: beautifulsoup4
+Requires-Dist: cachier>=2.2.1
+Requires-Dist: pystow>=0.1.0
+Requires-Dist: click
+Requires-Dist: click-default-group
+Requires-Dist: dataclasses-json
+Requires-Dist: tabulate
+Requires-Dist: more-click
+Requires-Dist: pyyaml
+Requires-Dist: tqdm
+Requires-Dist: bioregistry[align]>=0.10.0
+Requires-Dist: lxml
+Requires-Dist: pydantic>=2.0
+Requires-Dist: psycopg2-binary
+Provides-Extra: charts
+Requires-Dist: matplotlib; extra == "charts"
+Requires-Dist: seaborn; extra == "charts"
+Provides-Extra: docs
+Requires-Dist: sphinx>=8; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=3.0; extra == "docs"
+Requires-Dist: sphinx-click; extra == "docs"
+Requires-Dist: sphinx-automodapi; extra == "docs"
+Provides-Extra: slack
+Requires-Dist: slack-sdk; extra == "slack"
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: coverage; extra == "tests"
+Provides-Extra: twitter
+Requires-Dist: tweepy; extra == "twitter"
+Provides-Extra: web
+Requires-Dist: flask; extra == "web"
+Requires-Dist: bootstrap-flask; extra == "web"
+
+<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,iVBORw0KGgoAAAANSUhEUgAAACgAAAAoCAYAAACM/rhtAAAACXBIWXMAAAEnAAABJwGNvPDMAAAAGXRFWHRTb2Z0d2FyZQB3d3cuaW5rc2NhcGUub3Jnm+48GgAACi9JREFUWIWtmXl41MUZxz/z291sstmQO9mQG0ISwHBtOOSwgpUQhApWgUfEowKigKI81actypaqFbWPVkGFFKU0Vgs+YgvhEAoqEUESrnDlEEhCbkLYJtlkk9399Y/N/rKbzQXt96+Zed+Z9/t7Z+adeecnuA1s5yFVSGrLOAf2qTiEEYlUZKIAfYdKE7KoBLkQSc4XgkPfXxz/owmT41ZtiVtR3j94eqxQq5aDeASIvkVb12RBtt0mb5xZsvfa/5XgnqTMcI3Eq7IQjwM+7jJJo8YvNhK/qDBUOl8A7JZWWqqu01Jeg6Pd1nW4NuBjjax6eWrRruv/M8EDqTMflmXeB0Jcbb6RIRhmTCJ0ymgC0wYjadTd9nW0tWMu+In63NNU7c3FWtvgJpXrZVlakVGU8/ltEcwzGjU3miI/ABa72vwTB5K45AEi7x2PUEl9fZsHZLuDmgPHuLJpJ82lle6iTSH6mpXp+fnt/Sa4yzhbp22yfwFkgnMaBy17kPhFmQh1997qLxztNkq35XB505fINtf0iz1WvfTQ7Pxdlj4Jdnjuny5yvpEhjHh7FQOGD/YyZi4owS86HJ+QQMDpJaBf3jUXlHD21+8q0y4LDppV/vfNO7+jzV3Pa6SOac0E8I8fSPonpm7JAVR+eRhzwU/Ofj+e49tpT/HdtGXcyLvQJ8HAtCTGfmJCF2dwfpTMz4NszX/uqqdyr+xPyVwoEK+C03PGrDX4GkJ7NBJ+txH/hCgAit7cRlNxOY62dmzmZgwzJvZJUh2gI/xnRmoOHsfe3AqQ/kho0qXs+pLzLh3FgwdT54YKxLsAQq0mbf1zHuTsltZejemHJSrlgGGDPGTXc09zdM5qTi59jZbKOg+Zb1QYI95+XokEQogPDifPDnPJFQ8uCkl8FyGmACQtn4dhxp3KINX7jnHi0ZeJnT8dla8Plbu+48zzfyJ08kh8ggIACB4zlIAhsURm3EnML6eB6Fzep1a+SUt5DS2VddTs+4GQccPRhgV1kowIQRaChhMXAPxkIev/Vl+8R/HgnqTMmI4gjH/iQOIXZSqdzQUlXDB9RPyi+1DrdVx67WMursvCkDERXYxB0ROSIOKecURMG+tBzkXAhbYbZk6teNPLkwmPzUIX71wuMiw+MHx2nEJQrWIFHSdE4pIHlFDisLZxYe1HhIwfTtLK+RSu30rVnlxGvrOapOcW9DsW3vH6CgKS4zxIXlz3Fw8dSaMmcfEcV9XHYbc/DSCZMEkgFoJzY0TeO17pVL7jANbaBoauWUJlTi4VOw+T9sazBKYl0ZB/qV/kALThQRi3vOJB0lpzw0vPMONOtOHOqRcyi7bzkEqanJo3HogBMGROUrziaGundGsOsQsyUPn6UPx2NvELZxIybhinn3uLyx9uVwaW7XbqjxdQmr2X0uy93Dh+Dtlu9zCu9vdj1PsvEWwcii7OwJAXFnoRFCoVhoxJrmr0gOQWo9qBfaorXodOHq0o1x8roN3cSMyC6ZT942uQBIlL53Jl804sV6oY9/fXAGg4WcjFdZuxlFV7GNPFRzFs7VKCRiV7ejJrTa/eDr1rFKXZOQCocEyTgHQAyUdD4B2d4cF8pohg4zC0YUFU7z5C9Jy7sVvbKPtsH6GT0tCGBtFwspBTz/zRixyApbSKk8te5+aZ4l4JdUVQWpIScmQhjGocUjJCRhcTieSjURQTF89FtttpuVaLpaya8Knp1B3OQ5Zlag/nU//9cmScS6EnONrauWjazIQv3kCoVD3quUPS+uAXHU7z1SpATpEQchSA78AwD0WVnxa1XkdjURlCJRGQHMfN/EuEjk9jyr4NRN47Hltjc58Gm0sraTjZ/w3l5BLuKkZJdFzT1f5+3Sq3NZjRDNAjaX1orb2BX2wEmkA9fvGGbvW7Q+OlUu+2wlIqdx+h3dzkJVPrda5iQJ93p+DRqcQ/PhsAw8xJ6AfHdkhuIVvoEribLl/jxKOv4Gi34T8omgnb1yOk7sdTA01AiK3J6yoGgP+gaPwHOdOP6LlTlXb3mNYXAlI8da9/e0pJBZovV2BrakYzQK/I3bg0SsiiCqClqs/0wAPB6UOVo6k3+CdEETwm1aPtP+dLlLJPSKAHOYDWCoVLlYTkKAKcCU4vO7IrhErFsLVLPXZ+V0haDcN+v8xjB9strdQfPavUA0ckefRxWNuwVNS6rBRKQB44r+Lmc5f7TRAgaFQyYzb9Dv/4gd18ASQ8/gsC0zwJNJVcw97aeWmOcDtaAW6eLXZLBchTC8EhWXbW6o+cInhMipetuu9OUvTWNnwNodzx+krlvAQIGjmECV+spyH/Ak3F5QDok+OoPXicip2HiJiWTuH6rQx6eh7BxlT0STH4xUbSUl6Df/xAIqaO9bBVn3taKUuy/ZAwYZImpvx4FYjVRgQzOec9r1vK0TmrldMiIDkO45ZXegxLLrRW13P0/heQHQ4CUhIYvfElNIHOtWaztNJ4qZQBqfFKLg3OMz135rNY624ClB0tHJcomTA5ZMGnANbaBmoOHPMy5hvZebNuLCoj71frXIN0i9pDJzj24IsIlUTCo7NI3/KyQg5ArfMleEyKBzmA6r1HO8eV+dSEySEB2G3yRpwZP1c2f+n1GjB07RIlcwNoKi7j3G839EhQF2cg6fmHmbznPRKevJ/GorIedV1wtLVzJesrV9WqQtoIHRfWjreSjwGar1ZRui3Ho7PfwHBGb3jRg6S1roGeoIuNJGBIPKV/zSF31irOrn4HXAu9B1zduhtLecelQxZZ9xTtrgC342Df8IwQyaYqBMKEWo0xaw1BI4d4DNJSWcfF32fRWnuD5NWPEDZ5lIe8NDuHq1v+ha2xGdkho4szYJg1hbj501EH6OgJ5oIS8hf/oWPm5HqNrE51vdt4nC/7k+9bIIT8GYA2Ipixn5jwjQrrZsju0XT5GubTRfiEBqFPisUvOrzPPi0VdeQ9YcJ63bWmxbzphTk7XHKvA/DrlJkfAU+Bcy2N+fA3vZK0WVoxny4idOKIfn+IO7lTz7zRObWCjdMv7VnhruOV9dws9F8u4CsAS1k1J54wYS4o6arWaaS8hvLP998yuZtnisl7wuROLkdjsKzqqtfL45FjB8gzwZnIJy6dS8Jjs3p8ausvHG3tXN26mytZO5W8Rcjsbg1Qze/X45ELHY9I7wHLXG26+CgSl8zFkDGh3zdkF2S7nep9PzhzmnK3FEGwUWOwrJr6zTdeL529EnRhf3LmfCHEBkBZiNrwIAwZkwi9a5Qzh9D6dNvXYW3jZkEJ9UdOOYPwdY/gXgdiufuGuC2C4Hy3kWXrOhmeBLQeA6jV6GLC8Y0KR613Hn+2phZaK69jqah1P/hdsCKLLIfGtnbG+f3eyfHtEHTh38mzom2SY4WQWQjE9tnBE+XIZKuQNrqCcH9wSwRdMGGSJiTnpatwTJOFMIKcgvPVX/kNIcM1gSgC8iTZfii3aEL+7fyG+C+6O8izl1GE5gAAAABJRU5ErkJggg==" /></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:
+
+```bash
+$ 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:
+
+```bash
+$ 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:
+
+```console
+python3 -m pip install bioversions
+```
+
+The most recent code and data can be installed directly from GitHub with:
+
+```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
+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. Update with the following:
+
+```console
+python3 -m pip install cruft
+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
+`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 `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>

bioversions-0.5.554.dist-info/RECORD

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bioversions-0.5.552.dist-info/METADATA

@@ -1,166 +0,0 @@
-Metadata-Version: 2.1
-Name: bioversions
-Version: 0.5.552
-Summary: What's the current version for each biological database?
-Home-page: https://github.com/biopragmatics/bioversions
-Download-URL: https://github.com/biopragmatics/bioversions/releases
-Author: Charles Tapley Hoyt
-Author-email: cthoyt@gmail.com
-Maintainer: Charles Tapley Hoyt
-Maintainer-email: cthoyt@gmail.com
-License: MIT
-Project-URL: Bug Tracker, https://github.com/biopragmatics/bioversions/issues
-Keywords: databases,biological databases
-Classifier: Development Status :: 4 - Beta
-Classifier: Environment :: Console
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3 :: Only
-Requires-Python: >=3.8
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: requests
-Requires-Dist: requests-ftp
-Requires-Dist: beautifulsoup4
-Requires-Dist: cachier>=2.2.1
-Requires-Dist: pystow>=0.1.0
-Requires-Dist: click
-Requires-Dist: click-default-group
-Requires-Dist: dataclasses-json
-Requires-Dist: tabulate
-Requires-Dist: more-click
-Requires-Dist: pyyaml
-Requires-Dist: tqdm
-Requires-Dist: bioregistry[align]>=0.10.0
-Requires-Dist: pandas
-Requires-Dist: lxml
-Requires-Dist: psycopg2-binary
-Provides-Extra: charts
-Requires-Dist: matplotlib; extra == "charts"
-Requires-Dist: seaborn; extra == "charts"
-Provides-Extra: slack
-Requires-Dist: slack-sdk; extra == "slack"
-Provides-Extra: twitter
-Requires-Dist: tweepy; extra == "twitter"
-Provides-Extra: web
-Requires-Dist: flask; extra == "web"
-Requires-Dist: bootstrap-flask; extra == "web"
-
-<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://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://zenodo.org/badge/latestdoi/318852276">
-        <img src="https://zenodo.org/badge/318852276.svg" alt="DOI" />
-    </a>
-    <a href="https://github.com/psf/black">
-        <img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="Code style: black">
-    </a>
-    <a href="https://github.com/biopragmatics/bioregistry"$>
-        <img alt="Powered by the Bioregistry" src="https://img.shields.io/static/v1?label=Powered%20by&message=Bioregistry&color=BA274A&style=flat&logo=image/png;base64,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" />
-    </a>
-</p>
-
-What's the current version for each biological database?
-
-A daily updated static listing of all current versions (that are incorporated) can be found at
-https://biopragmatics.github.io/bioversions.
-
-## 🚀 Installation
-
-```bash
-$ pip install bioversions
-```
-
-## 💪 Usage
-
-```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:
-
-```bash
-$ 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:
-
-```bash
-$ wget "https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-$(bioversions get biogrid)/BIOGRID-ALL-$(bioversions get biogrid).mitab.zip"
-```
-
-## 🙏 Contributing
-
-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
-
-Code is licensed under the MIT License.
-
-### 🎁 Support
-
-The Bioversions service was 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 the Bioregistry is funded by the DARPA Young Faculty Award W911NF2010255 (PI:
-Benjamin M. Gyori).