An API client to bio.tools
Project description
bio.tools Client
An API client to bio.tools.
bio.tools
doesn't provide a first-party data download
(see this issue),
so this package implements an API wrapper to get the data in bulk.
💪 Getting Started
from biotools_client import get_raw_records
raw_records = get_raw_records()
Note, this takes about 2 hours when it's run since each page only includes 10 records and there's on the scale of 30K records (i.e., 3,000 requests need to be made).
Later, this package will implement a way to normalize the data from these records to be more comfortable to work with (e.g., removing missing records, annotating ORCID identifiers for authors, making better key names).
🚀 Installation
The most recent release can be installed from PyPI with:
pip install biotools_client
The most recent code and data can be installed directly from GitHub with:
pip install git+https://github.com/cthoyt/biotools-client.git
👐 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:
git clone git+https://github.com/cthoyt/biotools-client.git
cd biotools-client
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:
pip install cruft
cruft update
More info on Cruft's update command is available here.
🥼 Testing
After cloning the repository and installing tox
with pip install tox tox-uv
,
the unit tests in the tests/
folder can be run reproducibly with:
tox -e py
Additionally, these tests are automatically re-run with each commit in a GitHub Action.
📖 Building the Documentation
The documentation can be built locally using the following:
git clone git+https://github.com/cthoyt/biotools-client.git
cd biotools-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
. sphinx
plugins
like texext
can be added there. Additionally, they need to be added to the
extensions
list in docs/source/conf.py
.
The documentation can be deployed to ReadTheDocs using
this guide.
The .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.
Configuring ReadTheDocs
- Log in to ReadTheDocs with your GitHub account to install the integration at https://readthedocs.org/accounts/login/?next=/dashboard/
- Import your project by navigating to https://readthedocs.org/dashboard/import then clicking the plus icon next to your repository
- You can rename the repository on the next screen using a more stylized name (i.e., with spaces and capital letters)
- Click next, and you're good to go!
📦 Making a Release
Configuring Zenodo
Zenodo is a long-term archival system that assigns a DOI to each release of your package.
- 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.
- 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/biotools-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.
- Register for an account on the Python Package Index (PyPI)
- Navigate to https://pypi-hypernode.com/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
- 2-Factor authentication is required for PyPI since the end of 2023 (see this blog post from PyPI). This means you have to first issue account recovery codes, then set up 2-factor authentication
- Issue an API token from https://pypi-hypernode.com/manage/account/token
Configuring your machine's connection to PyPI
You have to do the following steps once per machine. Create a file in your home directory called
.pypirc
and include the following:
[distutils]
index-servers =
pypi
testpypi
[pypi]
username = __token__
password = <the API token you just got>
# This block is optional in case you want to be able to make test releases to the Test PyPI server
[testpypi]
repository = https://test.pypi.org/legacy/
username = __token__
password = <an API token from test PyPI>
Note that since PyPI is requiring token-based authentication, we use __token__
as the user, verbatim.
If you already have a .pypirc
file with a [distutils]
section, just make sure that there is an index-servers
key and that pypi
is in its associated list. More information on configuring the .pypirc
file can
be found here.
Uploading to PyPI
After installing the package in development mode and installing
tox
with pip install tox tox-uv
,
run the following from the shell:
tox -e finish
This script does the following:
- Uses Bump2Version to switch the version number in
the
pyproject.toml
,CITATION.cff
,src/biotools_client/version.py
, anddocs/source/conf.py
to not have the-dev
suffix - Packages the code in both a tar archive and a wheel using
build
- Uploads to PyPI using
twine
. - Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
- 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
- Navigate to https://github.com/cthoyt/biotools-client/releases/new to draft a new release
- Click the "Choose a Tag" dropdown and select the tag corresponding to the release you just made
- Click the "Generate Release Notes" button to get a quick outline of recent changes. Modify the title and description as you see fit
- Click the big green "Publish Release" button
This will trigger Zenodo to assign a DOI to your release as well.
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