A python package for integrating data from multiple resources
Project description
pyBioDataFuse
A python package for integrating data from multiple resources
💪 Getting Started
TODO show in a very small amount of space the MOST useful thing your package can do. Make it as short as possible! You have an entire set of docs for later.
Command Line Interface
The pyBiodatafuse command line tool is automatically installed. It can
be used from the shell with the --help
flag to show all subcommands:
$ pyBiodatafuse --help
TODO show the most useful thing the CLI does! The CLI will have documentation auto-generated by
sphinx
.
🚀 Installation
The most recent release can be installed from PyPI with:
$ pip install pyBiodatafuse
The most recent code and data can be installed directly from GitHub with:
$ pip install git+https://github.com/BioDataFuse/pyBiodatafuse.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/BioDataFuse/pyBiodatafuse.git
$ cd pyBiodatafuse
$ pip install -e .
🥼 Testing
After cloning the repository and installing tox
with pip install tox
, the unit tests in the tests/
folder can be
run reproducibly with:
$ tox
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/BioDataFuse/pyBiodatafuse.git
$ cd pyBiodatafuse
$ tox -e docs
$ open docs/build/html/index.html
The documentation automatically installs the package as well as the docs
extra specified in the setup.cfg
. sphinx
plugins
like texext
can be added there. Additionally, they need to be added to the
extensions
list in docs/source/conf.py
.
📦 Making a Release
After installing the package in development mode and installing
tox
with pip install tox
, the commands for making a new release are contained within the finish
environment
in tox.ini
. Run the following from the shell:
$ tox -e finish
This script does the following:
- Uses Bump2Version to switch the version number in the
setup.cfg
,src/pyBiodatafuse/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
. Be sure to have a.pypirc
file configured to avoid the need for manual input at this step - 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.
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