This archive is has been DISCONTINUED and is read-only.
The core synthesis functionality has been moved to https://github.com/BASIN-3D/basin3d.
The django web application framework has been moved to https://github.com/BASIN-3D/django-basin3d.
Broker for Assimilation, Synthesis and Integration of eNvironmental Diverse, Distributed Datasets
- BASIN-3D uses the GitFlow model of branching and code versioning in git.
- Code development will be peformed in a forked copy of the repo. Commits will not be made directly to the basin-3d repo. Developers will submit a pull request that is then merged by another team member, if another team member is available.
- Each pull request should contain only related modifications to a feature or bug fix.
- Sensitive information (secret keys, usernames etc) and configuration data (e.g database host port) should not be checked in to the repo.
- A practice of rebasing with the main repo should be used rather that merge commmits.
BASIN-D3 is a Django application which requires:
- Python (>= 3.6)
- Django (>=2.0,<2.1)**
** BASIN-3D may work on later versions of Django Application Framework, but it has not been tested.
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.
$ git clone [email protected]:<your bitbucket username>/basin-3d.git
$ cd basin-3d
Setup virtualenv for development and testing purposes. All basin-3d tests
are in basin3d.tests. They can be
There is an example project for testing in directory example-django.
Create an Anaconda environment
conda create -y -n basin3d python=3.6.5
Activate the new environment and prepare it for development
source activate basin3d
conda develop -npf -n basin3d .
Install BASIN-3D and its dependencies
python setup.py develop
pip install $(cat requirements.txt ) pytest-django pytest-cov
BASIN-3D stores datasource credentials. This requires an encryption secrect key.
cd example-django
mkdir -p .keyset
keyczart create --location=.keyset --purpose=crypt --name=basin3d
keyczart addkey --location=.keyset --status=primary
Migrate the database
./manage.py migrate
Run the tests
pytest -v --cov basin3d tests
Run the server
./manage.py runserver
Create a superuser
./manage.py createsuperuser
Sphinx is used to generate documentation. You first need to create a virtual environment for generating the docs.
$ source activate basin3d
$ pip install sphinx sphinx-autodoc-typehints
Generate the documentation
$ cd docs
$ make html
Review the generated documentation
$ open _build/html/index.html
Install a source distribution with pip:
$ pip install BASIN-3D-<version>.tar.gz
To get started read the setup documentation
We use SemVer for versioning. For the versions available, see the tags on this repository.
Workflow for tagging and building release:
- checkout the version to tag from
master git tag -a v[version]-[release] -m "Tagging release v[version]-[release]"- build distribution with
setup.py git push origin v[version]-[release]
See also the list of contributors who participated in this project.
Broker for Assimilation, Synthesis and Integration of eNvironmental Diverse, Distributed Datasets (BASIN-3D) Copyright (c) 2019, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.
If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Intellectual Property Office at [email protected].
NOTICE. This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit other to do so.
See LICENSE.md file for licensing details
This research is supported as part of the Watershed Function Scientific Focus Area funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award no. DE-AC02-05CH11231. This research used resources of the National Energy Research Scientific Computing Center (NERSC), U.S. Department of Energy Office of Science User Facility operated under Contract No. DE-AC02-05CH11231.