calvinmclean/atmosphere repository overview

⁠atmosphere :cloud:

Atmosphere addresses the growing needs for highly configurable and customized computational resources to support research efforts in plant sciences. Atmosphere is an integrative, private, self-service cloud computing platform designed to provide easy access to preconfigured, frequently used analysis routines, relevant algorithms, and data sets in an available-on-demand environment designed to accommodate computationally and data-intensive bioinformatics tasks.

⁠Installation

Install the required python packages

pip install -r requirements.txt

A separate environment is provided for developers

pip install -r dev_requirements.txt

The *requirements.txt files are generated using pip-tools⁠. See REQUIREMENTS.md⁠ for instructions on using pip-tools and upgrading packages in Atmosphere.

⁠Some Features

• A powerful web client for management and administration of virtual machines
• A fully RESTful API service for integrating with existing infrastructure components
• Virtual machine images preconfigured for computational science and iPlant's infrastructure

⁠Running scripts

There are several utility scripts in ./scripts. To run these:

cd <path to atmosphere>
export DJANGO_SETTINGS_MODULE='atmosphere.settings'
export PYTHONPATH="$PWD:$PYTHONPATH"
python scripts/<name of script>

⁠Contributing

See HACKING.md⁠.

⁠Coding Style

We rely on a tool to format the codebase. If you install from dev_requirements.txt, the yapf binary will be in your environment.

yapf --in-place --parallel   -- $(git ls-files | grep '\.py$')

When master is pulled, it's helpful to know if a pip install or a manage.py migrate is necessary. To get other helpful warnings:

ln -s $(pwd)/contrib/post-merge.hook $(pwd)/.git/hooks/post-merge

⁠Coding Conventions

⁠Import ordering

Imports should be grouped into the sections below and in sorted order.

1. Standard libraries
2. Third-party libraries
3. External project libraries
4. Local libraries

⁠License

See LICENSE.txt for license information

⁠Lead

• Edwin Skidmore [email protected]⁠

⁠Authors

The following individuals who have help/helped make :cloud: great appear in alphabetic order, by surname.

• Evan Briones [email protected]⁠
• Tharon Carlson [email protected]⁠
• Joseph Garcia [email protected]⁠
• Steven Gregory [email protected]⁠
• Jason Hansen [email protected]⁠
• Christopher James LaRose [email protected]⁠
• Amit Juneja [email protected]⁠
• Andrew Lenards [email protected]⁠
• Monica Lent [email protected]⁠
• Chris Martin [email protected]⁠
• Calvin Mclean [email protected]⁠
• Andre Mercer [email protected]⁠
• Connor Osborn [email protected]⁠
• J. Matt Peterson [email protected]⁠
• Julian Pistorius [email protected]⁠

Where the cloud lives!