atmosphere ☁️

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

• Use 4 space indentation
• Limit lines to 79 characters
• Remove unused imports
• Remove trailing whitespace
• See PEP8 - Style Guide for Python Code

It is recommended that you use the git pre-commit hook to ensure your code is compliant with our style guide.

ln -s $(pwd)/contrib/pre-commit.hook $(pwd)/.git/hooks/pre-commit

To automate running tests before a push use the git pre-push hook to ensure your code passes all the tests.

ln -s $(pwd)/contrib/pre-push.hook $(pwd).git/hooks/pre-push

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 edwin@cyverse.org

Authors

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

• Evan Briones cloud-alum@cyverse.org
• Tharon Carlson tharon@cyverse.org
• Joseph Garcia cloud-alum@cyverse.org
• Steven Gregory cloud-alum@cyverse.org
• Jason Hansen cloud-alum@cyverse.org
• Christopher James LaRose cloud-alum@cyverse.org
• Amit Juneja cloud-alum@cyverse.org
• Andrew Lenards lenards@cyverse.org
• Monica Lent cloud-alum@cyverse.org
• Chris Martin cmart@cyverse.org
• Calvin Mclean calvinmclean@cyverse.org
• Andre Mercer cloud-alum@cyverse.org
• Connor Osborn connor@cyverse.org
• J. Matt Peterson cloud-alum@cyverse.org
• Julian Pistorius julianp@cyverse.org

Where the cloud lives!