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The Kagami library (Kaga)

Project description

License: LGPL v3 Python 2.7 Python 3.7 PyPI version

Kagami Library

The Kagami library is a Python package to accelerate the development of novel computational biology algorithms. It is currently under rapid growth. Although the APIs are aimed to remain consistent within a major version, compatible between releases are not guaranteed. Please note that there is no plan to include documents anytime soon.

The Kagami library is distributed under the GNU Lesser General Public License v3.0.

Dependencies

  • Python >= 3.7.5
  • numpy >= 1.17.4
  • requests >= 2.22.0
  • tables >= 3.6.1

For RWrapper:

  • rpy2 >= 3.2.4
  • R >= 3.6.1

For pytest, test coverage, and profiling:

  • pytest >= 5.3.2
  • pytest-cov >= 2.8.1
  • pytest-profiling >= 1.7.0

Lower versions may work but have not been tested.

Installation

Using pip:

pip install kagami

Using Docker:

docker pull envomics/kagami

Testing

python -c "import kagami; kagami.test()"

Changelog

version 3.0

  • <input type="checkbox" checked="" disabled="" /> Migrate to Python 3.7
  • <input type="checkbox" checked="" disabled="" /> Add disk base for the Table
  • <input type="checkbox" checked="" disabled="" /> Add chunk mapping
  • <input type="checkbox" checked="" disabled="" /> Add numpy style indexing parameters for CoreTypes
  • <input type="checkbox" checked="" disabled="" /> Add attribute-like access to table index
  • <input type="checkbox" checked="" disabled="" /> Add dataframe-like assignment to table values
  • <input type="checkbox" checked="" disabled="" /> Add handy snippets and R-like functions
  • <input type="checkbox" checked="" disabled="" /> Clean None and na usage in map functions
  • <input type="checkbox" checked="" disabled="" /> Fix R wrapper init libraries multiple loading bug
  • <input type="checkbox" checked="" disabled="" /> Fix R wrapper library loading warning suppression
  • <input type="checkbox" checked="" disabled="" /> Update unit tests

Version 2.2

  • <input type="checkbox" checked="" disabled="" /> Add fixRepeat for NamedIndex and Table
  • <input type="checkbox" checked="" disabled="" /> Improve Table repr
  • <input type="checkbox" checked="" disabled="" /> Major refactor for package structure

Version 2.1

  • <input type="checkbox" checked="" disabled="" /> Add Dockerfile
  • <input type="checkbox" checked="" disabled="" /> Add setup script
  • <input type="checkbox" checked="" disabled="" /> Add level properties for factor type

Version 2.0

  • <input type="checkbox" checked="" disabled="" /> Add Factor CoreType
  • <input type="checkbox" checked="" disabled="" /> Add NamedIndex CoreType
  • <input type="checkbox" checked="" disabled="" /> Add StructuredArray CoreType
  • <input type="checkbox" checked="" disabled="" /> Add Table CoreType
  • <input type="checkbox" checked="" disabled="" /> Add HDF5 portals for StructuredArray and Table
  • <input type="checkbox" checked="" disabled="" /> Add RData portal for Table
  • <input type="checkbox" checked="" disabled="" /> Add Metadata class
  • <input type="checkbox" checked="" disabled="" /> Add functional programming support
  • <input type="checkbox" checked="" disabled="" /> Add BinWrapper
  • <input type="checkbox" checked="" disabled="" /> Add license
  • <input type="checkbox" checked="" disabled="" /> Update unit tests

Citation

If you use Kagami, DarkFusion or MOCA in a publication, we would appreciate citations: (coming soon)

Kagami is part of Albert's scientific toolbox.

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