The Kagami library (Kaga)
Project description
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)
Project details
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Filename, size | File type | Python version | Upload date | Hashes |
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