tcztzy / relatepy

Relate Python

Motivation

MyersGroup's Relate is written in C++. Frankly, I am not good at C++. So, I decide to write a wrapper over this project. Maybe I will refactor them all in Python/Cython is the performance loss is acceptable. Maybe I will integrate output file handling (e.g. plotting) in this project.

Install

$ pip install relatepy  # or
$ pip install git+https://github.com/tcztzy/relatepy

Build from source

Build requirements:

1. C++ compiler support C++17
2. Python interpreter and <Python.h> headers
3. zlib
4. Any build tools support PEP 517, such as build.

CMake is not required since we have Python's build tool chain.

$ git clone https://github.com/tcztzy/relatepy
$ cd relatepy
$ git submodule init
$ # C++20 had a <version> header, so you should remove the version file in gzstream directory
$ rm relate/include/src/gzstream/version
$ pip install build  # Any tools support PEP 517 would work
$ pip -m build

Environments

Set RELATEPY_RESOURCE_USAGE to enable the resource usage report (also need --verbosity=DEBUG).

Roadmap

• Refactoring
  • Chunk data
    • Manually
    • AnnData/Dask chunk
  • Paint
    • Logically equivalence
    • Simplified
    • Speed up
  • Build topology
  • Find equivalent branches
  • Get branch length
  • Combine sections
  • Finalize
• Visualizing scripting
  • Final results plotting
    • Effective population size
  • Intermediate process plotting
    • Painting