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Edge buffering for tree sequence recording.

Working out kinks in the idea... :)

Python dependencies

  • tskit
  • attrs
  • seaborn
  • pandas

Versions used here for the important things:

  • Python 3.8
  • tskit 2.3 (pip3 installed from PyPi)
  • attrs 19.3.0 (pip3 installed from PyPi)

C++ dependencies

  • A C++ compiler with complete C++17 support. For example, GCC >= 9.1
  • boost's program options library, sudo apt install libboost-program-options-dev
  • GSL, sudo apt install libgsl-dev
  • cmake, sudo apt install cmake
  • tbb, sudo apt install libtbb-dev

The tool chain used here is:

  • Pop! OS 20.04
  • g++ 9.3
  • boost 1.71
  • gsl 2.5
  • cmake 3.16.3
  • tbb

All packages are the OS versions.

Building the C++ example

cmake -Bbuild -DCMAKE_BUILD_TYPE=Release
cd build
make VERBOSE=1

Substitute Debug for Release to disable optimizations and add -g.

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Python testing ground for more efficent edge recording.

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