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DEVELOPING.md

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Developing

Building

Installing via pip -e does two things:

  1. Any changes to grgl's Python code will be immediately reflected in your current Python environment, without any additional calls to pip.
  2. When you run the pip command below, it compiles the C++ executables and copies them to the top-level of the grgl repository. Then when you run the Python code behind grg construct, grg convert, etc., it will find the executables there. If you make changes to the C++, you'll need to rerun the pip command below; that will rebuild the executables (grgl, grgp, grg-merge) and also rebuild the C++ code behind the Python API.
python3 -m venv /path/to/MyEnv
source /path/to/MyEnv/bin/activate
GRGL_COPY_BINS=1 pip install -v -e .

Other environment variables that control the Python-based build are:

  • GRGL_GSL=1: Turns on GNU scientific library, which is used to optionally compute p-values for GWAS
  • GRGL_DEBUG=1: Builds the unoptimized version with debug symbols.
  • GRGL_BGEN=1: Turns on BGEN input support for GRG construction

Utilities

There are two utilities gconverter and gindexer that are built when performing the build either via CMake or python. These utilities can be run with --help to see options; they are used for converting files (.vcf, .vcf.gz, and BGEN) to IGD and for indexing BGEN files (which is required before providing a BGEN input to GRG construction).

Testing

  • C++ unit tests are built as grgl_test, and running that executable will tell you the status of those tests.
  • An end-to-end test can be run via pytest test/endtoend/run_tests.py. These tests build GRGs using the currently installed grgl (so make sure you have built/installed your latest changes). The GRGs are then compared against known allele counts to make sure that the mutation to sample relationship was not broken by changes.

Code formatting

  • The code is formatted via clang-format, and CI workflows on Github will fail unless the code is formatted properly. Run ./format.sh from the top-level repo directory to format code. ./format-check.sh can be used to verify the code is properly formatted.