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Developer Build Instructions

System Dependencies

  • C++17 compiler
  • Python 3.8+

Run these commands to setup a fresh Ubuntu 22.04 instance (tested on x86 and Arm):

sudo apt update
sudo apt install -y g++ make pkg-config
sudo apt install -y python3 python-is-python3 python3.10-venv python-dev-is-python3

Clone the source code

git clone https://github.com/single-cell-data/TileDB-SOMA.git
cd TileDB-SOMA

Set up a Python Virtual Environment

Create a python virtual environment and install the developer requirements:

python -m venv test/tiledbsoma
source test/tiledbsoma/bin/activate
pip install -r apis/python/requirements_dev.txt

Python-only Development

Developers who do not need to modify the C++ code must use these build commands:

# remove old build artifacts
make clean

# build and install
pip install -v -e apis/python

# test
pytest apis/python

This approach leverages the build-system defined in pyproject.toml to reduce the number of dependencies required to build tiledbsoma.

Note - Running python setup.py develop is not supported.

Python and C++ Development

Developers who plan to modify the C++ code must use these build commands:

# clean, build, and install
make install

# test
make test

Note - These steps avoid issues when trying to use cmake from the pyproject.toml build-system overlay environment.

Note - All CI and local builds of python, R, and C++ leverage the ../scripts/bld build script, providing a common source for the build flows.

Note - Common developer use cases are captured in the Makefile described below.

Developer Makefile

The Makefile automates common developer use cases and promotes sharing of consistent build flows.

Usage: make rule [options]

Rules:
  install [options]   Build C++ library and install python module
  r-build [options]   Build C++ static library with "#define R_BUILD" for R
  update              Incrementally build C++ library and update python module
  test                Run tests
  clean               Remove build artifacts

Options:
  build=BUILD_TYPE    Cmake build type = Release|Debug|RelWithDebInfo|Coverage [Release]
  prefix=PREFIX       Install location [dist]
  tiledb=TILEDB_DIST  Absolute path to custom TileDB build 

Examples:
  Install Release build

    make install

  Install Debug build of libtiledbsoma and libtiledb

    make install build=Debug

  Install Release build with custom libtiledb

    make install tiledb=$PWD/../TileDB/dist

  Incrementally build C++ changes and update the python module

    make update

Notes

A build system with libfmt and libspdlog installed may conflict with the required versions for tiledbsoma. If that is the case, this configuration is known-good on Ubuntu 22.04:

sudo apt install libfmt-dev libspdlog-dev

Check:

$ dpkg -l | egrep "lib(spdlog|fmt)" | cut -c-80
ii  libfmt-dev:amd64                  8.1.1+ds1-2                             am
ii  libfmt8:amd64                     8.1.1+ds1-2                             am
ii  libspdlog-dev:amd64               1:1.9.2+ds-0.2                          am
ii  libspdlog1:amd64                  1:1.9.2+ds-0.2                          am

Similarly, for MacOS:

  • brew uninstall spdlog (if you have it)
  • brew uninstall fmt (if you have it)
  • brew uninstall tiledb (if you have it from brew)

All these will be installed for you using compatible versions.