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Developer Build Instructions

System Dependencies

  • C++20 compiler
  • Python 3.9+

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 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|ASAN|TSAN|LSAN|UBSAN|MSAN|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, libspdlog, or tiledb installed may conflict with the required versions for tiledbsoma. Suggestion is for you to not install these, and to let this project's superbuild install compatiable versions for you.

Specifically, uninstall the libfmt-dev and libspdlog-dev packages (or perhaps named spdlog and fmt, depending on the OS). As well, uninstall the tiledb package if you have that separately installed.

As a pro-tip: check the following is gone (and manually remove if necessary) /usr/lib/*/cmake/spdlog/spdlogConfig.cmake

If you do have reason to have fmt and spdlog installed, the following is a known-good configuration on Ubuntu 22.04:

$ 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

As for the tiledb package, if you have reason to have it installed as a separate package, please use the version matching libtiledbsoma/cmake/Modules/FindTileDB_EP.cmake.