longitudinal-tomography 3.7.0

Prerequisites

Linux

You need a C++ compiler like g++ installed. This is not required if installing a prebuilt package from acc-py or pypi.

Windows

On Windows computers MSVC >= 14.0 with the Windows 10 SDK is required.

In MinGW and WSL environments the standard g++ compiler works out of the box.

MacOS

You need to use a compiler other that the default provided on MacOS (gcc is symlinked to clang by default). The easiest way (and the way that us currently supported) is to install llvm and openmp with Homebrew: brew install llvm openmp.

Installation instructions

For MacOS see next section.

Clone the repository and run

pip install .

The C++ extension will be built on install using the native compiler in Linux and Windows (pybind11 should find it).

For development environments where it’s preferable to compile the C++ extension inplace, it’s possible to run the command

pip install -e .

which will compile the C++ extension using the available compiler (decided by setuptools).

MacOS

MacOS requires some special treatment for the extension to compile. You need to tell pip to use Homebrew clang and llvm instead of the default compiler and libraries. This can be done by setting the CC, LDFLAGS and CPPFLAGS environment variables. You also need to install the libomp package with Homebrew.

On arm64 (M1/M2) MacBooks, use the following: ..

export LDFLAGS=”-L/opt/homebrew/lib -L/opt/homebrew/opt/llvm/lib” export CPPFLAGS=”-I/opt/homebrew/include -I/opt/homebrew/opt/llvm/include” CC=/opt/homebrew/opt/llvm/bin/clang++ pip install .

Or use the -e flag for an editable installation. For Intel MacBooks, Homebrew packages are installed in a different location.

Hence, for Intel MacBooks, use the following:

export LDFLAGS="-L/usr/local/opt/homebrew/lib -L/usr/local/opt/homebrew/opt/llvm/lib"
export CPPFLAGS="-I/usr/local/opt/homebrew/include -I/usr/local/opt/homebrew/opt/llvm/include"
CC=/usr/local/opt/llvm/bin/clang++ pip install .

from longitudinal_tomography.cpp_routines import libtomo
libtomo.set_num_threads([num_threads])