Installation¶
tttrlib can either be installed from prebuilt binaries or from the source code. For most users it is recommended to install tttrlib using the prebuilt binaries. Below the installation using prebuilt binaries and the prerequisites to compile tttrlib are briefly outlined.
Prebuilt binaries¶
It is recommended to install tttrlib for Python environments via conda by.
conda install -c tpeulen tttrlib
Alternatively, tttrlib can be installed via pip.
pip install tttrlib
Compilation¶
tttrlib can be compiled and installed using the source code provided in the git repository. tttrlib is compiled in Docker environments. The continuous integration pipeline can be used as a reference to setup a compilation machine
git clone --recursive https://github.com/fluorescence-tools/tttrlib.git
cd tttrlib
python setup.py install
To compile tttrlib a set of prerequisites need to be fulfilled:
1. An installed compiler.
2. The `HDF5 <https://www.hdfgroup.org/>`_ library with C/C++ include files.
3. A recent 64bit `Python <https://www.python.org/>`_ installation with include files.
4. `cmake <https://cmake.org/>`_
5. `SWIG <http://www.swig.org/>`_
To debug and analyze the ouput of tttrlib in more detail it can be useful to build the library in Debug mode that outputs additional information to the standard standard logging stream. tttrlib can be build in debugging mode by.
python setup.py build_ext --debug
Windows¶
On windows tttrlib is best compiled with the Visual Studio 2017 <https://visualstudio.microsoft.com/>. For compilation the Visual Studion Community edition is sufficient. In addition to Visual Studio the libraries and the include files as listed above need to be installed. The prebuilt binaries are compiled on Windows 10 with using 64bit anaconda Python environments ``miniconda <https://docs.conda.io/en/latest/miniconda.html>`` using the conda build recipe that is provided with the
source code in the conda-recipe folder.
macOS¶
For MacOS the prebuilt binaries are compiled on MacOS 10.13 with the Apple clang compiler using a anaconda distribution and the provided conda-recipe.
Linux¶
The Linux prebuilt binaries are compiled on Ubuntu 18.04 in an anaconda distribution and the provided conda-recipe.
Conda¶
A conda recipe is provided in the folder ‘conda-recipe’ to build the tttrlib library with the conda build <https://docs.conda.io/projects/conda-build/en/latest/>_ environment.
conda install conda-build
conda build build-tools/conda-recipe
To build the library download the recipe, install the conda build package and use the provided recipe to build the library.