Installation troubleshooting

The requirements for the bamboost library are: h5py, mpi4py, numpy, pandas.

MPI

The mpi4py package requires a working MPI installation on the system. If the installation fails, it is likely that the MPI library is not installed.

HDF5

The h5py package requires the HDF5 library to be installed on the system. If the installation fails, it is likely that the HDF5 library is not installed.

Ubuntu/Debian

sudo apt install libhdf5-openmpi-dev

Fedora

sudo dnf install hdf5-openmpi-devel

Arch

sudo pacman -S hdf5-openmpi

Installation in editable mode

Bamboost can be installed in editable mode with

git clone [email protected]:cmbm-ethz/bamboost.git
cd bamboost
pip install -e .

Sometimes, bamboost hangs on import, i.e., from bamboost import managerresults in (unknown location). In this case you can try

pip install -e . --config-settings editable_mode=compat

which should fix the error.

Python version management

pyenv is a useful tool to manage development versions of python.

pyenv install --list # lists available versions
pyenv install 3.8-dev # installs python 3.8-dev
pyenv install 3.12.1 # installs python 3.12.1
pyenv global 3.12.1 # sets the global version
pyenv local 3.8-dev # sets the local version