Install packages in user environment¶

Basic User Installs¶

The Rubin Science Platform (RSP) comes with the rubin-env conda environment, including the LSST Science Pipelines, pre-installed and activated within the Notebook and Terminal. If it is necessary to extend the rubin-env environment by installing other Python packages, use the pip install command. In the RSP, pip actually invokes conda to do its work, ensuring that dependencies that are already present in rubin-env are used (if compatible). Packages installed with pip will be placed in a subdirectory of the home directory. These packages are only guaranteed to work when the conda environment in which they are installed is activated.

If it’s necessary to install other conda packages but don’t need to use them at the same time as the rubin-env and LSST Science Pipelines packages, install them into a new conda environment. Start by doing source /opt/lsst/software/stack/loadLSST.bash to initialize conda. Use the conda create -n myenv command to create the new environment. Use the conda activate myenv command to activate this environment. Use the mamba install {package} ... command to install one or more packages into the environment. (mamba is a faster version of conda for installing packages.) If the package to be installed is not available from the current channels, then the channel will have to be specified, e.g., mamba install -c {channel} {package}. When done using the environment and want to revert to the rubin-env one, use conda deactivate.

If it’s necessary to directly extend the rubin-env environment with other conda packages, the only way to do so at present is to clone the environment. This is a time- and space-consuming process, so we do not recommend it.

More Complex User Installs¶

Suppose one wishes to install a user package on the RSP that has dependencies on non-python libraries. Typically, these non-python libraries must be installed and built separately, and the LD_LIBRARY_PATH must be updated. Leanne Guy created a simple and effective tutorial notebook for working with user packages, using the install of the bagpipes Bayesian Analysis of Galaxies package as an example. (The bagpipes package depends on PyMultiNest, a python interface to the MultiNest package, which is written in C++.) The tutorial notebook runs through the steps to user install the bagpipes package and build its dependencies on the RSP so that it can be used both from the python command line shell and from inside a notebook.

The basic steps are:

Open a terminal in the Notebook aspect of the RSP.
Install the bagpipes package with pip:
```
pip install --user bagpipes
```
(The --user flag is necessary due to lack of root access.)

Among other packages, the above command installs PyMultiNest, a python interface for MultiNest. The MultiNest package itself is not included. Before we can use the bagpipes package, we must install MultiNest and update the LD_LIBRARY environment variable.
Install and build the dependencies – in this case, the MultiNest package – in the ~/local directory. In a terminal, execute:
```
cd ~/local
git clone https://github.com/JohannesBuchner/MultiNest
cd MultiNest/build
cmake ..
make
```

Update the LD_LIBRARY_PATH` in ``~/.bashrc file (for terminal-based access):

export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/local/MultiNest/lib

Update the LD_LIBRARY_PATH` in ``~/notebooks/.user_setups file (for notebook access):
```
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${HOME}/local/MultiNest/lib
```
After the first time perfoming Steps 4 and/or 5, log out and log back into the RSP.

For more information, please consult tutorial notebook for working with user packages.