Setting up

Before you can use the clm package, ensure that your system meets the following prerequisites:

Python 3.10 or later
Pip package manager

Clone the repository and enter it:

git clone https://github.com/skinniderlab/CLM.git
cd CLM

Creating a clm environment

All of clm’s dependencies are on PyPI. We have developed and tested clm on Python 3.10, but it should work on later Python versions as well. You can create a new virtual environment using venv, and install dependencies using pip.

Verify that Python 3.10 or newer is installed on your system.
```
python --version
```

Create a new environment and activate it.

python -m venv .venv
source .venv/bin/activate

In the activated environment, install all of clm’s dependencies.
```
pip install -r requirements.txt
```
In the activated environment, install the CLM package in editable mode.
```
pip install -e . --no-deps
```

Using a different Python version than the system default

If your Python version is not 3.10 or later, or if you’re getting errors when using a non-tested Python version, we recommend using the uv tool to create a virtual environment with the correct Python version. uv is quick to install and easy to use, both locally as well as on research clusters.

Once uv is installed:

Create a new environment with Python 3.10 and activate it.
```
uv venv --python 3.10
source .venv/bin/activate
```
In the activated environment, install all of clm’s dependencies.
```
uv pip install -r requirements.txt
```
In the activated environment, install the CLM package in editable mode.
```
uv pip install -e . --no-deps
```

clm environment using conda

If you prefer using conda, you can use the provided environment.yml file to create a new conda environment with all the necessary dependencies.

Note

clm can get all its dependencies from pypi using pip and does not need conda for environment management. Nevertheless, this might be the easiest option for most users who already have access to the conda executable locally or through a research cluster. The provided environment.yml file has the defaults channel disabled, and can be used to create a new conda environment with all the necessary dependencies. It can therefore be used without getting a business or enterprise license from Anaconda. (See Anaconda FAQs)

Create a new conda environment named clm with Python version 3.10.
```
conda create --name clm python=3.10 pip
```
Activate the environment.
```
conda activate clm
```
The command prompt will change to indicate the new conda environment by prepending (clm).
In the activated environment, install the dependencies provided in environment.yml:
```
conda env update --file environment.yml
```
In the activated environment, install the CLM package in editable mode.
```
pip install -e . --no-deps
```

Installation on specific clusters

The following instructions apply to installing and using clm on specific clusters at Princeton University where we have tested out the package in the past.

Della

Make sure that conda is in your path by loading the appropriate module:

module load anaconda3/2024.10

You can also load a different anaconda version. To see all available modules, run module avail anaconda3.

No further actions are required to install conda or python. You can go ahead and create a new conda environment as instructed above.

Argo

The default conda is recommended on argo systems. You do not need to load any modules or do anything special to use the conda command on argo. Click here for detailed information regarding conda on Argo.