Installation

Before you can use the paste3 package, ensure that your system meets the following prerequisites:

Python 3.12 or later
Pip package manager

Clone the repository and enter it:

git clone https://github.com/raphael-group/paste3.git
cd paste3

Creating a paste3 environment

All of paste3's dependencies are on PyPI. We have developed and tested paste3 on Python 3.12, 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 3.12 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 the paste3 package in editable mode, along with its dev and docs extras:
```
pip install -e .[dev,docs]
```

Using a different Python version than the system default

If your Python version is not 3.12 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 3.12 and activate it.
```
uv venv --python 3.12
source .venv/bin/activate
```
In the activated environment, install the package in editable mode, along with its dev and docs extras:
```
uv pip install -e .[dev,docs]
```

paste3 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 pinned to versions that have worked for us in the past.

Note

paste3 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 paste3 with Python version 3.12.
```
conda create --name paste3 python=3.12 pip
```
Activate the environment.
```
conda activate paste3
```
The command prompt will change to indicate the new conda environment by prepending (paste3).
In the activated environment, install the dependencies provided in environment.yml:
```
conda env update --file environment.yml
```
In the activated environment, install the package in editable mode without dependencies.
```
pip install -e . --no-deps
```