Installation

This documentation covers the installation process of pangeo-fish in a virtual Python environment.

In the following, we expect Conda to be installed on your Linux-based system.

For Windows users, we recommend WSL (2.0).

For more information, please refer to this page: pangeo on Windows.

For first use

If you are only interested in using pangeo-fish locally (i.e, without accessing remote data nor HPC resources), then all is needed is to create you create a virtual environment and install the package as well as its depedencies.

To do so, clone the pangeo-fish’s repository and navigate to it:

git clone https://github.com/pangeo-fish/pangeo-fish.git
cd pangeo-fish

Then, create a conda or micromamba environment with the following command: Still, we recommend using micromamba since it’s faster. Use either of the following commands:

# Using conda
conda env create -n pangeo-fish -f docs/environment.yaml

# Or using micromamba
micromamba create -n pangeo-fish -f docs/environment.yaml

And then just activate the environment

conda/micromamba activate pangeo-fish

This will create your environment with all the required libraries to make pangeo-fish work.

Finally, install the package itself from either its repository:

pip install -e .

… or from pip:

pip install pangeo-fish

For HPC use

This section details the additional steps to setup pangeo-fish for HPC use.

As such, we assume the reader has access to HPC resources such as Datarmor.

Please ensure to have completed the installation introduced above first!

Install the dask-hpcconfig package and set the environnement as a Jupyter kernel:

pip install dask-hpcconfig
ipython kernel install --name "pangeo-fish" --user

Besides, you can refer to this documentation on how to use pangeo on HPC.

All of those steps should create a Python environment able to run the different Jupyter notebooks available.

Help and Troubleshooting

In case of errors or difficulties upon installing pangeo-fish, you can report the issue here.