Python environment with useful tools

Python environment with useful tools#

Some Python tools are required for using GeoClaw, such as numpy and matplotlib. There are many other Python tools that are useful for dealing with geophysical data and/or more advanced plotting. The file requirements_geo.txt in this directory contains a list of things you might want to pip install. (Feel free to edit it to add or delete things based on your needs.)

You are strongly encouraged to create a new Python environment before pip installing a lot of software, and some operating systems now require this. The instructions below might be useful.

Building a Python virtual environment#

This procedure should work on a laptop (linux or MacOS) using the standard Python module venv.

mkdir ~/venv   # directory for virtual environments
python -m venv ~/venv/geo
source ~/venv/geo/bin/activate
python -m pip install --upgrade -r /path/to/requirements_geo.txt

Using the virtual environment#

When open a new shell or terminal window, the command

source ~/venv/geo/bin/activate

should activate the environment. You might want to put this in your .bashrc file, for example. Then if you start python, ipython, or a Jupyter lab in this environment, the packates listed in requirements_geo.txt (and their dependencies) should be available to import.

Building a conda environment on DesignSafe#

See also

https://designsafe-ci.org/user-guide/tools/jupyterhub/#installing

The following should work, but doesn’t seem to at the moment…

First launch JupyterHub from https://designsafe-ci.org/use-designsafe/tools-applications/analysis/jupyter/

Then start a terminal, and in this terminal:

conda config --add envs_dirs ~/MyData/Python_Envs  # directory for env
conda create --name geo  -y -c conda-forge pip python
conda activate geo 
python -m pip install --upgrade -r /path/to/requirements_geo.txt

pip install --src=$HOME/MyData/clawpack_src --user --no-build-isolation -e \
    git+https://github.com/clawpack/clawpack.git@v5.13.1#egg=clawpack
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