mirror of
https://github.com/JHUAPL/kaiju.git
synced 2026-01-08 22:58:05 -05:00
99 lines
3.1 KiB
ReStructuredText
99 lines
3.1 KiB
ReStructuredText
Building a python environment for ``kaiju`` on CentOS-Stream 9
|
|
==================================================================
|
|
|
|
.. Introduction
|
|
.. ------------
|
|
|
|
.. This file describes how to set up a python 3.8-based ``conda`` environment on an Intel-based machine running CentOS-Stream 9 which can be used to run the ``kaiju`` code.
|
|
|
|
.. These steps assume that ``pip`` (only) is used for installing additional packages, and packages are only taken from PyPI (and the default ``conda`` repository, if needed) - no other repositories are used.
|
|
|
|
.. *A NOTE OF EXPLANATION:* These instructions install ``miniconda3`` into a CentOS-Stream 9-specific subdirectory of the home directory, to maintain compatibility with instructions for other systems. Feel free to install ``miniconda3`` wherever is convenient.
|
|
|
|
.. Building the python environment
|
|
.. -------------------------------
|
|
|
|
.. .. code-block:: shell
|
|
|
|
.. # Download the installer.
|
|
.. cd $HOME
|
|
.. wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
|
|
|
|
.. # Run the installer.
|
|
.. # Install into $HOME/centos-stream-9/miniconda3, use all defaults.
|
|
.. bash ./Miniconda3-latest-MacOSX-x86_64.sh
|
|
|
|
.. # NOTE: This installation *should* run "conda init", which *should*
|
|
.. # add the conda setup code to ~/.bashrc or ~/.bash_profile.
|
|
|
|
.. # NOTE: This installation creates ~/.conda/environments.txt, but
|
|
.. # nothing else. This file just contains the path to the miniconda3
|
|
.. # installation directory.
|
|
|
|
.. # Turn off auto-activation of base environment.
|
|
.. # NOTE: This command creates ~/.condarc.
|
|
.. conda config --set auto_activate_base false
|
|
|
|
.. # Update everything to latest version.
|
|
.. conda update --all
|
|
|
|
.. # NOTE: This creates the directory ~/.cache/conda.
|
|
|
|
.. # Now create the environment for kaiju, specifying only the python version.
|
|
.. conda create -n kaiju-3.8 python=3.8
|
|
|
|
.. # NOTE: This adds the path to the new environment in
|
|
.. # ~/.conda/environments.txt.
|
|
|
|
.. # Activate the new environment.
|
|
.. conda activate kaiju-3.8
|
|
|
|
.. # Update everything to latest version.
|
|
.. conda update --all
|
|
|
|
.. # IMPORTANT: Use a pip cache specific to this machine.
|
|
.. export PIP_CACHE_DIR=$HOME/centos-stream-9/pip_cache
|
|
|
|
.. # Make sure CDF, HDF5, and GEOS have been built and installed.
|
|
|
|
.. # Install packages required by kaipy.
|
|
.. pip install -r requirements.txt
|
|
|
|
.. # Save the environment description.
|
|
.. conda list >& kaiju-3.8-centos-stream-9-YYYYMMDD.env
|
|
|
|
|
|
|
|
.. Where ``requirements.txt`` is a text file containing:
|
|
|
|
.. .. code-block::
|
|
|
|
.. ai.cdas
|
|
.. alive_progress
|
|
.. cartopy
|
|
.. cdasws
|
|
.. cdflib
|
|
.. configparser
|
|
.. dataclasses_json
|
|
.. h5py
|
|
.. jinja2
|
|
.. matplotlib
|
|
.. netCDF4
|
|
.. progressbar
|
|
.. pyhdf
|
|
.. pytest
|
|
.. scipy
|
|
.. spacepy
|
|
.. sunpy
|
|
.. xarray
|
|
|
|
|
|
.. Using the python environment
|
|
.. ----------------------------
|
|
|
|
.. Once your python environment is created, you must activate it for use with the ``kaiju`` software:
|
|
|
|
.. .. code-block:: shell
|
|
|
|
.. conda activate kaiju-3.8 # or whatever name you used for the python environment
|