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Instructions for fresh environment setup

  • Clone our repository: git clone [email protected]:niwa/kelp-detection.git
  • Create an .env file (contains LINZ LDS keys) and put into the root directory of the 'kelp-detection' repository
  • Create the conda environment from environment.yml in the repository root - conda env create -f environment.yml
  • Launch jupyter lab from the repositoriy root directory in the kelp conda environment
  • Open the notebooks/compare_test_sites.ipynb and run

Kelp Dashboard Demo

A demo dashboard for displaying Kelp extents across dates for MPI.

Usage

Either use launch_app.sh directly or use the code within to lauch using the commandline.

./launch_app.sh

Just follow the printed network URL.

Setup - Conda

Create environment

set +u
module load Miniforge3
source $(conda info --base)/etc/profile.d/conda.sh
conda config --add pkgs_dirs /nesi/nobackup/niwa03440/$USER/conda_pkgs
cd {PATH_TO_REPOSITORY}
conda env create -f streamlit.yml -p /nesi/project/niwa03440/conda/envs/streamlit
conda activate /nesi/project/niwa03440/conda/envs/streamlit
set -u

Activate environment

set +u
module load Miniforge3
source $(conda info --base)/etc/profile.d/conda.sh
conda activate /nesi/project/niwa03440/conda/envs/streamlit
set -u