UQSindy

Working repo for the PNNL MARS project "Probabilistic Model Discovery with Uncertainty Quantification"

Creating the environment from .yml file

With the .yml file it suffices to say

$CONDA env create -f environment.yml

where $CONDA is the conda (Anaconda/Miniconda) binary. If the Anaconda binaries were added to $PATH, then this is simply conda.

Activating and deactivating the environment

If it hasn't been done before, it is necessary to set up the shell to activate and deactivate environments. For that, do

$CONDA init
$CONDA config --set auto_activate_base false

and restart the shell. The last line will prevent the base environment from being loaded when the shell is launched (so that you have access from the shell to whatever Python you had first on your path, e.g., macOS's Python).

After restarting the shell, which conda should definitely point to the conda binary, and the remaining instructions assume that. If that's not the case, let David know!

Once the shell is set up, activating is done by

conda activate mars

which will add a (mars) prefix to the prompt. After this, which python and which jupyter should point to the mars environment's Python and Jupyter, respectively. You can then launch Jupyter the usual way: jupyter lab.

To deactivate the environment, do

conda deactivate

After this, which python should point to the whatever other Python you had on your path with first priority.

Environment for sunode

First check out sunode and step onto the downloaded folder, e.g.:

cd ~/src
git clone https://github.com/aseyboldt/sunode.git
cd sunode

With conda activated, and while stepping onto the sunode source folder, create a new environment mars-sunode:

conda create -n mars-sunode -q --yes -c conda-forge python=3.7 conda-build conda-verify coverage pytest hypothesis statsmodels
conda activate mars-sunode
conda-build -c conda-forge ./conda
conda install --yes -c $CONDA_PREFIX/conda-bld/ -c conda-forge sunode
conda install mkl-service
pip install pymc3 jupyterlab

After that you can deactivate and activate the mars-sunode environment at your convenience.