Prepare the environment

First follow these instructions to get a copy of the package as a local git repository.

Now that you have the repository, come inside and make your self comfortable. Run

cd seaduck

Tip

If you are running with sciserver’s Oceanography image or your own environment that already have the basic packages installed, you pretty much just need to run the following to get all the dependencies: conda env update --file ci/environment-ci.yml

If you want to create a new conda environment, run

conda create --name bubblebath
conda activate bubblebath

Tip

If you already have mamba installed, you can replace all conda in the commands with mamba.

I recommend installing the basic dependencies and the extra dependencies for tests at the same time. First, we create a file that combines the two yml file by running

pip install conda-merge
conda-merge environment.yml ci/environment-ci.yml > PleaseIgnore_env.yml

Now, let’s install them

conda env update --file PleaseIgnore_env.yml

Working with environment could be a headache sometimes. If some of the packages is unable to install on your machine, don’t sweat over it. Skip them for now, it is totally possible that some packages is not necessary for your purposes. You might be asking: “Hey! Is there a step that is absolutely not optional?” Yes, you need to install our package if you want to work on it.

pip install -e .

Install Jupyter kernel

First activate the environment you want to run notebooks on

conda activate bubblebath

Install ipykernel and activate it.

conda install -c anaconda ipykernel
python -m ipykernel install --user --name=bubblebath

If you are using a web page, you may need to refresh the web page.