This repository contains a suite of interactive Jupyter notebooks and Python scripts that will allow the user to reproduce the results and figures presented in:
B. Moore-Maley and S. E. Allen: Wind-driven upwelling and surface nutrient delivery in a semi-enclosed coastal sea, Ocean Sci., 2022.
A companion dataset has also been archived at the Canadian Federated Research Data Repository (FRDR):
Moore-Maley, B., S. E. Allen. SalishSeaCast hourly surface along-axis wind velocity, temperature and nitrate summary 2015-2019, Federated Research Data Repository, https://doi.org/10.20383/102.0546, 2022.
This dataset needs to be obtained before running the notebooks in this code repository. Alternatively, the file can be generated using the provided scripts, however this process requires about a day to complete.
Conda users can build the Python virtual environment necessary to run these scripts with the included environment.yaml file. From the Conda base environment, clone the repository to a working directory and build the environment:
$ git clone https://github.com/SalishSeaCast/SoG_upwelling_EOF_paper.git
$ cd SoG_upwelling_EOF_paper
$ conda update -n base conda
$ conda env create -f environment.yaml
$ source activate SoG_upwelling_EOF_paper
Next, add the scripts directory to your PYTHONPATH environment variable to access the tools module:
$ export PYTHONPATH=$PYTHONPATH:/path/to/SoG_upwelling_EOF_paper/scripts
If you choose to generate the aggregated results file yourself, the scripts/aggregate_results.py module is included for this task:
$ cd scripts
$ python3 aggregate_results.py /path/to/files/
Either way, once you have obtained the aggregated results file, the PCA results can then be generated:
$ cd scripts
$ python3 PCA.py /path/to/files/
Finally, any of the notebooks can by run by starting a Jupyter session and navigating to the notebooks directory:
$ jupyter lab
The SalishSeaCast analysis and documentation are copyright 2013-2022 by the Salish Sea MEOPAR Project Contributors and The University of British Columbia.
They are licensed under the Apache License, Version 2.0. http://www.apache.org/licenses/LICENSE-2.0 Please see the LICENSE file for details of the license.