josuemtzmo / tracpy

Fortran core of Tracmass + Python wrapping around the outside.

TracPy

Fortran core of TRACMASS + Python wrapping around the outside.

Set up for TracPy

I recommend setting up a good python environment for this work, as follows:

1. Install miniconda:

• download file from Continuum
• bash [download file]

1. Set conda-forge to be highest-priority channel (this helps the geography libraries like cartopy that connect to the geos library be all consistent)

• conda config --add channels conda-forge --force

1. Create environment called "tracpy" (some of the listed packages are required and some are just suggested because they are useful)

• conda create --name tracpy python=3.6 cartopy matplotlib ipython netCDF4 fiona shapely pandas xarray cmocean jupyter scipy numpy seaborn --yes

1. Need to also have octant:

• git clone https://github.com/hetland/octant.git
• cd octant
• pip install -e .

1. Make sure you installed tracpy:

• pip install -e .

1. To use environment:

• source activate tracpy

1. To stop using environment (in a given terminal window):

• source deactivate

1. To install more packages later:

• conda install [package name]

1. Run the manual in /docs with jupyter notebook

If you want to install locally, you can generally use the --user flag (e.g. pip install --user .).

To get the code

1. Make your new TracPy directory and change directories into it.
2. Clone the TracPy repository from GitHub. In the command prompt, type: git clone https://github.com/kthyng/tracpy.git
3. Install the package globally: pip install -e . This makes the package an editable install so that it can be updated with future additions to TracPy. Note that a required package is octant. To instead install the package locally: pip install --user .

To update the code later

1. Move into your TracPy directory.
2. Update your GitHub repository. git pull
3. Edit your install of TracPy. pip install -e . or pip install --force-reinstall -e . or, for local installation: pip install --ignore-installed --user .

To test the code

1. After making changes to the code, you can do some basic functionality testing with py.test or nosetests in the tests subdirectory.

To learn more about the module TracPy

Learn more by running a small test case. Internet required.

1. Open an iPython notebook server in the TracPy docs directory. ipython notebook
2. A webpage will open in your browser showing the available notebooks in the current directory. Open the notebook called manual.
3. The cells of the notebook can be run in order by pushing "shift" and "enter" together or the whole notebook can be run by selecting Cell > Run all. The notebook demonstrates how to initialize and run a numerical drifter experiment using TracPy.
4. Alternatively, a static PDF version of the manual can be viewed at http://nbviewer.ipython.org/urls/raw.github.com/kthyng/tracpy/master/docs/manual.ipynb.

To run your own projects

For projects, it is suggested to start a separate directory with its own initialization and run file for the simulation(s). Then TracPy can be imported as a module and the run script can be run from the project. An example set of projects can be found at https://github.com/kthyng/gisr.git.

To learn more about TRACMASS

• Döös, K., Kjellsson, J., & Jönsson, B. (2013). TRACMASS—A Lagrangian Trajectory Model. In Preventive Methods for Coastal Protection (pp. 225-249). Springer International Publishing.
• Döös, K., Rupolo, V., & Brodeau, L. (2011). Dispersion of surface drifters and model-simulated trajectories. Ocean Modelling, 39(3), 301-310.
• Döös, K., & Engqvist, A. (2007). Assessment of water exchange between a discharge region and the open sea–A comparison of different methodological concepts. Estuarine, Coastal and Shelf Science, 74(4), 709-721.
• TRACMASS on GitHub: https://github.com/TRACMASS