v0.3.0: Nutrient Simulation Module (NSM)

The ClearWater-modules package is a collection of water quality and vegetation process simulation modules written in modern Python and designed to flexibily couple with a variety of water transport models, such as RAS-2D, GSSHA, CE-Qual-W2, AdH, and others. These modules have been developed by the U.S. Army Engineer Research and Development Center (ERDC), Environmental Laboratory (EL).

This release adds the newly refactored and fully tested Nutrient Simulation Module (NSM) , which was originally developed in Fortran 95 by Zhong and Johnson (2016a, 2016b, 2016c) and released as version 1.0 in 2021.

What's Changed

• Implementation of use_sed_temp options by @xaviernogueira in #59
• Adding examples/dev_sandbox/prof.py by @xaviernogueira in #60
• Phosphorus, N2, and Pathogens and a very incomplete SedFlux by @kewalak in #61
• KW_Variables by @kewalak in #67
• Moving global variables and removing repeats by @kewalak in #73
• Pre-Initialize model xarray with timesteps by @sjordan29 in #77
• Algae Module Tests by @kewalak in #78
• Balgae Testing (and one Nitrogen Test) by @kewalak in #85
• Nitrogen Test by @kewalak in #86
• Ijm nsm v2 by @imscw95 in #87
• Phosphorus, N2, POM, and PX by @kewalak in #88
• Add dt to TSM by @sjordan29 in #89
• Create cprofile_tsm.py by @aufdenkampe in #91

Full Changelog: v0.2.0...v0.3.0

v0.2.0: OOP refactor; TSM fully functional

TSM module is fully functional with all model calculations verified as part of our pytest suite. Other improvements as well, and progress on NSM.

What's Changed

• Reset IM_TSM branch to IM_TSM_TEST to update reorganized module structure. by @imscw95 in #10
• Converting to PyTest (work in progress) by @xaviernogueira in #13
• TSM Refactor stage 1: Numba equations, constants, and pyproject by @xaviernogueira in #15
• Core model architecture refactor / modernization 🎉 by @xaviernogueira in #18
• KW_NSM by @kewalak in #26
• Move KW_NSM Branch Tests to tests_deprecated by @kewalak in #27
• Algae Variables by @kewalak in #28
• Ijm carbon cbod DOX updates by @imscw95 in #30
• Repo/package rename -> "clearwater_modules" by @xaviernogueira in #33
• Improved demo notebook to show a walk-thru on how to write a Model/Variables by @xaviernogueira in #34
• Automating tests! by @xaviernogueira in #35
• 31 figure out ifelse logic for process functions by @xaviernogueira in #36
• Update running_process_funcs.ipynb by @xaviernogueira in #38
• 37 add codecov tracking to our automated test suite by @xaviernogueira in #40
• Update README.md by @xaviernogueira in #42
• Ijm shared folder edits by @imscw95 in #32
• Ijm carbon cbod dox updates by @imscw95 in #46
• Ijm alk pom by @imscw95 in #47
• TSM Module by @xaviernogueira in #44
• 49 create convert static to state function by @xaviernogueira in #51
• Significant (~20-35% improvement) in increment_timestep() speed! by @xaviernogueira in #53
• Bug fix for EnergyBudget by @xaviernogueira in #56
• TSM tests are all passing! by @xaviernogueira in #58

New Contributors

• @imscw95 made their first contribution in #10
• @xaviernogueira made their first contribution in #13
• @kewalak made their first contribution in #26

Full Changelog: v0.1.0...v0.2.0

v0.1.0: Initial Release of ClearWater Modules in Python

The ClearWater-modules-python package is a collection of water quality and vegetation process simulation modules developed by the U.S. Army Engineer Research and Development Center (ERDC), Environmental Laboratory (EL).

This Python library is a port and modernization of the algorithms and structures originally written in Fortran 95, described by Zhong and Johnson (2016a, 2016b, 2016c) and released as version 1.0 in 2021.

This release captures the first round of development porting the following modules from Fortran to Python, as of December 22, 2022.

• TSM: Temperature Simulation Module (formerly TEMP)
• NSM: Nutrient Simulation Module 1 (NSM-I)
• GSM: General Constituent Simulation Module