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Changelog

  • 0.14.0.x simplified the setup of the gas exchange connections, documentation improvements
  • 0.13.0.8 added new testing framework, and 16 unit tests. Updated the documentation
  • 0.13.0.7 the isotope fractionation factor has been renamed from alpha to epsilon
  • 0.13.0.5 tinmestep keyword is now deprecated and should be replaced with max_timestep. min_time_step is now a configurable option.
  • 0.13.0.x The equations file is now a temporary file with a random name. This allows for the parallel execution of model code.
  • 0.13.0.x plot() will now return the figure and axes handles, and accepts the no_show option. This allows for the addition of manual plot elements in post-processing
  • May 10th v 0.13.0.0 fixes an error in the solubility calculation for oxygen and carbon dioxide. This will change the steady state results for pCO2 in existing models by about 4 ppm. This version renamed many classes. Existing models may need some editing.
    • Element -> ElementProperties
    • Species -> SpeciesProperties
    • Reservoir -> Species
    • ReservoirGroup -> Reservoir
    • ConnectionGroup -> ConnectionProperties
    • Connection -> Connect
    • SourceGroup -> SourceProperties
    • SinkGroup -> SinkProperties

    Since the respective ConnectionProperty, SourceProperty and SinkProperty objects which correlate with the former ConnectionGroup, SourceGroup SinkGroup classes. As such, existing code must be changed from

    Sink(
name="burial",
species=M.PO4,
register=M,  #
)

    to

    SinkProperties(
name="burial",
species=[M.PO4],
)

    and

    Connection(  #
source=M.S_b,  # source of flux
sink=M.D_b,  # target of flux
ctype="scale_with_concentration",
scale=M.S_b.volume / tau,
id="primary_production",
)

to

ConnectionProperties(  #
source=M.S_b,  # source of flux
sink=M.D_b,  # target of flux
ctype="scale_with_concentration",
scale=M.S_b.volume / tau,
id="primary_production",
species=[M.PO4],  # apply this only to PO4
)
  • May 1st, v 0.12.0.28 ESBMTK can now be installed via conda. Various documentation updates
  • Dec. v 0.12.0.x This is a breaking change that requires the following updates to the model definition.
    • Models that use isotope calculations need to ensure that sources and sink also specify the isotope keyword.
    • Weathering and Gas-exchange have now become connection properties, see the examples in the online documentation
    • Models that used carbonate_system_1_pp() no longer need to call this specifically, as this function is now called automatically
  • Oct. 12th, 2023 v 0.11.0.2 This is a breaking change. Added support to specify box area and volume explicitly, rather than as a function of hypsography. This is likely to affect existing geoemtry definitions since the (area/total area) parameter has changed meaning The area fraction is now calcualted automatically, and unless you split the model in specific basins the last parameter in the geometry list should always be 1 (i.e., [0, -350, 1]).

    Equilibrium constants are now calculated by pyCO2SYS. This facilitates a wide selection of parametrizations via the opt_k_carbonic and opt_pH_scale keywords in the Model definition. Options and defaults are the same as for pyCO2SYS.

  • Oct. 30th, 2023 v 0.10.0.11 This is a breaking change. Remineralization and photosynthesis must be implemented via functions, rather than transport connections. CS1 and CS2 are retired, and replaced by photosynthesis, organic-matter remineralization and carbonate-dissolution functions. I’ve started writing a user guide, see https://esbmtk.readthedocs.io/en/latest/ESBMTK-Tutorial.html

So far, only the very basics are covered. More to come!

  • July 28th, 2023, v 0.9.0.1 The ODEPACk backend is now fully functional, and the basic API is more or less stable.
  • Nov. 11th2022, v 0.9.0.0 Moved to odepack based backend. Removed now defunct code. The odepack backend does not yet support isotope calculations.
  • 0.8.0.0
    • Cleanup of naming scheme which is now strictly hierarchical.
    • Bulk connection dictionaries now have to be specified as source_to_sink instead of source2sink.
    • The connection naming scheme has been revamped. Please see esbmtk.connect.__set_name__() documentation for details.
    • Model concentration units must now match ‘mole/liter’ or ‘mol/kg’. Concentrations can still be specified as mmol/l or mmol/kg, but model output will be in mole/liter or kg. At present, the model does not provide for the automatic conversion of mol/l to mol/kg. Thus you must specify units in a consistent way.
    • The SeawaterConstants class now always returns values as mol/kg solution. Caveat Emptor.
    • The SeawaterConstants class no longer accepts the ‘model’ keyword
    • All of his will break existing models.
    • Models assume by default that they deal with ideal water, i.e., where the density equals one. To work with seawater, you must set ideal_water=False. In that case, you should also set the concentration_unit keyword to 'mol/kg' (solution).
    • Several classes now require the “register” keyword. You may need to fix your code accordingly
  • The flux and connection summary methods can be filtered by more than one keyword. Provide a filter string in the following format "keyword_1 keyword_2 and it will only return results that match both keywords.
  • Removed the dependency on the nptyping and number libraries
  • 0.7.3.9 Moved to setuptools build system. Lost of code fixes wrt isotope calculations, minor fixes in the carbonate module.
  • March 2nd0.7.3.4 Flux_summary now supports an exclude keyword. Hot fixed an error in the gas exchange code, which affected the total mass of atmosphere calculations. For the time being, the mass of the atmosphere is treated as constant.
  • 0.7.3.0 Flux data is no longer kept by default. This results in huge memory savings. esbmtk now requires python 3.9 or higher, and also depends on os and psutil. the scale with flux process now uses the ref_flux keyword instead of ref_reservoirs. Models must adapt their scripts accordingly. esbmtk objects no longer provide delta values by default. Rather they need to be calculated in the post-processing step via M.get_delta_values(). The f_0 keyword in the weathering connection is now called rate. Using the old keyword will result in a unit error.
  • January 8th0.7.2.2 Fixed several isotope calculation regressions. Added 31 Unit tests.