feat: Update version number to 0.14.0 with simplified

gas exchange connections setup and documentation improvements

CHANGELOG.org

@@ -1,4 +1,5 @@
 * 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.

CHANGELOG.rst

@@ -5,6 +5,8 @@
 1 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``

README.md

@@ -10,6 +10,13 @@
 <img alt="Documentation Status" src="https://readthedocs.org/projects/esbmtk/badge/?version=latest" />
 </a>
 
+<a href="https://img.shields.io/badge/Python-3.11-blue.svg">
+<img alt="Python 3.11 ready" src="https://www.python.org" />
+</a>
+
+<a href="https://doi.org/10.5281/zenodo.11959366">
+<img alt=Zenodo DOI src="https://zenodo.org/badge/DOI/10.5281/zenodo.11959366.svg" alt="DOI"></a>
+
 
 # ESBMTK - The  Earth Sciences Box Modeling Toolkit
 

docs/manual/manual-1.rst

@@ -62,9 +62,9 @@ which is easily encoded as a Python function
         a function of time. After Glover 2011, Modeling
         Methods for Marine Science.
 
-        :param C: tp.List of initial concentrations mol/m*3
+        :param C_0: tp.List of initial concentrations mol/m*3
         :param time: array of time points
-        :params V: lits of surface and deep ocean volume [m^3]
+        :params V: list of surface and deep ocean volume [m^3]
         :param F_w: River (weathering) flux of PO4 mol/s
         :param thx: thermohaline circulation in m*3/s
         :returns dCdt: tp.List of concentration changes mol/s
@@ -167,7 +167,6 @@ In the first step, one needs to define a model object that describes fundamental
         ConnectionProperties,  # the connection class
         SourceProperties,  # the source class
         SinkProperties,  # sink class
-        Q_,  # Quantity operator
     )
 
 Next we use the :py:class:`esbmtk.esbmtk.Model()`  class to create a model instance that defines basic model properties. Note that units are automatically translated into model units. While convenient, there are some important caveats: 
@@ -208,7 +207,7 @@ Most ESBMTK classes accept quantities, strings that represent quantities as well
 
     # boundary conditions
     F_w =  M.set_flux("45 Gmol", "year", M.P) # P @280 ppm (Filipelli 2002)
-    tau = Q_("100 year")  # PO4 residence time in surface boxq
+    tau = Q_("100 year")  # PO4 residence time in surface box
     F_b = 0.01  # About 1% of the exported P is buried in the deep ocean
     thc = "20*Sv"  # Thermohaline circulation in Sverdrup
 

docs/manual/manual-3.rst

@@ -75,7 +75,6 @@ Apart from density, this class will provide access to a host of instance paramet
         concentration_unit="mol/kg",
         opt_k_carbonic=13,  # Use Millero 2006
         opt_pH_scale=1,  # 1:total, 3:free scale
-        opt_buffers_mode=2, # carbonate, borate water alkalinity only
     )
 
 Caveats
@@ -217,40 +216,17 @@ ESBMTK implements gas exchange across the Air-Sea interface as a :py:class:`esbm
         name="CO2_At",
         species=M.CO2,
         species_ppm="280 ppm",
-        register=M,
     )
-
     Species2Species(  # Example for CO2
         source=M.CO2_At,  # GasReservoir
         sink=M.L_b.DIC,  # Reservoir
         species=M.CO2,
-        ref_species=M.H_b.CO2aq,
-        solubility=M.H_b.swc.SA_co2,
-        area=M.L_b.area,  # surface area
-        id="L_b_GEX",  # connection id
         piston_velocity="4.8 m/d",
-        water_vapor_pressure=M.H_b.swc.p_H2O,
-        register=M,
         ctype="gasexchange",
+        id="L_b_GEX",  # connection id
     )
 
-Defining gas transfer for O2  uses the same approach, but note the use of the ``solubility`` and ``ref_species`` keywords. At present, ESBMTK only carries the solubility constants for CO\ :sub:`2`\ and O\ :sub:`2`\.
-
-.. code:: ipython
-
-    Species2Species(  # Example for O2
-        source=M.O2_At,  # GasReservoir
-        sink=M.L_b.O2,  # Reservoir
-        species=M.O2,
-        ref_species=M.L_b.O2,
-        solubility=M._b.swc.SA_o2,
-        area=M._b.area,
-        piston_velocity="4.8 m/d",
-        water_vapor_pressure=M.L_b.swc.p_H2O,
-        id=f"O2_gas_exchange_L_b",
-        register=M,
-        ctype="gasexchange",
-    )
+Defining gas transfer for O2  uses the same approach. 
 
 pCO\ :sub:`2`\ Dependent Weathering
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -271,11 +247,10 @@ where :math:`A` denotes the area, :math:`f_0` the weathering flux at :math:`p_{0
         source=M.Fw.DIC,  # source of flux
         sink=M.L_b.DIC,
         reservoir_ref=M.CO2_At,  # pCO2
-        ctype="weathering",
-        id="wca",
         scale=1,  # optional, defaults to 1
         ex=0.2,  # exponent c
         pco2_0="280 ppm",  # reference pCO2
         rate="12 Tmol/a",  # rate at pco2_0
-        register=M,
+        ctype="weathering",
+        id="wca",
     )

tests/po4_1_test.py

@@ -5,7 +5,6 @@
     ConnectionProperties,  # the connection class
     SourceProperties,  # the source class
     SinkProperties,  # sink class
-    Q_,  # Quantity operator
 )
 # define the basic model parameters
 M = Model(
@@ -19,7 +18,7 @@
 tau * 12
 # boundary conditions
 F_w =  M.set_flux("45 Gmol", "year", M.P) # P @280 ppm (Filipelli 2002)
-tau = Q_("100 year")  # PO4 residence time in surface boxq
+tau = Q_("100 year")  # PO4 residence time in surface box
 F_b = 0.01  # About 1% of the exported P is buried in the deep ocean
 thc = "20*Sv"  # Thermohaline circulation in Sverdrup
 # Source definitions

tests/po4_2_test.py

@@ -5,7 +5,6 @@
     ConnectionProperties,  # the connection class
     SourceProperties,  # the source class
     SinkProperties,  # sink class
-    Q_,  # Quantity operator
 )
 # define the basic model parameters
 M = Model(
@@ -19,7 +18,7 @@
 tau * 12
 # boundary conditions
 F_w =  M.set_flux("45 Gmol", "year", M.P) # P @280 ppm (Filipelli 2002)
-tau = Q_("100 year")  # PO4 residence time in surface boxq
+tau = Q_("100 year")  # PO4 residence time in surface box
 F_b = 0.01  # About 1% of the exported P is buried in the deep ocean
 thc = "20*Sv"  # Thermohaline circulation in Sverdrup
 # Source definitions

tests/test_pH.py

@@ -3,9 +3,9 @@
 from esbmtk import Model, Reservoir, get_hplus
 import PyCO2SYS as pyco2
 
+
 def test_manual_ph_calculation():
-    """ Test convergence of interative pH calculation
-    """
+    """Test convergence of interative pH calculation"""
     M = Model(
         stop="1 yr",
         max_timestep="1 d",
@@ -38,7 +38,7 @@ def test_manual_ph_calculation():
             "S": 35,
         },
     )
-    
+
     hplus0 = M.S_b.swc.hplus
     hplus = hplus0 * 10
     for i in range(10):
@@ -52,11 +52,12 @@ def test_manual_ph_calculation():
             M.S_b.swc.KW,
             M.S_b.swc.KB,
         )
-        
+
     assert abs(hplus0 - hplus) < 1e-12
 
+
 def test_pyco2sys_ph_calculation():
-    """ Compare result of pH computation with the value
+    """Compare result of pH computation with the value
     provided by pyCO2sys
     """
     M = Model(
@@ -97,15 +98,15 @@ def test_pyco2sys_ph_calculation():
         temperature=M.S_b.swc.temperature,
         pressure=M.S_b.swc.pressure * 10,
         par1_type=1,
-        par1=M.S_b.TA.c[0] * 1E6,
+        par1=M.S_b.TA.c[0] * 1e6,
         par2_type=2,
-        par2=M.S_b.DIC.c[0] * 1E6,
+        par2=M.S_b.DIC.c[0] * 1e6,
         opt_k_carbonic=M.opt_k_carbonic,
         opt_pH_scale=M.opt_pH_scale,
         opt_buffers_mode=M.opt_buffers_mode,
     )
     results = pyco2.sys(**params)
-    pH = results['pH']
+    pH = results["pH"]
 
     hplus0 = M.S_b.swc.hplus
     hplus = hplus0 * 10

tests/test_po4_1.py

@@ -2,8 +2,6 @@
 import po4_1_test  # import script
 
 M = po4_1_test.M  # get model handle 
-tol = 1e-12  # tolerance
-
 test_values = [ # result, reference value
     (M.S_b.PO4.c[-1], 0.0000149597179598576),
     (M.D_b.PO4.c[-1], 0.0000219990964241379),

tests/test_po4_2.py

@@ -2,13 +2,10 @@
 import po4_2_test  # import script
 
 M = po4_2_test.M  # get model handle 
-tol = 1e-12  # tolerance
-
 test_values = [ # result, reference value
     (M.S_b.PO4.c[-1], 3.3378336265779095e-05),
     (M.D_b.PO4.c[-1], 4.9100854586867445e-05),
 ]
-
 # run tests
 @pytest.mark.parametrize("test_input, expected", test_values)
 def test_values(test_input, expected):

tests/test_po4_3.py

@@ -2,15 +2,12 @@
 import po4_3_test  # import script
 
 M = po4_3_test.M  # get model handle 
-tol = 1e-12  # tolerance
-
 test_values = [ # result, reference value
     (M.S_b.PO4.c[-1], 1.4999891897165636e-05),
     (M.S_b.DIC.c[-1], 0.0015899885410995674),
     (M.D_b.PO4.c[-1], 2.2058362084399994e-05),
     (M.D_b.DIC.c[-1], 0.002338186380946409),
 ]
-
 # run tests
 @pytest.mark.parametrize("test_input, expected", test_values)
 def test_values(test_input, expected):