Merge branch 'master' into dev

oscarbranson · Sep 14, 2023 · 72e2c61 · 72e2c61
2 parents c71623e + 5608f8e
commit 72e2c61
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Showing 3 changed files with 28 additions and 22 deletions.
diff --git a/cbsyst/__init__.py b/cbsyst/__init__.py
@@ -2,4 +2,4 @@
 from cbsyst.helpers import data_out, Bunch, pH_scale_converter
 from kgen import calc_Ks
 
-VERSION = '0.4.8'
+VERSION = '0.4.9'
diff --git a/cbsyst/cbsyst.py b/cbsyst/cbsyst.py
@@ -17,10 +17,10 @@ def Csys(
     CO2=None, HCO3=None, CO3=None,
     pCO2=None, fCO2=None,
     BT=None,
-    Ca=None, Mg=None,
+    Ca=0.0102821, Mg=0.0528171,
     T_in=25.0, T_out=None, 
     S_in=35.0, S_out=None,
-    P_in=None, P_out=None,
+    P_in=0.0, P_out=None,
     PT=0.0, SiT=0.0,
     ST=None, FT=None,
     pHsws=None, pHfree=None, pHNBS=None,
@@ -261,9 +261,9 @@ def Bsys(
     alphaB=None,
     T_in=25.0,
     S_in=35.0,
-    P_in=None,
-    Ca=None,
-    Mg=None,
+    P_in=0.0,
+    Ca=0.0102821,
+    Mg=0.0528171,
     ST=None,
     FT=None,
     pHsws=None,
@@ -429,9 +429,9 @@ def ABsys(
     alphaB=None,
     T_in=25.0,
     S_in=35.0,
-    P_in=None,
-    Ca=None,
-    Mg=None,
+    P_in=0.0,
+    Ca=0.0102821,
+    Mg=0.0528171,
     ST=None,
     FT=None,
     pHsws=None,
@@ -599,12 +599,12 @@ def CBsys(
     alphaB=None,
     T_in=25.0,
     S_in=35.0,
-    P_in=None,
+    P_in=0.0,
     T_out=None,
     S_out=None,
     P_out=None,
-    Ca=None,
-    Mg=None,
+    Ca=0.0102821,
+    Mg=0.0528171,
     PT=0.0,
     SiT=0.0,
     ST=None,

diff --git a/cbsyst/helpers.py b/cbsyst/helpers.py
@@ -32,7 +32,10 @@ def data_out(cbdat, path=None, include_constants=False):
     """
 
     cols = [
-        "pH",
+        "pHtot",
+        "pHfree",
+        "pHsws",
+        "pHNBS",
         "DIC",
         "fCO2",
         "pCO2",
@@ -49,33 +52,36 @@ def data_out(cbdat, path=None, include_constants=False):
         "ABT",
         "ABO3",
         "ABO4",
-        "T",
-        "S",
-        "P",
+        "T_in",
+        "S_in",
+        "P_in",
+        "T_out",
+        "S_out",
+        "P_out",
         "Ca",
         "Mg",
     ]
 
     consts = ["K0", "K1", "K2", "KB", "KW", "KS", "KspA", "KspC"]
 
-    size = cbdat.pH.size
+    size = cbdat.pHtot.size
     out = pd.DataFrame(index=range(size))
 
     for c in cols:
         if c in cbdat and cbdat[c] is not None:
-            if (np.ndim(cbdat[c]) == 1) & (cbdat[c].size == 1):
+            if (np.ndim(cbdat[c]) == 1) and (cbdat[c].size == 1):
                 cbdat[c] = cbdat[c][0]
             if c in cbdat:
                 out.loc[:, c] = cbdat[c]
 
     if include_constants:
         for c in consts:
             if c in cbdat.Ks and cbdat.Ks[c] is not None:
-                if (np.ndim(cbdat.Ks[c]) == 1) & (cbdat.Ks[c].size == 1):
+                if (np.ndim(cbdat.Ks[c]) == 1) and (cbdat.Ks[c].size == 1):
                     cbdat.Ks[c] = cbdat.Ks[c][0]
                 out.loc[:, "p" + c] = -np.log10(cbdat.Ks[c])
         if "alphaB" in cbdat and cbdat.alphaB is not None:
-            if (np.ndim(cbdat.alphaB) == 1) & (cbdat.alphaB.size == 1):
+            if (np.ndim(cbdat.alphaB) == 1) and (cbdat.alphaB.size == 1):
                 cbdat.alphaB = cbdat.alphaB[0]
             out.loc[:, "alphaB"] = cbdat.alphaB
 
@@ -369,12 +375,12 @@ def pH_scale_converter(pH, scale, Temp, Sal, Press=None, ST=None, FT=None):
         FT = calc_FT(Sal)
     TempK = Temp + 273.15
 
-    Ks = kgen.calc_Ks(TempC=Temp, Sal=Sal, Pres=Press)
+    Ks = Bunch(kgen.calc_Ks(temp_c=Temp, sal=Sal, p_bar=Press))
 
     inp = [None, None, None, None]
     inp[np.argwhere(scale == np.array(pH_scales))[0, 0]] = pH
 
-    return calc_pH_scales(*inp, TS, FT, TempK, Sal, Ks)
+    return calc_pH_scales(*inp, ST, FT, TempK, Sal, Ks)
 
 
 # TODO: function that correct pH for temperature