Bug fixes. (#52)

* Fix rates - first row is NaN

* Don't propagate uncertainties through cumsum.

* black

* Filter points where I == 0 in fe.

src/dgpost/transform/electrochemistry.py

@@ -16,7 +16,15 @@
 from yadg.dgutils import ureg
 import numpy as np
 import pandas as pd
-from dgpost.utils.helpers import load_data, name_to_chem, electrons_from_smiles
+from typing import Iterable
+from uncertainties import UFloat
+from uncertainties import unumpy as unp
+from dgpost.utils.helpers import (
+    load_data,
+    separate_data,
+    name_to_chem,
+    electrons_from_smiles,
+)
 
 
 @load_data(
@@ -177,6 +185,8 @@ def fe(
 
     """
     etot = abs(I) / (ureg("elementary_charge") * ureg("avogadro_constant"))
+    if isinstance(etot.m, Iterable):
+        etot.m[etot.m == 0] = np.NaN
     pretag = "fe" if output is None else output
     ret = {}
     for k, v in rate.items():
@@ -243,7 +253,11 @@ def charge(
 
     dQ = I * dt
 
-    Q = np.cumsum(dQ).to_base_units()
+    if any([isinstance(i.m, UFloat) for i in dQ]):
+        dQn, dQs, dQu = separate_data(dQ)
+        Q = ureg.Quantity(unp.uarray(np.cumsum(dQn), dQs), dQu).to_base_units()
+    else:
+        Q = np.cumsum(dQ).to_base_units()
 
     ret = {output: Q}
     return ret

src/dgpost/transform/rates.py

@@ -13,7 +13,6 @@
 
 """
 import pint
-
 from yadg.dgutils import ureg
 import pandas as pd
 import numpy as np
@@ -172,16 +171,16 @@ def batch_to_molar(
         c0 = ureg.Quantity(0, "mol/m³")
         for k, v in c.items():
             c[k] = np.insert(v, 0, c0)
-    elif isinstance(V.magnitude, Iterable) and len(V) == nts:
+    elif isinstance(V.m, Iterable) and len(V) == nts:
         V = V[1:]
 
     dt = np.diff(time)
-    dc = {k: np.diff(c_k) for k, c_k in c.items()}
+    dc = {k: np.diff(v) for k, v in c.items()}
     ret = {}
     for k, dc_k in dc.items():
         r = (dc_k / dt) * V
         if len(r) < nts:
-            r0 = ureg.Quantity(0, "mol/s")
+            r0 = ureg.Quantity(np.nan, "mol/s")
             r = np.insert(r, 0, r0)
         ret[f"{output}->{k}"] = r.to_base_units()
     return ret

tests/test_electrochemistry_fe.py

@@ -45,6 +45,24 @@
                 "fe->CO": ureg.Quantity(0.02858024),
             },
         ),
+        (  # ts2 - arrays, with I == 0, all Quantities, weird units
+            {
+                "I": ureg.Quantity([0, 100], "mA"),
+                "rate": {
+                    "H2": ureg.Quantity([0.6811524, 0.6811524], "mmol/hour"),
+                    "CH4": ureg.Quantity([0.1134709, 0.1134709], "mmol/hour"),
+                    "C2H4": ureg.Quantity([0.0239087, 0.0239087], "mmol/hour"),
+                    "CO": ureg.Quantity([0.0533184, 0.0533184], "mmol/hour"),
+                },
+                "charges": {"C": 4, "H": 1, "O": -2},
+            },
+            {
+                "fe->H2": ureg.Quantity([np.NaN, 0.36511734]),
+                "fe->CH4": ureg.Quantity([np.NaN, 0.24329496]),
+                "fe->C2H4": ureg.Quantity([np.NaN, 0.07689462]),
+                "fe->CO": ureg.Quantity([np.NaN, 0.02858024]),
+            },
+        ),
     ],
 )
 def test_electrochemistry_fe_direct(inputs, output):
@@ -53,7 +71,7 @@ def test_electrochemistry_fe_direct(inputs, output):
     print(ret)
     for k in inputs["rate"].keys():
         n = f"{tag}->{k}"
-        assert np.allclose(ret[n], output[n])
+        assert np.allclose(ret[n], output[n], equal_nan=True)
 
 
 @pytest.mark.parametrize(

tests/test_rates_batchtomolar.py

@@ -36,16 +36,20 @@
                 "V": ureg.Quantity(1, "l"),
             },
             {
-                "rate->A": ureg.Quantity([0.0, 10.0 / 60, 5.0 / 60, 5.0 / 60], "mol/s"),
-                "rate->B": ureg.Quantity([0.0, 5.0 / 60, 5.0 / 60, 1.0 / 60], "mol/s"),
+                "rate->A": ureg.Quantity(
+                    [np.NaN, 10.0 / 60, 5.0 / 60, 5.0 / 60], "mol/s"
+                ),
+                "rate->B": ureg.Quantity(
+                    [np.NaN, 5.0 / 60, 5.0 / 60, 1.0 / 60], "mol/s"
+                ),
             },
         ),
     ],
 )
 def test_rates_batchtomolar_direct(spec, ref):
     ret = rates.batch_to_molar(**spec)
     for k, v in ref.items():
-        assert np.allclose(v, ret[k])
+        assert np.allclose(v, ret[k], equal_nan=True)
 
 
 @pytest.mark.parametrize(