Merge pull request #44 from be-smith/bes/timestamp_bug_fix

Add try except around galvani timestamp. Not always present presumably due to the version of ec-lab used to write the file. Also minor bug fixes to the plotting library

Author: be-smith

src/navani/echem.py

@@ -76,7 +76,10 @@ def echem_file_loader(filepath: Union[str, Path], mass: float = None, area: floa
             gal_file = MPRfile(f)
 
         df = pd.DataFrame(data=gal_file.data)
-        df["timestamp"] = gal_file.timestamp + pd.to_timedelta(df["time/s"], unit="s")
+        try:
+            df["timestamp"] = gal_file.timestamp + pd.to_timedelta(df["time/s"], unit="s")
+        except AttributeError as e:
+            print("No timestamp detected in galvani export")
         df = biologic_processing(df)
 
     # arbin .res file - uses an sql server and requires mdbtools installed
@@ -909,7 +912,7 @@ def multi_cycle_plot(df: pd.DataFrame, cycles: ArrayLike, colormap: str = 'virid
         mask = df['half cycle'] == cycle
         ax.plot(df['Capacity'][mask], df['Voltage'][mask], color=cm(norm(np.ceil(cycle/2))))
 
-    cbar = fig.colorbar(sm)
+    cbar = fig.colorbar(sm, ax=ax)
     cbar.set_label('Cycle', rotation=270, labelpad=10)
     ax.set_ylabel('Voltage / V')
     ax.set_xlabel('Capacity / mAh')
@@ -985,7 +988,7 @@ def multi_dqdv_plot(df: pd.DataFrame,
 
         ax.plot(voltage, dqdv, color=cm(norm(np.ceil(cycle/2))))
 
-    cbar = fig.colorbar(sm)
+    cbar = fig.colorbar(sm, ax=ax)
     cbar.set_label('Cycle', rotation=270, labelpad=10)
     ax.set_xlabel('Voltage / V')
     ax.set_ylabel('dQ/dV / $mAhV^{-1}$')

tests/test_echem.py

@@ -97,7 +97,7 @@ def test_mpr_reader():
     df = ec.echem_file_loader(test_path)
     assert df.shape == (46102, 19)
 
-    cols = (
+    required_cols = (
         "state",
         "Capacity",
         "dQ/mA.h",
@@ -116,10 +116,11 @@ def test_mpr_reader():
         "control/V/mA",
         "I Range",
         "flags",
-        "timestamp",
     )
+    optional_cols = ("timestamp",)
 
-    assert set(cols) == set(df)
+    assert set(required_cols) <= set(df)
+    assert set(df) <= set(required_cols) | set(optional_cols)
 
     mask = df["half cycle"] == 1
     voltage, dqdv, capacity = ec.dqdv_single_cycle(