Merge pull request #43 from JuBiotech/reservoir-dtype

Treat reservoir ID in fluidics as int

Author: bertramgeinitz

bletl/__init__.py

@@ -11,6 +11,7 @@
     BLData,
     BLDParser,
     FilterTimeSeries,
+    FluidicsSource,
     IncompatibleFileError,
     InvalidLotNumberError,
     LotInformationError,

bletl/parsing/blpro.py

@@ -19,6 +19,7 @@
     BLData,
     BLDParser,
     FilterTimeSeries,
+    FluidicsSource,
     InvalidLotNumberError,
 )
 
@@ -346,7 +347,7 @@ def extract_fluidics(dfraw):
         ("Cycle", "cycle", int),
         ("Well", "well", int),
         ("Time", "time", float),
-        ("Reservoir", "reservoir", float),
+        ("Reservoir", "reservoir", FluidicsSource),
         ("MF_Volume", "mf_volume", float),
         ("Temp_Ch4", "volume", float),
     ]

bletl/types.py

@@ -3,7 +3,6 @@
 import enum
 import os
 import typing
-import warnings
 from typing import Dict, Optional, Tuple, Union
 
 import numpy
@@ -19,6 +18,20 @@ class BioLectorModel(enum.Enum):
     XT = "blXT"
 
 
+class FluidicsSource(enum.IntEnum):
+    """Number that identifies the source of volume changes."""
+
+    ReservoirA = 1
+
+    """Additions from reservoir A."""
+    ReservoirB = 2
+
+    """Additions from reservoir B."""
+
+    Pipetting = -1
+    """Additions from pipetting."""
+
+
 class BLData(dict):
     """Standardized data type for BioLector data."""
 

bletl/utils.py

@@ -1,9 +1,10 @@
 """Contains helper functions that do not depend on other modules within this package."""
 import datetime
+import enum
 import pathlib
 import re
 import urllib
-from typing import Optional, Sequence, Tuple, Union
+from typing import Optional, Sequence, Tuple
 
 import pandas
 
@@ -32,6 +33,9 @@ def __to_typed_cols__(
     for ocol, ncol, typ in ocol_ncol_type:
         if ocol is None or not ocol in dfin:
             dfout[ncol] = None
+        elif issubclass(typ, enum.Enum):
+            # Enum types are kept as object-series
+            dfout[ncol] = dfin[ocol].apply(lambda x: typ(x), convert_dtype=False)
         else:
             dfout[ncol] = dfin[ocol].astype(typ)
     return dfout

tests/test_core.py

@@ -635,3 +635,9 @@ def test_issue_38(self):
         assert bldata.fluidics.loc["E06", "volume"][-1] == 913.16
         assert bldata.fluidics.loc["F01", "volume"][-1] == 1202.719
         pass
+
+    def test_fluidics_source(self):
+        fp = dir_testfiles / "BLPro" / "18-FZJ-Test2--2018-02-07-10-01-11.csv"
+        bldata = bletl.parse(fp)
+        assert isinstance(bldata.fluidics["reservoir"][0], bletl.FluidicsSource)
+        pass