Merge branch 'develop' into SEEFOdataStuff

requirements.txt

-attrs==19.3.0
+attrs==20.1.0
 Click==7.1.2
 cycler==0.10.0
 dios==0.6.0
@@ -9,7 +9,7 @@ joblib==0.16.0
 llvmlite==0.34.0
 mlxtend==0.17.3
 matplotlib==3.3.1
-more-itertools==8.4.0
+more-itertools==8.5.0
 numba==0.51.1
 numpy==1.19.1
 outlier==0.2

saqc/core/core.py

@@ -60,6 +60,9 @@ def _prepInput(flagger, data, flags):
             raise TypeError("data should not use MultiIndex")
         data = dios.to_dios(data)
 
+    if not hasattr(data.columns, "str"):
+        raise TypeError("expected dataframe columns of type string")
+
     if not isinstance(flagger, BaseFlagger):
         # NOTE: we should generate that list automatically,
         #       it won't ever be complete otherwise

saqc/flagger/baseflagger.py

@@ -46,7 +46,7 @@ class BaseFlagger(ABC):
 
     @property
     def flags(self):
-        return self._flags
+        return self._flags.copy()
 
     def initFlags(self, data: diosT = None, flags: diosT = None) -> BaseFlaggerT:
         """
@@ -93,10 +93,10 @@ class BaseFlagger(ABC):
             raise TypeError(f"flagger of type '{self.__class__}' needed")
 
         if inplace:
-            self._flags = mergeDios(self.flags, other.flags, subset=subset, join=join)
+            self._flags = mergeDios(self._flags, other._flags, subset=subset, join=join)
             return self
         else:
-            return self.copy(flags=mergeDios(self.flags, other.flags, subset=subset, join=join))
+            return self.copy(flags=mergeDios(self._flags, other._flags, subset=subset, join=join))
 
     def slice(self, field: FieldsT = None, loc: LocT = None, drop: FieldsT = None, inplace=False) -> BaseFlaggerT:
         """ Return a potentially trimmed down copy of self. """
@@ -137,7 +137,9 @@ class BaseFlagger(ABC):
             field = slice(None) if field is None else self._check_field(field)
             indexer = (loc, field)
 
-        return self.flags.aloc[indexer]
+        # this is a bug in `dios.aloc`, which may return a shallow copied dios, if `slice(None)` is passed
+        # as row indexer. Thus is because pandas `.loc` return a shallow copy if a null-slice is passed to a series.
+        return self._flags.copy().aloc[indexer]
 
     def setFlags(self, field: str, loc: LocT = None, flag: FlagT = None, force: bool = False, inplace=False, **kwargs) -> BaseFlaggerT:
         """Overwrite existing flags at loc.
@@ -263,12 +265,12 @@ class BaseFlagger(ABC):
         # https://git.ufz.de/rdm-software/saqc/issues/46
         failed = []
         if isinstance(field, str):
-            if field not in self.flags:
+            if field not in self._flags:
                 failed += [field]
         else:
             try:
                 for f in field:
-                    if f not in self.flags:
+                    if f not in self._flags:
                         failed += [f]
             # not iterable, probably a slice or
             # any indexer we dont have to check

saqc/flagger/dmpflagger.py

@@ -74,14 +74,14 @@ class DmpFlagger(CategoricalFlagger):
 
         # implicit set self._flags, and make deepcopy of self aka. DmpFlagger
         newflagger = super().initFlags(data=data, flags=flags)
-        newflagger._causes = newflagger.flags.astype(str)
-        newflagger._comments = newflagger.flags.astype(str)
+        newflagger._causes = newflagger._flags.astype(str)
+        newflagger._comments = newflagger._flags.astype(str)
         newflagger._causes[:], newflagger._comments[:] = "", ""
         return newflagger
 
     def slice(self, field=None, loc=None, drop=None, inplace=False):
         newflagger = super().slice(field=field, loc=loc, drop=drop, inplace=inplace)
-        flags = newflagger.flags
+        flags = newflagger._flags
         newflagger._causes = self._causes.aloc[flags, ...]
         newflagger._comments = self._comments.aloc[flags, ...]
         return newflagger
@@ -94,7 +94,7 @@ class DmpFlagger(CategoricalFlagger):
 
     def merge(self, other: DmpFlaggerT, subset: Optional[List] = None, join: str = "merge", inplace=False):
         assert isinstance(other, DmpFlagger)
-        flags = mergeDios(self.flags, other.flags, subset=subset, join=join)
+        flags = mergeDios(self._flags, other._flags, subset=subset, join=join)
         causes = mergeDios(self._causes, other._causes, subset=subset, join=join)
         comments = mergeDios(self._comments, other._comments, subset=subset, join=join)
         if inplace:

sphinx-doc/requirements_sphinx.txt

 alabaster==0.7.12
 appdirs==1.4.4
 astor==0.8.1
-attrs==19.3.0
+attrs==20.1.0
 Babel==2.8.0
 black==20.8b1
 certifi==2020.6.20
@@ -24,7 +24,7 @@ Markdown==3.2.2
 MarkupSafe==1.1.1
 matplotlib==3.3.1
 mlxtend==0.17.2
-more-itertools==8.2.0
+more-itertools==8.5.0
 numba==0.51.1
 numpy==1.19.1
 outlier==0.2
@@ -44,7 +44,7 @@ python-intervals==1.10.0
 pytz==2019.3
 PyWavelets==1.1.1
 recommonmark==0.6.0
-regex==2020.6.8
+regex==2020.7.14
 requests==2.24.0
 scikit-learn==0.22.1
 scipy==1.4.1