Merge branch 'rf/rules' into 'master'

Rf/rules

See merge request fsl/ukbparse!109

CHANGELOG.rst

@@ -2,6 +2,19 @@
 ======================
 
 
+
+0.14.7 (Sunday 17th March 2019)
+-------------------------------
+
+
+Changed
+^^^^^^^
+
+
+* Changes to default cleaning rules - negative values for integer/categorical
+  types are no longer discarded.
+
+
 0.14.6 (Saturday 16th March 2019)
 ---------------------------------
 

ukbparse/__init__.py

@@ -6,7 +6,7 @@
 #
 
 
-__version__ = '0.14.6'
+__version__ = '0.14.7'
 """The ``ukbparse`` versioning scheme roughly follows Semantic Versioning
 conventions.
 """

ukbparse/data/datacodings_recoding.tsv

@@ -14,6 +14,7 @@ ID	RawLevels	NewLevels
 100013
 100011	10,3060,1030,12,24,600	1,2,3,4,5,6
 100012	0,13,35,57,79,912,1200	2,3,4,5,6,7
+100290	-10	0.5
 488	-1001	0
 493	0,-131,-141	1,2,3
 494	-1520,-2030,-3040,-4000	1,2,3,4

ukbparse/data/types.tsv

 Type	Clean
-Integer	makeNa('< 0')
-Categorical (single)	makeNa('< 0')
-Categorical (multiple)	makeNa('< 0')
\ No newline at end of file

ukbparse/data/variables_parentvalues.tsv

 ID	ParentValues	ChildValues
-757	v6142 == 1	0
 767	v6142 == 1	0
 777	v6142 == 1	0
 796	v6142 == 1 || v777 == 0	0

ukbparse/loadtables.py

@@ -421,7 +421,7 @@ def loadVariableTable(datafiles,
             warnings.filterwarnings('ignore', category=pd.errors.ParserWarning)
 
             if fname is not None:
-                log.debug('Loading %s table from %s', what, varfile)
+                log.debug('Loading %s table from %s', what, fname)
                 table = pd.read_csv(fname, '\t',
                                     index_col=0,
                                     dtype=dtypes,