making rpy2 an optional dependency to avoid libreadline issues on conda

CGATReport/Stats.py

@@ -750,12 +750,15 @@ def doMannWhitneyUTest(xvals, yvals):
     if len(xvals) == 0 or len(yvals) == 0:
         result = Result()
     else:
-        r_result = R['wilcox.test'](xvals, yvals, paired=False)
-        result = Result().fromR(
-            (("pvalue", 'p.value'),
-             ('alternative', None),
-             ('method', None)),
-            r_result)
+        if R:
+            r_result = R['wilcox.test'](xvals, yvals, paired=False)
+            result = Result().fromR(
+                (("pvalue", 'p.value'),
+                 ('alternative', None),
+                 ('method', None)),
+                r_result)
+        else:
+            raise ValueError("rpy2 not available")
 
     result.xobservations = len(xvals)
     result.yobservations = len(yvals)

CGATReport/Tracker.py

@@ -22,12 +22,6 @@
 import sqlalchemy.exc as exc
 import sqlalchemy.engine
 
-# for rpy2 for data frames
-try:
-    from rpy2.robjects import r as R
-except ImportError:
-    R = None
-
 from CGATReport import Utils
 from CGATReport import Stats
 

requires.txt

@@ -8,16 +8,18 @@ pandas>=0.16.0
 patsy>=0.2.1
 statsmodels>=0.5.0
 seaborn>=0.3.1
-rpy2>=2.6.0
 ggplot>=0.6.8
 sphinx>=1.0.5
 sphinxcontrib-programoutput>=0.8
 sqlalchemy>=0.7.0
-web.py>=0.37
+# Optional dependency
+# web.py>=0.37
 openpyxl>=2.0.3
 xlwt>=0.7.4
 mpld3>=0.2
 pillow>=2.7.0
+# rpy2 now an optional module
+# rpy2>=2.6.0
 # Disabled, as it requires pytz==2013b, which
 # conflicts with other packages that require a
 # more recent pytz.