Use .data property in diversity and Tajimas_D methods to avoid type error sgkit-dev#638

timothymillar · pentschev · commit f78216c0fd35 · 2021-09-16T05:54:43.000-07:00
diff --git a/sgkit/stats/popgen.py b/sgkit/stats/popgen.py
@@ -124,7 +124,7 @@ def diversity(
             {
                 variables.stat_diversity: (
                     ("variants", "cohorts"),
-                    pi,
+                    pi.data,
                 )
             }
         )
@@ -604,10 +604,12 @@ def Tajimas_D(
     D = d / d_stdev[:, np.newaxis]
 
     if has_windows(ds):
-        new_ds = create_dataset({variables.stat_Tajimas_D: (["windows", "cohorts"], D)})
+        new_ds = create_dataset(
+            {variables.stat_Tajimas_D: (["windows", "cohorts"], D.data)}
+        )
     else:
         new_ds = create_dataset(
-            {variables.stat_Tajimas_D: (["variants", "cohorts"], D)}
+            {variables.stat_Tajimas_D: (["variants", "cohorts"], D.data)}
         )
     return conditional_merge_datasets(ds, new_ds, merge)
 

Original file line number	Diff line number	Diff line change
`@@ -124,7 +124,7 @@ def diversity(`
`124`	`124`	`{`
`125`	`125`	`variables.stat_diversity: (`
`126`	`126`	`("variants", "cohorts"),`
`127`		`- pi,`
	`127`	`+ pi.data,`
`128`	`128`	`)`
`129`	`129`	`}`
`130`	`130`	`)`
`@@ -604,10 +604,12 @@ def Tajimas_D(`
`604`	`604`	`D = d / d_stdev[:, np.newaxis]`
`605`	`605`
`606`	`606`	`if has_windows(ds):`
`607`		`- new_ds = create_dataset({variables.stat_Tajimas_D: (["windows", "cohorts"], D)})`
	`607`	`+ new_ds = create_dataset(`
	`608`	`+ {variables.stat_Tajimas_D: (["windows", "cohorts"], D.data)}`
	`609`	`+ )`
`608`	`610`	`else:`
`609`	`611`	`new_ds = create_dataset(`
`610`		`- {variables.stat_Tajimas_D: (["variants", "cohorts"], D)}`
	`612`	`+ {variables.stat_Tajimas_D: (["variants", "cohorts"], D.data)}`
`611`	`613`	`)`
`612`	`614`	`return conditional_merge_datasets(ds, new_ds, merge)`
`613`	`615`