patching unittests

qiime2 · Oct 29, 2020 · 3bbc9c7 · 3bbc9c7
1 parent 2fc7e30
commit 3bbc9c7
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Showing 6 changed files with 6 additions and 86 deletions.
diff --git a/q2_gneiss/composition/__init__.py b/q2_gneiss/composition/__init__.py
@@ -8,11 +8,8 @@
 from ._composition import (
     ilr_hierarchical, ilr_phylogenetic, ilr_phylogenetic_ordination
 )
-from ._type import CladeMetadata
-from ._format import CladeMetadataDirectoryFormat, CladeMetadataFormat
 
 
 __all__ = [
-    "ilr_hierarchical", "ilr_phylogenetic", "ilr_phylogenetic_ordination",
-    "CladeMetadata", "CladeMetadataDirectoryFormat", "CladeMetadataFormat"
+    "ilr_hierarchical", "ilr_phylogenetic", "ilr_phylogenetic_ordination"
 ]
diff --git a/q2_gneiss/composition/_format.py b/q2_gneiss/composition/_format.py
diff --git a/q2_gneiss/composition/_method.py b/q2_gneiss/composition/_method.py
@@ -50,7 +50,7 @@ def ilr_phylogenetic_differential(
 def ilr_phylogenetic_ordination(table: pd.DataFrame, tree: skbio.TreeNode,
                                 pseudocount: float = 0.5,
                                 top_k_var: int = 10,
-                                clades: str = None) -> (
+                                clades: list = None) -> (
                                     OrdinationResults,
                                     skbio.TreeNode, pd.DataFrame
                                 ):
@@ -66,6 +66,8 @@ def ilr_phylogenetic_ordination(table: pd.DataFrame, tree: skbio.TreeNode,
     var = balances.var(axis=0).sort_values(ascending=False)
     if not clades:
         clades = var.index[:top_k_var]
+    else:
+        clades = clades[0].split(',')
     balances = balances[clades]
     balances.index.name = 'sampleid'
     # feature metadata

diff --git a/q2_gneiss/composition/_transformer.py b/q2_gneiss/composition/_transformer.py
diff --git a/q2_gneiss/composition/_type.py b/q2_gneiss/composition/_type.py
diff --git a/q2_gneiss/composition/tests/test_method.py b/q2_gneiss/composition/tests/test_method.py
@@ -138,7 +138,7 @@ def test_ilr_ordination(self):
             index=[1, 2, 3])
 
         exp_balances = exp_balances[['y0', 'y2', 'y1']]
-
+        exp_balances.index.name = 'sampleid'
         pdt.assert_frame_equal(res_ord.samples, exp_balances)
         exp_tree_str = ('((b:0.025,a:0.025)y1:0.2,'
                         '(c:0.025,d:0.025)y2:0.2)y0;\n')
@@ -150,6 +150,7 @@ def test_ilr_ordination(self):
                                [0.5, 0.707107, 0.000000]],
                               columns=['y0', 'y2', 'y1'],
                               index=['b', 'a', 'c', 'd'])
+        exp_md.index.name = 'featureid'
         pdt.assert_frame_equal(res_md, exp_md)