MAINT: organizes table/tree data consistently

qiime2 · May 19, 2020 · c4d7ed9 · c4d7ed9
1 parent 1083ff2
commit c4d7ed9
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Showing 3 changed files with 11 additions and 6 deletions.
diff --git a/q2_diversity_lib/tests/test_alpha.py b/q2_diversity_lib/tests/test_alpha.py
@@ -39,31 +39,32 @@ class FaithPDTests(TestPluginBase):
 
     def setUp(self):
         super().setUp()
-        # TODO: re-organize tables and trees
         self.empty_table_fp = self.get_data_path('empty_table.biom')
         self.empty_table_as_BIOMV210Format = \
             BIOMV210Format(self.empty_table_fp, mode='r')
         self.input_table_fp = self.get_data_path('faith_test_table.biom')
         self.input_table_as_BIOMV210Format = \
             BIOMV210Format(self.input_table_fp, mode='r')
-        self.input_tree_fp = self.get_data_path('faith_test.tree')
-        self.input_tree_as_NewickFormat = NewickFormat(self.input_tree_fp,
-                                                       mode='r')
         self.rf_table_fp = self.get_data_path('faith_test_table_rf.biom')
         self.rf_table_as_BIOMV210Format = \
             BIOMV210Format(self.rf_table_fp, mode='r')
         self.pa_table_fp = self.get_data_path('faith_test_table_pa.biom')
         self.pa_table_as_BIOMV210Format = \
             BIOMV210Format(self.pa_table_fp, mode='r')
+
         self.empty_tree_fp = self.get_data_path('empty.tree')
         self.empty_tree_as_NewickFormat = NewickFormat(self.empty_tree_fp,
                                                        mode='r')
+        self.input_tree_fp = self.get_data_path('faith_test.tree')
+        self.input_tree_as_NewickFormat = NewickFormat(self.input_tree_fp,
+                                                       mode='r')
         self.root_only_tree_fp = self.get_data_path('root_only.tree')
         self.root_only_tree_as_NewickFormat = \
             NewickFormat(self.root_only_tree_fp, mode='r')
         self.missing_tip_tree_fp = self.get_data_path('missing_tip.tree')
         self.missing_tip_tree_as_NewickFormat = \
             NewickFormat(self.missing_tip_tree_fp, mode='r')
+
         self.expected = pd.Series({'S1': 0.5, 'S2': 0.7, 'S3': 1.0,
                                    'S4': 100.5, 'S5': 101},
                                   name='faith_pd')

diff --git a/q2_diversity_lib/tests/test_beta.py b/q2_diversity_lib/tests/test_beta.py
@@ -223,6 +223,7 @@ def setUp(self):
                                              [0.25, 0.00, 0.00],
                                              [0.25, 0.00, 0.00]],
                                              ids=['S1', 'S2', 'S3'])
+
         self.table_fp = self.get_data_path('two_feature_table.biom')
         self.table_as_BIOMV210Format = BIOMV210Format(self.table_fp, mode='r')
         self.rf_table_fp = self.get_data_path('two_feature_rf_table.biom')
@@ -231,6 +232,7 @@ def setUp(self):
         self.p_a_table_fp = self.get_data_path('two_feature_p_a_table.biom')
         self.p_a_table_as_BIOMV210Format = BIOMV210Format(self.p_a_table_fp,
                                                           mode='r')
+
         self.tree_fp = self.get_data_path('three_feature.tree')
 
     def test_method(self):
@@ -286,11 +288,13 @@ def setUp(self):
             ids=('10084.PC.481', '10084.PC.593', '10084.PC.356',
                  '10084.PC.355', '10084.PC.354', '10084.PC.636',
                  '10084.PC.635', '10084.PC.607', '10084.PC.634'))
+
         self.table_fp = self.get_data_path('crawford.biom')
         self.table_as_BIOMV210Format = BIOMV210Format(self.table_fp, mode='r')
         self.rel_freq_table_fp = self.get_data_path('crawford_rf.biom')
         self.rf_table_as_BIOMV210Format = \
             BIOMV210Format(self.rel_freq_table_fp, mode='r')
+
         self.tree_fp = self.get_data_path('crawford.nwk')
 
     def test_method(self):

diff --git a/q2_diversity_lib/tests/test_util.py b/q2_diversity_lib/tests/test_util.py
@@ -94,14 +94,14 @@ def function_w_param(n_jobs=3):
             return n_jobs
         self.function_w_n_jobs_param = function_w_param
 
-        # TODO: re-organize tables and trees
         self.valid_table_fp = self.get_data_path('two_feature_table.biom')
         self.valid_table_as_BIOMV210Format = \
             BIOMV210Format(self.valid_table_fp, mode='r')
+        self.valid_table = biom.load_table(self.valid_table_fp)
+
         self.valid_tree_fp = self.get_data_path('three_feature.tree')
         self.valid_tree_as_NewickFormat = \
             NewickFormat(self.valid_tree_fp, mode='r')
-        self.valid_table = biom.load_table(self.valid_table_fp)
 
     def test_function_without_n_jobs_param(self):
         with self.assertRaisesRegex(TypeError, 'without \'n_jobs'):