make _to_dict() public (#472)

biocore · Dec 21, 2020 · d0a46ed · d0a46ed
1 parent a1acaff
commit d0a46ed
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Showing 2 changed files with 13 additions and 9 deletions.
diff --git a/empress/core.py b/empress/core.py
@@ -278,16 +278,20 @@ def make_empress(self):
         main_template = self._get_template()
 
         # _process_data does a lot of munging to the coordinates data and
-        # _to_dict puts the data into a dictionary-like object for consumption
-        data = self._to_dict()
+        # to_dict puts the data into a dictionary-like object for consumption
+        data = self.to_dict()
 
         plot = main_template.render(data)
 
         return plot
 
-    def _to_dict(self):
+    def to_dict(self):
         """Convert processed data into a dictionary
 
+        Warning: the object returned by to_dict will contain references to
+        internal variables. Exercise caution if modifying the value of objects
+        returned by to_dict.
+
         Returns
         -------
         dict

diff --git a/tests/python/test_core.py b/tests/python/test_core.py
@@ -297,7 +297,7 @@ def test_to_dict(self):
         viz = Empress(self.tree, self.table, self.sample_metadata,
                       shear_to_table=False)
 
-        obs = viz._to_dict()
+        obs = viz.to_dict()
         dict_a_cp = copy.deepcopy(DICT_A)
 
         # NOTE: Uncomment the following two lines of code to write the current
@@ -315,7 +315,7 @@ def test_to_dict_with_feature_metadata(self):
             self.tree, self.table, self.sample_metadata, self.feature_metadata,
             shear_to_table=False
         )
-        obs = viz._to_dict()
+        obs = viz.to_dict()
         dict_a_with_fm = copy.deepcopy(DICT_A)
         dict_a_with_fm["compressed_tip_metadata"] = {1: ["asdf", "qwer"]}
         dict_a_with_fm["compressed_int_metadata"] = {8: ["ghjk", "tyui"]}
@@ -333,7 +333,7 @@ def test_to_dict_with_metadata_nans(self):
         viz = Empress(self.tree, self.table, nan_sample_metadata,
                       nan_feature_metadata,
                       shear_to_table=False)
-        obs = viz._to_dict()
+        obs = viz.to_dict()
         dict_a_nan = copy.deepcopy(DICT_A)
 
         # [1][3] corresponds to Sample2, Metadata4
@@ -355,7 +355,7 @@ def test_to_dict_with_emperor(self):
                       ordination=self.pcoa,
                       shear_to_table=False,
                       filter_extra_samples=True)
-        obs = viz._to_dict()
+        obs = viz.to_dict()
 
         self.assertEqual(viz._emperor.width, '50vw')
         self.assertEqual(viz._emperor.height, '100vh; float: right')
@@ -418,7 +418,7 @@ def test_to_dict_tree_plot(self):
         dict_a_cp = copy.deepcopy(DICT_A)
         self._clear_copied_dict_a(dict_a_cp)
 
-        obs = viz._to_dict()
+        obs = viz.to_dict()
         self.assertEqual(obs, dict_a_cp)
 
     def test_to_dict_tree_plot_with_feature_metadata(self):
@@ -432,7 +432,7 @@ def test_to_dict_tree_plot_with_feature_metadata(self):
         dict_a_cp["compressed_int_metadata"] = {8: ["ghjk", "tyui"]}
         dict_a_cp["feature_metadata_columns"] = ["fmdcol1", "fmdcol2"]
 
-        obs = viz._to_dict()
+        obs = viz.to_dict()
         self.assertEqual(obs, dict_a_cp)
 
     def test_shear_tree_to_table(self):