change GatingResults 'sample' column name to 'sample_id', update a few related tests, & bump beta version

Author: whitews

src/flowkit/_models/gating_results.py

@@ -21,7 +21,7 @@ def __init__(self, results_dict, sample_id):
     @staticmethod
     def _get_pd_result_dict(res_dict, gate_name):
         return {
-            'sample': res_dict['sample'],
+            'sample_id': res_dict['sample'],
             'gate_path': res_dict['gate_path'],
             'parent': res_dict['parent'],
             'gate_name': gate_name,
@@ -60,7 +60,7 @@ def _process_results(self):
         df = pd.DataFrame(
             pd_list,
             columns=[
-                'sample',
+                'sample_id',
                 'gate_path',
                 'gate_name',
                 'gate_type',
@@ -73,10 +73,10 @@ def _process_results(self):
         )
         df['level'] = df.gate_path.map(lambda x: len(x) - 1)
 
-        self.report = df.sort_values(['sample', 'level', 'gate_name'])
+        self.report = df.sort_values(['sample_id', 'level', 'gate_name'])
 
     def _filter_gate_report(self, gate_name, gate_path=None):
-        results = self.report[(self.report['sample'] == self.sample_id) & (self.report['gate_name'] == gate_name)]
+        results = self.report[(self.report['sample_id'] == self.sample_id) & (self.report['gate_name'] == gate_name)]
 
         if gate_path is not None:
             results = results[results.gate_path == gate_path]
@@ -87,7 +87,7 @@ def _filter_gate_report(self, gate_name, gate_path=None):
 
     def get_gate_membership(self, gate_name, gate_path=None):
         """
-        Retrieve a boolean array indicating gate membership for the events in the GatingResults sample.
+        Retrieve a boolean array indicating gate membership for the Sample events in the GatingResults.
         Note, the same gate ID may be found in multiple gate paths, i.e. the gate ID can be ambiguous.
         In this case, specify the full gate path to retrieve gate indices.
 
@@ -106,7 +106,7 @@ def get_gate_membership(self, gate_name, gate_path=None):
             gate_path = gate_paths[0]
 
         # need to check for quadrant gates, as they need to be handled differently
-        gate_data = self.report[(self.report['sample'] == self.sample_id) & (self.report.gate_name == gate_name)]
+        gate_data = self.report[(self.report['sample_id'] == self.sample_id) & (self.report.gate_name == gate_name)]
         quad_parent_values = set(gate_data.quadrant_parent.to_list())
 
         if len(quad_parent_values) == 1 and None in quad_parent_values:

src/flowkit/_version.py

@@ -1,4 +1,4 @@
 """
 FlowKit version
 """
-__version__ = "1.3.0b0"
+__version__ = "1.3.0b1"

tests/workspace_tests.py

@@ -542,7 +542,7 @@ def test_analyze_single_sample(self):
         wsp.analyze_samples(sample_id=sample_id)
         report = wsp.get_analysis_report(group_name=sample_grp)
 
-        self.assertEqual(report['sample'].nunique(), 1)
+        self.assertEqual(report['sample_id'].nunique(), 1)
 
     def test_parse_wsp_sample_without_gates(self):
         wsp_path = "data/8_color_data_set/8_color_ICS_sample_without_gates.wsp"
@@ -570,7 +570,7 @@ def test_parse_wsp_sample_without_gates(self):
         self.assertEqual(time_count, 257482)
 
         report = wsp.get_analysis_report(group_name=sample_grp)
-        self.assertEqual(2, len(report['sample'].unique()))
+        self.assertEqual(2, len(report['sample_id'].unique()))
 
     def test_extract_sample_data(self):
         wsp_path = "data/8_color_data_set/8_color_ICS.wsp"