From 8f036415975d6e224e5e94277997329c0f1fa159 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Fri, 29 Oct 2021 09:49:28 +0300
Subject: Feature/biweight reimplementation (#47)

* add biweight reimplementation with pingouin

* delete biweight scripts and tests

* add python-pingouin to guix file

* delete biweight paths

* mypy fix:pingouin mising imports

* pep8 formatting && pylint fixes---
 tests/unit/computations/test_biweight.py    | 21 ---------------------
 tests/unit/computations/test_correlation.py | 11 -----------
 2 files changed, 32 deletions(-)
 delete mode 100644 tests/unit/computations/test_biweight.py

(limited to 'tests/unit')

diff --git a/tests/unit/computations/test_biweight.py b/tests/unit/computations/test_biweight.py
deleted file mode 100644
index ad404f1..0000000
--- a/tests/unit/computations/test_biweight.py
+++ /dev/null
@@ -1,21 +0,0 @@
-"""test for biweight script"""
-from unittest import TestCase
-from unittest import mock
-
-from gn3.computations.biweight import calculate_biweight_corr
-
-
-class TestBiweight(TestCase):
-    """test class for biweight"""
-
-    @mock.patch("gn3.computations.biweight.subprocess.check_output")
-    def test_calculate_biweight_corr(self, mock_check_output):
-        """test for calculate_biweight_corr func"""
-        mock_check_output.return_value = "0.1 0.5"
-        results = calculate_biweight_corr(command="Rscript",
-                                          path_to_script="./r_script.R",
-                                          trait_vals=[
-                                              1.2, 1.1, 1.9],
-                                          target_vals=[1.9, 0.4, 1.1])
-
-        self.assertEqual(results, (0.1, 0.5))
diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py
index fc52ec1..96d9c6d 100644
--- a/tests/unit/computations/test_correlation.py
+++ b/tests/unit/computations/test_correlation.py
@@ -5,7 +5,6 @@ from unittest import mock
 from collections import namedtuple
 
 from gn3.computations.correlations import normalize_values
-from gn3.computations.correlations import do_bicor
 from gn3.computations.correlations import compute_sample_r_correlation
 from gn3.computations.correlations import compute_all_sample_correlation
 from gn3.computations.correlations import filter_shared_sample_keys
@@ -98,16 +97,6 @@ class TestCorrelation(TestCase):
 
         self.assertEqual(results, expected_results)
 
-    @mock.patch("gn3.computations.correlations.calculate_biweight_corr")
-    def test_bicor(self, mock_biweight):
-        """Test for doing biweight mid correlation """
-        mock_biweight.return_value = (1.0, 0.0)
-
-        results = do_bicor(x_val=[1, 2, 3], y_val=[4, 5, 6])
-
-        self.assertEqual(results, (1.0, 0.0)
-                         )
-
     @mock.patch("gn3.computations.correlations.compute_corr_coeff_p_value")
     @mock.patch("gn3.computations.correlations.normalize_values")
     def test_compute_sample_r_correlation(self, norm_vals, compute_corr):
-- 
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