From 2f7ada913f756bb0856a5e5a6e0ea607832ada42 Mon Sep 17 00:00:00 2001
From: weiju <weiju.wu@gmail.com>
Date: Fri, 8 Mar 2024 10:22:24 -0800
Subject: [PATCH] changed preprocess_test to use pytest

---
 requirements.txt        |  1 -
 setup.py                |  2 +-
 test/preprocess_test.py | 25 +++++++------------------
 3 files changed, 8 insertions(+), 20 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index a5a8f1e..048eb1a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -12,4 +12,3 @@ graphviz>=0.20.1
 gql>=3.4.0
 chembl_webresource_client>=0.10.8
 tqdm>=4.64.0
-xmlrunner>=1.7.7
diff --git a/setup.py b/setup.py
index 71bc273..e515dda 100644
--- a/setup.py
+++ b/setup.py
@@ -17,7 +17,7 @@
                     'graphviz>=0.20.1',
                     'gql>=3.4.0',
                     'chembl_webresource_client>=0.10.8',
-                    'tqdm>=4.64.0', "xmlrunner>=1.7.7"]
+                    'tqdm>=4.64.0']
 setuptools.setup(
     name="isb_miner3",
     version="1.1.9",
diff --git a/test/preprocess_test.py b/test/preprocess_test.py
index c8f368c..e9278e5 100755
--- a/test/preprocess_test.py
+++ b/test/preprocess_test.py
@@ -1,15 +1,14 @@
 #!/usr/bin/env python3
 import sys
-import unittest
-import xmlrunner
+import pytest
 
-import pandas as pd
+#import pandas as pd
 from miner import miner
-import logging
+
+"""
 
 class PreprocessTest(unittest.TestCase):
 
-    """
     def test_remove_null_rows_min_0_remove_ok(self):
         df = pd.DataFrame([[0, 1, 2], [1, 2, 3], [0, 0, 0], [4, 5, 6]])
         df2 = miner.remove_null_rows(df)
@@ -51,24 +50,14 @@ def test_correct_batch_effects_no_tpm(self):
         for i in range(3):
             for j in range(3):
                 self.assertAlmostEquals(df2.values[i, j], -0.8164965809277261)
-    """
 
-    """
     def test_preprocess_main_simple(self):
         exp, conv_table = miner.preprocess('testdata/exp_data-001.csv', 'testdata/conv_table-001.tsv')
         self.assertEquals((10, 3), exp.shape)
         for i in range(3):
             for j in range(3):
                 self.assertAlmostEquals(exp.values[i, j], -0.8164965809277261)
-    """
+"""
 
-if __name__ == '__main__':
-    SUITE = []
-    LOG_FORMAT = '%(asctime)s %(message)s'
-    logging.basicConfig(format=LOG_FORMAT, level=logging.DEBUG,
-                        datefmt='%Y-%m-%d %H:%M:%S \t')
-    SUITE.append(unittest.TestLoader().loadTestsFromTestCase(PreprocessTest))
-    if len(sys.argv) > 1 and sys.argv[1] == 'xml':
-      xmlrunner.XMLTestRunner(output='test-reports').run(unittest.TestSuite(SUITE))
-    else:
-      unittest.TextTestRunner(verbosity=2).run(unittest.TestSuite(SUITE))
+def test_dummy():
+    pass