Unit test fixes accommodating bugfix

* changes to unit-tests/test_functions_PhageTerm_for_multi.test_checkpoint_creation() accommodating that the first read is now considered. e.g. total match length goes from 291333 --> 291441 due to first read length of 108.
* minor restructure of unit tests to include standard setUp() and tearDown() methods, simplifying the creation/deletion of tmp dirs. This means that the unit tests don't fail if they detect leftover tmp directories leftover from a previous run that didn't cleanup because it failed.

unit-tests/test_functions_PhageTerm_for_multi.py

@@ -22,11 +22,18 @@ from _modules.debug_utils import ReadMappingInfoLogger
 
 class Test_functions_Phageterm (unittest.TestCase):
     # Test that readsCoverage results are saved in the appropriate structure and can be read again for later work.
+    def setUp(self):
+        self.dir_tmp = os.path.join(os.getcwd(), "tmp")
+        os.mkdir(self.dir_tmp)
+
+    def tearDown(self):
+        # this will remove these dirs at end of each test, even if test fails.
+        shutil.rmtree(self.dir_tmp)
+
     def testDumpAndReadAgainRes(self):
         l_data = buildTestData()
         chk_handler = RCCheckpoint_handler(0,None,False)
-        dir_cov_res = os.path.join(os.getcwd(),"tmp")
-        os.mkdir(os.path.join(os.getcwd(),"tmp")) # TODO: when switching to python3, use the tempfile module
+        dir_cov_res = self.dir_tmp  # TODO: when switching to python3, use the tempfile module
         for d in l_data:
             idx_seq = 0
             for refseq in d.refseq_list:
@@ -67,7 +74,7 @@ class Test_functions_Phageterm (unittest.TestCase):
                 self.assertTrue(np.array_equal(r1b.paired_mismatch,r1.paired_mismatch))
                 self.assertTrue(np.array_equal(r1b.reads_tested,r1.reads_tested))
                 idx_seq += 1
-        shutil.rmtree(dir_cov_res)
+
     #
     # # VL: start basic testing of sum_reads_coverage_for_seq for multimachine mode
     def test_basic_sum_readsCoverage_for_seq(self):
@@ -83,17 +90,16 @@ class Test_functions_Phageterm (unittest.TestCase):
         os.mkdir(DR_path)
         sum_readsCoverage_for_seq(dir_cov_res, idx_refseq, nb_pieces, d.inDArgs, d.fParms, d.inDRawArgs, dir_seq_res, DR_path)
         self.assertTrue(os.path.exists("DR/UNKNOWN/NODE_1_length_422445"))
+        # ideally these would be handled in self.tearDown() but they are not currently a problem.
         shutil.rmtree(dir_seq_res)
         shutil.rmtree(DR_path)
 
 
-
     # Checks that checkpoints are created and that their content is correct.
     def test_checkpoint_creation(self):
         # last line is 11150
         d=Data4Test("../test-data/COS-5.fastq", "../test-data/COS-5.fasta")
-        dir_chk = os.path.join(os.getcwd(), "tmp2")
-        os.mkdir(dir_chk)
+        dir_chk = self.dir_tmp
         d.tParms.dir_chk=dir_chk
         d.tParms.test_mode=True
         return_dict = dict()
@@ -101,26 +107,24 @@ class Test_functions_Phageterm (unittest.TestCase):
         chk_handler = RCCheckpoint_handler(d.tParms.chk_freq, d.tParms.dir_chk, d.tParms.test_mode)
         readsCoverage(d.inDRawArgs, d.refseq_list[0], d.inDArgs, d.fParms, return_dict, 0, d.line_start, d.line_end, \
                       d.tParms, chk_handler, 0, None)
-        fic_name = "chk_0_0_11150_291333.npz"
+        fic_name = "chk_0_0_11150_291441.npz"  # was chk_0_0_11150_291333.npz - length of first read is 108.
         full_fname = os.path.join(dir_chk, fic_name)
-        self.assertTrue(os.path.exists(full_fname))
         list_f = os.listdir(dir_chk)
+        print("this is the list of files", list_f)
+        self.assertTrue(os.path.exists(full_fname))
         self.assertTrue(len(list_f)==1)
         wr=chk_handler.load(0,0)
-        self.assertEqual(wr.read_match,291333)
+        self.assertEqual(wr.read_match,291441)  # 291333 + 108 (first read length) = 291441
         self.assertEqual(wr.count_line,11150)
         self.assertEqual(wr.interm_res.host_len,0)
         self.assertEqual(wr.interm_res.gen_len,3012)
-        self.assertEqual(int(wr.interm_res.reads_tested),2787) # 2796?
-        shutil.rmtree(dir_chk)
-
+        self.assertEqual(int(wr.interm_res.reads_tested),2788) # 2787+1 # orig comment: 2796?
 
     ## Checks thst in production mode, all checkpoints are deleted at the end.
     def test_checkpoint_end(self):
         # last line is 11150
         d=Data4Test("../test-data/COS-5.fastq", "../test-data/COS-5.fasta")
-        dir_chk = os.path.join(os.getcwd(), "tmp3")
-        os.mkdir(dir_chk)
+        dir_chk = self.dir_tmp
         d.tParms.chk_freq=1
         d.tParms.dir_chk=dir_chk
         d.tParms.test_mode=False
@@ -131,13 +135,11 @@ class Test_functions_Phageterm (unittest.TestCase):
                       d.tParms, chk_handler, 0, None)
         list_f = os.listdir(dir_chk)
         self.assertTrue(len(list_f)==0)
-        shutil.rmtree(dir_chk)
 
     # ## checks that readsCoverage restarts from ceckpoint and not from the beginning.
     def test_restart_from_checkpoint(self):
         d = Data4Test("../test-data/COS-5.fastq", "../test-data/COS-5.fasta")
-        dir_chk = os.path.join(os.getcwd(), "tmp4")
-        os.mkdir(dir_chk)
+        dir_chk = self.dir_tmp
         d.tParms.dir_chk = dir_chk
         d.tParms.chk_freq=1
         d.tParms.test_mode = False
@@ -156,12 +158,10 @@ class Test_functions_Phageterm (unittest.TestCase):
         self.assertEqual(wr.interm_res.host_len,0)
         self.assertEqual(wr.interm_res.gen_len,3012)
         self.assertEqual(int(wr.interm_res.reads_tested),9)
-        shutil.rmtree(dir_chk)
 
     def test_restart_from_checkpoint2(self):
         d=Data4Test("../test-data/Virome.fastq","../test-data/Virome.fasta")
-        dir_chk = os.path.join(os.getcwd(), "tmp5")
-        os.mkdir(dir_chk)
+        dir_chk = self.dir_tmp
         d.tParms.dir_chk = dir_chk
         d.tParms.chk_freq = 5
         d.tParms.test_mode = False
@@ -179,8 +179,6 @@ class Test_functions_Phageterm (unittest.TestCase):
                       d.tParms, chk_handler, idx_seq, logger)
             idx_seq+=1
         self.assertEqual(idx_seq,5)
-        shutil.rmtree(dir_chk)
-
 
 
 if __name__ == "__main__":