From 60f369c76cba1af3e112e5f8ab31e5f6acee0e39 Mon Sep 17 00:00:00 2001
From: Veronique Legrand <vlegrand@pasteur.fr>
Date: Fri, 13 Oct 2023 11:54:00 +0200
Subject: [PATCH] updated path of source module in broken test
---
unit-tests/Data4Test.py | 4 ++--
unit-tests/test_functions_PhageTerm_for_multi.py | 10 +++++-----
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/unit-tests/Data4Test.py b/unit-tests/Data4Test.py
index 3ab4de9..20ebf2a 100755
--- a/unit-tests/Data4Test.py
+++ b/unit-tests/Data4Test.py
@@ -1,7 +1,7 @@
import os
-from _modules.IData_handling import genomeFastaRecovery,totReads
-from _modules.main_utils import inputRawDataArgs,functionalParms,InputDerivedDataArgs,technicalParms
+from phagetermvirome.IData_handling import genomeFastaRecovery,totReads
+from phagetermvirome.main_utils import inputRawDataArgs,functionalParms,InputDerivedDataArgs,technicalParms
TEST_DIR_PATH = os.path.dirname(os.path.abspath(__file__))
TEST_DATA_PATH = os.path.join(TEST_DIR_PATH, "..", "test-data")
diff --git a/unit-tests/test_functions_PhageTerm_for_multi.py b/unit-tests/test_functions_PhageTerm_for_multi.py
index 7e84e11..bfcec89 100755
--- a/unit-tests/test_functions_PhageTerm_for_multi.py
+++ b/unit-tests/test_functions_PhageTerm_for_multi.py
@@ -6,7 +6,7 @@
import sys
sys.path.append("..")
-sys.path.append("../_modules")
+sys.path.append("../phagetermvirome")
import unittest
import numpy as np
@@ -14,9 +14,9 @@ import os
import shutil
from Data4Test import buildTestData, Data4Test
-from _modules.functions_PhageTerm import readsCoverage
-from _modules.readsCoverage_res import loadRCRes,RCRes,RCCheckpoint_handler
-from _modules.debug_utils import ReadMappingInfoLogger
+from phagetermvirome.functions_PhageTerm import readsCoverage
+from phagetermvirome.readsCoverage_res import loadRCRes,RCRes,RCCheckpoint_handler
+from phagetermvirome.debug_utils import ReadMappingInfoLogger
@@ -71,7 +71,7 @@ class Test_functions_Phageterm (unittest.TestCase):
#
# # VL: start basic testing of sum_reads_coverage_for_seq for multimachine mode
def test_basic_sum_readsCoverage_for_seq(self):
- from _modules.seq_processing import sum_readsCoverage_for_seq
+ from phagetermvirome.seq_processing import sum_readsCoverage_for_seq
d=Data4Test("data/G-janv_S2_R1_001.fastq.500","data/seq1_2_3.fasta", paired="data/G-janv_S2_R2_001.fastq.500", \
hostseq="", seed=20, edge=500, insert_max=1000, limit_coverage=11, virome=0)
dir_cov_res=os.path.join(os.getcwd(),"data")
--
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