MIN Remove path manipulations

Author: luispedro

gmsc_mapper/main.py

@@ -1,7 +1,6 @@
 import subprocess
 import argparse
 import sys
-sys.path.append("..")
 import os
 from os import path
 import pandas as pd

tests/test_filter_length.py

@@ -1,5 +1,3 @@
-import sys
-sys.path.append("..")
 from gmsc_mapper.filter_length import filter_length
 import pytest
 import os
@@ -11,7 +9,7 @@ def test_filter_length():
         assert len(f.readlines()) == 4
     filtered_file = filter_length("./tests/test_filter_length.faa",os.path.dirname(os.path.realpath(__file__)),100)
     with gzip.open(filtered_file,"rt") as f:
-        assert len(f.readlines()) == 6  
+        assert len(f.readlines()) == 6
 
 if __name__ == '__main__':
-    pytest.main()
+    pytest.main()

tests/test_generate_fasta.py

@@ -1,5 +1,3 @@
-import sys
-sys.path.append("..")
 from gmsc_mapper.main import generate_fasta
 from gmsc_mapper.fasta import fasta_iter
 import pytest
@@ -18,4 +16,4 @@ def test_generate_fasta():
     assert fasta_list == known_list
 
 if __name__ == '__main__':
-    pytest.main()
+    pytest.main()

tests/test_habitat.py

@@ -1,5 +1,3 @@
-import sys
-sys.path.append("..")
 from gmsc_mapper.map_habitat import smorf_habitat
 import pytest
 import os
@@ -19,4 +17,4 @@ def test_habitat():
     assert habitat_dict == known_habitat
 
 if __name__ == '__main__':
-    pytest.main()
+    pytest.main()

tests/test_predict.py

@@ -1,5 +1,3 @@
-import sys
-sys.path.append("..")
 from gmsc_mapper.predict import predict_genes,filter_smorfs
 from gmsc_mapper.fasta import fasta_iter
 import pytest
@@ -30,4 +28,4 @@ def test_filter():
     assert filter_dict == known_filtered
 
 if __name__ == '__main__':
-    pytest.main()
+    pytest.main()

tests/test_quality.py

@@ -1,5 +1,3 @@
-import sys
-sys.path.append("..")
 from gmsc_mapper.map_quality import smorf_quality
 import pytest
 import os
@@ -18,4 +16,4 @@ def test_smorf_quality():
     assert quality_dict == known_quality
 
 if __name__ == '__main__':
-    pytest.main()
+    pytest.main()

tests/test_taxonomy.py

@@ -1,5 +1,3 @@
-import sys
-sys.path.append("..")
 from gmsc_mapper.map_taxonomy import store_index,smorf_taxonomy,deep_lca
 import pytest
 import os
@@ -30,6 +28,6 @@ def test_deep_lca():
         for line in f:
             deep_lca_taxonomy.append(line.replace("\n",""))
     assert deep_lca_taxonomy == known_taxonomy
-    
+
 if __name__ == '__main__':
     pytest.main()

tests/test_translate.py

@@ -1,5 +1,3 @@
-import sys
-sys.path.append("..")
 from gmsc_mapper.translate import translate_gene,check_frame
 from gmsc_mapper.fasta import fasta_iter
 import pytest
@@ -28,4 +26,4 @@ def test_translate():
     assert translate_dict == known_translated
 
 if __name__ == '__main__':
-    pytest.main()
+    pytest.main()