fix: testing suits

tests/test_scripts_dgicev.py

@@ -9,7 +9,7 @@
 import pytest
 
 
-@pytest.mark.optional
+@pytest.mark.skip(reason="Only for testing purposes")
 def bam_to_sam(bam_file):
     """Converts a BAM file to SAM format and returns it as a string.
 
@@ -28,7 +28,7 @@ def bam_to_sam(bam_file):
         return temp_sam.read().decode()
 
 
-@pytest.mark.optional
+@pytest.mark.skip(reason="Only for testing purposes")
 def test_read_run_error_free():
     """Test the read.py script by piping SAM data to it."""
     input_bam = "tests/data/REF_aln_trim_subsample.bam"

tests/test_silo_input_transformer.py

@@ -6,8 +6,6 @@
 
 import pytest
 
-import silo_input_transformer
-
 logging.basicConfig(level=logging.INFO)
 
 config_path = "silo_input_transformer/config.yaml"
@@ -18,6 +16,9 @@
 )
 def test_transform():
     """Test to run Rust based Silo input transformer, fail for error."""
+
+    import silo_input_transformer
+
     result = silo_input_transformer.run_with_config(config_path)  # type: ignore
     logging.info(f"Result from Rust: {result}")
     return result