Add warning messages for empty alignment files and tests

Co-authored-by: Adamtaranto <2160099+Adamtaranto@users.noreply.github.com>

Author: Copilot

src/flexidot/utils/alignments.py

@@ -133,7 +133,13 @@ def parse_blast6(
                 }
             )
 
-    logging.info(f'Parsed {len(alignments)} alignments from BLAST6 file: {filepath}')
+    if len(alignments) == 0:
+        logging.warning(
+            f'No alignments found in BLAST6 file: {filepath}. '
+            'Plot will be generated without alignment overlays.'
+        )
+    else:
+        logging.info(f'Parsed {len(alignments)} alignments from BLAST6 file: {filepath}')
     return alignments
 
 
@@ -260,7 +266,13 @@ def parse_paf(
                 }
             )
 
-    logging.info(f'Parsed {len(alignments)} alignments from PAF file: {filepath}')
+    if len(alignments) == 0:
+        logging.warning(
+            f'No alignments found in PAF file: {filepath}. '
+            'Plot will be generated without alignment overlays.'
+        )
+    else:
+        logging.info(f'Parsed {len(alignments)} alignments from PAF file: {filepath}')
     return alignments
 
 

tests/test_gff_handling.py

@@ -3,6 +3,7 @@
 from pathlib import Path
 
 
+from flexidot.utils.alignments import load_alignments
 from flexidot.utils.file_handling import read_gffs
 
 # Test data paths
@@ -66,3 +67,39 @@ def test_read_multiple_gffs_with_empty(self):
         # Should still work and return data from the non-empty file
         assert len(feat_dict) > 0
         assert 'Seq2' in feat_dict
+
+
+class TestEmptyAlignments:
+    """Tests for empty alignment file handling."""
+
+    def test_empty_blast6_file(self, tmp_path):
+        """Test reading an empty BLAST6 file."""
+        empty_file = tmp_path / 'empty.blast6'
+        empty_file.write_text('')
+
+        alignments = load_alignments(str(empty_file), file_format='blast6')
+        assert alignments == []
+
+    def test_empty_paf_file(self, tmp_path):
+        """Test reading an empty PAF file."""
+        empty_file = tmp_path / 'empty.paf'
+        empty_file.write_text('')
+
+        alignments = load_alignments(str(empty_file), file_format='paf')
+        assert alignments == []
+
+    def test_blast6_file_with_only_comments(self, tmp_path):
+        """Test reading a BLAST6 file with only comments."""
+        comment_file = tmp_path / 'comments.blast6'
+        comment_file.write_text('# This is a comment\n# Another comment\n')
+
+        alignments = load_alignments(str(comment_file), file_format='blast6')
+        assert alignments == []
+
+    def test_paf_file_with_only_comments(self, tmp_path):
+        """Test reading a PAF file with only comments."""
+        comment_file = tmp_path / 'comments.paf'
+        comment_file.write_text('# This is a comment\n# Another comment\n')
+
+        alignments = load_alignments(str(comment_file), file_format='paf')
+        assert alignments == []