Added cmakelist

Author: TimoLassmann

.github/workflows/wheels.yml

@@ -48,8 +48,8 @@ jobs:
 
         # Linux specific settings
         CIBW_BEFORE_ALL_LINUX: >
-          yum install -y cmake3 openmp-devel ||
-          (apt-get update && apt-get install -y cmake libomp-dev)
+          yum install -y cmake3 ||
+          (apt-get update && apt-get install -y cmake)
         CIBW_REPAIR_WHEEL_COMMAND_LINUX: auditwheel repair -w {dest_dir} {wheel}
 
         # macOS specific settings  

python/kalign/__init__.py

@@ -10,9 +10,9 @@
 from importlib import import_module
 from typing import Any, List, Literal, Optional, Union
 
-from . import _core, io, utils
+from . import _core
 
-__version__ = "3.4.1"
+__version__ = "3.4.5"
 __author__ = "Timo Lassmann"
 __email__ = "timo.lassmann@telethonkids.org.au"
 
@@ -410,7 +410,8 @@ def write_alignment(
 
     mapped_format = format_map[format_lower]
 
-    # Use appropriate writer from io module
+    # Use appropriate writer from io module (lazy import to avoid circular imports)
+    from . import io
     if mapped_format == "fasta":
         io.write_fasta(sequences, output_file, ids=ids)
     elif mapped_format == "clustal":
@@ -496,8 +497,6 @@ def generate_test_sequences(
     "set_num_threads",
     "get_num_threads",
     "kalign",
-    "io",
-    "utils",
     "DNA",
     "DNA_INTERNAL",
     "RNA",