Fix partis imports to use installed package instead of submodule

Updated parse_cluster.py and write_lh_annotations.py to import from
the partis-bcr PyPI package (installed via requirements.txt) instead of
the deprecated lib/partis submodule path.

Changes:
- Removed manual sys.path manipulation for lib/partis
- Changed imports from python.utils to partis.utils
- Changed imports from python.glutils to partis.glutils
- Changed imports from python.clusterpath to partis.clusterpath

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>

Author: jgallowa07

scripts/parse_cluster.py

@@ -14,11 +14,9 @@
 import colored_traceback.always
 from util_functions import write_to_fasta
 
-default_partis_path = os.path.join(os.getcwd(), "lib/partis")
-sys.path.append(default_partis_path)
-import python.utils as utils
-import python.glutils as glutils
-from python.clusterpath import ClusterPath
+import partis.utils as utils
+import partis.glutils as glutils
+from partis.clusterpath import ClusterPath
 
 
 def show_available_clusters(cpath, ipartition, ptn):

scripts/write_lh_annotations.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python3
+
 from __future__ import absolute_import
 import math
 import copy
@@ -8,9 +9,7 @@
 import sys
 from io import open
 from six.moves import zip
-default_partis_path = os.path.join(os.getcwd(), 'lib/partis')
-sys.path.append(default_partis_path)
-import python.utils as utils
+import partis.utils as utils
 
 # reads sampled trees/annotation pairs, collapses duplicate annotations while keeping tracking of all the trees that contributed, then writes all [best] unique annotations to linearham_run_all[best].yaml
 #  This does not add the inferred ancestral sequences to the annotations (atm this is done in partis/test/linearham-run.py, although maybe it'd make sense to do it here)