Description: fetch extend.py and logger.py helpers from parsnp namespace
 This fixes failures to import logger and extend when running parsnp.  This
 patch comes along with installing the missing helpers in dist-packages/parsnp.
Author: Étienne Mollier <emollier@debian.org>
Forwarded: not-needed
Last-Update: 2022-04-14
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- parsnp.orig/extend.py
+++ parsnp/extend.py
@@ -14,7 +14,7 @@
 import numpy as np
 from Bio.AlignIO.MafIO import MafWriter, MafIterator
 from Bio.AlignIO.MauveIO import MauveWriter, MauveIterator
-from logger import logger
+from parsnp.logger import logger
 import time
 #%%
 
--- parsnp.orig/parsnp
+++ parsnp/parsnp
@@ -8,7 +8,7 @@
 from tempfile import TemporaryDirectory
 import re
 import logging
-from logger import logger
+from parsnp.logger import logger
 import multiprocessing
 import argparse
 import signal
@@ -17,7 +17,7 @@
 from Bio import SeqIO
 from glob import glob
 
-import extend as ext
+import parsnp.extend as ext
 
 __version__ = "1.7.4"
 reroot_tree = True #use --midpoint-reroot