1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
|
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
|
