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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
@@ -9,7 +9,7 @@
import bisect
import numpy as np
from tqdm import tqdm
-from logger import logger, TqdmToLogger, MIN_TQDM_INTERVAL
+from parsnp.logger import logger, TqdmToLogger, MIN_TQDM_INTERVAL
import spoa
#%%
--- parsnp.orig/parsnp
+++ parsnp/parsnp
@@ -13,7 +13,7 @@
from tempfile import TemporaryDirectory
import re
import logging
-from logger import logger, TqdmToLogger, MIN_TQDM_INTERVAL
+from parsnp.logger import logger, TqdmToLogger, MIN_TQDM_INTERVAL
import argparse
import signal
from multiprocessing import Pool
@@ -1731,7 +1731,7 @@
if args.extend_lcbs:
logger.warning("The LCB extension module is experimental. Runtime may be significantly increased and extended alignments may not be as high quality as the original core-genome. Extensions off of existing LCBs are in a separate xmfa file.")
import partition
- import extend as ext
+ import parsnp.extend as ext
orig_parsnp_xmfa = parsnp_output
extended_parsnp_xmfa = orig_parsnp_xmfa + ".extended"
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