[med-svn] [Git][med-team/srst2][master] remove dependency on python3-mock
Alexandre Detiste (@detiste-guest)
gitlab at salsa.debian.org
Sun Jan 7 16:23:07 GMT 2024
Alexandre Detiste pushed to branch master at Debian Med / srst2
Commits:
f5ce5399 by Alexandre Detiste at 2024-01-07T17:21:24+01:00
remove dependency on python3-mock
- - - - -
2 changed files:
- debian/control
- debian/patches/2to3.patch
Changes:
=====================================
debian/control
=====================================
@@ -10,7 +10,6 @@ Build-Depends: debhelper-compat (= 13),
python3-setuptools,
markdown,
dos2unix,
- python3-mock <!nocheck>,
python3-scipy <!nocheck>,
bowtie2 <!nocheck>,
samtools <!nocheck>
=====================================
debian/patches/2to3.patch
=====================================
@@ -6,7 +6,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
--- a/README.md
+++ b/README.md
-@@ -70,7 +70,7 @@ Current release - v0.2.0 - July 28, 2016
+@@ -70,7 +70,7 @@
-----
Dependencies:
@@ -15,7 +15,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
* scipy, numpy http://www.scipy.org/install.html
* bowtie2 (v2.1.0 or later) http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
* SAMtools v0.1.18 https://sourceforge.net/projects/samtools/files/samtools/0.1.18/ (NOTE: later versions can be used, but better results are obtained with v0.1.18, especially at low read depths (<20x))
-@@ -171,7 +171,7 @@ Updates in v0.1.3
+@@ -171,7 +171,7 @@
### 1 - Install dependencies
@@ -24,7 +24,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
* scipy http://www.scipy.org/install.html
* bowtie2 v2.1.0 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
* SAMtools v0.1.18 https://sourceforge.net/projects/samtools/files/samtools/0.1.18/ (NOTE 0.1.19 DOES NOT WORK)
-@@ -541,13 +541,13 @@ IN ADDITION TO THE NOVEL ALLELES FILE OU
+@@ -541,13 +541,13 @@
For genes:
```
@@ -40,7 +40,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
```
# More basic usage examples
-@@ -787,7 +787,7 @@ cdhit-est -i rawseqs.fasta -o rawseqs_cd
+@@ -787,7 +787,7 @@
2 - Parse the cluster output and tabulate the results, check for inconsistencies between gene names and the sequence clusters, and generate individual fasta files for each cluster to facilitate further checking:
```
@@ -49,7 +49,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
```
For comparing gene names to cluster assignments, this script assumes very basic nomenclature of the form gene-allele, ie a gene symbol followed by '-' followed by some more specific allele designation. E.g. adk-1, blaCTX-M-15. The full name of the gene (adk-1, blaCTX-M-15) will be stored as the allele, and the bit before the '-' will be stored as the name of the gene cluster (adk, blaCTX). This won't always give you exactly what you want, because there really are no standards for gene nomenclature! But it will work for many cases, and you can always modify the script if you need to parse names in a different way. Note though that this only affects how sensible the gene cluster nomenclature is going to be in your srst2 results, and will not affect the behaviour of the clustering (which is purely sequence based using cdhit) or srst2 (which will assign a top scoring allele per cluster, the cluster name may not be perfect but the full allele name will always be reported anyway).
-@@ -820,13 +820,13 @@ To type these virulence genes using SRST
+@@ -820,13 +820,13 @@
1 - Extract virulence genes by genus from the main VFDB file, `CP_VFs.ffn`:
```
@@ -65,7 +65,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
```
2 - Run CD-HIT to cluster the sequences for this genus, at 90% nucleotide identity:
-@@ -838,13 +838,13 @@ cd-hit -i Clostridium.fsa -o Clostridium
+@@ -838,13 +838,13 @@
3 - Parse the cluster output and tabulate the results using the specific Virulence gene DB compatible script:
```
@@ -83,7 +83,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
The output file, `Clostridium_VF_clustered.fasta`, should now be ready to use with srst2 (`--gene_db Clostridium_VF_clustered.fasta`).
--- a/database_clustering/README.md
+++ b/database_clustering/README.md
-@@ -59,7 +59,7 @@ cdhit-est -i rawseqs.fasta -o rawseqs_cd
+@@ -59,7 +59,7 @@
2 - Parse the cluster output and tabulate the results, check for inconsistencies between gene names and the sequence clusters, and generate individual fasta files for each cluster to facilitate further checking:
@@ -92,7 +92,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
For comparing gene names to cluster assignments, this script assumes very basic nomenclature of the form gene-allele, ie a gene symbol followed by '-' followed by some more specific allele designation. E.g. adk-1, blaCTX-M-15. The full name of the gene (adk-1, blaCTX-M-15) will be stored as the allele, and the bit before the '-' will be stored as the name of the gene cluster (adk, blaCTX). This won't always give you exactly what you want, because there really are no standards for gene nomenclature! But it will work for many cases, and you can always modify the script if you need to parse names in a different way. Note though that this only affects how sensible the gene cluster nomenclature is going to be in your srst2 results, and will not affect the behaviour of the clustering (which is purely sequence based using cdhit) or srst2 (which will assign a top scoring allele per cluster, the cluster name may not be perfect but the full allele name will always be reported anyway).
-@@ -89,11 +89,11 @@ To type these virulence genes using SRST
+@@ -89,11 +89,11 @@
gunzip VFDB_setB_nt.fas.gz
@@ -106,7 +106,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
- Run CD-HIT to cluster the sequences for this genus, at 90% nucleotide identity:
-@@ -101,8 +101,8 @@ cd-hit-est -i Clostridium.fsa -o Clostri
+@@ -101,8 +101,8 @@
- Parse the cluster output and tabulate the results using the specific Virulence gene DB compatible script:
@@ -119,7 +119,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
+python3 csv_to_gene_db.py -t Clostridium_cdhit90.csv -o Clostridium_VF_clustered.fasta -s 5
--- a/database_clustering/align_plot_tree_min3.py
+++ b/database_clustering/align_plot_tree_min3.py
-@@ -11,44 +11,44 @@ fasta_directory = "/home/UNIMELB/hdashno
+@@ -11,44 +11,44 @@
# Get the filenames of all files in the input directory "fasta_directory"
files = []
for f in os.listdir(fasta_directory):
@@ -196,7 +196,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
# take csv table detailing clustering etc and sequences for gene DB, write as fasta
# expected csv file format:
# seqID,clusterid,gene,allele,(DNAseq),other....
-@@ -45,18 +45,18 @@ if __name__ == "__main__":
+@@ -45,18 +45,18 @@
if options.output_file == "":
DoError("Please specify output fasta file using -o")
if options.seq_col != "":
@@ -218,7 +218,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
# read contents of a table and print as fasta
f = file(options.table_file,"r")
-@@ -82,7 +82,7 @@ if __name__ == "__main__":
+@@ -82,7 +82,7 @@
if seqs_file_id in input_seqs:
record = SeqRecord(input_seqs[seqs_file_id],id=db_id, description=db_id)
else:
@@ -239,7 +239,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
#example usage:
#/srst2/database_clustering/get_all_vfdb.sh ./CP_VFs.ffn ./VFDB
-@@ -12,7 +12,7 @@ fi
+@@ -12,7 +12,7 @@
VFDBFILE=$(readlink -e $1)
OUTPUTFOLDER=$2
@@ -248,7 +248,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
DBCLUSTERINGSCRIPTFOLDER=$(dirname $(readlink -e $0))
#if the specified output folder doesn't exist, then create it
-@@ -22,7 +22,7 @@ fi
+@@ -22,7 +22,7 @@
cd ${OUTPUTFOLDER}
#extract virulence genes from all available genera into separate files
@@ -257,7 +257,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
#loop over each genus' *.fsa file and generate the gene database fasta file
for FSAFILE in *.fsa; do
-@@ -36,10 +36,10 @@ for FSAFILE in *.fsa; do
+@@ -36,10 +36,10 @@
cd-hit -i ${FILENAME} -o ${GENUS}/${GENUS}_cdhit90 -c 0.9 > ${GENUS}/${GENUS}_cdhit90.stdout
#Parse the cluster output and tabulate the results using the specific Virulence gene DB compatible script:
@@ -280,7 +280,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
#example usage:
#/srst2/database_clustering/get_genus_vfdb.sh ./CP_VFs.ffn Bacillus ./VFDB
-@@ -12,7 +12,7 @@ fi
+@@ -12,7 +12,7 @@
VFDBFILE=$(readlink -e $1)
GENUS=$2
OUTPUTFOLDER=$3
@@ -289,7 +289,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
DBCLUSTERINGSCRIPTFOLDER=$(dirname $(readlink -e $0))
#if the specified output folder doesn't exist, then create it
-@@ -24,13 +24,13 @@ cd ${OUTPUTFOLDER}
+@@ -24,13 +24,13 @@
echo Generating virulence gene database for ${GENUS}
FILENAME=${GENUS}.fsa
#extract virulence genes from all available genera into separate files
@@ -317,7 +317,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
#
# Basic analysis of SRST2 output
# Authors - Kathryn Holt (kholt at unimelb.edu.au)
-@@ -62,7 +62,7 @@ def compile_results(args,mlst_results,db
+@@ -62,7 +62,7 @@
if mlst_cols == 0:
mlst_header_string = test_string
else:
@@ -326,7 +326,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
test_string_split = test_string.split("\t")
this_mlst_cols = len(test_string)
-@@ -107,7 +107,7 @@ def compile_results(args,mlst_results,db
+@@ -107,7 +107,7 @@
if variable not in variable_list:
variable_list.append(variable)
@@ -335,7 +335,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
if "Sample" in sample_list:
sample_list.remove("Sample")
-@@ -177,8 +177,8 @@ def compile_results(args,mlst_results,db
+@@ -177,8 +177,8 @@
# log ST counts
if len(mlst_results_master) > 0:
@@ -354,7 +354,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
'''
Download MLST datasets from this site: http://pubmlst.org/data/ by
-@@ -23,7 +23,7 @@ from argparse import ArgumentParser
+@@ -23,7 +23,7 @@
import xml.dom.minidom as xml
import urllib2 as url
import re, os, glob
@@ -363,7 +363,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
def parse_args():
parser = ArgumentParser(description='Download MLST datasets by species'
-@@ -125,12 +125,12 @@ def main():
+@@ -125,12 +125,12 @@
if info != None:
found_species.append(info)
if len(found_species) == 0:
@@ -379,7 +379,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
exit(2)
assert len(found_species) == 1
-@@ -176,22 +176,22 @@ def main():
+@@ -176,22 +176,22 @@
log_file.close()
species_all_fasta_file.close()
@@ -423,7 +423,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
'''
This script generates SRST2 jobs for the Grid Engine (qsub) scheduling system
(http://gridscheduler.sourceforge.net/). It allows many samples to be processed in parallel. After
-@@ -98,7 +98,7 @@ def read_file_sets(args):
+@@ -98,7 +98,7 @@
(baseName,read) = m.groups()
reverse_reads[baseName] = fastq
else:
@@ -432,7 +432,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
else:
# matches default Illumina file naming format, e.g. m.groups() = ('samplename', '_S1', '_L001', '_R1', '_001')
baseName, read = m.groups()[0], m.groups()[3]
-@@ -107,8 +107,8 @@ def read_file_sets(args):
+@@ -107,8 +107,8 @@
elif read == "_R2":
reverse_reads[baseName] = fastq
else:
@@ -443,7 +443,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
fileSets[file_name_before_ext] = fastq
num_single_readsets += 1
# store in pairs
-@@ -119,17 +119,17 @@ def read_file_sets(args):
+@@ -119,17 +119,17 @@
else:
fileSets[sample] = [forward_reads[sample]] # no reverse found
num_single_readsets += 1
@@ -465,7 +465,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
return fileSets
-@@ -139,7 +139,7 @@ class CommandError(Exception):
+@@ -139,7 +139,7 @@
def run_command(command, **kwargs):
'Execute a shell command and check the exit status and any O/S exceptions'
command_str = ' '.join(command)
@@ -474,7 +474,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
try:
exit_status = call(command, **kwargs)
except OSError as e:
-@@ -209,9 +209,9 @@ def bowtie_index(fasta_files):
+@@ -209,9 +209,9 @@
for fasta in fasta_files:
built_index = fasta + '.1.bt2'
if os.path.exists(built_index):
@@ -486,7 +486,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
run_command([get_bowtie_execs()[1], fasta, fasta])
def get_samtools_exec():
-@@ -229,9 +229,9 @@ def samtools_index(fasta_files):
+@@ -229,9 +229,9 @@
for fasta in fasta_files:
built_index = fasta + '.fai'
if os.path.exists(built_index):
@@ -498,7 +498,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
run_command([get_samtools_exec(), 'faidx', fasta])
def main():
-@@ -283,7 +283,7 @@ def main():
+@@ -283,7 +283,7 @@
cmd += " " + args.other_args
# print and run command
@@ -515,7 +515,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
'''
This script generates SRST2 jobs for the SLURM scheduling system (http://slurm.schedmd.com/). It
allows many samples to be processed in parallel. After they all complete, the results can be
-@@ -102,7 +102,7 @@ def read_file_sets(args):
+@@ -102,7 +102,7 @@
(baseName,read) = m.groups()
reverse_reads[baseName] = fastq
else:
@@ -524,7 +524,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
else:
# matches default Illumina file naming format, e.g. m.groups() = ('samplename', '_S1', '_L001', '_R1', '_001')
baseName, read = m.groups()[0], m.groups()[3]
-@@ -111,8 +111,8 @@ def read_file_sets(args):
+@@ -111,8 +111,8 @@
elif read == "_R2":
reverse_reads[baseName] = fastq
else:
@@ -535,7 +535,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
fileSets[file_name_before_ext] = fastq
num_single_readsets += 1
# store in pairs
-@@ -123,17 +123,17 @@ def read_file_sets(args):
+@@ -123,17 +123,17 @@
else:
fileSets[sample] = [forward_reads[sample]] # no reverse found
num_single_readsets += 1
@@ -557,7 +557,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
return fileSets
-@@ -143,7 +143,7 @@ class CommandError(Exception):
+@@ -143,7 +143,7 @@
def run_command(command, **kwargs):
'Execute a shell command and check the exit status and any O/S exceptions'
command_str = ' '.join(command)
@@ -566,7 +566,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
try:
exit_status = call(command, **kwargs)
except OSError as e:
-@@ -213,9 +213,9 @@ def bowtie_index(fasta_files):
+@@ -213,9 +213,9 @@
for fasta in fasta_files:
built_index = fasta + '.1.bt2'
if os.path.exists(built_index):
@@ -578,7 +578,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
run_command([get_bowtie_execs()[1], fasta, fasta])
def get_samtools_exec():
-@@ -233,9 +233,9 @@ def samtools_index(fasta_files):
+@@ -233,9 +233,9 @@
for fasta in fasta_files:
built_index = fasta + '.fai'
if os.path.exists(built_index):
@@ -590,7 +590,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
run_command([get_samtools_exec(), 'faidx', fasta])
def main():
-@@ -292,10 +292,10 @@ def main():
+@@ -292,10 +292,10 @@
cmd += " " + args.other_args
# print and run command
@@ -616,7 +616,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
#
# Authors - Michael Inouye (minouye at unimelb.edu.au), Harriet Dashnow (h.dashnow at gmail.com),
# Kathryn Holt (kholt at unimelb.edu.au), Bernie Pope (bjpope at unimelb.edu.au)
-@@ -30,7 +30,7 @@ from itertools import groupby
+@@ -30,7 +30,7 @@
from operator import itemgetter
from collections import OrderedDict
try:
@@ -625,7 +625,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
except:
srst2_version = "version unknown"
-@@ -306,8 +306,8 @@ def parse_fai(fai_file,db_type,delimiter
+@@ -306,8 +306,8 @@
gene_clusters.append(gene_cluster)
if len(delimiter_check) > 0:
@@ -636,7 +636,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
return size, gene_clusters, unique_gene_symbols, unique_allele_symbols, gene_cluster_symbols
-@@ -505,12 +505,12 @@ def score_alleles(args, mapping_files_pr
+@@ -505,12 +505,12 @@
avg_depth_allele, coverage_allele, mismatch_allele, indel_allele, missing_allele,
size_allele, next_to_del_depth_allele, run_type,unique_gene_symbols, unique_allele_symbols):
# sort into hash for each gene locus
@@ -651,7 +651,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
)
allele_to_gene = dict_of_dicts_inverted_ind(depth_by_gene)
-@@ -553,7 +553,7 @@ def score_alleles(args, mapping_files_pr
+@@ -553,7 +553,7 @@
# Fit linear model to observed Pval distribution vs expected Pval distribution (QQ plot)
pvals.sort(reverse=True)
len_obs_pvals = len(pvals)
@@ -660,7 +660,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
exp_pvals2 = [-log(float(ep) / (len_obs_pvals + 1), 10) for ep in exp_pvals]
# Slope is score
-@@ -698,7 +698,7 @@ def run_bowtie(mapping_files_pre,sample_
+@@ -698,7 +698,7 @@
try:
command += ['-u',str(int(args.stop_after))]
except ValueError:
@@ -669,7 +669,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
if args.other:
x = args.other
-@@ -732,7 +732,7 @@ def get_pileup(args, mapping_files_pre,
+@@ -732,7 +732,7 @@
logging.info('Generate and sort BAM file...')
out_file_bam = mapping_files_pre + ".unsorted.bam"
view_command = [samtools_exec, 'view']
@@ -678,7 +678,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
view_command += ['-@', str(args.threads)]
view_command += ['-b', '-o', out_file_bam, '-q', str(args.mapq), '-S', bowtie_sam_mod]
run_command(view_command)
-@@ -806,12 +806,12 @@ def calculate_ST(allele_scores, ST_db, g
+@@ -806,12 +806,12 @@
try:
clean_st = ST_db[allele_string]
except KeyError:
@@ -695,7 +695,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
clean_st = "NF"
else:
clean_st = "ND"
-@@ -848,7 +848,7 @@ def parse_ST_database(ST_filename,gene_n
+@@ -848,7 +848,7 @@
ST_db = {} # key = allele string, value = ST
gene_names = []
num_gene_cols_expected = len(gene_names_from_fai)
@@ -704,7 +704,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
with open(ST_filename) as f:
count = 0
for line in f:
-@@ -858,23 +858,23 @@ def parse_ST_database(ST_filename,gene_n
+@@ -858,23 +858,23 @@
gene_names = line_split[1:min(num_gene_cols_expected+1,len(line_split))]
for g in gene_names_from_fai:
if g not in gene_names:
@@ -735,7 +735,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
return (ST_db, gene_names)
def get_allele_name_from_db(allele,run_type,args,unique_allele_symbols=False,unique_cluster_symbols=False):
-@@ -936,7 +936,7 @@ def group_allele_dict_by_gene(by_allele,
+@@ -936,7 +936,7 @@
def dict_of_dicts_inverted_ind(dd):
res = dict()
@@ -744,7 +744,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
res.update(dict((key2,key) for key2 in val))
return res
-@@ -946,7 +946,7 @@ def parse_scores(run_type,args,scores, h
+@@ -946,7 +946,7 @@
unique_cluster_symbols,unique_allele_symbols, pileup_file):
# sort into hash for each gene locus
@@ -753,7 +753,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
if coverage_allele[allele] > args.min_coverage ),
run_type,args,
unique_cluster_symbols,unique_allele_symbols)
-@@ -957,7 +957,7 @@ def parse_scores(run_type,args,scores, h
+@@ -957,7 +957,7 @@
for gene in scores_by_gene:
gene_hash = scores_by_gene[gene]
@@ -762,7 +762,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
(top_allele,top_score) = scores_sorted[0]
# check if depth is adequate for confident call
-@@ -1462,7 +1462,7 @@ def map_fileSet_to_db(args, sample_name,
+@@ -1462,7 +1462,7 @@
logging.info("Printing all MLST scores to " + scores_output_file)
scores_output = file(scores_output_file, 'w')
scores_output.write("Allele\tScore\tAvg_depth\tEdge1_depth\tEdge2_depth\tPercent_coverage\tSize\tMismatches\tIndels\tTruncated_bases\tDepthNeighbouringTruncation\tMmaxMAF\n")
@@ -771,7 +771,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
score = scores[allele]
scores_output.write('\t'.join([allele, str(score), str(avg_depth_allele[allele]), \
str(hash_edge_depth[allele][0]), str(hash_edge_depth[allele][1]), \
-@@ -1547,7 +1547,7 @@ def compile_results(args,mlst_results,db
+@@ -1547,7 +1547,7 @@
if mlst_cols == 0:
mlst_header_string = test_string
else:
@@ -780,7 +780,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
test_string_split = test_string.split("\t")
this_mlst_cols = len(test_string_split)
if (mlst_cols == 0) or (mlst_cols == this_mlst_cols):
-@@ -1637,8 +1637,8 @@ def compile_results(args,mlst_results,db
+@@ -1637,8 +1637,8 @@
# log ST counts
if len(mlst_results_master) > 0:
@@ -791,7 +791,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
sts.sort()
for st in sts:
logging.info("ST" + st + "\t" + str(st_counts[st]))
-@@ -1656,9 +1656,9 @@ def main():
+@@ -1656,9 +1656,9 @@
if not os.path.exists(output_dir):
try:
os.makedirs(output_dir)
@@ -803,7 +803,7 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
if args.log is True:
logfile = args.output + ".log"
-@@ -1703,9 +1703,9 @@ def main():
+@@ -1703,9 +1703,9 @@
if not args.mlst_definitions:
# print warning to screen to alert user, may want to stop and restart
@@ -826,12 +826,19 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
--- a/tests/test_slurm_srst2.py
+++ b/tests/test_slurm_srst2.py
-@@ -1,4 +1,4 @@
+@@ -1,10 +1,10 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
import os
import sys
+ import unittest
+
+-from mock import patch
++from unittest.mock import patch
+
+ sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'scripts')))
+
--- a/tests/test_srst2.py
+++ b/tests/test_srst2.py
@@ -1,11 +1,11 @@
@@ -842,8 +849,9 @@ Bug-Upstream: https://github.com/katholt/srst2/issues/122
import sys
import unittest
- from mock import MagicMock, patch
+-from mock import MagicMock, patch
-from StringIO import StringIO
++from unittest.mock import MagicMock, patch
+from io import StringIO
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'scripts')))
View it on GitLab: https://salsa.debian.org/med-team/srst2/-/commit/f5ce539956acde49fc10b57f4d358560d1f3c4a5
--
View it on GitLab: https://salsa.debian.org/med-team/srst2/-/commit/f5ce539956acde49fc10b57f4d358560d1f3c4a5
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