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debian/changelog
View file @ 9207cab9
......@@ -9,6 +9,7 @@ spades (3.13.1-1) UNRELEASED; urgency=medium
* Move source package lintian overrides to debian/source.
* Set upstream metadata fields: Repository.
* Make sure Python3 interpreter is used in scripts
* Specify yaml loader
-- Andreas Tille <tille@debian.org> Tue, 08 Oct 2019 18:17:07 +0200
......
debian/control
View file @ 9207cab9
......@@ -9,7 +9,7 @@ Priority: optional
Build-Depends: debhelper-compat (= 12),
dh-python,
cmake,
python-all-dev,
python3-dev,
zlib1g-dev,
libbz2-dev,
libboost-dev,
......
debian/patches/python3.patch
View file @ 9207cab9
......@@ -115,6 +115,24 @@ Description: Make sure Python3 interpreter is used in scripts
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
@@ -214,7 +214,7 @@ def run_iteration(configs_dir, execution
lines = []
with open(cfg_file) as infile:
for line in infile:
- for src, target in replacements.iteritems():
+ for src, target in list(replacements.iteritems()):
line = line.replace(src, target)
lines.append(line)
with open(cfg_file, 'w') as outfile:
@@ -275,7 +275,7 @@ def run_scaffold_correction(configs_dir,
lines = []
with open(cfg_file) as infile:
for line in infile:
- for src, target in replacements.iteritems():
+ for src, target in list(replacements.iteritems()):
line = line.replace(src, target)
lines.append(line)
with open(cfg_file, 'w') as outfile:
--- a/assembler/src/spades_pipeline/truspades/reference_construction.py
+++ b/assembler/src/spades_pipeline/truspades/reference_construction.py
@@ -1,4 +1,4 @@
......
debian/patches/series
View file @ 9207cab9
......@@ -19,3 +19,4 @@ fix-bool-cast
spelling
gcc7.patch
python3.patch
yaml_load.patch
debian/patches/yaml_load.patch 0 → 100644
View file @ 9207cab9
Author: Andreas Tille <tille@debian.org>
Last-Update: Tue, 12 Nov 2019 17:11:17 +0100
Description: Specify yaml loader
see https://github.com/yaml/pyyaml/wiki/PyYAML-yaml.load(input)-Deprecation
--- a/assembler/spades.py
+++ b/assembler/spades.py
@@ -107,7 +107,7 @@ def print_used_values(cfg, log):
" or --meta flag if processing metagenomic dataset)")
log.info(" Reads:")
- dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename, 'r'))
+ dataset_data = pyyaml.load(open(cfg["dataset"].yaml_filename, 'r'), Loader=yaml.FullLoader)
dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(cfg["dataset"].yaml_filename))
support.pretty_print_reads(dataset_data, log)