[med-svn] [Git][med-team/spades][master] 4 commits: d/t/run-upstreams-tests: make tests a bit more verbose.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Jun 25 15:41:11 BST 2022
Étienne Mollier pushed to branch master at Debian Med / spades
Commits:
95071fcf by Étienne Mollier at 2022-06-25T14:28:47+02:00
d/t/run-upstreams-tests: make tests a bit more verbose.
- - - - -
393ccb17 by Étienne Mollier at 2022-06-25T16:13:05+02:00
Adjust 0003_accept-system-bwa.patch: import support functions.
Closes: #1011968
- - - - -
5c254e6b by Étienne Mollier at 2022-06-25T16:15:07+02:00
Refresh yaml_load.patch.
- - - - -
88edc557 by Étienne Mollier at 2022-06-25T16:15:59+02:00
initialize changelog
- - - - -
4 changed files:
- debian/changelog
- debian/patches/0003_accept-system-bwa.patch
- debian/patches/yaml_load.patch
- debian/tests/run-upstreams-tests
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+spades (3.15.4+dfsg-3) UNRELEASED; urgency=medium
+
+ * d/t/run-upstreams-tests: make tests a bit more verbose.
+ * Adjust 0003_accept-system-bwa.patch: import support functions.
+ (Closes: #1011968)
+ * Refresh yaml_load.patch.
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 25 Jun 2022 16:15:22 +0200
+
spades (3.15.4+dfsg-2) unstable; urgency=medium
* Team upload.
=====================================
debian/patches/0003_accept-system-bwa.patch
=====================================
@@ -13,9 +13,9 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
In case you consider taking over the patch I'd suggest to take it over into
some common import file.
---- a/assembler/src/spades_pipeline/support.py
-+++ b/assembler/src/spades_pipeline/support.py
-@@ -70,6 +70,22 @@ def warning(warn_str, log=None, prefix="
+--- spades.orig/assembler/src/spades_pipeline/support.py
++++ spades/assembler/src/spades_pipeline/support.py
+@@ -70,6 +70,22 @@
sys.stdout.write("\n\n%s %s\n\n\n" % (prefix, warn_str))
sys.stdout.flush()
@@ -38,7 +38,7 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
def wsl_check():
def in_wsl():
-@@ -130,7 +146,14 @@ def check_binaries(binary_dir, log):
+@@ -131,7 +147,14 @@
for binary in ["spades-hammer", "spades-ionhammer", "spades-core", "spades-bwa"]:
binary_path = os.path.join(binary_dir, binary)
if not os.path.isfile(binary_path):
@@ -54,9 +54,9 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
def check_file_existence(input_filename, message="", log=None):
---- a/assembler/src/spades_pipeline/options_parser.py
-+++ b/assembler/src/spades_pipeline/options_parser.py
-@@ -992,7 +992,10 @@ def add_to_cfg(cfg, log, bin_home, spade
+--- spades.orig/assembler/src/spades_pipeline/options_parser.py
++++ spades/assembler/src/spades_pipeline/options_parser.py
+@@ -992,7 +992,10 @@
if (not args.only_error_correction) and args.mismatch_corrector:
cfg["mismatch_corrector"] = empty_config()
cfg["mismatch_corrector"].__dict__["skip-masked"] = None
@@ -68,9 +68,18 @@ Description: Enable using Debian packaged bwa instead of bwa-spades
cfg["mismatch_corrector"].__dict__["threads"] = args.threads
cfg["mismatch_corrector"].__dict__["output-dir"] = args.output_dir
cfg["run_truseq_postprocessing"] = options_storage.run_truseq_postprocessing
---- a/assembler/src/spades_pipeline/scripts/postprocessing_script.py
-+++ b/assembler/src/spades_pipeline/scripts/postprocessing_script.py
-@@ -78,7 +94,10 @@ def main():
+--- spades.orig/assembler/src/spades_pipeline/scripts/postprocessing_script.py
++++ spades/assembler/src/spades_pipeline/scripts/postprocessing_script.py
+@@ -15,6 +15,8 @@
+ from os.path import abspath, dirname, realpath, join, isfile
+ from site import addsitedir
+
++sys.path += [("/usr/share/spades/spades_pipeline")]
++import support
+
+ def parse_args():
+ parser = argparse.ArgumentParser()
+@@ -78,7 +80,10 @@
# run command
if isfile(args.result_scaffolds_filename):
shutil.move(args.result_scaffolds_filename, args.assembled_scaffolds_filename)
=====================================
debian/patches/yaml_load.patch
=====================================
@@ -3,9 +3,9 @@ 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
-@@ -114,7 +114,7 @@ def print_used_values(cfg, log):
+--- spades.orig/assembler/spades.py
++++ spades/assembler/spades.py
+@@ -114,7 +114,7 @@
" for RNA-Seq use '--rna'.")
log.info(" Reads:")
@@ -14,7 +14,7 @@ Description: Specify yaml loader
dataset_data = support.relative2abs_paths(dataset_data, os.path.dirname(cfg["dataset"].yaml_filename))
support.pretty_print_reads(dataset_data, log)
-@@ -350,7 +350,7 @@ def clear_configs(cfg, log, command_befo
+@@ -334,7 +334,7 @@
spades_commands_fpath = os.path.join(cfg["common"].output_dir, "run_spades.yaml")
with open(spades_commands_fpath) as stream:
@@ -23,7 +23,7 @@ Description: Specify yaml loader
restart_from_stage_id = None
for num in range(len(old_pipeline)):
-@@ -385,7 +385,7 @@ def clear_configs(cfg, log, command_befo
+@@ -369,7 +369,7 @@
def get_first_incomplete_command(filename):
with open(filename) as stream:
@@ -32,9 +32,9 @@ Description: Specify yaml loader
first_incomplete_stage_id = 0
while first_incomplete_stage_id < len(old_pipeline):
---- a/assembler/src/tools/reads_utils/reads_quality.py
-+++ b/assembler/src/tools/reads_utils/reads_quality.py
-@@ -148,7 +148,7 @@ print("Analyzing datasets")
+--- spades.orig/assembler/src/tools/reads_utils/reads_quality.py
++++ spades/assembler/src/tools/reads_utils/reads_quality.py
+@@ -148,7 +148,7 @@
for dataset in datasets:
try:
@@ -43,9 +43,9 @@ Description: Specify yaml loader
except pyyaml.YAMLError as exc:
support.warning('skipping ' + dataset + ': exception caught while parsing YAML file (' + options_storage.dataset_yaml_filename + '):\n' + str(exc))
continue
---- a/assembler/src/spades_pipeline/options_parser.py
-+++ b/assembler/src/spades_pipeline/options_parser.py
-@@ -1062,14 +1062,14 @@ def postprocessing(args, cfg, dataset_da
+--- spades.orig/assembler/src/spades_pipeline/options_parser.py
++++ spades/assembler/src/spades_pipeline/options_parser.py
+@@ -1062,14 +1062,14 @@
if load_processed_dataset:
if os.path.isfile(processed_dataset_fpath):
try:
@@ -62,9 +62,9 @@ Description: Specify yaml loader
except pyyaml.YAMLError:
_, exc, _ = sys.exc_info()
support.error(
---- a/assembler/src/spades_pipeline/scripts/compress_all.py
-+++ b/assembler/src/spades_pipeline/scripts/compress_all.py
-@@ -38,7 +38,7 @@ def compress_dataset_files(input_file, e
+--- spades.orig/assembler/src/spades_pipeline/scripts/compress_all.py
++++ spades/assembler/src/spades_pipeline/scripts/compress_all.py
+@@ -38,7 +38,7 @@
except:
from joblib import Parallel, delayed
@@ -73,7 +73,7 @@ Description: Specify yaml loader
remove_not_corrected_reads(output_dir)
is_changed = False
if gzip_output:
-@@ -80,7 +80,7 @@ def compress_dataset_files(input_file, e
+@@ -80,7 +80,7 @@
if not_used_yaml_file != "":
is_changed = True
@@ -82,9 +82,9 @@ Description: Specify yaml loader
dataset_data += not_used_dataset_data
log.info("\n== Info about datasets not used in error correction stage is loaded")
---- a/assembler/src/spades_pipeline/scripts/postprocessing_script.py
-+++ b/assembler/src/spades_pipeline/scripts/postprocessing_script.py
-@@ -80,7 +80,7 @@ def main():
+--- spades.orig/assembler/src/spades_pipeline/scripts/postprocessing_script.py
++++ spades/assembler/src/spades_pipeline/scripts/postprocessing_script.py
+@@ -66,7 +66,7 @@
elif sys.version.startswith("3."):
import pyyaml3 as pyyaml
@@ -93,9 +93,9 @@ Description: Specify yaml loader
# init python_lib_folder
python_modules_home = abspath(dirname(realpath(__file__)))
---- a/assembler/src/spades_pipeline/stages/correction_stage.py
-+++ b/assembler/src/spades_pipeline/stages/correction_stage.py
-@@ -25,7 +25,7 @@ def prepare_config_corr(filename, cfg, e
+--- spades.orig/assembler/src/spades_pipeline/stages/correction_stage.py
++++ spades/assembler/src/spades_pipeline/stages/correction_stage.py
+@@ -25,7 +25,7 @@
import pyyaml2 as pyyaml
elif sys.version.startswith("3."):
import pyyaml3 as pyyaml
@@ -104,9 +104,9 @@ Description: Specify yaml loader
data["dataset"] = cfg.dataset
data["output_dir"] = cfg.output_dir
data["work_dir"] = cfg.tmp_dir
---- a/assembler/src/spades_pipeline/stages/spades_stage.py
-+++ b/assembler/src/spades_pipeline/stages/spades_stage.py
-@@ -30,7 +30,7 @@ def get_read_length(output_dir, K, ext_p
+--- spades.orig/assembler/src/spades_pipeline/stages/spades_stage.py
++++ spades/assembler/src/spades_pipeline/stages/spades_stage.py
+@@ -30,7 +30,7 @@
import pyyaml2 as pyyaml
elif sys.version.startswith("3."):
import pyyaml3 as pyyaml
@@ -115,17 +115,17 @@ Description: Specify yaml loader
max_read_length = int(est_params_data["nomerge max read length"])
log.info("Max read length detected as %d" % max_read_length)
if max_read_length == 0:
---- a/assembler/src/spades_pipeline/truspades/moleculo_filter_contigs.py
-+++ b/assembler/src/spades_pipeline/truspades/moleculo_filter_contigs.py
-@@ -37,4 +37,4 @@ class ContigLengthFilter:
+--- spades.orig/assembler/src/spades_pipeline/truspades/moleculo_filter_contigs.py
++++ spades/assembler/src/spades_pipeline/truspades/moleculo_filter_contigs.py
+@@ -37,4 +37,4 @@
return len(contig.seq) >= self.min_length
# def Filter(contigs, left_reads, right_reads, length_threshold, pattern):
-# dataset_data = pyyaml.load(yaml_file, 'r')
+# dataset_data = pyyaml.load(yaml_file, 'r', Loader=pyyaml.FullLoader)
---- a/assembler/src/test/teamcity/teamcity_kmertools/teamcity_gbuilder.py
-+++ b/assembler/src/test/teamcity/teamcity_kmertools/teamcity_gbuilder.py
-@@ -63,7 +63,7 @@ def load_info(info_filename):
+--- spades.orig/assembler/src/test/teamcity/teamcity_kmertools/teamcity_gbuilder.py
++++ spades/assembler/src/test/teamcity/teamcity_kmertools/teamcity_gbuilder.py
+@@ -63,7 +63,7 @@
elif sys.version.startswith('3.'):
import pyyaml3 as pyyaml
@@ -134,9 +134,9 @@ Description: Specify yaml loader
return info
---- a/assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmercount.py
-+++ b/assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmercount.py
-@@ -63,7 +63,7 @@ def load_info(info_filename):
+--- spades.orig/assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmercount.py
++++ spades/assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmercount.py
+@@ -63,7 +63,7 @@
elif sys.version.startswith('3.'):
import pyyaml3 as pyyaml
@@ -145,9 +145,9 @@ Description: Specify yaml loader
return info
---- a/assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmerestimating.py
-+++ b/assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmerestimating.py
-@@ -63,7 +63,7 @@ def load_info(info_filename):
+--- spades.orig/assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmerestimating.py
++++ spades/assembler/src/test/teamcity/teamcity_kmertools/teamcity_kmerestimating.py
+@@ -63,7 +63,7 @@
elif sys.version.startswith('3.'):
import pyyaml3 as pyyaml
=====================================
debian/tests/run-upstreams-tests
=====================================
@@ -1,7 +1,7 @@
#!/bin/sh
# autopkgtest check: Run the spades tests for each tool.
# Author: Sascha Steinbiss <satta at debian.org>
-set -e
+set -ex
WORKDIR=$(mktemp -d)
trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/54973e8fab65ecec4d19150ee0ade1563d161a0d...88edc5574662f6d3b8b46b6087817b251175dee6
--
View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/54973e8fab65ecec4d19150ee0ade1563d161a0d...88edc5574662f6d3b8b46b6087817b251175dee6
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