[med-svn] [Git][med-team/qcumber][master] 3 commits: Recommends: dwgsim
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Apr 5 10:06:45 BST 2022
Andreas Tille pushed to branch master at Debian Med / qcumber
Commits:
332135d9 by Andreas Tille at 2022-04-05T10:16:30+02:00
Recommends: dwgsim
- - - - -
e78f90c3 by Andreas Tille at 2022-04-05T10:54:20+02:00
Replace deprecated yaml.load() by yaml.safe_load()
- - - - -
543c094b by Andreas Tille at 2022-04-05T11:06:25+02:00
debian/get-minikrakendb
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/get-minikrakendb
- debian/patches/series
- + debian/patches/yaml_load.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+qcumber (2.3.0-3) UNRELEASED; urgency=medium
+
+ * Recommends: dwgsim
+ * Replace yaml.load() by yaml.safe_load()
+ * Fix debian/get-minikrakendb
+
+ -- Andreas Tille <tille at debian.org> Tue, 05 Apr 2022 10:16:12 +0200
+
qcumber (2.3.0-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -34,6 +34,7 @@ Depends: ${python3:Depends},
r-cran-ggplot2,
r-cran-quantreg,
snakemake
+Recommends: dwgsim
Conflicts: qc-pipeline
Provides: qc-pipeline
Replaces: qc-pipeline
=====================================
debian/get-minikrakendb
=====================================
@@ -2,7 +2,7 @@
conffile=/etc/qcumber/config.txt
krakendb=`sed '/\[PATH\]/,$d' $conffile | grep "^kraken_db" | head -n 1 | sed 's/^kraken_db *= *\([^ ]\+\) *$/\1/'`
-KRAKENDBDIR="echo krakendb | sed 's?/minikraken_20141208/*$//'"
+KRAKENDBDIR=`echo $krakendb | sed 's?/minikraken_20141208/*$??'`
check_krakendb_md5 () {
if ! grep -q "$1.*$2" minikraken.md5 ; then
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ check_fasta.patch
make_executable.patch
fix_html_file_licenses.patch
add-python-shebang.patch
+yaml_load.patch
=====================================
debian/patches/yaml_load.patch
=====================================
@@ -0,0 +1,89 @@
+Description: Replace deprecated yaml.load() by yaml.safe_load()
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 05 Apr 2022 10:16:12 +0200
+
+--- a/QCumber-2
++++ b/QCumber-2
+@@ -174,7 +174,7 @@ def main():
+ configfile = default_configfile
+
+ if configfile:
+- config_args = yaml.load(open(configfile, "r"))
++ config_args = yaml.safe_load(open(configfile, "r"))
+ keep_args = dict()
+ for arg in config_args.keys():
+ print(arg)
+@@ -193,7 +193,7 @@ def main():
+ if arguments["rename"]:
+ arguments["rename"] = os.path.abspath(arguments["rename"])
+
+- parameter = yaml.load(
++ parameter = yaml.safe_load(
+ open(os.path.join(
+ os.path.dirname(os.path.realpath(__file__)),
+ "config",
+@@ -206,7 +206,7 @@ def main():
+ with open(os.path.join(qcumber_path,
+ 'filenames.yaml'),
+ 'r') as filetype_h:
+- filename_types = yaml.load(filetype_h)
++ filename_types = yaml.safe_load(filetype_h)
+ all_files = []
+ for file_or_dir in arguments["input"]:
+ if os.path.isdir(file_or_dir):
+--- a/input_utils.py
++++ b/input_utils.py
+@@ -1149,7 +1149,7 @@ def ordered_load(stream, Loader=yaml.Loa
+ OrderedLoader.add_constructor(
+ yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG,
+ construct_mapping)
+- return yaml.load(stream, OrderedLoader)
++ return yaml.safe_load(stream, OrderedLoader)
+
+
+ def longest_common_prefix(str1, str2):
+--- a/modules/init.snakefile
++++ b/modules/init.snakefile
+@@ -48,7 +48,7 @@ classification_path= main_path + "/Class
+
+ try:
+ with open('samples.yaml', 'r') as sample_h:
+- sample_info_new = yaml.load(sample_h)
++ sample_info_new = yaml.safe_load(sample_h)
+ sample_info_new_complex = dict((x, y)
+ for x, y in sample_info.items()
+ if isinstance(y, list))
+@@ -168,7 +168,7 @@ def plot_summary(csv, outfile):
+ plt.savefig(outfile)
+
+ #------------------------------------------< make config files >-------------------------------------------------------#
+-parameter = yaml.load(open(os.path.join(geninfo_config["QCumber_path"], "config", "parameter.txt"), "r"))
++parameter = yaml.safe_load(open(os.path.join(geninfo_config["QCumber_path"], "config", "parameter.txt"), "r"))
+
+ sample_dict = dict([(geninfo_config["Sample information"]["rename"][get_name(x)], x) for x in sum(geninfo_config["Sample information"]["samples"].values(), [])])
+
+@@ -192,7 +192,7 @@ unique_samples = dict(joined_samples, **
+ (x, geninfo_config["Sample information"]["samples"][x]) for x in geninfo_config["Sample information"]["samples"].keys()
+ if x not in sum(geninfo_config["Sample information"]["join_lanes"].values(), [])))
+
+-cmd_input = yaml.load(open("config.yaml","r"))
++cmd_input = yaml.safe_load(open("config.yaml","r"))
+ if config["reference"] or config["index"]:
+ config["nomapping"] = False
+ else:
+--- a/test/test_qcumber2.py
++++ b/test/test_qcumber2.py
+@@ -138,11 +138,11 @@ def main():
+ else:
+ try:
+ with open(test_run_c_file, 'r') as testrun_conf_file:
+- user_config_dict = yaml.load(testrun_conf_file)
++ user_config_dict = yaml.safe_load(testrun_conf_file)
+ except FileNotFoundError:
+ try:
+ with open(default_test_run_c_file, 'r') as testrun_conf_file:
+- user_config_dict = yaml.load(testrun_conf_file)
++ user_config_dict = yaml.safe_load(testrun_conf_file)
+ except FileNotFoundError:
+ eprint('No config file found!')
+ except yaml.YAMLError as exc:
View it on GitLab: https://salsa.debian.org/med-team/qcumber/-/compare/c28dd51885520dfd931ee43ded1d33d601212b55...543c094b82bfedb8b870144e58838bd003b23ac4
--
View it on GitLab: https://salsa.debian.org/med-team/qcumber/-/compare/c28dd51885520dfd931ee43ded1d33d601212b55...543c094b82bfedb8b870144e58838bd003b23ac4
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