[med-svn] [Git][med-team/spades][master] 5 commits: initialize changelog.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Oct 23 16:01:07 BST 2022
Étienne Mollier pushed to branch master at Debian Med / spades
Commits:
7ed02086 by Étienne Mollier at 2022-10-23T15:38:01+02:00
initialize changelog.
- - - - -
95cf2c9e by Étienne Mollier at 2022-10-23T16:57:49+02:00
d/control: add missing build-deps following llvm reorganization.
This fixes failure to build from source caught by archive rebuild.
Closes: #1022309
- - - - -
25e942f1 by Étienne Mollier at 2022-10-23T16:58:23+02:00
yaml_load.patch: update to fix new pyyaml.load calls.
Closes: #1022086
- - - - -
6da1e5a4 by Étienne Mollier at 2022-10-23T16:58:39+02:00
d/copyright: bump copyright year.
- - - - -
919244fc by Étienne Mollier at 2022-10-23T17:00:45+02:00
ready to upload to unstable.
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/yaml_load.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+spades (3.15.5+dfsg-2) unstable; urgency=medium
+
+ * d/control: add missing build-deps following llvm reorganization.
+ (Closes: #1022309)
+ * yaml_load.patch: update to fix new pyyaml.load calls. (Closes: #1022086)
+ * d/copyright: bump copyright year.
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 23 Oct 2022 16:59:13 +0200
+
spades (3.15.5+dfsg-1) unstable; urgency=medium
* New upstream version 3.15.5+dfsg
=====================================
debian/control
=====================================
@@ -9,12 +9,16 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-python,
+ clang-format,
+ clang-tidy,
+ clang-tools,
cmake,
python3-all,
zlib1g-dev,
libbz2-dev,
libbam-dev,
libbamtools-dev,
+ libc++-dev,
libhts-dev,
libnlopt-dev,
libnlopt-cxx-dev,
=====================================
debian/copyright
=====================================
@@ -30,6 +30,7 @@ Files: debian/*
Copyright: 2014-2016 Andreas Tille <tille at debian.org>
2015-2016 Afif Elghraoui <afif at debian.org>
2016 Sascha Steinbiss <sascha at steinbiss.name>
+ 2021-2022 Étienne Mollier <emollier at debian.org>
License: GPL-2+
Files: assembler/src/projects/ionhammer/seqeval/*
=====================================
debian/patches/yaml_load.patch
=====================================
@@ -1,7 +1,9 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 12 Nov 2019 17:11:17 +0100
+Last-Update: 2022-10-23
Description: Specify yaml loader
see https://github.com/yaml/pyyaml/wiki/PyYAML-yaml.load(input)-Deprecation
+Reviewed-By: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1022086
--- spades.orig/assembler/spades.py
+++ spades/assembler/spades.py
@@ -156,3 +158,65 @@ Description: Specify yaml loader
return info
+--- spades.orig/assembler/src/spades_pipeline/stages/before_start_stage.py
++++ spades/assembler/src/spades_pipeline/stages/before_start_stage.py
+@@ -29,7 +29,7 @@
+ self.tmp_files = []
+
+ if (os.path.isfile(os.path.join(output_dir, "run_spades.yaml"))):
+- previous_pipeline = pyyaml.load(open(os.path.join(output_dir, "run_spades.yaml")))
++ previous_pipeline = pyyaml.load(open(os.path.join(output_dir, "run_spades.yaml")), Loader=pyyaml.FullLoader)
+ for previous_stage in previous_pipeline:
+ self.tmp_files += previous_stage["del_after"]
+
+--- spades.orig/assembler/src/spades_pipeline/stages/error_correction_stage.py
++++ spades/assembler/src/spades_pipeline/stages/error_correction_stage.py
+@@ -47,7 +47,7 @@
+ import pyyaml2 as pyyaml
+ elif sys.version.startswith("3."):
+ import pyyaml3 as pyyaml
+- data = pyyaml.load(open(filename))
++ data = pyyaml.load(open(filename), Loader=pyyaml.FullLoader)
+ data["dataset"] = cfg.dataset_yaml_filename
+ data["working_dir"] = cfg.tmp_dir
+ data["output_dir"] = cfg.output_dir
+--- spades.orig/assembler/src/test/teamcity/teamcity_kmertools/teamcity_readfilter.py
++++ spades/assembler/src/test/teamcity/teamcity_kmertools/teamcity_readfilter.py
+@@ -63,7 +63,7 @@
+ elif sys.version.startswith('3.'):
+ import pyyaml3 as pyyaml
+
+- info = pyyaml.load(open(info_filename, 'r'))
++ info = pyyaml.load(open(info_filename, 'r'), Loader=pyyaml.FullLoader)
+ return info
+
+
+--- spades.orig/assembler/src/test/teamcity/teamcity_workflow/workflow_base.py
++++ spades/assembler/src/test/teamcity/teamcity_workflow/workflow_base.py
+@@ -67,7 +67,7 @@
+ elif sys.version.startswith('3.'):
+ import pyyaml3 as pyyaml
+
+- info = pyyaml.load(open(info_filename, 'r'))
++ info = pyyaml.load(open(info_filename, 'r'), Loader=pyyaml.FullLoader)
+ return info
+
+
+--- spades.orig/assembler/src/test/teamcity/teamcity_workflow/workflow_kmer.py
++++ spades/assembler/src/test/teamcity/teamcity_workflow/workflow_kmer.py
+@@ -27,7 +27,7 @@
+ def get_kmer_list(path):
+ run_spades_yaml = os.path.join(path, "run_spades.yaml")
+
+- stages = pyyaml.load(open(run_spades_yaml))
++ stages = pyyaml.load(open(run_spades_yaml), Loader=pyyaml.FullLoader)
+ kmers = []
+ for stage in stages:
+ stage_name = stage['STAGE']
+@@ -62,4 +62,4 @@
+ return 12
+
+
+-workflow_base.main(check_test=check_kmer_set)
+\ No newline at end of file
++workflow_base.main(check_test=check_kmer_set)
View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/1de58481d8bfcccbd24e042d8f7081bf9a27ae19...919244fc220185bc65370ddbf8480977c6215af4
--
View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/1de58481d8bfcccbd24e042d8f7081bf9a27ae19...919244fc220185bc65370ddbf8480977c6215af4
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