Nilesh Patra pushed to branch master at Debian Med / python-pybedtools
Commits: 9d07b327 by Nilesh Patra at 2022-10-23T16:19:47+05:30 Add patch to replace yaml.load calls with yaml.safe_load (Closes: #1022076) - - - - - a7840a98 by Nilesh Patra at 2022-10-23T16:24:30+05:30 Change B-D from python3-nose to python3-pytest (Closes: #1018560) - - - - - 59b201e0 by Nilesh Patra at 2022-10-23T16:25:18+05:30 Bump Standards-Version to 4.6.1 (no changes needed) - - - - - 81ae9819 by Nilesh Patra at 2022-10-23T16:25:18+05:30 Upload to unstable - - - - - 4 changed files: - debian/changelog - debian/control - debian/patches/series - + debian/patches/yaml_safe_load.patch Changes: ===================================== debian/changelog ===================================== @@ -1,8 +1,12 @@ -python-pybedtools (0.9.0-2) UNRELEASED; urgency=medium +python-pybedtools (0.9.0-2) unstable; urgency=medium - * Drop lintian-overrides + * Team Upload. + * Add patch to replace yaml.load calls with + yaml.safe_load (Closes: #1022076) + * Change B-D from python3-nose to python3-pytest (Closes: #1018560) + * Bump Standards-Version to 4.6.1 (no changes needed) - -- Andreas Tille <[email protected]> Thu, 17 Feb 2022 15:26:18 +0100 + -- Nilesh Patra <[email protected]> Sun, 23 Oct 2022 16:24:34 +0530 python-pybedtools (0.9.0-1) unstable; urgency=medium ===================================== debian/control ===================================== @@ -13,7 +13,7 @@ Build-Depends: debhelper-compat (= 13), python3-setuptools, python3-pysam, python3-matplotlib, - python3-nose, + python3-pytest, python3-numpy, python3-numpydoc, python3-pandas, @@ -24,7 +24,7 @@ Build-Depends: debhelper-compat (= 13), python3-sphinx, r-base-core, zlib1g-dev -Standards-Version: 4.6.0 +Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/python-pybedtools Vcs-Git: https://salsa.debian.org/med-team/python-pybedtools.git Homepage: https://daler.github.io/pybedtools/ ===================================== debian/patches/series ===================================== @@ -2,3 +2,4 @@ spelling define_filenotfounderror_python2.patch remove_badges_from_documentation.patch add_missing_shebang.patch +yaml_safe_load.patch ===================================== debian/patches/yaml_safe_load.patch ===================================== @@ -0,0 +1,29 @@ +Description: Use yaml.safe_load instead of yaml.load which is deprecated +Author: Nilesh Patra <[email protected]> +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1022076 +Last-Update: 2022-10-23 +--- a/pybedtools/contrib/plotting.py ++++ b/pybedtools/contrib/plotting.py +@@ -524,7 +524,7 @@ + """ + import yaml + +- conf = yaml.load(open(yaml_config)) ++ conf = yaml.safe_load(open(yaml_config)) + + disallowed = ["method", "method_kwargs"] + for dis in disallowed: +--- a/pybedtools/test/test_iter.py ++++ b/pybedtools/test/test_iter.py +@@ -130,9 +130,9 @@ + labels = [] + for config_fn in yamltestdesc: + if hasattr(yaml, "FullLoader"): +- test_cases = yaml.load(open(config_fn).read(), Loader=yaml.FullLoader) ++ test_cases = yaml.safe_load(open(config_fn).read(), Loader=yaml.FullLoader) + else: +- test_cases = yaml.load(open(config_fn).read()) ++ test_cases = yaml.safe_load(open(config_fn).read()) + for test_case in test_cases: + kw = test_case["kwargs"] + View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/-/compare/1c1546f423ab564b3b7d36e338523bc7d0f0725a...81ae981964a7719d0e77f6d6b5cddbe314ea483c -- View it on GitLab: https://salsa.debian.org/med-team/python-pybedtools/-/compare/1c1546f423ab564b3b7d36e338523bc7d0f0725a...81ae981964a7719d0e77f6d6b5cddbe314ea483c You're receiving this email because of your account on salsa.debian.org.
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