[med-svn] [Git][med-team/python-pybedtools][master] 4 commits: Add patch to replace yaml.load calls with yaml.safe_load (Closes: #1022076)

[Nilesh Patra (@nilesh)]

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 <tille at debian.org>  Thu, 17 Feb 2022 15:26:18 +0100
+ -- Nilesh Patra <nilesh at debian.org>  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 <nilesh at debian.org>
+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
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