[med-svn] [Git][med-team/snakemake][debian_for_upstream_5.14.0_which_requires_conda] 3 commits: Upload to unstable

[Rebecca N. Palmer]

Rebecca N. Palmer pushed to branch debian_for_upstream_5.14.0_which_requires_conda at Debian Med / snakemake


Commits:
13a15261 by Andreas Tille at 2020-04-09T11:17:36+02:00
Upload to unstable

- - - - -
ddcda055 by Rebecca N. Palmer at 2020-04-09T14:27:49+01:00
Use Python 3 in subprocess calls.

- - - - -
c8284853 by Rebecca N. Palmer at 2020-04-09T14:58:47+01:00
Merge branch 'master' into debian_for_upstream_5.14.0_which_requires_conda

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/py3_subprocess.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,11 +1,5 @@
 snakemake (5.14.0-1) UNRELEASED; urgency=medium
 
-  * Team upload.
-
-  [ Rebecca N. Palmer ]
-  * Exclude lazy_property to make Sphinx succeed.
-    Closes: #955056
-
   [ Andreas Tille ]
   * New upstream version
   * Remove trailing whitespace in debian/changelog (routine-update)
@@ -14,7 +8,18 @@ snakemake (5.14.0-1) UNRELEASED; urgency=medium
   * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
     Repository-Browse.
 
- -- Andreas Tille <tille at debian.org>  Thu, 09 Apr 2020 10:39:25 +0200
+  [ Rebecca N. Palmer ]
+  * Use Python 3 in subprocess calls.
+
+ -- Rebecca N. Palmer <rebecca_palmer at zoho.com>  Thu, 09 Apr 2020 14:57:00 +0100
+
+snakemake (5.10.0-3) unstable; urgency=medium
+
+  [ Rebecca N. Palmer ]
+  * Exclude lazy_property to make Sphinx succeed.
+    Closes: #955056
+
+ -- Andreas Tille <tille at debian.org>  Thu, 09 Apr 2020 11:09:24 +0200
 
 snakemake (5.10.0-2) unstable; urgency=medium
 


=====================================
debian/patches/py3_subprocess.patch
=====================================
@@ -0,0 +1,29 @@
+Description: Use Python 3 in subprocess calls
+
+TODO - are any of the ones in snakemake/script.py:execute_script a problem?
+
+Author: Rebecca N. Palmer <rebecca_palmer at zoho.com>
+Forwarded: no
+
+--- snakemake-5.14.0.orig/tests/test_linting.py
++++ snakemake-5.14.0/tests/test_linting.py
+@@ -18,7 +18,7 @@ def test_lint(lint, case):
+         out = (
+             sp.check_output(
+                 [
+-                    "python",
++                    "python3",
+                     "-m",
+                     "snakemake",
+                     "--lint",
+--- snakemake-5.14.0.orig/tests/test_tibanna.py
++++ snakemake-5.14.0/tests/test_tibanna.py
+@@ -8,7 +8,7 @@ from common import *
+ # run tibanna test before any moto-related tests because they apparently render AWS environment variables invalid or uneffective.
+ def test_tibanna():
+     workdir = dpath("test_tibanna")
+-    subprocess.check_call(["python", "cleanup.py"], cwd=workdir)
++    subprocess.check_call(["python3", "cleanup.py"], cwd=workdir)
+ 
+     os.environ["TEST_ENVVAR1"] = "test"
+     os.environ["TEST_ENVVAR2"] = "test"


=====================================
debian/patches/series
=====================================
@@ -12,3 +12,4 @@
 boto3_is_just_boto
 python3
 workaround_sphinx_issue.patch
+py3_subprocess.patch



View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/f671d67b08614c65e4da995dc1d3cba2a7ee2ba4...c828485311e9ad238e27c94d3a76e366b458564d

-- 
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/f671d67b08614c65e4da995dc1d3cba2a7ee2ba4...c828485311e9ad238e27c94d3a76e366b458564d
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