[med-svn] [Git][med-team/snakemake][master] Not invoking "python" binary that is python3 in Debian

[Steffen Möller (@moeller)]

Steffen Möller pushed to branch master at Debian Med / snakemake


Commits:
01102433 by Steffen Moeller at 2021-10-19T02:17:47+02:00
Not invoking "python" binary that is python3 in Debian

- - - - -


2 changed files:

- + debian/patches/python2to3.patch
- debian/patches/series


Changes:

=====================================
debian/patches/python2to3.patch
=====================================
@@ -0,0 +1,60 @@
+Author: Steffen Moeller
+Description: Tests have a series of invocations of the former python executable.
+Forwarded: not needed since Debian-specific.
+
+Index: snakemake/tests/test_github_issue627/Snakefile
+===================================================================
+--- snakemake.orig/tests/test_github_issue627/Snakefile
++++ snakemake/tests/test_github_issue627/Snakefile
+@@ -2,7 +2,7 @@ rule:
+     shell:
+         """
+         set +e
+-        python -m snakemake --cores 1 -p --profile . -s Snakefile.internal
++        python3 -m snakemake --cores 1 -p --profile . -s Snakefile.internal
+         RETVAL=$?
+         set -e
+ 
+Index: snakemake/tests/test_github_issue627/job.py
+===================================================================
+--- snakemake.orig/tests/test_github_issue627/job.py
++++ snakemake/tests/test_github_issue627/job.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import time
+ 
+Index: snakemake/tests/test_github_issue_14/pythonTest.py
+===================================================================
+--- snakemake.orig/tests/test_github_issue_14/pythonTest.py
++++ snakemake/tests/test_github_issue_14/pythonTest.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import sys
+ import os
+ import local_script
+Index: snakemake/tests/test_issue916/pythonTest.py
+===================================================================
+--- snakemake.orig/tests/test_issue916/pythonTest.py
++++ snakemake/tests/test_issue916/pythonTest.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import sys
+ import os
+ import local_script
+Index: snakemake/tests/test_tibanna/README.md
+===================================================================
+--- snakemake.orig/tests/test_tibanna/README.md
++++ snakemake/tests/test_tibanna/README.md
+@@ -5,7 +5,7 @@ tibanna deploy_unicorn --usergroup=johan
+ ```
+ # run the following to do a test run
+ pip install -U tibanna
+-python cleanup.py  # first delete output files that are already on s3
++python3 cleanup.py  # first delete output files that are already on s3
+ export TIBANNA_DEFAULT_STEP_FUNCTION_NAME=tibanna_unicorn_johannes
+ snakemake --tibanna --use-conda --configfile=config.json --default-remote-prefix=snakemake-tibanna-test/1
+ ```


=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ python3.patch
 workaround_sphinx_issue.patch
 remove_ccbysa_snippets.patch
 fix_test_pytest.patch
+python2to3.patch



View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/011024338e72a6bf0cadb111aa739680ebbd0862

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View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/011024338e72a6bf0cadb111aa739680ebbd0862
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