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 -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/011024338e72a6bf0cadb111aa739680ebbd0862 You're receiving this email because of your account on salsa.debian.org.
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