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|
Author: Steffen Moeller
Description: Tests have a series of invocations of the former python executable.
Forwarded: not needed since Debian-specific.
--- a/tests/test_github_issue627/Snakefile
+++ b/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
--- a/tests/test_github_issue627/job.py
+++ b/tests/test_github_issue627/job.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
import time
--- a/tests/test_github_issue_14/pythonTest.py
+++ b/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
--- a/tests/test_issue916/pythonTest.py
+++ b/tests/test_issue916/pythonTest.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
import sys
import os
import local_script
--- a/tests/test_tibanna/README.md
+++ b/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
```
--- a/snakemake/script.py
+++ b/snakemake/script.py
@@ -637,7 +637,7 @@ class PythonScript(ScriptBase):
def _get_python_version(self):
out = self._execute_cmd(
- "python -c \"import sys; print(f'{sys.version_info.major}.{sys.version_info.minor}')\"",
+ "python3 -c \"import sys; print(f'{sys.version_info.major}.{sys.version_info.minor}')\"",
read=True,
)
try:
@@ -651,7 +651,7 @@ class PythonScript(ScriptBase):
py_exec = sys.executable
if self.container_img is not None:
# use python from image
- py_exec = "python"
+ py_exec = "python3"
elif self.conda_env is not None or self.env_modules is not None:
if self._is_python_env():
py_version = self._get_python_version()
@@ -660,7 +660,7 @@ class PythonScript(ScriptBase):
if py_version >= MIN_PY_VERSION:
# Python version is new enough, make use of environment
# to execute script
- py_exec = "python"
+ py_exec = "python3"
else:
logger.warning(
"Environment defines Python "
--- a/snakemake/unit_tests/templates/ruletest.py.jinja2
+++ b/snakemake/unit_tests/templates/ruletest.py.jinja2
@@ -26,7 +26,7 @@ def test_{{ ruletest.name }}():
# Run the test job.
sp.check_output([
- "python",
+ "python3",
"-m",
"snakemake",
"{{ ruletest.target }}",
@@ -53,4 +53,4 @@ def test_{{ ruletest.name }}():
# To modify this behavior, you can inherit from common.OutputChecker in here
# and overwrite the method `compare_files(generated_file, expected_file),
# also see common.py.
- common.OutputChecker(data_path, expected_path, workdir).check()
\ No newline at end of file
+ common.OutputChecker(data_path, expected_path, workdir).check()
|
