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Description: Use Python 3 in subprocess calls
TODO - are any of the ones in snakemake/script.py:execute_script a problem?
Author: Michael R. Crusoe <michael.crusoe@gmail.com>, Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no
--- a/tests/test_delete_all_output/Snakefile
+++ b/tests/test_delete_all_output/Snakefile
@@ -10,9 +10,9 @@ rule delete_all_output:
"""
echo $PATH
ls
- python -m snakemake --cores 1 -s Snakefile_inner all && \
+ python3 -m snakemake --cores 1 -s Snakefile_inner all && \
rm nothere && \
- python -m snakemake --cores 1 -s Snakefile_inner --delete-all-output all && \
+ python3 -m snakemake --cores 1 -s Snakefile_inner --delete-all-output all && \
test -f infile && test ! -f intermediate && test ! -f somedir/final && \
test ! -d empty_dir && test ! -L dangling && test ! -d full_dir
"""
@@ -21,8 +21,8 @@ rule delete_temp_output:
output: touch("delete_temp_output")
shell:
"""
- python -m snakemake --cores 1 -s Snakefile_inner --notemp temp && \
- python -m snakemake --cores 1 -s Snakefile_inner --delete-temp-output temp && \
+ python3 -m snakemake --cores 1 -s Snakefile_inner --notemp temp && \
+ python3 -m snakemake --cores 1 -s Snakefile_inner --delete-temp-output temp && \
test -f infile && test ! -f temp_intermediate && \
test ! -d temp_empty_dir && test ! -d temp_full_dir && test -f temp_keep
"""
--- a/tests/test_list_untracked/Snakefile
+++ b/tests/test_list_untracked/Snakefile
@@ -2,4 +2,4 @@ shell.executable("bash")
rule run_test:
output: "leftover_files"
- shell: "python -m snakemake -s Snakefile_inner --list-untracked 2> {output}"
+ shell: "python3 -m snakemake -s Snakefile_inner --list-untracked 2> {output}"
--- a/tests/tests.py
+++ b/tests/tests.py
@@ -1293,7 +1293,7 @@ def test_convert_to_cwl():
workdir = dpath("test_convert_to_cwl")
# run(workdir, export_cwl=os.path.join(workdir, "workflow.cwl"))
shell(
- "cd {workdir}; PYTHONPATH={src} python -m snakemake --export-cwl workflow.cwl",
+ "cd {workdir}; PYTHONPATH={src} python3 -m snakemake --export-cwl workflow.cwl",
src=os.getcwd(),
)
shell("cd {workdir}; cwltool --singularity workflow.cwl")
@@ -1395,7 +1395,7 @@ def test_filegraph():
dot_path = dot_path.replace("\\", "/")
# make sure the calls work
- shell("cd {workdir};python -m snakemake --filegraph > {dot_path}")
+ shell("cd {workdir};python3 -m snakemake --filegraph > {dot_path}")
# make sure the output can be interpreted by dot
with open(dot_path, "rb") as dot_file, open(pdf_path, "wb") as pdf_file:
@@ -1882,8 +1882,8 @@ def test_github_issue1384():
shell(
"""
cd {tmpdir}
- python -m snakemake --generate-unit-tests
- pytest -v .tests/unit
+ python3 -m snakemake --generate-unit-tests
+ python3 -m pytest -v .tests/unit
"""
)
finally:
--- a/tests/test_profile/Snakefile
+++ b/tests/test_profile/Snakefile
@@ -1,3 +1,3 @@
rule:
shell:
- "python -m snakemake --cores 1 --profile . -s Snakefile.internal"
+ "python3 -m snakemake --cores 1 --profile . -s Snakefile.internal"
--- a/tests/test_linting.py
+++ b/tests/test_linting.py
@@ -18,7 +18,7 @@ def test_lint(lint, case):
out = (
sp.check_output(
[
- "python",
+ "python3",
"-m",
"snakemake",
"--lint",
--- a/tests/test_tibanna.py
+++ b/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"
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