generate unit test with snakemake but missing quote for configfile in generated test scripts #843
Description
snakemake 5.31.1
I ran my workflow with success a first time
snakemake --configfile config/config_test_rapidrun.yaml -s Snakefile --cores 8 --use-conda
and then I ran again my workflow to generate unit test scripts using --generate-unit-tests
snakemake --configfile config/config_test_rapidrun.yaml -s Snakefile --cores 8 --use-conda --generate-unit-tests
I ran pytest3
python3 -m pytest .tests/unit/
Then all the tests failed. It appears that the path of the configfile is not quoted inside the scripts:
Instance of error:
========================================================================== ERRORS ==========================================================================
____________________________________________________ ERROR collecting .tests/unit/test_trim_primers.py _____________________________________________________
../../../miniconda3/envs/snakemake_rapidrun/lib/python3.9/site-packages/_pytest/python.py:578: in _importtestmodule
mod = import_path(self.fspath, mode=importmode)
../../../miniconda3/envs/snakemake_rapidrun/lib/python3.9/site-packages/_pytest/pathlib.py:531: in import_path
importlib.import_module(module_name)
../../../miniconda3/envs/snakemake_rapidrun/lib/python3.9/importlib/__init__.py:127: in import_module
return _bootstrap._gcd_import(name[level:], package, level)
<frozen importlib._bootstrap>:1030: in _gcd_import
???
<frozen importlib._bootstrap>:1007: in _find_and_load
???
<frozen importlib._bootstrap>:986: in _find_and_load_unlocked
???
<frozen importlib._bootstrap>:680: in _load_unlocked
???
../../../miniconda3/envs/snakemake_rapidrun/lib/python3.9/site-packages/_pytest/assertion/rewrite.py:161: in exec_module
source_stat, co = _rewrite_test(fn, self.config)
../../../miniconda3/envs/snakemake_rapidrun/lib/python3.9/site-packages/_pytest/assertion/rewrite.py:354: in _rewrite_test
tree = ast.parse(source, filename=fn_)
../../../miniconda3/envs/snakemake_rapidrun/lib/python3.9/ast.py:50: in parse
return compile(source, filename, mode, flags,
E File "/home/pguerin/working/edna/snakemake_rapidrun_swarm/.tests/unit/test_trim_primers.py", line 37
E /home/pguerin/working/edna/snakemake_rapidrun_swarm/config/config_test_rapidrun.yaml
E ^
E SyntaxError: invalid syntax
And the faulty code:
# Run the test job.
sp.check_output([
"python",
"-m",
"snakemake",
"results/04_trim_primers/projet1/chond/sample2.fastq",
"-F",
"-j1",
"--keep-target-files",
"--configfile",
/home/pguerin/working/edna/snakemake_rapidrun_swarm/config/config_test_rapidrun.yaml
"--use-conda",
"--directory",
workdir,
])