--generate-unit-tests will raise error in 8.20.1 or newer version #3137
Description
Snakemake version
8.21.0
or
8.20.*
Describe the bug
Snakefile:
rule a:
output:
"test",
shell:
"touch {output} "error:
❯ snakemake --generate-unit-tests
Found existing alias for "snakemake". You should use: "snk"
Building DAG of jobs...
Generating unit tests for each rule...
Traceback (most recent call last):
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/snakemake/cli.py", line 2053, in args_to_api
dag_api.generate_unit_tests(args.generate_unit_tests)
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/snakemake/api.py", line 604, in _handle_no_exec
return method(self, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/snakemake/api.py", line 616, in generate_unit_tests
self.workflow_api._workflow.generate_unit_tests(path=path)
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/snakemake/workflow.py", line 828, in generate_unit_tests
unit_tests.generate(
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/snakemake/unit_tests/__init__.py", line 52, in generate
env.get_template("common.py.jinja2").render(version=__version__),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/jinja2/environment.py", line 1013, in get_template
return self._load_template(name, globals)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/jinja2/environment.py", line 972, in _load_template
template = self.loader.load(self, name, self.make_globals(globals))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/jinja2/loaders.py", line 126, in load
source, filename, uptodate = self.get_source(environment, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/jinja2/loaders.py", line 347, in get_source
raise TemplateNotFound(template)
jinja2.exceptions.TemplateNotFound: common.py.jinja2Logs
❯ mamba create -n 20241013_test_snk snakemake
❯ mamba activate 20241013_test_snk
❯ snakemake --version
Found existing alias for "snakemake". You should use: "snk" 8.21.0
❯ snakemake
Found existing alias for "snakemake". You should use: "snk" Assuming unrestricted shared filesystem usage.
Building DAG of jobs...
Using shell: /usr/bin/bash Provided cores: 16
Rules claiming more threads will be scaled down. Job stats:
job count ----- ------- a 1
total 1
Select jobs to execute... Execute 1 jobs...
[Sun Oct 13 11:10:55 2024] localrule a:
output: test
jobid: 0
reason: Missing output files: test
resources: tmpdir=/tmp
[Sun Oct 13 11:10:55 2024]
Finished job 0.
1 of 1 steps (100%) done
Complete log: .snakemake/log/2024-10-13T111055.778607.snakemake.log
❯ snakemake --generate-unit-tests
Found existing alias for "snakemake". You should use: "snk"
Building DAG of jobs...
Generating unit tests for each rule...
Traceback (most recent call last):
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/snakemake/cli.py", line 2053, in args_to_api
dag_api.generate_unit_tests(args.generate_unit_tests)
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/snakemake/api.py", line 604, in _handle_no_exec
return method(self, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/snakemake/api.py", line 616, in generate_unit_tests
self.workflow_api._workflow.generate_unit_tests(path=path)
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/snakemake/workflow.py", line 828, in generate_unit_tests
unit_tests.generate(
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/snakemake/unit_tests/__init__.py", line 52, in generate
env.get_template("common.py.jinja2").render(version=__version__),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/jinja2/environment.py", line 1013, in get_template
return self._load_template(name, globals)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/jinja2/environment.py", line 972, in _load_template
template = self.loader.load(self, name, self.make_globals(globals))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/jinja2/loaders.py", line 126, in load
source, filename, uptodate = self.get_source(environment, name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jiangy/1/miniforge3/envs/20241013_test_snk/lib/python3.12/site-packages/jinja2/loaders.py", line 347, in get_source
raise TemplateNotFound(template)
jinja2.exceptions.TemplateNotFound: common.py.jinja2Additional context
In version 8.20.1 will also raise error:
❯ mamba install -y snakemake=8.20.1
❯ snakemake --version
Found existing alias for "snakemake". You should use: "snk"
8.20.1
❯ snakemake --generate-unit-tests Found existing alias for "snakemake". You should use: "snk"
Building DAG of jobs...
Generating unit tests for each rule...
Traceback (most recent call last):
.....
jinja2.exceptions.TemplateNotFound: common.py.jinja2
In 8.18.1, it works well.
❯ mamba install -y snakemake=8.18.1
❯ snakemake --version
Found existing alias for "snakemake". You should use: "snk"
8.18.1
❯ snakemake --generate-unit-tests
Found existing alias for "snakemake". You should use: "snk"
Building DAG of jobs...
Generating unit tests for each rule...
Generating unit test for rule a: .tests/unit/test_a.py.