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--restart, Toil still thinks it's finished and I get
[2021-09-24T14:33:48+1000] [MainThread] [W] [toil.common] Requested restart but the workflow has already been completed; allowing exports to rerun.. What I actually want it to do here is cache the jobs that are unchanged and re-run those that have changed. Is this possible at all in toil?
+character is a filename to
%2B. This results in a error:
Cannot make job: Invalid filename: 'P233%2B35_structure.txt' contains illegal characters
The two lines with no test coverage are annotated at https://github.com/common-workflow-language/cwltool/pull/1446/files#annotation_2008443310
For local checking you'll need to run all the tests with
Hm, that fails. ```$ make diff-cover
python --version 2>&1 | grep "Python 3"
python -m pytest -rs --cov --cov-config=.coveragerc --cov-report=
ERROR: usage: main.py [options] [file_or_dir] [file_or_dir] [...]
main.py: error: unrecognized arguments: -n --cov --cov-config=.coveragerc --cov-report=
Makefile:155: recipe for target 'testcov' failed
make: * [testcov] Error 4
make install-depseemed to do the trick.
So when I run
make diff-cover on that PR locally I get:
cwltool/command_line_tool.py (62.5%): Missing lines 207,256-257
revmap_fileand the new test. I get the impression that the test (in its current setup) can only check that what you put in as filename, also gets out (i.e. the external filename representation). I guess that's why only the
ifclause is covered by the test. I guess the
elseclause will only be executed if you supply an internal filename representation (at least, that's what I'm guessing right now). I'm not sure how I would have to supply an internal filename representation in that current test, because it uses a
CommandLineTool, which is an external thingy.
internalin this case refers to a path within a software (docker) container
DockerRequirementat https://github.com/common-workflow-language/cwltool/pull/1446/files#diff-39c8c56d7c38aab05d7eb4a8a765fcc4ea98d28bc4d0fedd22bce834e28dc843R123 is enough?
file:///reference to a tmpdir
(tmp_path / "outdir").as_uri()