This week was not as productive as I wanted because I had several tough deadlines in the university and I had to cope with that, luckily I successfully passed an exam and presented a coursework. In my proposal I mentioned a two week period of exams, when I might work less, this week may be counted as one of the two. The next week is not going to be easy also, but I will definitely have more time and will work as planned.

Nevertheless, I managed to start/complete the following points:

  • I started a pull request to workflows repository with my automatically wrapped CNVkit tools. I requested for help with testing data, perhaps I had to be more insistent. The next week I am going to get a successful check from repository’s Travis CI, for now I just lack proper data.

  • I changed the structure of templates so that they can be divided into smaller parts, that’s definitely a need because Jinja2 templates look unreadable when there’s a lot of code in one file. It allowed me to add an option of plugging hand-written outputs to a formed CWL tool, which might be useful when argparse2cwl can’t recognize output arguments. I also need to test an option with forming outputs considering “output” keyword in the name of an argument.

  • I rewrote interface to argparse2cwl, now a user can get information about a2c arguments with passing -ha or --help_arg2cwl option to any tool he/she wants to wrap. I also think about making a standalone instrument, so calling argparse2cwl will look not like $ python <tool name> --generate_cwl_tool, but like $ arg2cwl python <tool name>. It will be a little more explicit way of working with our program; also it will allow to specify usual -h for getting help.

  • I made a dead simple test for checking the general program running process. Regarding testing, there are two parts of what should be tested: the Python code that I wrote and CWL tools which are produced on the output. The first part is not easy, actually it is a large part of the project, but at least it is clear what to do. Testing tools, on the contrary, is a very tricky part. For now, I can only assure the syntax of the formed tool doesn’t violate the standard, and only by running cwl-runner from the command line (I can not import cwltool, because it doesn’t support Python3, as far as I know). I don’t have tests for checking whether executing jobs with CWL tools produces the same result as running tools without wrappers. I need test data for creating jobs, and that is where I need community’s help; I can do it alone, but it will take a lot of time in questions where someone competent can instantly show me where to find what I need.

To sum up, on the next week I will bring my PR to a working state, cover some small parts in argparse API and make some changes to CWL tool forming, but mainly I will concentrate on testing code that I wrote.