fairagro / m4.4_sciwin_client

🦀 SciWIn Client: Reproducible computational Workflows made easy!
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Explicit In/Outputs for `s4n run` #18

Open JensKrumsieck opened 4 weeks ago

JensKrumsieck commented 4 weeks ago

Think of and implement an explicit commandline syntax for inputs and outputs that are not infered by the parser

aleidel commented 1 week ago

https://github.com/fairagro/m4.4_sciwin_client/tree/feature/fixed_in_out

Currently user would use command similar to: s4n tool create --inputs tests/test_data/input.txt tests/test_data/input2.txt --outputs res.txt python tests/test_data/echo2.py --test tests/test_data/input.txt -t2 tests/test_data/input2.txt --out res.txt

There is an extra method for parsing the input/output because the actual command is just the trailing argument without -- , which leads to problems with automatic separation if a value delimiter ' ' is used for inputs and outputs (could also use other delimiter e.g. ',' --inputs tests/test_data/input.txt,tests/test_data/input2.txt but then the user can not insert spaces which would be unintuitive).

Assumptions: input and outputs contain a '.' which might not be true for all inputs or outputs