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README.md

pypi2cwl forms CWL tool descriptions from PyPi packages using argparse2cwl. It installs the package if it hasn't been installed before, downloads the source code to a new directory, parses command-line scripts from package's setup.py and runs argparse2cwl against those scripts.

Installing

$ pip install pypi2cwl

Usage

$ pypi2cwl <package_name> [options]

Options (some of them are inherited from argparse2cwl):

  • -go, --generate_outputs: flag for generating outputs not only from arguments that are instances of argparse.FileType('w'), but also from every argument which contains output keyword in its name. For instance, argument --output-file with no type will also be placed to output section. However, --output-directory argument will also be treated like file, so generated tools must be checked carefully when this option is selected.

  • -d, --directory: directory for storing tool descriptions.

  • -v, --venv: this flag must be used if pypi2cwl is run inside a virtual environment. Then a package, if it wasn't installed before, will be installed locally.

  • --no-clean: the source package won't be deleted after running, so setup.py inside the package can be edited

Troubleshooting

Sometimes setup() function cannot be parsed directly from package's setup.py. If pypi2cwl has exited with warning could not import setup function and a path to setup.py file, follow the path provided in the message, edit setup.py so setup function is available in the main body of the program and is executed during importing setup.py, and run pypi2cwl again with --no-clean option. The edits don't affect the program's behavior, because only the downloaded copy of the package is edited.

Limitations

pypi2cwl cannot process packages where:

a) tools are not defined as command-line scripts in setup.py

b) argument parsers other than argparse (for instance, sys.argv) are used.


In these cases you should manually generate tool descriptions using argparse2cwl.