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.
$ pip install pypi2cwl
$ pypi2cwl <package_name> [options]
Options (some of them are inherited from
--generate_outputs: flag for generating outputs not only from arguments that are instances of
argparse.FileType('w'), but also from every argument which contains
outputkeyword in its name. For instance, argument
--output-filewith no type will also be placed to output section. However,
--output-directoryargument will also be treated like file, so generated tools must be checked carefully when this option is selected.
--directory: directory for storing tool descriptions.
--venv: this flag must be used if
pypi2cwlis 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.pyinside the package can be edited
setup() function cannot be parsed directly from package's
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 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.
pypi2cwl cannot process packages where:
a) tools are not defined as command-line scripts in
b) argument parsers other than
argparse (for instance,
sys.argv) are used.
In these cases you should manually generate tool descriptions using