CLI: Export Pydra interfaces

[Lestropie]

https://github.com/nipype/pydra

Similar to existing __print_usage_*__ hidden command-line functions, it should be possible to auto-export---from both C++ and Python---the requisite interface information for Pydra.

Pinging @tclose.

[Lestropie]

Code links:

• C++:

  • Catching special options: https://github.com/MRtrix3/mrtrix3/blob/3.0.4/core/app.cpp#L1035
  • __print_full_usage__ implementation: https://github.com/MRtrix3/mrtrix3/blob/3.0.4/core/app.cpp#L659
  • __print_usage_markdown__ implementation: https://github.com/MRtrix3/mrtrix3/blob/3.0.4/core/app.cpp#L687
  • __print_usage_rst__ implementation: https://github.com/MRtrix3/mrtrix3/blob/3.0.4/core/app.cpp#L798

• Python:

  • Catching special options: https://github.com/MRtrix3/mrtrix3/blob/3.0.4/lib/mrtrix3/app.py#L134
  • __print_full_usage__ implementation: https://github.com/MRtrix3/mrtrix3/blob/3.0.4/lib/mrtrix3/app.py#L874
  • __print_usage_markdown__ implementation: https://github.com/MRtrix3/mrtrix3/blob/3.0.4/lib/mrtrix3/app.py#L919
  • __print_usage_rst__ implementation: https://github.com/MRtrix3/mrtrix3/blob/3.0.4/lib/mrtrix3/app.py#L992
  • Note that type information of Python command-line arguments / options is currently limited; will be enhanced by: run.command(): Support for command-line piping #1392 (currently under development; see Python Command Line Changes ankitasanil/mrtrix3#1)

[tclose]

Ok, cool. So we would only need to write something in the mold of std::string full_usage() to print out the Pydra interfaces?

Could then look into a GH Action to update the Pydra package with new Mrtrix releases

[Lestropie]

Correct.

For eg. online documentation, a script generates that documentation, and that same script is re-run in CI to check for differences, so that software interface and online documentation are guaranteed to have correspondence. So that content is encapsulated within the repository itself, including the versions that correspond to prior tagged releases. For Pydra, is there a preference for having that interface information embedded within the relevant repository vs. stored somewhere externally?

[tclose]

For Pydra, is there a preference for having that interface information embedded within the relevant repository vs. stored somewhere externally?

The standard place to store the interfaces is in their own repo, e.g. https://github.com/nipype/pydra-mrtrix3, typically because they are managed by people external to the tool's dev team, but storing them in the main MRtrix3 repo would be ideal IMO.

[tclose]

Just checked with the Mattermost channel, and storing them in the mrtrix repo is preferred if possible