Upgrade from ISMRMRD to MRD v2

[naegelejd]

No description provided.

[naegelejd]

This is a very large PR that overhauls the entire Gadgetron code base to upgrade from ISMRMRD to MRDv2, switch to a pure streaming architecture, and remove socket networking from the codebase.

Specifically, this PR:

1. Upgrades all tested Gadgets/Toolboxes to use MRDv2 instead of ISMRMRD
   • A few untested Gadgets remain because it would be better to add a test and keep them
2. Removes all networking code
   • Removed gadgetron_ismrmrd_client
   • Greatly simplified apps/gadgetron
3. Removes all Readers and Writers
   • gadgetron now reads/writes only the MRD Protocol (via stdin/stdout or --input/--output)
4. Refactors end-to-end tests to use PyTest
   • Eliminated Siemens dat conversion
   • Test data has been converted to MRDv2 using test/integration/convert_test_data.py
5. Removes everything Windows-related
6. Ports the CI pipeline to GitHub Actions
   • Docker images are published only when a new release (tag) is pushed
   • Conda package is not yet published (it would conflict with existing gadgetron package)

[hansenms]

Overall this looks great. Huge amount of work here. Much more to do, but this sets us up with a basis to work off. Made some minor comments about some additional stuff we can remove and then maybe some things for next steps:

General Comments:

• It would be good with a scheme to parallelize the data download for the tests.
• Perhaps add a readme to say that the test case conversion tools are temporary. We will remove those once we have MRD data converters.
• Next step should be removing XML files and runtime linking.
• We should remove Doxygen (nobody needs that, intellisense is what we use) and Readthedocs and use approach from Tyger.
• We should come up with some other approach to distributed.
• We should have some general "tail" gadget where you choose output format with a parameter.

[naegelejd]

The repository settings required a follow-up review. I addressed your feedback and opened issues for next steps.