There is an issue resuming the pipeline from an intermediate stage after pipeline completion. I ran the pipeline with PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python python -m evla_pipe.run_pipeline test.sdm/ and it completed successfully (aside from some failed stages, including EVLA_Flag_baddeformatters).
I then made edits to EVLA_Flag_baddeformatters.py. To test my changes, I tried to resume the pipeline from the EVLA_Flag_baddeformatters stage by running PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python python -m evla_pipe.run_pipeline --resume-from EVLA_Flag_baddeformatters test.sdm/. The pipeline completed successfully and the EVLA_Flag_baddeformatters stage now completes without errors, but stages which did not fail before are now failing with ERROR: No measurement set specified in pipeline_context['msname'].