Fix workflow tests that are failing (#410)
This PR updates the tests so that all the examples run and if an example
fails then the test results in a failure as well. Changes include:
- Reformatting design_macrocyclic_binder.sh and
design_macrocyclic_monomer.sh to be submitted correctly by
test_diffusion.py
- Reducing the total length in design_tetrahedral_oligos.sh to reduce
run time of this test
- Changes to test_diffusion.py and main.yml to be able to run the
examples in different chunks so examples can run in parallel and to make
sure that if an example errors out, that the tests does not pass.
Currently design_ppi_scaffolded, design_timbarrel, and
design_ppi_flexible_peptide_with_secondarystructure_specification are
failing which should be addressed in other, future PRs.