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.

Author: woodsh17

.github/workflows/main.yml

@@ -69,6 +69,13 @@ jobs:
         uv pip install --no-cache-dir -e . --no-deps
         rm -rf ~/.cache # /app/RFdiffusion/tests
 
+    - name: Preseed DGL backend
+      shell: bash
+      run: |
+        mkdir -p "$HOME/.dgl"
+        printf '{"backend": "pytorch"}' > "$HOME/.dgl/config.conf"
+        echo "DGLBACKEND=pytorch" >> "$GITHUB_ENV"
+
     - name: Download weights
       run: |
         mkdir models
@@ -87,8 +94,29 @@ jobs:
     - name: Setup and Run ppi_scaffolds tests
       run: |
         tar -xvf examples/ppi_scaffolds_subset.tar.gz -C examples
-        cd tests && uv run python test_diffusion.py
+        total_chunks=$(nproc)
+        cd tests 
+
+        #launch all chunks in background and record PIDs + labels
+        pids=""
+        for chunk_index in $(seq 1 $total_chunks); do
+          echo "Running chunk $chunk_index of $total_chunks"
+          uv run python test_diffusion.py --total_chunks $total_chunks --chunk_index $chunk_index &
+          pids="$pids $!"
+        done
+
+        # wait for each and track failures
+        fail=0
+        for pid in $pids; do
+          if ! wait "$pid"; then
+            echo "A chunk (PID $pid) failed"
+            fail=1
+          else
+            echo "A chunk (PID $pid) passed"
+          fi
+        done
 
+        exit "$fail"
 
     # - name: Test with pytest
     #   run: |

examples/design_macrocyclic_binder.sh

@@ -1,18 +1,15 @@
 #!/bin/bash
 
-prefix=./outputs/diffused_binder_cyclic2
+# Note that in the example below the indices in the
+# input_pdbs/7zkr_GABARAP.pdb file have been shifted
+# by +2 in chain A relative to pdbID 7zkr.
 
-# Note that the indices in this pdb file have been 
-# shifted by +2 in chain A relative to pdbID 7zkr.
-pdb='./input_pdbs/7zkr_GABARAP.pdb'
-
-num_designs=10
-script="../scripts/run_inference.py"
-$script --config-name base \
-inference.output_prefix=$prefix \
-inference.num_designs=$num_designs \
+../scripts/run_inference.py \
+--config-name base \
+inference.output_prefix=example_outputs/diffused_binder_cyclic2 \
+inference.num_designs=10 \
 'contigmap.contigs=[12-18 A3-117/0]' \
-inference.input_pdb=$pdb \
+inference.input_pdb=./input_pdbs/7zkr_GABARAP.pdb \
 inference.cyclic=True \
 diffuser.T=50 \
 inference.cyc_chains='a' \

examples/design_macrocyclic_monomer.sh

@@ -1,17 +1,15 @@
 #!/bin/bash 
 
-prefix=./outputs/uncond_cycpep
-# Note that the indices in this pdb file have been 
-# shifted by +2 in chain A relative to pdbID 7zkr.
-pdb='./input_pdbs/7zkr_GABARAP.pdb'
+# Note that in the example below the indices in the 
+# input_pdbs/7zkr_GABARAP.pdb file have been shifted
+# by +2 in chain A relative to pdbID 7zkr.
 
-num_designs=10
-script="../scripts/run_inference.py"
-$script --config-name base \
-inference.output_prefix=$prefix \
-inference.num_designs=$num_designs \
+../scripts/run_inference.py \
+--config-name base \
+inference.output_prefix=example_outputs/uncond_cycpep \
+inference.num_designs=10 \
 'contigmap.contigs=[12-18]' \
-inference.input_pdb=$pdb \
+inference.input_pdb=input_pdbs/7zkr_GABARAP.pdb \
 inference.cyclic=True \
 diffuser.T=50 \
 inference.cyc_chains='a'

examples/design_tetrahedral_oligos.sh

@@ -5,6 +5,6 @@
 # This external potential promotes contacts both within (with a relative weight of 1) and between chains (relative weight 0.1)
 # We specify that we want to apply these potentials to all chains, with a guide scale of 2.0 (a sensible starting point)
 # We decay this potential with quadratic form, so that it is applied more strongly initially
-# We specify a total length of 1200aa, so each chain is 100 residues long
+# We specify a total length of 1200aa, so each chain is 100 residues long - length updated to 600aa, so each chain is 50 residues long for testing to run faster
 
-python ../scripts/run_inference.py --config-name=symmetry inference.symmetry="tetrahedral" inference.num_designs=10 inference.output_prefix="example_outputs/tetrahedral_oligo" 'potentials.guiding_potentials=["type:olig_contacts,weight_intra:1,weight_inter:0.1"]' potentials.olig_intra_all=True potentials.olig_inter_all=True potentials.guide_scale=2.0 potentials.guide_decay="quadratic" 'contigmap.contigs=[1200-1200]'
+python ../scripts/run_inference.py --config-name=symmetry inference.symmetry="tetrahedral" inference.num_designs=10 inference.output_prefix="example_outputs/tetrahedral_oligo" 'potentials.guiding_potentials=["type:olig_contacts,weight_intra:1,weight_inter:0.1"]' potentials.olig_intra_all=True potentials.olig_inter_all=True potentials.guide_scale=2.0 potentials.guide_decay="quadratic" 'contigmap.contigs=[600-600]'