Fix workflow tests that are failing

.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]'