From a18f99614aee57101707240c282b0f4409dcc78c Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Fri, 10 Oct 2025 09:35:57 -0500
Subject: [PATCH 01/22] Address 'command' referenced before assignment error in
 tests

---
 tests/test_diffusion.py | 24 +++++++++++++++++-------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/tests/test_diffusion.py b/tests/test_diffusion.py
index f3eaeccd..993e38f3 100644
--- a/tests/test_diffusion.py
+++ b/tests/test_diffusion.py
@@ -118,15 +118,25 @@ def _write_command(self, bash_file, test_f) -> None:
                 inference.final_step=48
         """
         out_lines=[]
+        command_lines = []
+        in_command = False
         with open(bash_file, "r") as f:
-            lines = f.readlines()
-            for line in lines:
-                if not (line.startswith("python") or line.startswith("../")):
+            for line in f:
+                stripped = line.strip()
+                if stripped.startswith("python") or stripped.startswith("../"):
+                    in_command = True
+                if in_command:
+                    # Remove trailing line continuation slashes
+                    if stripped.endswith("\\"):
+                        command_lines.append(stripped[:-1].strip())
+                    else:
+                        command_lines.append(stripped)
+                        in_command = False # End of command
+                else: 
                     out_lines.append(line)
-                else:
-                    command = line.strip()
-            if not command.startswith("python"):
-                command = f'python {command}'
+        if not command_lines:
+            raise ValueError(f"No valid python command found in {bash_file}")
+        command = " ".join(command_lines)
         # get the partial_T
         if "partial_T" in command:
             final_step = int(command.split("partial_T=")[1].split(" ")[0]) - 2

From 2d157302d341c3d8b8d8ef2e02a955d419f51e55 Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Fri, 10 Oct 2025 09:36:45 -0500
Subject: [PATCH 02/22] Adjusting command format for
 design_macrocyclic_binder.sh and design_macrocyclic_monomer.sh

---
 examples/design_macrocyclic_binder.sh  | 19 ++++++++-----------
 examples/design_macrocyclic_monomer.sh | 18 ++++++++----------
 2 files changed, 16 insertions(+), 21 deletions(-)

diff --git a/examples/design_macrocyclic_binder.sh b/examples/design_macrocyclic_binder.sh
index c0c69f0b..1fe5a851 100755
--- a/examples/design_macrocyclic_binder.sh
+++ b/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' \
diff --git a/examples/design_macrocyclic_monomer.sh b/examples/design_macrocyclic_monomer.sh
index 96eda600..3aa1ac3d 100755
--- a/examples/design_macrocyclic_monomer.sh
+++ b/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'

From a45c3f9da7cfd5d3733d33d142ed8e980a7cf6b3 Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Fri, 10 Oct 2025 13:41:05 -0500
Subject: [PATCH 03/22] Fail tests when example scripts exit non-zero

---
 tests/test_diffusion.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/tests/test_diffusion.py b/tests/test_diffusion.py
index 993e38f3..f84af956 100644
--- a/tests/test_diffusion.py
+++ b/tests/test_diffusion.py
@@ -48,10 +48,12 @@ def setUp(self):
         print(f"Running commands in {self.out_f}, two steps of diffusion, deterministic=True")
 
         self.results = {}
+        self.exec_status = {}
 
         for bash_file in sorted( glob.glob(f"{self.out_f}/*.sh"), reverse=False):
             test_name = os.path.basename(bash_file)[:-len('.sh')]
             res, output = execute(f"Running {test_name}", f'bash {bash_file}', return_='tuple', add_message_and_command_line_to_output=True)
+            self.exec_status[test_name] = (exit_code, output)
 
             self.results[test_name] = dict(
                 state = 'failed' if res else 'passed',
@@ -61,6 +63,13 @@ def setUp(self):
             #subprocess.run(["bash", bash_file], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
             #subprocess.run(["bash", bash_file])
 
+    def test_examples_run_without_errors(self):
+        for name, (exit_code, output) in sorted(self.exec_status.items()):
+            with self.subTest(example=name):
+                self.assertEqual(exit_code, 0,
+                                 msg=f"Example '{name}' exited with {exit_code}\n{output}")
+
+
 
     def test_commands(self):
         """

From f43a81d59d6999759667db97269d0fea3693c277 Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Fri, 10 Oct 2025 13:53:59 -0500
Subject: [PATCH 04/22] Changing number of designs for examples from 10 to 2 to
 speed up tests

---
 examples/design_cyclic_oligos.sh                                | 2 +-
 examples/design_dihedral_oligos.sh                              | 2 +-
 examples/design_macrocyclic_binder.sh                           | 2 +-
 examples/design_macrocyclic_monomer.sh                          | 2 +-
 examples/design_motifscaffolding.sh                             | 2 +-
 examples/design_motifscaffolding_inpaintseq.sh                  | 2 +-
 examples/design_motifscaffolding_with_target.sh                 | 2 +-
 examples/design_nickel.sh                                       | 2 +-
 examples/design_partialdiffusion.sh                             | 2 +-
 examples/design_partialdiffusion_multipleseq.sh                 | 2 +-
 examples/design_partialdiffusion_withseq.sh                     | 2 +-
 examples/design_ppi.sh                                          | 2 +-
 examples/design_ppi_flexible_peptide.sh                         | 2 +-
 ...pi_flexible_peptide_with_secondarystructure_specification.sh | 2 +-
 examples/design_ppi_scaffolded.sh                               | 2 +-
 examples/design_tetrahedral_oligos.sh                           | 2 +-
 examples/design_timbarrel.sh                                    | 2 +-
 examples/design_unconditional.sh                                | 2 +-
 examples/design_unconditional_w_contact_potential.sh            | 2 +-
 examples/design_unconditional_w_monomer_ROG.sh                  | 2 +-
 20 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/examples/design_cyclic_oligos.sh b/examples/design_cyclic_oligos.sh
index db9a0896..0f620816 100755
--- a/examples/design_cyclic_oligos.sh
+++ b/examples/design_cyclic_oligos.sh
@@ -7,4 +7,4 @@
 # We decay this potential with quadratic form, so that it is applied more strongly initially
 # We specify a total length of 480aa, so each chain is 80 residues long
 
-python ../scripts/run_inference.py --config-name=symmetry inference.symmetry="C6" inference.num_designs=10 inference.output_prefix="example_outputs/C6_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=[480-480]'
+python ../scripts/run_inference.py --config-name=symmetry inference.symmetry="C6" inference.num_designs=2 inference.output_prefix="example_outputs/C6_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=[480-480]'
diff --git a/examples/design_dihedral_oligos.sh b/examples/design_dihedral_oligos.sh
index 0d64a6fe..ac2f6a6f 100755
--- a/examples/design_dihedral_oligos.sh
+++ b/examples/design_dihedral_oligos.sh
@@ -7,4 +7,4 @@
 # We decay this potential with quadratic form, so that it is applied more strongly initially
 # We specify a total length of 320aa, so each chain is 80 residues long
 
-python ../scripts/run_inference.py --config-name=symmetry inference.symmetry="D2" inference.num_designs=10 inference.output_prefix="example_outputs/D2_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=[320-320]'
+python ../scripts/run_inference.py --config-name=symmetry inference.symmetry="D2" inference.num_designs=2 inference.output_prefix="example_outputs/D2_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=[320-320]'
diff --git a/examples/design_macrocyclic_binder.sh b/examples/design_macrocyclic_binder.sh
index 1fe5a851..7db500db 100755
--- a/examples/design_macrocyclic_binder.sh
+++ b/examples/design_macrocyclic_binder.sh
@@ -7,7 +7,7 @@
 ../scripts/run_inference.py \
 --config-name base \
 inference.output_prefix=example_outputs/diffused_binder_cyclic2 \
-inference.num_designs=10 \
+inference.num_designs=2 \
 'contigmap.contigs=[12-18 A3-117/0]' \
 inference.input_pdb=/input_pdbs/7zkr_GABARAP.pdb \
 inference.cyclic=True \
diff --git a/examples/design_macrocyclic_monomer.sh b/examples/design_macrocyclic_monomer.sh
index 3aa1ac3d..d0cc3188 100755
--- a/examples/design_macrocyclic_monomer.sh
+++ b/examples/design_macrocyclic_monomer.sh
@@ -7,7 +7,7 @@
 ../scripts/run_inference.py \
 --config-name base \
 inference.output_prefix=example_outputs/uncond_cycpep \
-inference.num_designs=10 \
+inference.num_designs=2 \
 'contigmap.contigs=[12-18]' \
 inference.input_pdb=input_pdbs/7zkr_GABARAP.pdb \
 inference.cyclic=True \
diff --git a/examples/design_motifscaffolding.sh b/examples/design_motifscaffolding.sh
index f5a80ddf..2c9088e8 100755
--- a/examples/design_motifscaffolding.sh
+++ b/examples/design_motifscaffolding.sh
@@ -8,4 +8,4 @@
 #   - 10-40 residues (randomly sampled)
 # We generate 10 designs
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_motifscaffolding inference.input_pdb=input_pdbs/5TPN.pdb 'contigmap.contigs=[10-40/A163-181/10-40]' inference.num_designs=10
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_motifscaffolding inference.input_pdb=input_pdbs/5TPN.pdb 'contigmap.contigs=[10-40/A163-181/10-40]' inference.num_designs=2
diff --git a/examples/design_motifscaffolding_inpaintseq.sh b/examples/design_motifscaffolding_inpaintseq.sh
index 8a06444b..08a1c61d 100755
--- a/examples/design_motifscaffolding_inpaintseq.sh
+++ b/examples/design_motifscaffolding_inpaintseq.sh
@@ -12,4 +12,4 @@
 # We generate 10 designs
 # We then specify that residues 163-168 (inclusive), 170-171 (inclusive) and 179 (inclusive) on the A chain of the input, should be masked in the input
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_motifscaffolding_inpaintseq inference.input_pdb=input_pdbs/5TPN.pdb 'contigmap.contigs=[10-40/A163-181/10-40]' inference.num_designs=10 'contigmap.inpaint_seq=[A163-168/A170-171/A179]'
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_motifscaffolding_inpaintseq inference.input_pdb=input_pdbs/5TPN.pdb 'contigmap.contigs=[10-40/A163-181/10-40]' inference.num_designs=2 'contigmap.inpaint_seq=[A163-168/A170-171/A179]'
diff --git a/examples/design_motifscaffolding_with_target.sh b/examples/design_motifscaffolding_with_target.sh
index b52d7402..fcb32c5d 100755
--- a/examples/design_motifscaffolding_with_target.sh
+++ b/examples/design_motifscaffolding_with_target.sh
@@ -11,4 +11,4 @@
 # We generate 10 designs
 # As in the paper (at least for some of the designs we tested), we use the complex-finetuned model
 
-python ../scripts/run_inference.py inference.output_prefix=example_outputs/design_motifscaffolding_with_target inference.input_pdb=input_pdbs/1YCR.pdb 'contigmap.contigs=[A25-109/0 0-70/B17-29/0-70]' contigmap.length=70-120 inference.num_designs=10 inference.ckpt_override_path=../models/Complex_base_ckpt.pt
+python ../scripts/run_inference.py inference.output_prefix=example_outputs/design_motifscaffolding_with_target inference.input_pdb=input_pdbs/1YCR.pdb 'contigmap.contigs=[A25-109/0 0-70/B17-29/0-70]' contigmap.length=70-120 inference.num_designs=2 inference.ckpt_override_path=../models/Complex_base_ckpt.pt
diff --git a/examples/design_nickel.sh b/examples/design_nickel.sh
index 8239680f..560951ec 100755
--- a/examples/design_nickel.sh
+++ b/examples/design_nickel.sh
@@ -17,4 +17,4 @@
 
 ckpt='../models/Base_epoch8_ckpt.pt'
 
-python ../scripts/run_inference.py inference.symmetry="C4" inference.num_designs=15 inference.output_prefix=example_outputs/design_nickel 'potentials.guiding_potentials=["type:olig_contacts,weight_intra:1,weight_inter:0.06"]' potentials.olig_intra_all=True potentials.olig_inter_all=True potentials.guide_scale=2 potentials.guide_decay="quadratic" inference.input_pdb=input_pdbs/nickel_symmetric_motif.pdb 'contigmap.contigs=[50/A2-4/50/0 50/A7-9/50/0 50/A12-14/50/0 50/A17-19/50/0]' inference.ckpt_override_path=$ckpt
+python ../scripts/run_inference.py inference.symmetry="C4" inference.num_designs=2 inference.output_prefix=example_outputs/design_nickel 'potentials.guiding_potentials=["type:olig_contacts,weight_intra:1,weight_inter:0.06"]' potentials.olig_intra_all=True potentials.olig_inter_all=True potentials.guide_scale=2 potentials.guide_decay="quadratic" inference.input_pdb=input_pdbs/nickel_symmetric_motif.pdb 'contigmap.contigs=[50/A2-4/50/0 50/A7-9/50/0 50/A12-14/50/0 50/A17-19/50/0]' inference.ckpt_override_path=$ckpt
diff --git a/examples/design_partialdiffusion.sh b/examples/design_partialdiffusion.sh
index 1e1fdc24..3330ad9a 100755
--- a/examples/design_partialdiffusion.sh
+++ b/examples/design_partialdiffusion.sh
@@ -7,4 +7,4 @@
 # But, in either case, the contig length must sum to the length of the input pdb file
 # We generate 10 designs, and noise and denoise 10 steps (20% of the full trajectory)
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_partialdiffusion inference.input_pdb=input_pdbs/2KL8.pdb 'contigmap.contigs=[79-79]' inference.num_designs=10 diffuser.partial_T=10
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_partialdiffusion inference.input_pdb=input_pdbs/2KL8.pdb 'contigmap.contigs=[79-79]' inference.num_designs=2 diffuser.partial_T=10
diff --git a/examples/design_partialdiffusion_multipleseq.sh b/examples/design_partialdiffusion_multipleseq.sh
index 1962ff03..36fe03fd 100755
--- a/examples/design_partialdiffusion_multipleseq.sh
+++ b/examples/design_partialdiffusion_multipleseq.sh
@@ -6,4 +6,4 @@
 # Note the ranges do not necessarily need to lie on the same chain as in this example.
 # However, positions are 0-indexed over the whole sequence--not per-chain-- so care must be taken when providing ranges to provide_seq.
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_partialdiffusion_peptidewithmultiplesequence inference.input_pdb=input_pdbs/peptide_complex_ideal_helix.pdb 'contigmap.contigs=["172-172/0 34-34"]' diffuser.partial_T=10 inference.num_designs=10 'contigmap.provide_seq=[172-177,200-205]'
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_partialdiffusion_peptidewithmultiplesequence inference.input_pdb=input_pdbs/peptide_complex_ideal_helix.pdb 'contigmap.contigs=["172-172/0 34-34"]' diffuser.partial_T=10 inference.num_designs=2 'contigmap.provide_seq=[172-177,200-205]'
diff --git a/examples/design_partialdiffusion_withseq.sh b/examples/design_partialdiffusion_withseq.sh
index ab585c74..95c5d73d 100755
--- a/examples/design_partialdiffusion_withseq.sh
+++ b/examples/design_partialdiffusion_withseq.sh
@@ -11,4 +11,4 @@
 # This contig will lead to the whole input pdb being noise by 10 steps (partial_T=10)
 # However, we provide the sequence of the peptide (the last 20 residues in the contig), with provide_seq=[172-205]. This is 0-indexed
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_partialdiffusion_peptidewithsequence inference.input_pdb=input_pdbs/peptide_complex_ideal_helix.pdb 'contigmap.contigs=["172-172/0 34-34"]' diffuser.partial_T=10 inference.num_designs=10 'contigmap.provide_seq=[172-205]'
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_partialdiffusion_peptidewithsequence inference.input_pdb=input_pdbs/peptide_complex_ideal_helix.pdb 'contigmap.contigs=["172-172/0 34-34"]' diffuser.partial_T=10 inference.num_designs=2 'contigmap.provide_seq=[172-205]'
diff --git a/examples/design_ppi.sh b/examples/design_ppi.sh
index 5e217b21..8354ef7b 100755
--- a/examples/design_ppi.sh
+++ b/examples/design_ppi.sh
@@ -8,4 +8,4 @@
 # We tell diffusion to target three specific residues on the target, specifically residues 59, 83 and 91 of the A chain
 # We make 10 designs, and reduce the noise added during inference to 0, to improve the quality of the designs
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_ppi inference.input_pdb=input_pdbs/insulin_target.pdb 'contigmap.contigs=[A1-150/0 70-100]' 'ppi.hotspot_res=[A59,A83,A91]' inference.num_designs=10 denoiser.noise_scale_ca=0 denoiser.noise_scale_frame=0
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_ppi inference.input_pdb=input_pdbs/insulin_target.pdb 'contigmap.contigs=[A1-150/0 70-100]' 'ppi.hotspot_res=[A59,A83,A91]' inference.num_designs=2 denoiser.noise_scale_ca=0 denoiser.noise_scale_frame=0
diff --git a/examples/design_ppi_flexible_peptide.sh b/examples/design_ppi_flexible_peptide.sh
index 1af54c71..5960f6b3 100755
--- a/examples/design_ppi_flexible_peptide.sh
+++ b/examples/design_ppi_flexible_peptide.sh
@@ -9,4 +9,4 @@
 # We make 10 designs
 # We mask (diffuse) the structure of the peptide using the inpaint_str flag. This has the effect of having RFdiffusion simultaneously design a binder and predict the structure of the peptide within the complex.
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_ppi_flexible_peptide inference.input_pdb=input_pdbs/3IOL.pdb 'contigmap.contigs=[B10-35/0 70-100]' 'ppi.hotspot_res=[B28,B29]' inference.num_designs=10 'contigmap.inpaint_str=[B10-35]'
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_ppi_flexible_peptide inference.input_pdb=input_pdbs/3IOL.pdb 'contigmap.contigs=[B10-35/0 70-100]' 'ppi.hotspot_res=[B28,B29]' inference.num_designs=2 'contigmap.inpaint_str=[B10-35]'
diff --git a/examples/design_ppi_flexible_peptide_with_secondarystructure_specification.sh b/examples/design_ppi_flexible_peptide_with_secondarystructure_specification.sh
index 6e0dfc88..96015db4 100755
--- a/examples/design_ppi_flexible_peptide_with_secondarystructure_specification.sh
+++ b/examples/design_ppi_flexible_peptide_with_secondarystructure_specification.sh
@@ -10,4 +10,4 @@
 # We then specify that we want this to adopt a helical conformation
 # If you wanted to specify that it should adopt a strand conformation, you would specify `contigmap.inpaint_str_strand`
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_ppi_flexible_peptide_with_secondarystructure inference.input_pdb=input_pdbs/tau_peptide.pdb 'contigmap.contigs=[70-100/0 B165-178]' inference.num_designs=10 'contigmap.inpaint_str=[B165-178]' scaffoldguided.scaffoldguided=True 'contigmap.inpaint_str_helix=[B165-178]'
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_ppi_flexible_peptide_with_secondarystructure inference.input_pdb=input_pdbs/tau_peptide.pdb 'contigmap.contigs=[70-100/0 B165-178]' inference.num_designs=2 'contigmap.inpaint_str=[B165-178]' scaffoldguided.scaffoldguided=True 'contigmap.inpaint_str_helix=[B165-178]'
diff --git a/examples/design_ppi_scaffolded.sh b/examples/design_ppi_scaffolded.sh
index 63ca165e..96e1ecf0 100755
--- a/examples/design_ppi_scaffolded.sh
+++ b/examples/design_ppi_scaffolded.sh
@@ -7,4 +7,4 @@
 # We then provide a path to a directory of different scaffolds (we've provided some for you to use, from Cao et al., 2022)
 # We generate 10 designs, and reduce the noise added during inference to 0 (which improves the quality of designs)
 
-../scripts/run_inference.py scaffoldguided.target_path=input_pdbs/insulin_target.pdb inference.output_prefix=example_outputs/design_ppi_scaffolded scaffoldguided.scaffoldguided=True 'ppi.hotspot_res=[A59,A83,A91]' scaffoldguided.target_pdb=True scaffoldguided.target_ss=target_folds/insulin_target_ss.pt scaffoldguided.target_adj=target_folds/insulin_target_adj.pt scaffoldguided.scaffold_dir=./ppi_scaffolds/ inference.num_designs=10 denoiser.noise_scale_ca=0 denoiser.noise_scale_frame=0
+../scripts/run_inference.py scaffoldguided.target_path=input_pdbs/insulin_target.pdb inference.output_prefix=example_outputs/design_ppi_scaffolded scaffoldguided.scaffoldguided=True 'ppi.hotspot_res=[A59,A83,A91]' scaffoldguided.target_pdb=True scaffoldguided.target_ss=target_folds/insulin_target_ss.pt scaffoldguided.target_adj=target_folds/insulin_target_adj.pt scaffoldguided.scaffold_dir=./ppi_scaffolds/ inference.num_designs=2 denoiser.noise_scale_ca=0 denoiser.noise_scale_frame=0
diff --git a/examples/design_tetrahedral_oligos.sh b/examples/design_tetrahedral_oligos.sh
index 231e14a9..4d9fcfd0 100755
--- a/examples/design_tetrahedral_oligos.sh
+++ b/examples/design_tetrahedral_oligos.sh
@@ -7,4 +7,4 @@
 # 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
 
-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=2 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]'
diff --git a/examples/design_timbarrel.sh b/examples/design_timbarrel.sh
index 410254ed..dc679908 100755
--- a/examples/design_timbarrel.sh
+++ b/examples/design_timbarrel.sh
@@ -8,4 +8,4 @@
 # We add 0-5 residues (randomly sampled) to the N and the C-terminus
 # This will allow the generation of diverse TIM barrels with slightly different length helices and strands
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_tim_barrel scaffoldguided.scaffoldguided=True scaffoldguided.target_pdb=False scaffoldguided.scaffold_dir=tim_barrel_scaffold/ inference.num_designs=10 denoiser.noise_scale_ca=0.5 denoiser.noise_scale_frame=0.5 scaffoldguided.sampled_insertion=0-5 scaffoldguided.sampled_N=0-5 scaffoldguided.sampled_C=0-5
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_tim_barrel scaffoldguided.scaffoldguided=True scaffoldguided.target_pdb=False scaffoldguided.scaffold_dir=tim_barrel_scaffold/ inference.num_designs=2 denoiser.noise_scale_ca=0.5 denoiser.noise_scale_frame=0.5 scaffoldguided.sampled_insertion=0-5 scaffoldguided.sampled_N=0-5 scaffoldguided.sampled_C=0-5
diff --git a/examples/design_unconditional.sh b/examples/design_unconditional.sh
index 3ece16f7..78887776 100755
--- a/examples/design_unconditional.sh
+++ b/examples/design_unconditional.sh
@@ -4,4 +4,4 @@
 # We tell RFdiffusion that designs should be 100-200 residues in length (randomly sampled each design)
 # We generate 10 such designs
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_unconditional 'contigmap.contigs=[100-200]' inference.num_designs=10
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_unconditional 'contigmap.contigs=[100-200]' inference.num_designs=2
diff --git a/examples/design_unconditional_w_contact_potential.sh b/examples/design_unconditional_w_contact_potential.sh
index 999a9c04..b2743723 100755
--- a/examples/design_unconditional_w_contact_potential.sh
+++ b/examples/design_unconditional_w_contact_potential.sh
@@ -4,4 +4,4 @@
 # We tell RFdiffusion that designs should be 100-200 residues in length (randomly sampled each design)
 # We generate 10 such designs
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_unconditional_w_contact_potential 'contigmap.contigs=[100-200]' inference.num_designs=10 'potentials.guiding_potentials=["type:monomer_contacts,weight:0.05"]'
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_unconditional_w_contact_potential 'contigmap.contigs=[100-200]' inference.num_designs=2 'potentials.guiding_potentials=["type:monomer_contacts,weight:0.05"]'
diff --git a/examples/design_unconditional_w_monomer_ROG.sh b/examples/design_unconditional_w_monomer_ROG.sh
index b34a0a72..079caa6b 100755
--- a/examples/design_unconditional_w_monomer_ROG.sh
+++ b/examples/design_unconditional_w_monomer_ROG.sh
@@ -7,4 +7,4 @@
 # We use the monomer_ROG potential, with guide scale 2 and quadratic decay
 # Note that this potential is probably not necessary in this kind of case, but is provided as an example
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_monomer_ROG_unconditional 'contigmap.contigs=[100-200]' inference.num_designs=10 'potentials.guiding_potentials=["type:monomer_ROG,weight:1,min_dist:5"]' potentials.guide_scale=2 potentials.guide_decay="quadratic"
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_monomer_ROG_unconditional 'contigmap.contigs=[100-200]' inference.num_designs=2 'potentials.guiding_potentials=["type:monomer_ROG,weight:1,min_dist:5"]' potentials.guide_scale=2 potentials.guide_decay="quadratic"

From 778f8d4b28f7cfd6e54c61c76ffd47de6d38bd2a Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Fri, 10 Oct 2025 15:21:04 -0500
Subject: [PATCH 05/22] Fix input_pdb path in design_macrocyclic_binder and fix
 incorrect call to res in test_diffusion.py

---
 examples/design_macrocyclic_binder.sh | 2 +-
 tests/test_diffusion.py               | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/design_macrocyclic_binder.sh b/examples/design_macrocyclic_binder.sh
index 7db500db..99170417 100755
--- a/examples/design_macrocyclic_binder.sh
+++ b/examples/design_macrocyclic_binder.sh
@@ -9,7 +9,7 @@
 inference.output_prefix=example_outputs/diffused_binder_cyclic2 \
 inference.num_designs=2 \
 'contigmap.contigs=[12-18 A3-117/0]' \
-inference.input_pdb=/input_pdbs/7zkr_GABARAP.pdb \
+inference.input_pdb=./input_pdbs/7zkr_GABARAP.pdb \
 inference.cyclic=True \
 diffuser.T=50 \
 inference.cyc_chains='a' \
diff --git a/tests/test_diffusion.py b/tests/test_diffusion.py
index f84af956..2e8ba44d 100644
--- a/tests/test_diffusion.py
+++ b/tests/test_diffusion.py
@@ -53,7 +53,7 @@ def setUp(self):
         for bash_file in sorted( glob.glob(f"{self.out_f}/*.sh"), reverse=False):
             test_name = os.path.basename(bash_file)[:-len('.sh')]
             res, output = execute(f"Running {test_name}", f'bash {bash_file}', return_='tuple', add_message_and_command_line_to_output=True)
-            self.exec_status[test_name] = (exit_code, output)
+            self.exec_status[test_name] = (res, output)
 
             self.results[test_name] = dict(
                 state = 'failed' if res else 'passed',

From a9b748be37b34792043b195e955dec5270da8b77 Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Tue, 14 Oct 2025 11:44:50 -0500
Subject: [PATCH 06/22] Add print statement to list failed examples

---
 tests/test_diffusion.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/tests/test_diffusion.py b/tests/test_diffusion.py
index 2e8ba44d..32ea9bea 100644
--- a/tests/test_diffusion.py
+++ b/tests/test_diffusion.py
@@ -25,6 +25,8 @@ class TestSubmissionCommands(unittest.TestCase):
     outputs are the same as the reference outputs.
     """
 
+    failed_tests = []
+
     def setUp(self):
         """
         Grabs files from the examples folder
@@ -66,9 +68,16 @@ def setUp(self):
     def test_examples_run_without_errors(self):
         for name, (exit_code, output) in sorted(self.exec_status.items()):
             with self.subTest(example=name):
+                if exit_code != 0:
+                    self.__class__.failed_tests.append(f"{name}")
                 self.assertEqual(exit_code, 0,
                                  msg=f"Example '{name}' exited with {exit_code}\n{output}")
 
+        sys.stderr.write("\n==== EXAMPLE FAILURE SUMMARY ====\n")
+        for line in self.__class__.failed_tests:
+            sys.stderr.write(f" - {line}\n")
+        sys.stderr.write("=========================\n\n")
+        sys.stderr.flush()
 
 
     def test_commands(self):
@@ -169,7 +178,6 @@ def _write_command(self, bash_file, test_f) -> None:
             f.write(output_command)
 
 
-
 def execute_through_pty(command_line):
     import pty, select
 

From 5dff3eb188675093229d50a9f854a9d253df70d3 Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Fri, 17 Oct 2025 10:39:26 -0500
Subject: [PATCH 07/22] These changes split the examples up in chunks and runs
 the different chunks to speed up the workflow.

---
 .github/workflows/main.yml |  10 +-
 tests/test_diffusion.py    | 244 +++++++++++++++++++++++++++----------
 2 files changed, 188 insertions(+), 66 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 6b23c5dc..89a694ff 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -87,7 +87,15 @@ 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) 
+        for chunk_index in $(seq 1 $total_chunks); do
+          echo "Running chunk $chunk_index of $total_chunks"
+          uv run python tests/test_diffusion.py --total-chunks $total_chunks --chunk-index $chunk_index &
+        done
+
+        wait
+        echo "All chunks completed."
+        #cd tests && uv run python test_diffusion.py
 
 
     # - name: Test with pytest
diff --git a/tests/test_diffusion.py b/tests/test_diffusion.py
index 32ea9bea..71829775 100644
--- a/tests/test_diffusion.py
+++ b/tests/test_diffusion.py
@@ -11,6 +11,7 @@
 
 script_dir = os.path.dirname(os.path.abspath(__file__))
 
+
 class TestSubmissionCommands(unittest.TestCase):
     """
     Test harness for checking that commands in the examples folder,
@@ -27,12 +28,37 @@ class TestSubmissionCommands(unittest.TestCase):
 
     failed_tests = []
 
+    # number of chunks to split examples into
+    total_chunks = 1
+    # which chunk to run
+    chunk_index = 1
+
     def setUp(self):
         """
         Grabs files from the examples folder
         """
         submissions = glob.glob(f"{script_dir}/../examples/*.sh")
         # get datetime for output folder, in YYYY_MM_DD_HH_MM_SS format
+        chunks = self.__class__.total_chunks
+        idx = self.__class__.chunk_index
+        if chunks < 1:
+            raise ValueError("total_chunks must be at least 1")
+        if idx < 1 or idx > chunks:
+            raise ValueError(
+                "chunk_index must be between 1 and total_chunks (inclusive)"
+            )
+        if chunks > 1:
+            submissions = [
+                submissions[i]
+                for i in range(len(submissions))
+                if i % chunks == (idx - 1)
+            ]
+            print(
+                f"Running chunk {idx}/{chunks}, {len(submissions)} submissions to run"
+            )
+        if not submissions:
+            raise ValueError("No submissions selected for chunk {idx} of {chunks}")
+
         now = datetime.datetime.now()
         now = now.strftime("%Y_%m_%d_%H_%M_%S")
         self.out_f = f"{script_dir}/tests_{now}"
@@ -41,37 +67,54 @@ def setUp(self):
         # Make sure we have access to all the relevant files
         exclude_dirs = ["outputs", "example_outputs"]
         for filename in os.listdir(f"{script_dir}/../examples"):
-            if filename not in exclude_dirs and not os.path.islink(os.path.join(script_dir, filename)) and os.path.isdir(os.path.join(f'{script_dir}/../examples', filename)):
-                os.symlink(os.path.join(f'{script_dir}/../examples', filename), os.path.join(script_dir, filename))
+            if (
+                filename not in exclude_dirs
+                and not os.path.islink(os.path.join(script_dir, filename))
+                and os.path.isdir(os.path.join(f"{script_dir}/../examples", filename))
+            ):
+                os.symlink(
+                    os.path.join(f"{script_dir}/../examples", filename),
+                    os.path.join(script_dir, filename),
+                )
 
         for submission in submissions:
             self._write_command(submission, self.out_f)
 
-        print(f"Running commands in {self.out_f}, two steps of diffusion, deterministic=True")
+        print(
+            f"Running commands in {self.out_f}, two steps of diffusion, deterministic=True"
+        )
 
         self.results = {}
         self.exec_status = {}
 
-        for bash_file in sorted( glob.glob(f"{self.out_f}/*.sh"), reverse=False):
-            test_name = os.path.basename(bash_file)[:-len('.sh')]
-            res, output = execute(f"Running {test_name}", f'bash {bash_file}', return_='tuple', add_message_and_command_line_to_output=True)
+        for bash_file in sorted(glob.glob(f"{self.out_f}/*.sh"), reverse=False):
+            test_name = os.path.basename(bash_file)[: -len(".sh")]
+            res, output = execute(
+                f"Running {test_name}",
+                f"bash {bash_file}",
+                return_="tuple",
+                add_message_and_command_line_to_output=True,
+            )
             self.exec_status[test_name] = (res, output)
 
             self.results[test_name] = dict(
-                state = 'failed' if res else 'passed',
-                log = output,
+                state="failed" if res else "passed",
+                log=output,
             )
 
-            #subprocess.run(["bash", bash_file], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
-            #subprocess.run(["bash", bash_file])
+            # subprocess.run(["bash", bash_file], stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+            # subprocess.run(["bash", bash_file])
 
     def test_examples_run_without_errors(self):
         for name, (exit_code, output) in sorted(self.exec_status.items()):
             with self.subTest(example=name):
                 if exit_code != 0:
                     self.__class__.failed_tests.append(f"{name}")
-                self.assertEqual(exit_code, 0,
-                                 msg=f"Example '{name}' exited with {exit_code}\n{output}")
+                self.assertEqual(
+                    exit_code,
+                    0,
+                    msg=f"Example '{name}' exited with {exit_code}\n{output}",
+                )
 
         sys.stderr.write("\n==== EXAMPLE FAILURE SUMMARY ====\n")
         for line in self.__class__.failed_tests:
@@ -79,51 +122,57 @@ def test_examples_run_without_errors(self):
         sys.stderr.write("=========================\n\n")
         sys.stderr.flush()
 
-
     def test_commands(self):
         """
         Runs all the commands in the test_f folder
         """
-        reference=f'{script_dir}/reference_outputs'
+        reference = f"{script_dir}/reference_outputs"
         os.makedirs(reference, exist_ok=True)
-        test_files=glob.glob(f"{self.out_f}/example_outputs/*pdb")
-        print(f'{self.out_f=} {test_files=}')
+        test_files = glob.glob(f"{self.out_f}/example_outputs/*pdb")
+        print(f"{self.out_f=} {test_files=}")
 
         # first check that we have the right number of outputs
-        #self.assertEqual(len(test_files), len(glob.glob(f"{self.out_f}/*.sh"))), "One or more of the example commands didn't produce an output (check the example command is formatted correctly)"
+        # self.assertEqual(len(test_files), len(glob.glob(f"{self.out_f}/*.sh"))), "One or more of the example commands didn't produce an output (check the example command is formatted correctly)"
 
         result = self.defaultTestResult()
         for test_file in test_files:
             with self.subTest(test_file=test_file):
-                test_pdb=iu.parse_pdb(test_file)
+                test_pdb = iu.parse_pdb(test_file)
                 if not os.path.exists(f"{reference}/{os.path.basename(test_file)}"):
                     copyfile(test_file, f"{reference}/{os.path.basename(test_file)}")
-                    print(f"Created reference file {reference}/{os.path.basename(test_file)}")
+                    print(
+                        f"Created reference file {reference}/{os.path.basename(test_file)}"
+                    )
                 else:
-                    ref_pdb=iu.parse_pdb(f"{reference}/{os.path.basename(test_file)}")
-                    rmsd=calc_rmsd(test_pdb['xyz'][:,:3].reshape(-1,3), ref_pdb['xyz'][:,:3].reshape(-1,3))[0]
+                    ref_pdb = iu.parse_pdb(f"{reference}/{os.path.basename(test_file)}")
+                    rmsd = calc_rmsd(
+                        test_pdb["xyz"][:, :3].reshape(-1, 3),
+                        ref_pdb["xyz"][:, :3].reshape(-1, 3),
+                    )[0]
                     try:
                         self.assertAlmostEqual(rmsd, 0, 2)
                         result.addSuccess(self)
                         print(f"Subtest {test_file} passed")
 
-                        state = 'passed'
-                        log = f'Subtest {test_file} passed'
+                        state = "passed"
+                        log = f"Subtest {test_file} passed"
 
                     except AssertionError as e:
                         result.addFailure(self, e)
                         print(f"Subtest {test_file} failed")
 
-                        state = 'failed'
-                        log = f'Subtest {test_file} failed:\n{e!r}'
+                        state = "failed"
+                        log = f"Subtest {test_file} failed:\n{e!r}"
 
-                    self.results[ 'pdb-diff.' + test_file.rpartition('/')[-1] ] = dict(state = state, log = log)
+                    self.results["pdb-diff." + test_file.rpartition("/")[-1]] = dict(
+                        state=state, log=log
+                    )
 
-        with open('.results.json', 'w') as f: json.dump(self.results, f, sort_keys=True, indent=2)
+        with open(".results.json", "w") as f:
+            json.dump(self.results, f, sort_keys=True, indent=2)
 
         self.assertTrue(result.wasSuccessful(), "One or more subtests failed")
 
-
     def _write_command(self, bash_file, test_f) -> None:
         """
         Takes a bash file from the examples folder, and writes
@@ -135,7 +184,7 @@ def _write_command(self, bash_file, test_f) -> None:
             else:
                 inference.final_step=48
         """
-        out_lines=[]
+        out_lines = []
         command_lines = []
         in_command = False
         with open(bash_file, "r") as f:
@@ -149,8 +198,8 @@ def _write_command(self, bash_file, test_f) -> None:
                         command_lines.append(stripped[:-1].strip())
                     else:
                         command_lines.append(stripped)
-                        in_command = False # End of command
-                else: 
+                        in_command = False  # End of command
+                else:
                     out_lines.append(line)
         if not command_lines:
             raise ValueError(f"No valid python command found in {bash_file}")
@@ -161,16 +210,17 @@ def _write_command(self, bash_file, test_f) -> None:
         else:
             final_step = 48
 
-        output_command = f"{command} inference.deterministic=True inference.final_step={final_step}"
+        output_command = (
+            f"{command} inference.deterministic=True inference.final_step={final_step}"
+        )
         # replace inference.num_designs with 1
         if "inference.num_designs=" in output_command:
             output_command = f'{output_command.split("inference.num_designs=")[0]}inference.num_designs=1 {" ".join(output_command.split("inference.num_designs=")[1].split(" ")[1:])}'
         else:
-            output_command = f'{output_command} inference.num_designs=1'
+            output_command = f"{output_command} inference.num_designs=1"
         # replace 'example_outputs' with f'{self.out_f}/example_outputs'
         output_command = f'{output_command.split("example_outputs")[0]}{self.out_f}/example_outputs{output_command.split("example_outputs")[1]}'
 
-
         # write the new command
         with open(f"{test_f}/{os.path.basename(bash_file)}", "w") as f:
             for line in out_lines:
@@ -184,21 +234,32 @@ def execute_through_pty(command_line):
     if sys.platform == "darwin":
 
         master, slave = pty.openpty()
-        p = subprocess.Popen(command_line, shell=True, stdout=slave, stdin=slave,
-                             stderr=subprocess.STDOUT, close_fds=True)
+        p = subprocess.Popen(
+            command_line,
+            shell=True,
+            stdout=slave,
+            stdin=slave,
+            stderr=subprocess.STDOUT,
+            close_fds=True,
+        )
 
         buffer = []
         while True:
             try:
                 if select.select([master], [], [], 0.2)[0]:  # has something to read
                     data = os.read(master, 1 << 22)
-                    if data: buffer.append(data)
+                    if data:
+                        buffer.append(data)
 
-                elif (p.poll() is not None)  and  (not select.select([master], [], [], 0.2)[0] ): break  # process is finished and output buffer if fully read
+                elif (p.poll() is not None) and (
+                    not select.select([master], [], [], 0.2)[0]
+                ):
+                    break  # process is finished and output buffer if fully read
 
-            except OSError: break  # OSError will be raised when child process close PTY descriptior
+            except OSError:
+                break  # OSError will be raised when child process close PTY descriptior
 
-        output = b''.join(buffer).decode(encoding='utf-8', errors='backslashreplace')
+        output = b"".join(buffer).decode(encoding="utf-8", errors="backslashreplace")
 
         os.close(master)
         os.close(slave)
@@ -206,7 +267,7 @@ def execute_through_pty(command_line):
         p.wait()
         exit_code = p.returncode
 
-        '''
+        """
         buffer = []
         while True:
             if select.select([master], [], [], 0.2)[0]:  # has something to read
@@ -227,13 +288,19 @@ def execute_through_pty(command_line):
 
         output = b''.join(buffer).decode(encoding='utf-8', errors='backslashreplace')
         exit_code = p.returncode
-        '''
+        """
 
     else:
 
         master, slave = pty.openpty()
-        p = subprocess.Popen(command_line, shell=True, stdout=slave, stdin=slave,
-                             stderr=subprocess.STDOUT, close_fds=True)
+        p = subprocess.Popen(
+            command_line,
+            shell=True,
+            stdout=slave,
+            stdin=slave,
+            stderr=subprocess.STDOUT,
+            close_fds=True,
+        )
 
         os.close(slave)
 
@@ -241,10 +308,12 @@ def execute_through_pty(command_line):
         while True:
             try:
                 data = os.read(master, 1 << 22)
-                if data: buffer.append(data)
-            except OSError: break  # OSError will be raised when child process close PTY descriptior
+                if data:
+                    buffer.append(data)
+            except OSError:
+                break  # OSError will be raised when child process close PTY descriptior
 
-        output = b''.join(buffer).decode(encoding='utf-8', errors='backslashreplace')
+        output = b"".join(buffer).decode(encoding="utf-8", errors="backslashreplace")
 
         os.close(master)
 
@@ -254,39 +323,84 @@ def execute_through_pty(command_line):
     return exit_code, output
 
 
-
-def execute(message, command_line, return_='status', until_successes=False, terminate_on_failure=True, silent=False, silence_output=False, silence_output_on_errors=False, add_message_and_command_line_to_output=False):
-    if not silent: print(message);  print(command_line); sys.stdout.flush();
+def execute(
+    message,
+    command_line,
+    return_="status",
+    until_successes=False,
+    terminate_on_failure=True,
+    silent=False,
+    silence_output=False,
+    silence_output_on_errors=False,
+    add_message_and_command_line_to_output=False,
+):
+    if not silent:
+        print(message)
+        print(command_line)
+        sys.stdout.flush()
     while True:
 
-        #exit_code, output = execute_through_subprocess(command_line)
-        #exit_code, output = execute_through_pexpect(command_line)
+        # exit_code, output = execute_through_subprocess(command_line)
+        # exit_code, output = execute_through_pexpect(command_line)
         exit_code, output = execute_through_pty(command_line)
 
-        if (exit_code  and  not silence_output_on_errors) or  not (silent or silence_output): print(output); sys.stdout.flush();
+        if (exit_code and not silence_output_on_errors) or not (
+            silent or silence_output
+        ):
+            print(output)
+            sys.stdout.flush()
 
-        if exit_code and until_successes: pass  # Thats right - redability COUNT!
-        else: break
+        if exit_code and until_successes:
+            pass  # Thats right - redability COUNT!
+        else:
+            break
 
-        print( "Error while executing {}: {}\n".format(message, output) )
+        print("Error while executing {}: {}\n".format(message, output))
         print("Sleeping 60s... then I will retry...")
-        sys.stdout.flush();
+        sys.stdout.flush()
         time.sleep(60)
 
-    if add_message_and_command_line_to_output: output = message + '\nCommand line: ' + command_line + '\n' + output
+    if add_message_and_command_line_to_output:
+        output = message + "\nCommand line: " + command_line + "\n" + output
 
-    if return_ == 'tuple'  or  return_ == tuple: return(exit_code, output)
+    if return_ == "tuple" or return_ == tuple:
+        return (exit_code, output)
 
     if exit_code and terminate_on_failure:
         print("\nEncounter error while executing: " + command_line)
-        if return_==True: return True
+        if return_ == True:
+            return True
         else:
-            print('\nEncounter error while executing: ' + command_line + '\n' + output);
-            raise BenchmarkError('\nEncounter error while executing: ' + command_line + '\n' + output)
+            print("\nEncounter error while executing: " + command_line + "\n" + output)
+            raise BenchmarkError(
+                "\nEncounter error while executing: " + command_line + "\n" + output
+            )
 
-    if return_ == 'output': return output
-    else: return exit_code
+    if return_ == "output":
+        return output
+    else:
+        return exit_code
 
 
 if __name__ == "__main__":
-    unittest.main()
+    import argparse
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "--total_chunks",
+        type=int,
+        default=1,
+        help="total number of chunks to split the examples into (default: 1)",
+    )
+    parser.add_argument(
+        "--chunk_index",
+        type=int,
+        default=1,
+        help="Which chunk to run (1-based index, default:1)",
+    )
+    args, remaining = parser.parse_known_args()
+
+    TestSubmissionCommands.total_chunks = args.total_chunks
+    TestSubmissionCommands.chunk_index = args.chunk_index
+
+    unittest.main(argv=[sys.argv[0]] + remaining)

From e2378c73581772e64ef866affe2a62d43409a470 Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Fri, 17 Oct 2025 10:51:44 -0500
Subject: [PATCH 08/22] Change num_designs in examples back to 10, since this
 is reset in test_diffusion.py

---
 examples/design_cyclic_oligos.sh                                | 2 +-
 examples/design_dihedral_oligos.sh                              | 2 +-
 examples/design_macrocyclic_binder.sh                           | 2 +-
 examples/design_macrocyclic_monomer.sh                          | 2 +-
 examples/design_motifscaffolding.sh                             | 2 +-
 examples/design_motifscaffolding_inpaintseq.sh                  | 2 +-
 examples/design_motifscaffolding_with_target.sh                 | 2 +-
 examples/design_nickel.sh                                       | 2 +-
 examples/design_partialdiffusion.sh                             | 2 +-
 examples/design_partialdiffusion_multipleseq.sh                 | 2 +-
 examples/design_partialdiffusion_withseq.sh                     | 2 +-
 examples/design_ppi.sh                                          | 2 +-
 examples/design_ppi_flexible_peptide.sh                         | 2 +-
 ...pi_flexible_peptide_with_secondarystructure_specification.sh | 2 +-
 examples/design_ppi_scaffolded.sh                               | 2 +-
 examples/design_tetrahedral_oligos.sh                           | 2 +-
 examples/design_timbarrel.sh                                    | 2 +-
 examples/design_unconditional.sh                                | 2 +-
 examples/design_unconditional_w_contact_potential.sh            | 2 +-
 examples/design_unconditional_w_monomer_ROG.sh                  | 2 +-
 20 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/examples/design_cyclic_oligos.sh b/examples/design_cyclic_oligos.sh
index 0f620816..db9a0896 100755
--- a/examples/design_cyclic_oligos.sh
+++ b/examples/design_cyclic_oligos.sh
@@ -7,4 +7,4 @@
 # We decay this potential with quadratic form, so that it is applied more strongly initially
 # We specify a total length of 480aa, so each chain is 80 residues long
 
-python ../scripts/run_inference.py --config-name=symmetry inference.symmetry="C6" inference.num_designs=2 inference.output_prefix="example_outputs/C6_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=[480-480]'
+python ../scripts/run_inference.py --config-name=symmetry inference.symmetry="C6" inference.num_designs=10 inference.output_prefix="example_outputs/C6_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=[480-480]'
diff --git a/examples/design_dihedral_oligos.sh b/examples/design_dihedral_oligos.sh
index ac2f6a6f..0d64a6fe 100755
--- a/examples/design_dihedral_oligos.sh
+++ b/examples/design_dihedral_oligos.sh
@@ -7,4 +7,4 @@
 # We decay this potential with quadratic form, so that it is applied more strongly initially
 # We specify a total length of 320aa, so each chain is 80 residues long
 
-python ../scripts/run_inference.py --config-name=symmetry inference.symmetry="D2" inference.num_designs=2 inference.output_prefix="example_outputs/D2_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=[320-320]'
+python ../scripts/run_inference.py --config-name=symmetry inference.symmetry="D2" inference.num_designs=10 inference.output_prefix="example_outputs/D2_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=[320-320]'
diff --git a/examples/design_macrocyclic_binder.sh b/examples/design_macrocyclic_binder.sh
index 99170417..1067a01e 100755
--- a/examples/design_macrocyclic_binder.sh
+++ b/examples/design_macrocyclic_binder.sh
@@ -7,7 +7,7 @@
 ../scripts/run_inference.py \
 --config-name base \
 inference.output_prefix=example_outputs/diffused_binder_cyclic2 \
-inference.num_designs=2 \
+inference.num_designs=10 \
 'contigmap.contigs=[12-18 A3-117/0]' \
 inference.input_pdb=./input_pdbs/7zkr_GABARAP.pdb \
 inference.cyclic=True \
diff --git a/examples/design_macrocyclic_monomer.sh b/examples/design_macrocyclic_monomer.sh
index d0cc3188..3aa1ac3d 100755
--- a/examples/design_macrocyclic_monomer.sh
+++ b/examples/design_macrocyclic_monomer.sh
@@ -7,7 +7,7 @@
 ../scripts/run_inference.py \
 --config-name base \
 inference.output_prefix=example_outputs/uncond_cycpep \
-inference.num_designs=2 \
+inference.num_designs=10 \
 'contigmap.contigs=[12-18]' \
 inference.input_pdb=input_pdbs/7zkr_GABARAP.pdb \
 inference.cyclic=True \
diff --git a/examples/design_motifscaffolding.sh b/examples/design_motifscaffolding.sh
index 2c9088e8..f5a80ddf 100755
--- a/examples/design_motifscaffolding.sh
+++ b/examples/design_motifscaffolding.sh
@@ -8,4 +8,4 @@
 #   - 10-40 residues (randomly sampled)
 # We generate 10 designs
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_motifscaffolding inference.input_pdb=input_pdbs/5TPN.pdb 'contigmap.contigs=[10-40/A163-181/10-40]' inference.num_designs=2
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_motifscaffolding inference.input_pdb=input_pdbs/5TPN.pdb 'contigmap.contigs=[10-40/A163-181/10-40]' inference.num_designs=10
diff --git a/examples/design_motifscaffolding_inpaintseq.sh b/examples/design_motifscaffolding_inpaintseq.sh
index 08a1c61d..8a06444b 100755
--- a/examples/design_motifscaffolding_inpaintseq.sh
+++ b/examples/design_motifscaffolding_inpaintseq.sh
@@ -12,4 +12,4 @@
 # We generate 10 designs
 # We then specify that residues 163-168 (inclusive), 170-171 (inclusive) and 179 (inclusive) on the A chain of the input, should be masked in the input
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_motifscaffolding_inpaintseq inference.input_pdb=input_pdbs/5TPN.pdb 'contigmap.contigs=[10-40/A163-181/10-40]' inference.num_designs=2 'contigmap.inpaint_seq=[A163-168/A170-171/A179]'
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_motifscaffolding_inpaintseq inference.input_pdb=input_pdbs/5TPN.pdb 'contigmap.contigs=[10-40/A163-181/10-40]' inference.num_designs=10 'contigmap.inpaint_seq=[A163-168/A170-171/A179]'
diff --git a/examples/design_motifscaffolding_with_target.sh b/examples/design_motifscaffolding_with_target.sh
index fcb32c5d..b52d7402 100755
--- a/examples/design_motifscaffolding_with_target.sh
+++ b/examples/design_motifscaffolding_with_target.sh
@@ -11,4 +11,4 @@
 # We generate 10 designs
 # As in the paper (at least for some of the designs we tested), we use the complex-finetuned model
 
-python ../scripts/run_inference.py inference.output_prefix=example_outputs/design_motifscaffolding_with_target inference.input_pdb=input_pdbs/1YCR.pdb 'contigmap.contigs=[A25-109/0 0-70/B17-29/0-70]' contigmap.length=70-120 inference.num_designs=2 inference.ckpt_override_path=../models/Complex_base_ckpt.pt
+python ../scripts/run_inference.py inference.output_prefix=example_outputs/design_motifscaffolding_with_target inference.input_pdb=input_pdbs/1YCR.pdb 'contigmap.contigs=[A25-109/0 0-70/B17-29/0-70]' contigmap.length=70-120 inference.num_designs=10 inference.ckpt_override_path=../models/Complex_base_ckpt.pt
diff --git a/examples/design_nickel.sh b/examples/design_nickel.sh
index 560951ec..fe303068 100755
--- a/examples/design_nickel.sh
+++ b/examples/design_nickel.sh
@@ -17,4 +17,4 @@
 
 ckpt='../models/Base_epoch8_ckpt.pt'
 
-python ../scripts/run_inference.py inference.symmetry="C4" inference.num_designs=2 inference.output_prefix=example_outputs/design_nickel 'potentials.guiding_potentials=["type:olig_contacts,weight_intra:1,weight_inter:0.06"]' potentials.olig_intra_all=True potentials.olig_inter_all=True potentials.guide_scale=2 potentials.guide_decay="quadratic" inference.input_pdb=input_pdbs/nickel_symmetric_motif.pdb 'contigmap.contigs=[50/A2-4/50/0 50/A7-9/50/0 50/A12-14/50/0 50/A17-19/50/0]' inference.ckpt_override_path=$ckpt
+python ../scripts/run_inference.py inference.symmetry="C4" inference.num_designs=10 inference.output_prefix=example_outputs/design_nickel 'potentials.guiding_potentials=["type:olig_contacts,weight_intra:1,weight_inter:0.06"]' potentials.olig_intra_all=True potentials.olig_inter_all=True potentials.guide_scale=2 potentials.guide_decay="quadratic" inference.input_pdb=input_pdbs/nickel_symmetric_motif.pdb 'contigmap.contigs=[50/A2-4/50/0 50/A7-9/50/0 50/A12-14/50/0 50/A17-19/50/0]' inference.ckpt_override_path=$ckpt
diff --git a/examples/design_partialdiffusion.sh b/examples/design_partialdiffusion.sh
index 3330ad9a..1e1fdc24 100755
--- a/examples/design_partialdiffusion.sh
+++ b/examples/design_partialdiffusion.sh
@@ -7,4 +7,4 @@
 # But, in either case, the contig length must sum to the length of the input pdb file
 # We generate 10 designs, and noise and denoise 10 steps (20% of the full trajectory)
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_partialdiffusion inference.input_pdb=input_pdbs/2KL8.pdb 'contigmap.contigs=[79-79]' inference.num_designs=2 diffuser.partial_T=10
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_partialdiffusion inference.input_pdb=input_pdbs/2KL8.pdb 'contigmap.contigs=[79-79]' inference.num_designs=10 diffuser.partial_T=10
diff --git a/examples/design_partialdiffusion_multipleseq.sh b/examples/design_partialdiffusion_multipleseq.sh
index 36fe03fd..1962ff03 100755
--- a/examples/design_partialdiffusion_multipleseq.sh
+++ b/examples/design_partialdiffusion_multipleseq.sh
@@ -6,4 +6,4 @@
 # Note the ranges do not necessarily need to lie on the same chain as in this example.
 # However, positions are 0-indexed over the whole sequence--not per-chain-- so care must be taken when providing ranges to provide_seq.
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_partialdiffusion_peptidewithmultiplesequence inference.input_pdb=input_pdbs/peptide_complex_ideal_helix.pdb 'contigmap.contigs=["172-172/0 34-34"]' diffuser.partial_T=10 inference.num_designs=2 'contigmap.provide_seq=[172-177,200-205]'
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_partialdiffusion_peptidewithmultiplesequence inference.input_pdb=input_pdbs/peptide_complex_ideal_helix.pdb 'contigmap.contigs=["172-172/0 34-34"]' diffuser.partial_T=10 inference.num_designs=10 'contigmap.provide_seq=[172-177,200-205]'
diff --git a/examples/design_partialdiffusion_withseq.sh b/examples/design_partialdiffusion_withseq.sh
index 95c5d73d..ab585c74 100755
--- a/examples/design_partialdiffusion_withseq.sh
+++ b/examples/design_partialdiffusion_withseq.sh
@@ -11,4 +11,4 @@
 # This contig will lead to the whole input pdb being noise by 10 steps (partial_T=10)
 # However, we provide the sequence of the peptide (the last 20 residues in the contig), with provide_seq=[172-205]. This is 0-indexed
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_partialdiffusion_peptidewithsequence inference.input_pdb=input_pdbs/peptide_complex_ideal_helix.pdb 'contigmap.contigs=["172-172/0 34-34"]' diffuser.partial_T=10 inference.num_designs=2 'contigmap.provide_seq=[172-205]'
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_partialdiffusion_peptidewithsequence inference.input_pdb=input_pdbs/peptide_complex_ideal_helix.pdb 'contigmap.contigs=["172-172/0 34-34"]' diffuser.partial_T=10 inference.num_designs=10 'contigmap.provide_seq=[172-205]'
diff --git a/examples/design_ppi.sh b/examples/design_ppi.sh
index 8354ef7b..5e217b21 100755
--- a/examples/design_ppi.sh
+++ b/examples/design_ppi.sh
@@ -8,4 +8,4 @@
 # We tell diffusion to target three specific residues on the target, specifically residues 59, 83 and 91 of the A chain
 # We make 10 designs, and reduce the noise added during inference to 0, to improve the quality of the designs
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_ppi inference.input_pdb=input_pdbs/insulin_target.pdb 'contigmap.contigs=[A1-150/0 70-100]' 'ppi.hotspot_res=[A59,A83,A91]' inference.num_designs=2 denoiser.noise_scale_ca=0 denoiser.noise_scale_frame=0
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_ppi inference.input_pdb=input_pdbs/insulin_target.pdb 'contigmap.contigs=[A1-150/0 70-100]' 'ppi.hotspot_res=[A59,A83,A91]' inference.num_designs=10 denoiser.noise_scale_ca=0 denoiser.noise_scale_frame=0
diff --git a/examples/design_ppi_flexible_peptide.sh b/examples/design_ppi_flexible_peptide.sh
index 5960f6b3..1af54c71 100755
--- a/examples/design_ppi_flexible_peptide.sh
+++ b/examples/design_ppi_flexible_peptide.sh
@@ -9,4 +9,4 @@
 # We make 10 designs
 # We mask (diffuse) the structure of the peptide using the inpaint_str flag. This has the effect of having RFdiffusion simultaneously design a binder and predict the structure of the peptide within the complex.
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_ppi_flexible_peptide inference.input_pdb=input_pdbs/3IOL.pdb 'contigmap.contigs=[B10-35/0 70-100]' 'ppi.hotspot_res=[B28,B29]' inference.num_designs=2 'contigmap.inpaint_str=[B10-35]'
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_ppi_flexible_peptide inference.input_pdb=input_pdbs/3IOL.pdb 'contigmap.contigs=[B10-35/0 70-100]' 'ppi.hotspot_res=[B28,B29]' inference.num_designs=10 'contigmap.inpaint_str=[B10-35]'
diff --git a/examples/design_ppi_flexible_peptide_with_secondarystructure_specification.sh b/examples/design_ppi_flexible_peptide_with_secondarystructure_specification.sh
index 96015db4..6e0dfc88 100755
--- a/examples/design_ppi_flexible_peptide_with_secondarystructure_specification.sh
+++ b/examples/design_ppi_flexible_peptide_with_secondarystructure_specification.sh
@@ -10,4 +10,4 @@
 # We then specify that we want this to adopt a helical conformation
 # If you wanted to specify that it should adopt a strand conformation, you would specify `contigmap.inpaint_str_strand`
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_ppi_flexible_peptide_with_secondarystructure inference.input_pdb=input_pdbs/tau_peptide.pdb 'contigmap.contigs=[70-100/0 B165-178]' inference.num_designs=2 'contigmap.inpaint_str=[B165-178]' scaffoldguided.scaffoldguided=True 'contigmap.inpaint_str_helix=[B165-178]'
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_ppi_flexible_peptide_with_secondarystructure inference.input_pdb=input_pdbs/tau_peptide.pdb 'contigmap.contigs=[70-100/0 B165-178]' inference.num_designs=10 'contigmap.inpaint_str=[B165-178]' scaffoldguided.scaffoldguided=True 'contigmap.inpaint_str_helix=[B165-178]'
diff --git a/examples/design_ppi_scaffolded.sh b/examples/design_ppi_scaffolded.sh
index 96e1ecf0..63ca165e 100755
--- a/examples/design_ppi_scaffolded.sh
+++ b/examples/design_ppi_scaffolded.sh
@@ -7,4 +7,4 @@
 # We then provide a path to a directory of different scaffolds (we've provided some for you to use, from Cao et al., 2022)
 # We generate 10 designs, and reduce the noise added during inference to 0 (which improves the quality of designs)
 
-../scripts/run_inference.py scaffoldguided.target_path=input_pdbs/insulin_target.pdb inference.output_prefix=example_outputs/design_ppi_scaffolded scaffoldguided.scaffoldguided=True 'ppi.hotspot_res=[A59,A83,A91]' scaffoldguided.target_pdb=True scaffoldguided.target_ss=target_folds/insulin_target_ss.pt scaffoldguided.target_adj=target_folds/insulin_target_adj.pt scaffoldguided.scaffold_dir=./ppi_scaffolds/ inference.num_designs=2 denoiser.noise_scale_ca=0 denoiser.noise_scale_frame=0
+../scripts/run_inference.py scaffoldguided.target_path=input_pdbs/insulin_target.pdb inference.output_prefix=example_outputs/design_ppi_scaffolded scaffoldguided.scaffoldguided=True 'ppi.hotspot_res=[A59,A83,A91]' scaffoldguided.target_pdb=True scaffoldguided.target_ss=target_folds/insulin_target_ss.pt scaffoldguided.target_adj=target_folds/insulin_target_adj.pt scaffoldguided.scaffold_dir=./ppi_scaffolds/ inference.num_designs=10 denoiser.noise_scale_ca=0 denoiser.noise_scale_frame=0
diff --git a/examples/design_tetrahedral_oligos.sh b/examples/design_tetrahedral_oligos.sh
index 4d9fcfd0..231e14a9 100755
--- a/examples/design_tetrahedral_oligos.sh
+++ b/examples/design_tetrahedral_oligos.sh
@@ -7,4 +7,4 @@
 # 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
 
-python ../scripts/run_inference.py --config-name=symmetry inference.symmetry="tetrahedral" inference.num_designs=2 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=[1200-1200]'
diff --git a/examples/design_timbarrel.sh b/examples/design_timbarrel.sh
index dc679908..410254ed 100755
--- a/examples/design_timbarrel.sh
+++ b/examples/design_timbarrel.sh
@@ -8,4 +8,4 @@
 # We add 0-5 residues (randomly sampled) to the N and the C-terminus
 # This will allow the generation of diverse TIM barrels with slightly different length helices and strands
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_tim_barrel scaffoldguided.scaffoldguided=True scaffoldguided.target_pdb=False scaffoldguided.scaffold_dir=tim_barrel_scaffold/ inference.num_designs=2 denoiser.noise_scale_ca=0.5 denoiser.noise_scale_frame=0.5 scaffoldguided.sampled_insertion=0-5 scaffoldguided.sampled_N=0-5 scaffoldguided.sampled_C=0-5
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_tim_barrel scaffoldguided.scaffoldguided=True scaffoldguided.target_pdb=False scaffoldguided.scaffold_dir=tim_barrel_scaffold/ inference.num_designs=10 denoiser.noise_scale_ca=0.5 denoiser.noise_scale_frame=0.5 scaffoldguided.sampled_insertion=0-5 scaffoldguided.sampled_N=0-5 scaffoldguided.sampled_C=0-5
diff --git a/examples/design_unconditional.sh b/examples/design_unconditional.sh
index 78887776..3ece16f7 100755
--- a/examples/design_unconditional.sh
+++ b/examples/design_unconditional.sh
@@ -4,4 +4,4 @@
 # We tell RFdiffusion that designs should be 100-200 residues in length (randomly sampled each design)
 # We generate 10 such designs
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_unconditional 'contigmap.contigs=[100-200]' inference.num_designs=2
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_unconditional 'contigmap.contigs=[100-200]' inference.num_designs=10
diff --git a/examples/design_unconditional_w_contact_potential.sh b/examples/design_unconditional_w_contact_potential.sh
index b2743723..999a9c04 100755
--- a/examples/design_unconditional_w_contact_potential.sh
+++ b/examples/design_unconditional_w_contact_potential.sh
@@ -4,4 +4,4 @@
 # We tell RFdiffusion that designs should be 100-200 residues in length (randomly sampled each design)
 # We generate 10 such designs
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_unconditional_w_contact_potential 'contigmap.contigs=[100-200]' inference.num_designs=2 'potentials.guiding_potentials=["type:monomer_contacts,weight:0.05"]'
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_unconditional_w_contact_potential 'contigmap.contigs=[100-200]' inference.num_designs=10 'potentials.guiding_potentials=["type:monomer_contacts,weight:0.05"]'
diff --git a/examples/design_unconditional_w_monomer_ROG.sh b/examples/design_unconditional_w_monomer_ROG.sh
index 079caa6b..b34a0a72 100755
--- a/examples/design_unconditional_w_monomer_ROG.sh
+++ b/examples/design_unconditional_w_monomer_ROG.sh
@@ -7,4 +7,4 @@
 # We use the monomer_ROG potential, with guide scale 2 and quadratic decay
 # Note that this potential is probably not necessary in this kind of case, but is provided as an example
 
-../scripts/run_inference.py inference.output_prefix=example_outputs/design_monomer_ROG_unconditional 'contigmap.contigs=[100-200]' inference.num_designs=2 'potentials.guiding_potentials=["type:monomer_ROG,weight:1,min_dist:5"]' potentials.guide_scale=2 potentials.guide_decay="quadratic"
+../scripts/run_inference.py inference.output_prefix=example_outputs/design_monomer_ROG_unconditional 'contigmap.contigs=[100-200]' inference.num_designs=10 'potentials.guiding_potentials=["type:monomer_ROG,weight:1,min_dist:5"]' potentials.guide_scale=2 potentials.guide_decay="quadratic"

From 6d0036b4809704b412012c194db8c694432da810 Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Fri, 17 Oct 2025 10:57:53 -0500
Subject: [PATCH 09/22] Fix typo in main.yml in test_diffusion options

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 89a694ff..c41bc94a 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -90,7 +90,7 @@ jobs:
         total_chunks=$(nproc) 
         for chunk_index in $(seq 1 $total_chunks); do
           echo "Running chunk $chunk_index of $total_chunks"
-          uv run python tests/test_diffusion.py --total-chunks $total_chunks --chunk-index $chunk_index &
+          uv run python tests/test_diffusion.py --total_chunks $total_chunks --chunk_index $chunk_index &
         done
 
         wait

From a629d43e928409c1e27f5396b376f1bcaca9a3be Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Fri, 17 Oct 2025 11:04:32 -0500
Subject: [PATCH 10/22] Add step to cd into tests directory in main.yml

---
 .github/workflows/main.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index c41bc94a..56743674 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -87,10 +87,11 @@ jobs:
     - name: Setup and Run ppi_scaffolds tests
       run: |
         tar -xvf examples/ppi_scaffolds_subset.tar.gz -C examples
-        total_chunks=$(nproc) 
+        total_chunks=$(nproc)
+        cd tests 
         for chunk_index in $(seq 1 $total_chunks); do
           echo "Running chunk $chunk_index of $total_chunks"
-          uv run python tests/test_diffusion.py --total_chunks $total_chunks --chunk_index $chunk_index &
+          uv run python test_diffusion.py --total_chunks $total_chunks --chunk_index $chunk_index &
         done
 
         wait

From 17f315b2de6d84c0ac189164b2c8d5c52fe8ac46 Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Fri, 17 Oct 2025 12:45:28 -0500
Subject: [PATCH 11/22] Add index of chunk to test directory name

---
 tests/test_diffusion.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_diffusion.py b/tests/test_diffusion.py
index 71829775..e73c9cd8 100644
--- a/tests/test_diffusion.py
+++ b/tests/test_diffusion.py
@@ -61,7 +61,7 @@ def setUp(self):
 
         now = datetime.datetime.now()
         now = now.strftime("%Y_%m_%d_%H_%M_%S")
-        self.out_f = f"{script_dir}/tests_{now}"
+        self.out_f = f"{script_dir}/tests_{now}_{idx}"
         os.mkdir(self.out_f)
 
         # Make sure we have access to all the relevant files

From 260692d6c2ce4a565fd60cf636c825c3317cc123 Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Mon, 20 Oct 2025 08:48:02 -0500
Subject: [PATCH 12/22] Edits to test_diffusion to make change setUp to
 setUpClass to make this a class method so examples run only once

---
 tests/test_diffusion.py | 42 +++++++++++++++++++++++------------------
 1 file changed, 24 insertions(+), 18 deletions(-)

diff --git a/tests/test_diffusion.py b/tests/test_diffusion.py
index e73c9cd8..10231d11 100644
--- a/tests/test_diffusion.py
+++ b/tests/test_diffusion.py
@@ -33,14 +33,19 @@ class TestSubmissionCommands(unittest.TestCase):
     # which chunk to run
     chunk_index = 1
 
-    def setUp(self):
+    out_f = None
+    results = {}
+    exec_status = {}
+
+    @classmethod
+    def setUpClass(cls):
         """
-        Grabs files from the examples folder
+        Class-level setup: Grabs files from the examples folder, discover & rewrite example commands, then execute them once.
         """
         submissions = glob.glob(f"{script_dir}/../examples/*.sh")
         # get datetime for output folder, in YYYY_MM_DD_HH_MM_SS format
-        chunks = self.__class__.total_chunks
-        idx = self.__class__.chunk_index
+        chunks = cls.total_chunks
+        idx = cls.chunk_index
         if chunks < 1:
             raise ValueError("total_chunks must be at least 1")
         if idx < 1 or idx > chunks:
@@ -61,8 +66,8 @@ def setUp(self):
 
         now = datetime.datetime.now()
         now = now.strftime("%Y_%m_%d_%H_%M_%S")
-        self.out_f = f"{script_dir}/tests_{now}_{idx}"
-        os.mkdir(self.out_f)
+        cls.out_f = f"{script_dir}/tests_{now}_{idx}"
+        os.mkdir(cls.out_f)
 
         # Make sure we have access to all the relevant files
         exclude_dirs = ["outputs", "example_outputs"]
@@ -78,16 +83,16 @@ def setUp(self):
                 )
 
         for submission in submissions:
-            self._write_command(submission, self.out_f)
+            cls._write_command(submission, cls.out_f)
 
         print(
-            f"Running commands in {self.out_f}, two steps of diffusion, deterministic=True"
+            f"Running commands in {cls.out_f}, two steps of diffusion, deterministic=True"
         )
 
-        self.results = {}
-        self.exec_status = {}
+        cls.results = {}
+        cls.exec_status = {}
 
-        for bash_file in sorted(glob.glob(f"{self.out_f}/*.sh"), reverse=False):
+        for bash_file in sorted(glob.glob(f"{cls.out_f}/*.sh"), reverse=False):
             test_name = os.path.basename(bash_file)[: -len(".sh")]
             res, output = execute(
                 f"Running {test_name}",
@@ -95,9 +100,9 @@ def setUp(self):
                 return_="tuple",
                 add_message_and_command_line_to_output=True,
             )
-            self.exec_status[test_name] = (res, output)
+            cls.exec_status[test_name] = (res, output)
 
-            self.results[test_name] = dict(
+            cls.results[test_name] = dict(
                 state="failed" if res else "passed",
                 log=output,
             )
@@ -106,7 +111,7 @@ def setUp(self):
             # subprocess.run(["bash", bash_file])
 
     def test_examples_run_without_errors(self):
-        for name, (exit_code, output) in sorted(self.exec_status.items()):
+        for name, (exit_code, output) in sorted(self.__class__.exec_status.items()):
             with self.subTest(example=name):
                 if exit_code != 0:
                     self.__class__.failed_tests.append(f"{name}")
@@ -128,8 +133,8 @@ def test_commands(self):
         """
         reference = f"{script_dir}/reference_outputs"
         os.makedirs(reference, exist_ok=True)
-        test_files = glob.glob(f"{self.out_f}/example_outputs/*pdb")
-        print(f"{self.out_f=} {test_files=}")
+        test_files = glob.glob(f"{self.__class__.out_f}/example_outputs/*pdb")
+        print(f"{self.__class__.out_f=} {test_files=}")
 
         # first check that we have the right number of outputs
         # self.assertEqual(len(test_files), len(glob.glob(f"{self.out_f}/*.sh"))), "One or more of the example commands didn't produce an output (check the example command is formatted correctly)"
@@ -173,7 +178,8 @@ def test_commands(self):
 
         self.assertTrue(result.wasSuccessful(), "One or more subtests failed")
 
-    def _write_command(self, bash_file, test_f) -> None:
+    @classmethod
+    def _write_command(cls, bash_file, test_f) -> None:
         """
         Takes a bash file from the examples folder, and writes
         a version of it to the test_f folder.
@@ -219,7 +225,7 @@ def _write_command(self, bash_file, test_f) -> None:
         else:
             output_command = f"{output_command} inference.num_designs=1"
         # replace 'example_outputs' with f'{self.out_f}/example_outputs'
-        output_command = f'{output_command.split("example_outputs")[0]}{self.out_f}/example_outputs{output_command.split("example_outputs")[1]}'
+        output_command = f'{output_command.split("example_outputs")[0]}{cls.out_f}/example_outputs{output_command.split("example_outputs")[1]}'
 
         # write the new command
         with open(f"{test_f}/{os.path.basename(bash_file)}", "w") as f:

From a570b2b8bdce98e979d875cde81d5f9ed0f3d225 Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Tue, 21 Oct 2025 09:57:15 -0500
Subject: [PATCH 13/22] Edit main.yml workflow so if an example fails, the test
 doesn't pass

---
 .github/workflows/main.yml | 27 +++++++++++++++++++++++++--
 1 file changed, 25 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 56743674..6b79b1c1 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -86,17 +86,40 @@ jobs:
 
     - name: Setup and Run ppi_scaffolds tests
       run: |
+        set -euo pipefail
         tar -xvf examples/ppi_scaffolds_subset.tar.gz -C examples
         total_chunks=$(nproc)
         cd tests 
+
+        #launch all chunks in background and record PIDs + labels
+        decalre -a pics
+        declare -a label_by_pid
+
         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 $chunk_index &
+          pid=$!
+          pids+=("$pid")
+          label_by_pid["$pid"]="chunk_$chunk_index"
+        done
+
+        # wait for each and track failures
+        fail=0
+        for pid in "${pids[@]}"; do
+          if ! wait "$pid"; do
+            echo "${label_by_pid[$pid]} failed (PID $pid)"
+            fail=1
+          else
+            echo "✅ ${label_by_pid[$pid]} passed (PID $pid)"
+          fi
         done
 
-        wait
+        # make step fail if any chunk failed
+        if [ "$fail" -ne 0 ]; then
+          echo "One or more chunks failed."
+          exit 1
+        fi
         echo "All chunks completed."
-        #cd tests && uv run python test_diffusion.py
 
 
     # - name: Test with pytest

From 4dd3a5f8c05e3fe06fd231f5299b0e47da093348 Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Tue, 21 Oct 2025 10:02:56 -0500
Subject: [PATCH 14/22] Remove -o option from pipefail

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 6b79b1c1..822d7d7f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -86,7 +86,7 @@ jobs:
 
     - name: Setup and Run ppi_scaffolds tests
       run: |
-        set -euo pipefail
+        set -eu pipefail
         tar -xvf examples/ppi_scaffolds_subset.tar.gz -C examples
         total_chunks=$(nproc)
         cd tests 

From 56feb3bb4ab497e656ba185579aed06e5c32647a Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Tue, 21 Oct 2025 10:09:12 -0500
Subject: [PATCH 15/22] Remove set pipefail

---
 .github/workflows/main.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 822d7d7f..baf7afa6 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -86,7 +86,6 @@ jobs:
 
     - name: Setup and Run ppi_scaffolds tests
       run: |
-        set -eu pipefail
         tar -xvf examples/ppi_scaffolds_subset.tar.gz -C examples
         total_chunks=$(nproc)
         cd tests 
@@ -110,7 +109,7 @@ jobs:
             echo "${label_by_pid[$pid]} failed (PID $pid)"
             fail=1
           else
-            echo "✅ ${label_by_pid[$pid]} passed (PID $pid)"
+            echo "${label_by_pid[$pid]} passed (PID $pid)"
           fi
         done
 

From dc1867dadf5f9ac6cb8b97e647eee67f0b6f8d23 Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Tue, 21 Oct 2025 16:29:06 -0500
Subject: [PATCH 16/22] Edit main.yml so workflow runs

---
 .github/workflows/main.yml | 24 +++++++-----------------
 1 file changed, 7 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index baf7afa6..a19916ef 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -91,35 +91,25 @@ jobs:
         cd tests 
 
         #launch all chunks in background and record PIDs + labels
-        decalre -a pics
-        declare -a label_by_pid
-
+        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 $chunk_index &
-          pid=$!
-          pids+=("$pid")
-          label_by_pid["$pid"]="chunk_$chunk_index"
+          pids="$pids $!"
         done
 
         # wait for each and track failures
         fail=0
-        for pid in "${pids[@]}"; do
-          if ! wait "$pid"; do
-            echo "${label_by_pid[$pid]} failed (PID $pid)"
+        for pid in $pids; do
+          if ! wait "$pid"; then
+            echo "A chunk (PID $pid) failed"
             fail=1
           else
-            echo "${label_by_pid[$pid]} passed (PID $pid)"
+            echo "A chunk (PID $pid) passed"
           fi
         done
 
-        # make step fail if any chunk failed
-        if [ "$fail" -ne 0 ]; then
-          echo "One or more chunks failed."
-          exit 1
-        fi
-        echo "All chunks completed."
-
+        exit "$fail"
 
     # - name: Test with pytest
     #   run: |

From 4d870c07da5e645393ee85a557b41e799d8b6371 Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Wed, 22 Oct 2025 10:03:07 -0500
Subject: [PATCH 17/22] In setUpClass check that directory doesn't already
 exists, so tests do not fail before running examples

---
 tests/test_diffusion.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/tests/test_diffusion.py b/tests/test_diffusion.py
index 10231d11..8de5c03e 100644
--- a/tests/test_diffusion.py
+++ b/tests/test_diffusion.py
@@ -74,13 +74,16 @@ def setUpClass(cls):
         for filename in os.listdir(f"{script_dir}/../examples"):
             if (
                 filename not in exclude_dirs
-                and not os.path.islink(os.path.join(script_dir, filename))
+                and not os.path.exists(os.path.join(script_dir, filename))
                 and os.path.isdir(os.path.join(f"{script_dir}/../examples", filename))
             ):
-                os.symlink(
-                    os.path.join(f"{script_dir}/../examples", filename),
-                    os.path.join(script_dir, filename),
-                )
+                try:
+                    os.symlink(
+                        os.path.join(f"{script_dir}/../examples", filename),
+                        os.path.join(script_dir, filename),
+                    )
+                except FileExistsError:
+                    pass
 
         for submission in submissions:
             cls._write_command(submission, cls.out_f)

From be5b7b6b89dbba576e2001087879a140bc532f44 Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Wed, 22 Oct 2025 15:13:35 -0500
Subject: [PATCH 18/22] Preseed DGL so avoid examples that are ran at the same
 time failing

---
 .github/workflows/main.yml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index a19916ef..b2dd2e3d 100644
--- a/.github/workflows/main.yml
+++ b/.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

From 681874e6ea19e763a5ccb35d1a434c9b3f6d8179 Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Wed, 22 Oct 2025 15:16:41 -0500
Subject: [PATCH 19/22] Reduce length for design_tetrahedral_oligos to 600 to
 reduce run time

---
 examples/design_tetrahedral_oligos.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/design_tetrahedral_oligos.sh b/examples/design_tetrahedral_oligos.sh
index 231e14a9..5aab7887 100755
--- a/examples/design_tetrahedral_oligos.sh
+++ b/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]'

From 4aea4fd65a8cbdbb5c6fff13dba36927a48b738c Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Thu, 23 Oct 2025 12:26:00 -0500
Subject: [PATCH 20/22] Change design_nickel.sh num_designs back to 15

---
 examples/design_nickel.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/design_nickel.sh b/examples/design_nickel.sh
index fe303068..8239680f 100755
--- a/examples/design_nickel.sh
+++ b/examples/design_nickel.sh
@@ -17,4 +17,4 @@
 
 ckpt='../models/Base_epoch8_ckpt.pt'
 
-python ../scripts/run_inference.py inference.symmetry="C4" inference.num_designs=10 inference.output_prefix=example_outputs/design_nickel 'potentials.guiding_potentials=["type:olig_contacts,weight_intra:1,weight_inter:0.06"]' potentials.olig_intra_all=True potentials.olig_inter_all=True potentials.guide_scale=2 potentials.guide_decay="quadratic" inference.input_pdb=input_pdbs/nickel_symmetric_motif.pdb 'contigmap.contigs=[50/A2-4/50/0 50/A7-9/50/0 50/A12-14/50/0 50/A17-19/50/0]' inference.ckpt_override_path=$ckpt
+python ../scripts/run_inference.py inference.symmetry="C4" inference.num_designs=15 inference.output_prefix=example_outputs/design_nickel 'potentials.guiding_potentials=["type:olig_contacts,weight_intra:1,weight_inter:0.06"]' potentials.olig_intra_all=True potentials.olig_inter_all=True potentials.guide_scale=2 potentials.guide_decay="quadratic" inference.input_pdb=input_pdbs/nickel_symmetric_motif.pdb 'contigmap.contigs=[50/A2-4/50/0 50/A7-9/50/0 50/A12-14/50/0 50/A17-19/50/0]' inference.ckpt_override_path=$ckpt

From ead721f32670eae379612d9e545690c3f288d251 Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Fri, 24 Oct 2025 09:48:03 -0500
Subject: [PATCH 21/22] Remove try block with except FileExistsError that isn't
 needed

---
 tests/test_diffusion.py | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/tests/test_diffusion.py b/tests/test_diffusion.py
index 8de5c03e..2bc6bfd6 100644
--- a/tests/test_diffusion.py
+++ b/tests/test_diffusion.py
@@ -77,13 +77,10 @@ def setUpClass(cls):
                 and not os.path.exists(os.path.join(script_dir, filename))
                 and os.path.isdir(os.path.join(f"{script_dir}/../examples", filename))
             ):
-                try:
-                    os.symlink(
-                        os.path.join(f"{script_dir}/../examples", filename),
-                        os.path.join(script_dir, filename),
-                    )
-                except FileExistsError:
-                    pass
+                os.symlink(
+                    os.path.join(f"{script_dir}/../examples", filename),
+                    os.path.join(script_dir, filename),
+                )
 
         for submission in submissions:
             cls._write_command(submission, cls.out_f)

From dd7643d6406cfbb1332eccaa36e6c0fc786251de Mon Sep 17 00:00:00 2001
From: woodsh17 <hmwoods14@gmail.com>
Date: Wed, 12 Nov 2025 13:45:07 -0600
Subject: [PATCH 22/22] Revert "Remove try block with except FileExistsError
 that isn't needed" After running the test, I found that this was needed This
 reverts commit ead721f32670eae379612d9e545690c3f288d251.

---
 tests/test_diffusion.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/tests/test_diffusion.py b/tests/test_diffusion.py
index 2bc6bfd6..8de5c03e 100644
--- a/tests/test_diffusion.py
+++ b/tests/test_diffusion.py
@@ -77,10 +77,13 @@ def setUpClass(cls):
                 and not os.path.exists(os.path.join(script_dir, filename))
                 and os.path.isdir(os.path.join(f"{script_dir}/../examples", filename))
             ):
-                os.symlink(
-                    os.path.join(f"{script_dir}/../examples", filename),
-                    os.path.join(script_dir, filename),
-                )
+                try:
+                    os.symlink(
+                        os.path.join(f"{script_dir}/../examples", filename),
+                        os.path.join(script_dir, filename),
+                    )
+                except FileExistsError:
+                    pass
 
         for submission in submissions:
             cls._write_command(submission, cls.out_f)