fix an issue with dim_pairwise not being propagated and try to get Alexs end2end test working on github actions

Author: lucidrains

alphafold3_pytorch/alphafold3.py

@@ -1735,6 +1735,7 @@ def __init__(
         self.pairwise_conditioner = PairwiseConditioning(
             dim_pairwise_trunk = dim_pairwise_trunk,
             dim_pairwise_rel_pos_feats = dim_pairwise_rel_pos_feats,
+            dim_pairwise = dim_pairwise,
             **pairwise_cond_kwargs
         )
 

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "alphafold3-pytorch"
-version = "0.1.135"
+version = "0.1.136"
 description = "Alphafold 3 - Pytorch"
 authors = [
     { name = "Phil Wang", email = "[email protected]" }

tests/test_af3.py

@@ -476,6 +476,7 @@ def test_alphafold3(
 
     alphafold3 = Alphafold3(
         dim_atom_inputs = 77,
+        dim_pairwise = 64,
         atoms_per_window = atoms_per_window,
         dim_template_feats = 44,
         num_dist_bins = 38,

tests/test_input.py

@@ -160,6 +160,12 @@ def test_pdbinput_input():
     # training
 
     alphafold3 = Alphafold3(
+        dim_atom=8,
+        dim_atompair=8,
+        dim_input_embedder_token=8,
+        dim_single=8,
+        dim_pairwise=8,
+        dim_token=8,
         dim_atom_inputs=3,
         dim_atompair_inputs=1,
         atoms_per_window=27,
@@ -168,7 +174,7 @@ def test_pdbinput_input():
         confidence_head_kwargs=dict(pairformer_depth=1),
         template_embedder_kwargs=dict(pairformer_stack_depth=1),
         msa_module_kwargs=dict(depth=1),
-        pairformer_stack=dict(depth=2),
+        pairformer_stack=dict(depth=1),
         diffusion_module_kwargs=dict(
             atom_encoder_depth=1,
             token_transformer_depth=1,