Strict type-checking + unit tests across the foundry shared library

models/rf3/configs/datasets/pdb_and_distillation.yaml

@@ -9,7 +9,6 @@ defaults:
     - monomer_distillation
     - na_complex_distillation
     - disorder_distillation
-    # - domain_distillation
     # - rna_monomer_distillation
   - val/af3_validation@val.af3_validation
   - val/af3_validation@val.quick_af3_validation_with_templating
@@ -28,8 +27,6 @@ train:
     probability: 0.02
   disorder_distillation:
     probability: 0.02
-  # multidomain_distillation:
-  #   probability: 0.06
   # rna_monomer_distillation:
   #   probability: 0.04
 

pyproject.toml

@@ -258,10 +258,7 @@ module = [
 ignore_errors = true
 
 # NOTE: the rf3 enablement ratchet (0014) is fully cleared — there is no rf3 module-level
-# mypy exemption here. The one module that cannot type-check, `rf3.data.paired_msa`
-# (broken against the installed atomworks; needs a `PandasDataset`-API refactor), carries
-# a file-level `# mypy: ignore-errors` directive in the module itself, so the suppression
-# is visible where the code is and the module stays inside mypy's `files` scope.
+# mypy exemption here, and every rf3 module type-checks with no in-file suppressions.
 
 # Per-module strictness ratchet (direction (b)). The global baseline above leaves
 # disallow_untyped_defs / check_untyped_defs off; fully-annotated modules opt into strict
@@ -274,6 +271,33 @@ module = [
     "foundry.utils.alignment",
     "foundry.utils.weights",
     "foundry.utils.rotation_augmentation",
+    "foundry.utils.instantiators",
+    "foundry.utils.ddp",
+    "foundry.utils.squashfs",
+    "foundry.utils.logging",
+    "foundry.utils.datasets",
+    "foundry.training.schedulers",
+    "foundry.training.EMA",
+    "foundry.training.checkpoint",
+    "foundry.common",
+    "foundry.constants",
+    "foundry.metrics.metric",
+    "foundry.metrics.losses",
+    "foundry.callbacks.callback",
+    "foundry.callbacks.timing_logging",
+    "foundry.callbacks.metrics_logging",
+    "foundry.callbacks.train_logging",
+    "foundry.callbacks.health_logging",
+    "foundry.inference_engines.base",
+    "foundry.inference_engines.checkpoint_registry",
+    "foundry.hydra.resolvers",
+    "foundry.model.layers.blocks",
+    "foundry.utils.xpu.single_xpu_strategy",
+    "foundry.utils.xpu.xpu_accelerator",
+    "foundry.utils.xpu.xpu_precision",
+    "foundry.testing.fixtures",
+    "foundry.testing.pytest_hooks",
+    "foundry_cli.download_checkpoints",
 ]
 disallow_untyped_defs = true
 check_untyped_defs = true