Merge pull request #311 from macrocosm-os/staging

Staging

Author: mccrindlebrian

blacklist.txt

@@ -0,0 +1,5 @@
+5DcBFgjEPuUtXCWJURUX5mDnmWLw1RukwfvJAgJZD5cHCftb
+5F9XbpH9fhYsWQFSZ789EHWdFnzthcVfXLno4WE7YJUBK8nF
+5Dm2K8EKo4kvX5cK782w6wwemuPckXi92dVmprTzhg24TyJV
+5C5vSVadd2XPX2zyTLvnyRAtLchF68gwkKGFgryjbJn83cU4
+5CcGFU5VQmqefkybdf3D2hmJrrqp5HSKfmzmXrjRbbUkWgMs

folding/__init__.py

@@ -1,12 +1,8 @@
 from .protocol import JobSubmissionSynapse
 from .validators.protein import Protein
 
-__version__ = "1.4.0"
+__version__ = "1.4.1"
 version_split = __version__.split(".")
-__spec_version__ = (
-    (10000 * int(version_split[0]))
-    + (100 * int(version_split[1]))
-    + (1 * int(version_split[2]))
-)
+__spec_version__ = (10000 * int(version_split[0])) + (100 * int(version_split[1])) + (1 * int(version_split[2]))
 
 __OPENMM_VERSION_TAG__ = "8.2"

folding/base/neuron.py

@@ -85,7 +85,7 @@ def __init__(self, config=None):
         else:
             self.wallet = bt.wallet(config=self.config)
             self.subtensor = bt.subtensor(config=self.config)
-            self.metagraph = self.subtensor.metagraph(self.config.netuid, lite = False)
+            self.metagraph = self.subtensor.metagraph(self.config.netuid, lite=False)
 
             # Check OpenMM version if we are not in mock mode.
             self.check_openmm_version()
@@ -126,9 +126,7 @@ def check_openmm_version(self):
 
     def setup_wandb_logging(self):
         if os.path.isfile(f"{self.config.neuron.full_path}/wandb_ids.pkl"):
-            self.wandb_ids = load_pkl(
-                f"{self.config.neuron.full_path}/wandb_ids.pkl", "rb"
-            )
+            self.wandb_ids = load_pkl(f"{self.config.neuron.full_path}/wandb_ids.pkl", "rb")
         else:
             self.wandb_ids = {}
 
@@ -161,7 +159,7 @@ def sync(self):
         self.save_state()
 
     def weight_setter(self):
-        """ method to set weights for the validator. """
+        """method to set weights for the validator."""
         try:
             logger.info("Attempting to set weights...")
             weights_are_set = self.set_weights()
@@ -188,9 +186,7 @@ def should_sync_metagraph(self):
         """
         Check if enough epoch blocks have elapsed since the last checkpoint to sync.
         """
-        return (
-            self.block - self.metagraph.last_update[self.uid]
-        ) > self.config.neuron.metagraph_resync_length
+        return (self.block - self.metagraph.last_update[self.uid]) > self.config.neuron.metagraph_resync_length
 
     def should_set_weights(self) -> bool:
         # Don't set weights on initialization.
@@ -206,9 +202,7 @@ def should_set_weights(self) -> bool:
             return False
 
         # Define appropriate logic for when set weights.
-        return (
-            self.block - self.metagraph.last_update[self.uid]
-        ) > self.config.neuron.epoch_length
+        return (self.block - self.metagraph.last_update[self.uid]) > self.config.neuron.epoch_length
 
     def save_state(self):
         pass

folding/organic/validator.py

@@ -40,12 +40,8 @@ def __init__(
         self._validator: BaseNeuron = validator
 
         protected_args = ["ff", "water", "box"]
-        simulation_args = list(
-            SimulationConfig(ff="organic", water="organic", box="cube").to_dict().keys()
-        )
-        self.simulation_args = [
-            arg for arg in simulation_args if arg not in protected_args
-        ]
+        simulation_args = list(SimulationConfig(ff="organic", water="organic", box="cube").to_dict().keys())
+        self.simulation_args = [arg for arg in simulation_args if arg not in protected_args]
 
     async def _on_organic_entry(self, synapse: OrganicSynapse) -> bt.Synapse:
         """
@@ -55,9 +51,7 @@ async def _on_organic_entry(self, synapse: OrganicSynapse) -> bt.Synapse:
 
         config: dict = synapse.get_simulation_params()
         self._organic_queue.add(config)
-        logger.success(
-            f"Query received: organic queue size = {self._organic_queue.size}"
-        )
+        logger.success(f"Query received: organic queue size = {self._organic_queue.size}")
 
         # TODO: This is still False on the API side.... Why!???!
         synapse.is_processed = True
@@ -77,21 +71,15 @@ async def start_loop(self):
                 logs = await self.forward()
 
                 total_elapsed_time = logs.get("total_elapsed_time", 0)
-                logger.info(
-                    f"Organic scoring iteration completed in {total_elapsed_time:.2f} seconds."
-                )
+                logger.info(f"Organic scoring iteration completed in {total_elapsed_time:.2f} seconds.")
 
                 logger.warning(
                     f"Sleeping for {self._validator.config.neuron.organic_trigger_frequency} seconds before next organic check."
                 )
-                await asyncio.sleep(
-                    self._validator.config.neuron.organic_trigger_frequency
-                )
+                await asyncio.sleep(self._validator.config.neuron.organic_trigger_frequency)
 
             except Exception as e:
-                logger.error(
-                    f"Error occured during organic scoring iteration:\n{e}"
-                )
+                logger.error(f"Error occured during organic scoring iteration:\n{e}")
                 await asyncio.sleep(1)
 
     async def sample(self) -> dict[str, Any]:

folding/store.py

@@ -95,10 +95,10 @@ def _job_to_dict(self, job: "Job") -> dict:
         """Convert a Job object to a dictionary for database storage."""
         data = job.to_dict()
 
-        # Convert Python list or dict objects to JSON strings for sqlite 
+        # Convert Python list or dict objects to JSON strings for sqlite
         data_to_update = {}
         for k, v in data.items():
-            if isinstance(v, (list,dict)):
+            if isinstance(v, (list, dict)):
                 data_to_update[k] = json.dumps(v)
 
         data.update(data_to_update)
@@ -220,7 +220,7 @@ def update_gjp_job(self, job: "Job", gjp_address: str, keypair, job_id: str):
         """
 
         body = get_epistula_body(job=job)
-        
+
         body_bytes = self.epistula.create_message_body(body)
         headers = self.epistula.generate_header(hotkey=keypair, body=body_bytes)
 

folding/utils/epistula_utils.py

@@ -27,13 +27,11 @@ def get_epistula_body(job: "Job") -> dict:
     body["is_organic"] = body.get("is_organic", False)
     body["update_interval"] = body.pop("update_interval").total_seconds()
     body["max_time_no_improvement"] = body.pop("max_time_no_improvement").total_seconds()
-    body["best_loss_at"] = (
-         body["best_loss_at"] if pd.notna(body["best_loss_at"]) else datetime.now(timezone.utc)
-    )
+    body["best_loss_at"] = body["best_loss_at"] if pd.notna(body["best_loss_at"]) else datetime.now(timezone.utc)
     body["best_hotkey"] = "" if body["best_hotkey"] is None else body["best_hotkey"]
     body["best_loss"] = 0.0 if body["best_loss"] == np.inf else body["best_loss"]
-    
-    body["best_cpt_links"] = json.dumps(body.pop("best_cpt_links")) if body["best_cpt_links"] else [""]
+
+    body["best_cpt_links"] = body.pop("best_cpt_links") if body["best_cpt_links"] else [""]
     body["epsilon"] = int(body.pop("epsilon"))
     body.pop("event")
     body.pop("job_id")

folding/utils/logger.py

@@ -19,6 +19,7 @@
     diagnose=False,
 )
 
+
 def setup_file_logging(log_path, retention):
     """Setup file logging with rotation"""
     logger.add(
@@ -32,9 +33,11 @@ def setup_file_logging(log_path, retention):
         format=FORMAT,
     )
 
+
 def add_events_level():
     """Add custom EVENTS level if it doesn't exist"""
     if "EVENTS" not in logger._core.levels:
         logger.level("EVENTS", no=38, icon="📝")
 
-__all__ = ['logger', 'setup_file_logging', 'add_events_level']
+
+__all__ = ["logger", "setup_file_logging", "add_events_level"]

folding/utils/s3_utils.py

@@ -34,7 +34,6 @@ def create_s3_client(
     access_key_id: str = S3_CONFIG["access_key_id"],
     secret_access_key: str = S3_CONFIG["secret_access_key"],
 ) -> boto3.client:
-
     """Creates a configured S3 client using the environment variables defined in S3_CONFIG.
 
     Raises:
@@ -86,7 +85,6 @@ async def upload_to_s3(
         input_time = datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
 
         for file_type in ["pdb", "cpt"]:
-
             if file_type == "cpt":
                 file_path = os.path.join(validator_directory, simulation_cpt)
             else:
@@ -96,7 +94,11 @@ async def upload_to_s3(
             logger.debug(f"putting file: {file_path} at {location} with type {file_type}")
 
             key = await asyncio.to_thread(
-                handler.put, file_path=file_path, location=location, public=True, file_type=file_type
+                handler.put,
+                file_path=file_path,
+                location=location,
+                public=True,
+                file_type=file_type,
             )
             s3_links[file_type] = os.path.join("https://nyc3.digitaloceanspaces.com/vali-s3-demo-do/", key)
             await asyncio.sleep(0.10)