fix(edits): use a valid timestamp when locks are overridden, instead of None; add fallback for get earliest ts

Author: akhileshh

pychunkedgraph/graph/chunkedgraph.py

@@ -1022,9 +1022,13 @@ def get_earliest_timestamp(self):
         from datetime import timedelta
 
         for op_id in range(100):
-            _, timestamp = self.client.read_log_entry(op_id)
+            _log, timestamp = self.client.read_log_entry(op_id)
             if timestamp is not None:
                 return timestamp - timedelta(milliseconds=500)
+            if _log:
+                return self.client._read_byte_row(serializers.serialize_uint64(op_id))[
+                    attributes.OperationLogs.Status
+                ][-1].timestamp
 
     def get_operation_ids(self, node_ids: typing.Sequence):
         response = self.client.read_nodes(node_ids=node_ids)

pychunkedgraph/graph/operation.py

@@ -31,7 +31,7 @@
 from .cutting import run_multicut
 from .exceptions import PreconditionError
 from .exceptions import PostconditionError
-from .utils.generic import get_bounding_box as get_bbox
+from .utils.generic import get_bounding_box as get_bbox, get_valid_timestamp
 from ..logging.log_db import TimeIt
 
 
@@ -432,6 +432,8 @@ def execute(
                 lock.locked_root_ids,
                 np.array([lock.operation_id] * len(lock.locked_root_ids)),
             )
+            if timestamp is None:
+                timestamp = get_valid_timestamp(timestamp)
 
             log_record_before_edit = self._create_log_record(
                 operation_id=lock.operation_id,
@@ -865,7 +867,7 @@ def __init__(
         self.path_augment = path_augment
         self.disallow_isolating_cut = disallow_isolating_cut
         self.do_sanity_check = do_sanity_check
-        if np.any(np.in1d(self.sink_ids, self.source_ids)):
+        if np.any(np.isin(self.sink_ids, self.source_ids)):
             raise PreconditionError(
                 "Supervoxels exist in both sink and source, "
                 "try placing the points further apart."
@@ -914,8 +916,8 @@ def _apply(
             supervoxels = np.concatenate(
                 [agg.supervoxels for agg in l2id_agglomeration_d.values()]
             )
-            mask0 = np.in1d(edges.node_ids1, supervoxels)
-            mask1 = np.in1d(edges.node_ids2, supervoxels)
+            mask0 = np.isin(edges.node_ids1, supervoxels)
+            mask1 = np.isin(edges.node_ids2, supervoxels)
             edges = edges[mask0 & mask1]
         if len(edges) == 0:
             raise PreconditionError("No local edges found.")

pychunkedgraph/graph/utils/generic.py

@@ -98,7 +98,7 @@ def time_min():
 
 def get_valid_timestamp(timestamp):
     if timestamp is None:
-        timestamp = datetime.datetime.utcnow()
+        timestamp = datetime.datetime.now(datetime.timezone.utc)
     if timestamp.tzinfo is None:
         timestamp = pytz.UTC.localize(timestamp)
     # Comply to resolution of BigTables TimeRange