replacing with timezone aware defaults

caveclient/chunkedgraph.py

@@ -204,7 +204,7 @@ def _process_timestamp(self, timestamp):
             if self._default_timestamp is not None:
                 return self._default_timestamp
             else:
-                return datetime.datetime.utcnow()
+                return datetime.datetime.now(datetime.timezone.utc)
         else:
             return timestamp
 
@@ -816,11 +816,10 @@ def get_latest_roots(self, root_id, timestamp=None, timestamp_future=None):
             timestamp = timestamp_future
 
         if timestamp is None:
-            timestamp = datetime.datetime.utcnow()
+            timestamp = datetime.datetime.now(datetime.timezone.utc)
 
         # or if timestamp_root is less than timestamp_future
-
-        if timestamp is None or timestamp_root < timestamp:
+        if (timestamp is None) or (timestamp_root < timestamp):
             lineage_graph = self.get_lineage_graph(
                 root_id,
                 timestamp_past=timestamp_root,
@@ -1114,14 +1113,16 @@ def get_past_ids(self, root_ids, timestamp_past=None, timestamp_future=None):
     def get_delta_roots(
         self,
         timestamp_past: datetime.datetime,
-        timestamp_future: datetime.datetime = datetime.datetime.utcnow(),
+        timestamp_future: datetime.datetime = datetime.datetime.now(
+            datetime.timezone.utc
+        ),
     ):
         """get the list of roots that have changed between timetamp_past and timestamp_future
 
 
         Args:
             timestamp_past (datetime.datetime): past timepoint to query
-            timestamp_future (datetime.datetime, optional): future timepoint to query. Defaults to datetime.datetime.utcnow().
+            timestamp_future (datetime.datetime, optional): future timepoint to query. Defaults to datetime.datetime.now(datetime.timezone.utc).
 
         Returns:
             old_roots (np.ndarray): roots that have expired in that interval

caveclient/materializationengine.py

@@ -111,7 +111,7 @@ def concatenate_position_columns(df, inplace=False):
 
 def convert_timestamp(ts: datetime):
     if ts == "now":
-        ts = datetime.utcnow()
+        ts = datetime.now(timezone.utc)
 
     if isinstance(ts, datetime):
         if ts.tzinfo is None:
@@ -1181,7 +1181,7 @@ def live_live_query(
             allow_missing_lookups (bool, optional): If there are annotations without supervoxels and rootids yet, allow results. Defaults to False.
             random_sample: (int, optional) : if given, will do a tablesample of the table to return that many annotations
         Example:
-         live_live_query("table_name",datetime.datetime.utcnow(),
+         live_live_query("table_name",datetime.datetime.now(datetime.timezone.utc),
             joins=[[table_name, table_column, joined_table, joined_column],
                      [joined_table, joincol2, third_table, joincol_third]]
             suffixes={
@@ -1350,7 +1350,7 @@ def live_query(
         Args:
             table: 'str'
             timestamp (datetime.datetime): time to materialize (in utc)
-                pass datetime.datetime.utcnow() for present time
+                pass datetime.datetime.now(datetime.timezone.utc) for present time
             filter_in_dict (dict , optional):
                 keys are column names, values are allowed entries.
                 Defaults to None.
@@ -1850,7 +1850,7 @@ def live_live_query(
             allow_invalid_root_ids (bool, optional): If True, ignore root ids not valid at the given timestamp, otherwise raise an Error. Defaults to False.
             random_sample (int, optional): If given, will do a tablesample of the table to return that many annotations
         Example:
-         live_live_query("table_name",datetime.datetime.utcnow(),
+         live_live_query("table_name",datetime.datetime.now(datetime.timezone.utc),
             joins=[[table_name, table_column, joined_table, joined_column],
                      [joined_table, joincol2, third_table, joincol_third]]
             suffixes={

docs/guide/materialization.rst

@@ -212,15 +212,15 @@ that is more recent that the most recent version available.  For convience, you
 
 
 to automatically update the results of your query to a time in the future, such as now.
-For example, to pass now, use ```datetime.datetime.utcnow```.  Note all timestamps are in UTC
+For example, to pass now, use ```datetime.datetime.now(datetime.timezone.utc)```.  Note all timestamps are in UTC
 throughout the codebase. 
 
 .. code:: python
 
     import datetime
     synapse_table = client.info.get_datastack_info()['synapse_table']
     df=client.materialize.live_query(synapse_table,
-                                      datetime.datetime.utcnow(),
+                                      datetime.datetime.now(datetime.timezone.utc),
                                       filter_equal_dict = {'post_pt_root_id': MYID})
 
 This will raise an ValueError exception if the IDs passed in your filters are not valid at the timestamp given
@@ -232,11 +232,11 @@ You can also pass a timestamp directly to query_table and it will call live_quer
     import datetime
     synapse_table = client.info.get_datastack_info()['synapse_table']
     df=client.materialize.query_table(synapse_table,
-                                      timestamp=datetime.datetime.utcnow(),
+                                      timestamp=datetime.datetime.now(datetime.timezone.utc),
                                       filter_equal_dict = {'post_pt_root_id': MYID})
 
 
-Also, keep in mind if you run multiple queries and at each time pass ``datetime.datetime.utcnow()``,
+Also, keep in mind if you run multiple queries and at each time pass ``datetime.datetime.now(datetime.timezone.utc)``,
 there is no gauruntee that the IDs will be consistent from query to query, as proofreading might be happening
 at any time.  For larger scale analysis constraining oneself to a materialized version will ensure consistent results.
 
@@ -312,7 +312,7 @@ The one required argument for ``live_query`` is the timestamp.
     nuc_df = client.materialize.tables.nucleus_detection_v0(
         id=my_ids
     ).live_query(
-        timestamp=datetime.datetime.utcnow(),
+        timestamp=datetime.datetime.now(datetime.timezone.utc),
     )
 
 The live query functions have similar but slightly different arguments: ``timestamp`` (required), ``offset``, ``limit``, ``split_positions``,

tests/test_chunkedgraph.py

@@ -47,7 +47,7 @@ def test_get_roots(self, myclient):
         url = chunkedgraph_endpoints_v1["get_roots"].format_map(endpoint_mapping)
         svids = np.array([97557743795364048, 75089979126506763], dtype=np.uint64)
         root_ids = np.array([864691135217871271, 864691135566275148], dtype=np.uint64)
-        now = datetime.datetime.utcnow()
+        now = datetime.datetime.now(datetime.timezone.utc)
         query_d = package_timestamp(now)
         qurl = url + "?" + urlencode(query_d)
         responses.add(
@@ -231,7 +231,7 @@ def test_delta_roots(self, myclient):
         endpoint_mapping = self._default_endpoint_map
         url = chunkedgraph_endpoints_v1["delta_roots"].format_map(endpoint_mapping)
 
-        now = datetime.datetime.utcnow()
+        now = datetime.datetime.now(datetime.timezone.utc)
         timestamp_past = now - datetime.timedelta(days=1)
         query_d = package_timestamp(timestamp_past, name="timestamp_past")
         query_d.update(package_timestamp(now, name="timestamp_future"))
@@ -434,7 +434,7 @@ def test_past_ids(self, myclient):
                 "864691136577570580": [864691136721486702, 864691133958789149],
             },
         }
-        now = datetime.datetime.utcnow()
+        now = datetime.datetime.now(datetime.timezone.utc)
         timestamp_past = now - datetime.timedelta(days=7)
 
         query_d = package_timestamp(timestamp_past, name="timestamp_past")
@@ -470,7 +470,7 @@ def test_lineage_graph(self, myclient):
         url = chunkedgraph_endpoints_v1["handle_lineage_graph"].format_map(
             endpoint_mapping
         )
-        now = datetime.datetime.utcnow()
+        now = datetime.datetime.now(datetime.timezone.utc)
         timestamp_past = now - datetime.timedelta(days=7)
 
         query_d = package_timestamp(timestamp_past, name="timestamp_past")