Address various deprecation warnings in pytest output

CHANGELOG.md

@@ -12,6 +12,7 @@ Write the date in place of the "Unreleased" in the case a new version is release
 ### Fixed
 
 - Adapt to change in dask public API in dask 2024.9.0.
+- Address miscellaneous deprecations in dependencies.
 
 ## v0.1.0b8 (2024-09-06)
 

tiled/_tests/test_sync.py

@@ -65,7 +65,7 @@ def populate_internal(client):
         awkward.Array([1, [2, 3]]), key="d", metadata={"color": "red"}, specs=["alpha"]
     )
     # sparse
-    coo = sparse.COO(coords=[[2, 5]], data=[1.3, 7.5], shape=(10,))
+    coo = sparse.COO(coords=numpy.array([[2, 5]]), data=[1.3, 7.5], shape=(10,))
     client.write_sparse(key="e", coords=coo.coords, data=coo.data, shape=coo.shape)
 
     # nested

tiled/adapters/tiff.py

@@ -242,10 +242,10 @@ def read(self, slice: Optional[NDSlice] = ...) -> NDArray[Any]:
             return self._seq.asarray()
         if isinstance(slice, int):
             # e.g. read(slice=0) -- return an entire image
-            return tifffile.TiffFile(self._seq.files[slice]).asarray()
+            return tifffile.TiffFile(self._seq[slice]).asarray()
         if isinstance(slice, builtins.slice):
             # e.g. read(slice=(...)) -- return a slice along the image axis
-            return tifffile.TiffSequence(self._seq.files[slice]).asarray()
+            return tifffile.TiffSequence(self._seq[slice]).asarray()
         if isinstance(slice, tuple):
             if len(slice) == 0:
                 return self._seq.asarray()
@@ -255,10 +255,10 @@ def read(self, slice: Optional[NDSlice] = ...) -> NDArray[Any]:
             # Could be int or slice (0, slice(...)) or (0,....); the_rest is converted to a list
             if isinstance(image_axis, int):
                 # e.g. read(slice=(0, ....))
-                arr = tifffile.TiffFile(self._seq.files[image_axis]).asarray()
+                arr = tifffile.TiffFile(self._seq[image_axis]).asarray()
             elif image_axis is Ellipsis:
                 # Return all images
-                arr = tifffile.TiffSequence(self._seq.files).asarray()
+                arr = tifffile.TiffSequence(self._seq).asarray()
                 the_rest.insert(0, Ellipsis)  # Include any leading dimensions
             elif isinstance(image_axis, builtins.slice):
                 arr = self.read(slice=image_axis)

tiled/authn_database/core.py

@@ -1,6 +1,6 @@
+import datetime
 import hashlib
 import uuid as uuid_module
-from datetime import datetime
 
 from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.future import select
@@ -77,7 +77,7 @@ async def purge_expired(db, cls):
     """
     Remove expired entries.
     """
-    now = datetime.utcnow()
+    now = datetime.datetime.now(datetime.UTC)
     num_expired = 0
     statement = (
         select(cls)
@@ -146,7 +146,7 @@ async def lookup_valid_session(db, session_id):
         return None
     if (
         session.expiration_time is not None
-        and session.expiration_time < datetime.utcnow()
+        and session.expiration_time < datetime.datetime.now(datetime.UTC)
     ):
         await db.delete(session)
         await db.commit()
@@ -171,7 +171,7 @@ async def lookup_valid_pending_session_by_device_code(db, device_code):
         return None
     if (
         pending_session.expiration_time is not None
-        and pending_session.expiration_time < datetime.utcnow()
+        and pending_session.expiration_time < datetime.datetime.now(datetime.UTC)
     ):
         await db.delete(pending_session)
         await db.commit()
@@ -189,7 +189,7 @@ async def lookup_valid_pending_session_by_user_code(db, user_code):
         return None
     if (
         pending_session.expiration_time is not None
-        and pending_session.expiration_time < datetime.utcnow()
+        and pending_session.expiration_time < datetime.datetime.now(datetime.UTC)
     ):
         await db.delete(pending_session)
         await db.commit()
@@ -228,7 +228,7 @@ async def lookup_valid_api_key(db, secret):
     Look up an API key. Ensure that it is valid.
     """
 
-    now = datetime.utcnow()
+    now = datetime.datetime.now(datetime.UTC)
     hashed_secret = hashlib.sha256(secret).digest()
     api_key = (
         await db.execute(

tiled/examples/xdi.py

@@ -80,7 +80,7 @@ def read_xdi(data_uri, structure=None, metadata=None, specs=None, access_policy=
 
         # TODO validate
 
-        df = pd.read_table(file, delim_whitespace=True, names=col_labels)
+        df = pd.read_table(file, sep=r"\s+", names=col_labels)
 
     return DataFrameAdapter.from_pandas(
         df,

tiled/server/app.py

@@ -270,9 +270,9 @@ async def index(
             principal=Security(get_current_principal, scopes=[]),
         ):
             return templates.TemplateResponse(
+                request,
                 "index.html",
                 {
-                    "request": request,
                     # This is used to construct the link to the React UI.
                     "root_url": get_root_url(request),
                     # If defined, this adds a Binder link to the page.

tiled/server/authentication.py

@@ -1,9 +1,9 @@
+import datetime
 import enum
 import hashlib
 import secrets
 import uuid as uuid_module
 import warnings
-from datetime import datetime, timedelta
 from pathlib import Path
 from typing import Optional
 
@@ -67,7 +67,7 @@
 from .utils import API_KEY_COOKIE_NAME, get_authenticators, get_base_url
 
 ALGORITHM = "HS256"
-UNIT_SECOND = timedelta(seconds=1)
+UNIT_SECOND = datetime.timedelta(seconds=1)
 
 # Max API keys and Sessions allowed to Principal.
 # This is here for at least two reasons:
@@ -77,13 +77,13 @@
 API_KEY_LIMIT = 100
 SESSION_LIMIT = 200
 
-DEVICE_CODE_MAX_AGE = timedelta(minutes=15)
+DEVICE_CODE_MAX_AGE = datetime.timedelta(minutes=15)
 DEVICE_CODE_POLLING_INTERVAL = 5  # seconds
 
 
 def utcnow():
     "UTC now with second resolution"
-    return datetime.utcnow().replace(microsecond=0)
+    return datetime.datetime.now(datetime.UTC).replace(microsecond=0)
 
 
 class Mode(enum.Enum):
@@ -759,7 +759,9 @@ async def generate_apikey(db, principal, apikey_params, request):
             ),
         )
     if apikey_params.expires_in is not None:
-        expiration_time = utcnow() + timedelta(seconds=apikey_params.expires_in)
+        expiration_time = utcnow() + datetime.timedelta(
+            seconds=apikey_params.expires_in
+        )
     else:
         expiration_time = None
     # The standard 32 byes of entropy,

tiled/server/core.py

@@ -1,5 +1,6 @@
 import collections.abc
 import dataclasses
+import datetime
 import itertools
 import math
 import operator
@@ -8,7 +9,6 @@
 import types
 import uuid
 from collections import defaultdict
-from datetime import datetime, timedelta
 from hashlib import md5
 from typing import Any
 
@@ -225,7 +225,9 @@ async def construct_entries_response(
             keys = tree.keys()[offset : offset + limit]  # noqa: E203
         items = [(key, None) for key in keys]
     # This value will not leak out. It just used to seed comparisons.
-    metadata_stale_at = datetime.utcnow() + timedelta(days=1_000_000)
+    metadata_stale_at = datetime.datetime.now(datetime.UTC) + datetime.timedelta(
+        days=1_000_000
+    )
     must_revalidate = getattr(tree, "must_revalidate", True)
     for key, entry in items:
         resource = await construct_resource(

tiled/server/router.py

@@ -1,9 +1,9 @@
 import dataclasses
+import datetime
 import inspect
 import os
 import re
 import warnings
-from datetime import datetime, timedelta
 from functools import partial
 from pathlib import Path
 from typing import Any, List, Optional
@@ -149,7 +149,7 @@ async def about(
             },
             meta={"root_path": request.scope.get("root_path") or "" + "/api"},
         ).model_dump(),
-        expires=datetime.utcnow() + timedelta(seconds=600),
+        expires=datetime.datetime.now(datetime.UTC) + datetime.timedelta(seconds=600),
     )