Merge pull request #59 from CederGroupHub/Update-to-python=3.10-minimum

Update black.yaml, ci.yaml, and page.yaml to python 3.10

.github/workflows/black.yaml

@@ -13,8 +13,8 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.9"  # Specify the Python version you need
+          python-version: "3.10"  # Specify the Python version you need
       - name: Install Black
-        run: pip install black==22.3.0
+        run: pip install black
       - name: Run Black
         run: black ./alab_management

.github/workflows/ci.yaml

@@ -16,7 +16,7 @@ jobs:
     timeout-minutes: 60
     strategy:
       matrix:
-        python-version: [ "3.8", "3.9", "3.10" ]
+        python-version: ["3.10"]
     services:
       rabbitmq:
         image: "rabbitmq:3.9"
@@ -37,7 +37,7 @@ jobs:
         uses: actions/setup-python@v2
         with:
           # python-version: ${{ matrix.python-version }}
-          python-version: "3.9"
+          python-version: "3.10"
           # cache: 'pip'
           # cache-dependency-path:
       - name: Set up environment

.github/workflows/page.yaml

@@ -19,7 +19,7 @@ jobs:
       - name: Set up python
         uses: actions/setup-python@v2
         with:
-          python-version: '3.8'
+          python-version: '3.10'
       - name: Set up dependencies
         run: pip install --quiet .
       - name: Compile sphinx

alab_management/builders/experimentbuilder.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import Any, Dict, List, Literal, Optional, Set, Union
+from typing import Any, Literal
 
 from .samplebuilder import SampleBuilder
 
@@ -13,20 +13,20 @@ class ExperimentBuilder:
       name (str): The name of the experiment.
     """
 
-    def __init__(self, name: str, tags: Optional[List[str]] = None, **metadata):
+    def __init__(self, name: str, tags: list[str] | None = None, **metadata):
         """
         Args:
           name (str): The name of the experiment.
           tags (List[str]): A list of tags to attach to the experiment.
         """
         self.name = name
-        self._samples: List[SampleBuilder] = []
-        self._tasks: Dict[str, Dict[str, Any]] = {}
+        self._samples: list[SampleBuilder] = []
+        self._tasks: dict[str, dict[str, Any]] = {}
         self.tags = tags or []
         self.metadata = metadata
 
     def add_sample(
-        self, name: str, tags: Optional[List[str]] = None, **metadata
+        self, name: str, tags: list[str] | None = None, **metadata
     ) -> SampleBuilder:
         """
         Add a sample to the batch. Each sample already has multiple tasks binded to it. Each
@@ -53,8 +53,8 @@ def add_task(
         self,
         task_id: str,
         task_name: str,
-        task_kwargs: Dict[str, Any],
-        samples: List[SampleBuilder],
+        task_kwargs: dict[str, Any],
+        samples: list[SampleBuilder],
     ) -> None:
         """
         This function adds a task to the sample. You should use this function only for special cases which
@@ -78,7 +78,7 @@ def add_task(
             "samples": [sample.name for sample in samples],
         }
 
-    def to_dict(self) -> Dict[str, Any]:
+    def to_dict(self) -> dict[str, Any]:
         """
         Return a dictionary that can be used to generate an input file for the `experiment`
         to run.
@@ -88,9 +88,9 @@ def to_dict(self) -> Dict[str, Any]:
             A dictionary that can be used to generate an input file for the `experiment` to run.
 
         """
-        samples: List[Dict[str, Any]] = []
+        samples: list[dict[str, Any]] = []
         # tasks = []
-        tasks: List[Dict[str, Union[str, Set[int], List]]] = []
+        tasks: list[dict[str, str | set[int] | list]] = []
         task_ids = {}
 
         for sample in self._samples:

alab_management/builders/samplebuilder.py

@@ -1,6 +1,6 @@
 """Build the sample object."""
 
-from typing import TYPE_CHECKING, Any, Dict, List, Optional
+from typing import TYPE_CHECKING, Any
 
 from bson import ObjectId  # type: ignore
 
@@ -23,11 +23,11 @@ def __init__(
         self,
         name: str,
         experiment: "ExperimentBuilder",
-        tags: Optional[List[str]] = None,
+        tags: list[str] | None = None,
         **metadata,
     ):
         self.name = name
-        self._tasks: List[str] = []  # type: ignore
+        self._tasks: list[str] = []  # type: ignore
         self.experiment = experiment
         self.metadata = metadata
         self._id = str(ObjectId())
@@ -49,7 +49,7 @@ def add_task(
         if task_id not in self._tasks:
             self._tasks.append(task_id)
 
-    def to_dict(self) -> Dict[str, Any]:
+    def to_dict(self) -> dict[str, Any]:
         """Return Sample as a dictionary.
 
         This looks like:

alab_management/builders/utils.py

@@ -1,6 +1,6 @@
 """This module contains utility functions for the builders module."""
 
-from typing import TYPE_CHECKING, List, Union
+from typing import TYPE_CHECKING
 
 from bson import ObjectId  # type: ignore
 
@@ -13,7 +13,7 @@
 
 def append_task(
     task: "BaseTask",
-    samples: Union[SampleBuilder, List[SampleBuilder]],
+    samples: SampleBuilder | list[SampleBuilder],
 ):
     """
     Used to add basetask to a SampleBuilder's tasklist during Experiment construction.

alab_management/config.py

@@ -27,12 +27,12 @@
 import os
 from pathlib import Path
 from types import MappingProxyType as FrozenDict
-from typing import Any, Dict
+from typing import Any
 
 import toml
 
 
-def freeze_config(config_: Dict[str, Any]) -> FrozenDict:
+def freeze_config(config_: dict[str, Any]) -> FrozenDict:
     """
     Convert the config dict to frozen config.
 

alab_management/dashboard/routes/experiment.py

@@ -1,7 +1,7 @@
 """This is a dashboard that displays data from the ALab database."""
 
 from datetime import datetime, timedelta
-from typing import Any, Dict, List, Optional
+from typing import Any
 
 from bson import ObjectId  # type: ignore
 from bson.errors import InvalidId  # type: ignore
@@ -180,11 +180,11 @@ def query_experiment_results(exp_id: str):
 def cancel_experiment(exp_id: str):
     try:
         exp_id = ObjectId(exp_id)
-        experiment: Optional[Dict[str, Any]] = experiment_view.get_experiment(exp_id)
+        experiment: dict[str, Any] | None = experiment_view.get_experiment(exp_id)
         if experiment is None:
             return {"status": "error", "reason": "Experiment not found"}, 400
 
-        tasks: List[Dict[str, Any]] = experiment["tasks"]
+        tasks: list[dict[str, Any]] = experiment["tasks"]
         # tasks = experiment_view.get_experiment(exp_id)["tasks"]
 
         for task in tasks:

alab_management/device_manager.py

@@ -6,11 +6,12 @@
 DeviceManager class, which will handle all the request to run certain methods on the real device.
 """
 
+from collections.abc import Callable
 from concurrent.futures import Future
 from enum import Enum, auto
 from functools import partial
 from threading import Thread
-from typing import Any, Callable, Dict, NoReturn, Optional, cast
+from typing import Any, NoReturn, cast
 from uuid import uuid4
 
 import dill
@@ -171,9 +172,7 @@ def callback_publish(channel, delivery_tag, props, response):
             channel.basic_ack(delivery_tag=cast(int, delivery_tag))
 
         try:
-            device_entry: Optional[Dict[str, Any]] = self._device_view.get_device(
-                device
-            )
+            device_entry: dict[str, Any] | None = self._device_view.get_device(device)
 
             # check if the device is currently occupied by this task
             if self._check_status and (
@@ -217,7 +216,7 @@ def on_message(
               "kwargs": Dict,
           }
         """
-        body: Dict[str, Any] = dill.loads(_body)
+        body: dict[str, Any] = dill.loads(_body)
 
         thread = Thread(
             target=self._execute_command_wrapper,
@@ -266,15 +265,15 @@ def __init__(self, task_id: ObjectId, timeout: int = None):
         #  taskid, or can be random? I think this dies with the resourcerequest context manager anyways?
         self._rpc_reply_queue_name = str(uuid4()) + DEFAULT_CLIENT_QUEUE_SUFFIX
         self._task_id = task_id
-        self._waiting: Dict[ObjectId, Future] = {}
+        self._waiting: dict[ObjectId, Future] = {}
 
         self._conn = get_rabbitmq_connection()
         self._channel = self._conn.channel()
         self._channel.queue_declare(
             self._rpc_reply_queue_name, exclusive=False, auto_delete=True
         )
 
-        self._thread: Optional[Thread] = None
+        self._thread: Thread | None = None
 
         self._channel.basic_consume(
             queue=self._rpc_reply_queue_name,

alab_management/device_view/dbattributes.py

@@ -1,4 +1,4 @@
-from typing import Any, Union
+from typing import Any
 
 from pymongo.collection import Collection  # type: ignore
 
@@ -71,7 +71,7 @@ def __init__(
         device_collection: Collection,
         device_name: str,
         attribute_name: str,
-        default_value: Union[list, None] = None,
+        default_value: list | None = None,
     ):
         self._collection = device_collection
         self.attribute_name = attribute_name
@@ -284,7 +284,7 @@ def __init__(
         device_collection: Collection,
         device_name: str,
         attribute_name: str,
-        default_value: Union[dict, None] = None,
+        default_value: dict | None = None,
     ):
         self._collection = device_collection
         self.attribute_name = attribute_name

alab_management/device_view/device.py

@@ -5,9 +5,10 @@
 import threading
 import time
 from abc import ABC, abstractmethod
+from collections.abc import Callable
 from queue import Empty, PriorityQueue
 from traceback import format_exc
-from typing import Any, Callable, Dict, List, Optional, Union
+from typing import Any
 from unittest.mock import Mock
 
 from alab_management.logger import DBLogger
@@ -23,7 +24,7 @@ def _UNSPECIFIED(_):
 
 def mock(
     return_constant: Any = _UNSPECIFIED,
-    object_type: Union[List[Any], Any] = _UNSPECIFIED,
+    object_type: list[Any] | Any = _UNSPECIFIED,
 ):
     """
     A decorator used for mocking functions during simulation.
@@ -143,7 +144,7 @@ class BaseDevice(ABC):
         kwargs: keyword arguments that will be passed to the device class
     """
 
-    def __init__(self, name: str, description: Optional[str] = None, *args, **kwargs):
+    def __init__(self, name: str, description: str | None = None, *args, **kwargs):
         """
         Initialize a device object, you can set up connection to
         the device in this method. The device will only be initialized
@@ -253,7 +254,7 @@ def disconnect(self):
 
     @property
     @abstractmethod
-    def sample_positions(self) -> List[SamplePosition]:
+    def sample_positions(self) -> list[SamplePosition]:
         """
         The sample positions describe the position that can hold a sample. The name of sample
         position will be the unique identifier of this sample position. It does not store any
@@ -298,7 +299,7 @@ def is_running(self) -> bool:
 
     # methods to store Device values inside the database. Lists and dictionaries are supported.
     def list_in_database(
-        self, name: str, default_value: Optional[Union[list, None]] = None
+        self, name: str, default_value: list | None | None = None
     ) -> ListInDatabase:
         """
         Create a list attribute that is stored in the database.
@@ -320,7 +321,7 @@ def list_in_database(
         )
 
     def dict_in_database(
-        self, name: str, default_value: Optional[Union[dict, None]] = None
+        self, name: str, default_value: dict | None | None = None
     ) -> DictInDatabase:
         """
         Create a dict attribute that is stored in the database.
@@ -353,7 +354,7 @@ def _apply_default_db_values(self):
             if any(isinstance(attribute, t) for t in [ListInDatabase, DictInDatabase]):
                 attribute.apply_default_value()
 
-    def request_maintenance(self, prompt: str, options: List[Any]):
+    def request_maintenance(self, prompt: str, options: list[Any]):
         """
         Request maintenance input from the user. This will display a prompt to the user and wait for them to select
         an option. The selected option will be returned.
@@ -365,7 +366,7 @@ def request_maintenance(self, prompt: str, options: List[Any]):
         return request_maintenance_input(prompt=prompt, options=options)
 
     def retrieve_signal(
-        self, signal_name: str, within: Optional[datetime.timedelta] = None
+        self, signal_name: str, within: datetime.timedelta | None = None
     ):
         """Retrieve a signal from the database.
 
@@ -423,8 +424,8 @@ def __init__(self, device: BaseDevice):
         self.is_logging = False
         self.queue: PriorityQueue = PriorityQueue()
 
-        self._logging_thread: Optional[threading.Thread] = None
-        self._start_time: Optional[datetime.datetime] = None
+        self._logging_thread: threading.Thread | None = None
+        self._start_time: datetime.datetime | None = None
 
     def get_methods_to_log(self):
         """
@@ -567,7 +568,7 @@ def stop(self):
         self.is_logging = False
         self._logging_thread.join()
 
-    def retrieve_signal(self, signal_name, within: Optional[datetime.timedelta] = None):
+    def retrieve_signal(self, signal_name, within: datetime.timedelta | None = None):
         """Retrieve a signal from the database.
 
         Args:
@@ -599,7 +600,7 @@ def retrieve_signal(self, signal_name, within: Optional[datetime.timedelta] = No
             )
 
 
-_device_registry: Dict[str, BaseDevice] = {}
+_device_registry: dict[str, BaseDevice] = {}
 
 
 def add_device(device: BaseDevice):
@@ -609,7 +610,7 @@ def add_device(device: BaseDevice):
     _device_registry[device.name] = device
 
 
-def get_all_devices() -> Dict[str, BaseDevice]:
+def get_all_devices() -> dict[str, BaseDevice]:
     """
     Get all the device names in the device registry. This is a shallow copy of the registry.