update page dependency

.github/workflows/page.yaml

@@ -28,7 +28,7 @@ jobs:
           python -m sphinx -T -E -b html -d _build/doctrees -D language=en ./docs/source _build/html
       - name: Deploy
         uses: peaceiris/actions-gh-pages@v3
-        if: ${{ github.ref == 'refs/heads/master' }}
+        if: ${{ github.ref == 'refs/heads/main' }}
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: _build/html

alab_management/builders/samplebuilder.py

@@ -53,12 +53,15 @@ def to_dict(self) -> dict[str, Any]:
         """Return Sample as a dictionary.
 
         This looks like:
-        {
-            "_id": str(ObjectId),
-            "name": str,
-            "tags": List[str],
-            "metadata": Dict[str, Any],
-        }
+
+        .. code-block::
+
+            {
+                "_id": str(ObjectId),
+                "name": str,
+                "tags": List[str],
+                "metadata": Dict[str, Any],
+            }
 
         Returns
         -------

alab_management/device_manager.py

@@ -324,14 +324,14 @@ def create_device_wrapper(
 
     def call(self, device_name: str, method: str, *args, **kwargs) -> Any:
         """
-        Call a method inside the device with name ``device_name``. *args, **kwargs will be feeded into
+        Call a method inside the device with name ``device_name``. args, kwargs will be feeded into
         the method directly.
 
         Args:
             device_name: the name of device, which is defined by administer.
             method: the class method to call
-            *args: positional arguments to feed into the method function
-            **kwargs: keyword arguments to feed into the method function
+            args: positional arguments to feed into the method function
+            kwargs: keyword arguments to feed into the method function
 
         Returns
         -------

alab_management/device_view/dbattributes.py

@@ -21,28 +21,27 @@ def value_in_database(name: str, default_value: Any) -> property:
     Example usage when defining a new Device:
 
         .. code-block:: python
-        from alab_management.device_view import BaseDevice, value_in_database
 
-        class MyDevice(BaseDevice):
-            my_attribute = value_in_database("my_attribute", 0)
+          from alab_management.device_view import BaseDevice, value_in_database
 
-            def __init__(self, name: str, **kwargs):
-                super().__init__(name, **kwargs)
-                self.name = name
-                self.my_attribute #initial call to the property, which sets the default value in the database
+          class MyDevice(BaseDevice):
+              my_attribute = value_in_database("my_attribute", 0)
 
-        ....
-        #first instantiation
+              def __init__(self, name: str, **kwargs):
+                  super().__init__(name, **kwargs)
+                  self.name = name
+                  self.my_attribute #initial call to the property, which sets the default value in the database
 
-        mydevice = MyDevice(name = "mydevice_1")
-        mydevice.my_attribute = 5 #sets the value in the database
-
-        ....
-        #future instantiation
-        mydevice = MyDevice(name = "mydevice_1")
-        mydevice.my_attribute #retrieves value from db and returns 5
+          ....
+          #first instantiation
 
+          mydevice = MyDevice(name = "mydevice_1")
+          mydevice.my_attribute = 5 #sets the value in the database
 
+          ....
+          #future instantiation
+          mydevice = MyDevice(name = "mydevice_1")
+          mydevice.my_attribute #retrieves value from db and returns 5
     """
 
     def getter(self) -> Any:

alab_management/device_view/device.py

@@ -202,7 +202,8 @@ def __init__(self, address: str, port: int = 502, *args, **kwargs):
     @property
     @abstractmethod
     def description(self) -> str:
-        """A short description of the device. This will be stored in the database + displayed in the dashboard. This
+        """
+        A short description of the device. This will be stored in the database + displayed in the dashboard. This
         must be declared in subclasses of BaseDevice!.
         """
         return self._description
@@ -380,18 +381,21 @@ def request_maintenance(self, prompt: str, options: list[Any]):
     def retrieve_signal(
         self, signal_name: str, within: datetime.timedelta | None = None
     ):
-        """Retrieve a signal from the database.
-
-        Args: signal_name (str): device signal name. This should match the signal_name passed to the
-        `@log_device_signal` decorator within (Optional[datetime.timedelta], optional): timedelta defining how far
-        back to pull logs from (relative to current time). Defaults to None.
-
-        Returns ------- Dict: Dictionary of signal result. Single value vs lists depends on whether `within` was None
-        or not, respectively. Form is: { "device_name": "device_name", "signal_name": "signal_name",
-        "value": "signal_value" or ["signal_value_1", "signal_value_2", ...]], "timestamp": "timestamp" or [
-        "timestamp_1", "timestamp_2", ...] }
+        """
+        Retrieve a signal from the database.
 
+        Args:
+            signal_name (str): device signal name. This should match the signal_name passed to the
+              ``@log_device_signal`` decorator
+            within (Optional[datetime.timedelta], optional):
+              timedelta defining how far back to pull logs from (relative to current time). Defaults to None.
 
+        Returns
+        -------
+            Dict: Dictionary of signal result. Single value vs lists depends on whether ``within`` was None
+            or not, respectively. Form is: { "device_name": "device_name", "signal_name": "signal_name",
+            "value": "signal_value" or ["signal_value_1", "signal_value_2", ...]], "timestamp": "timestamp" or [
+            "timestamp_1", "timestamp_2", ...] }
         """
         return self._signalemitter.retrieve_signal(signal_name, within)
 
@@ -441,11 +445,12 @@ def __init__(self, device: BaseDevice):
 
     def get_methods_to_log(self):
         """
-        Log the data from all methods decorated with `@log_signal` to the database.
+        Log the data from all methods decorated with ``@log_signal`` to the database.
 
-        Collected all the methods that are decorated with `@log_signal` and return a dictionary of the form:
+        Collected all the methods that are decorated with ``@log_signal`` and return a dictionary of the form:
 
         .. code-block::
+
             {
                 <method_name>: {
                     "interval": <interval_seconds>,

alab_management/lab_view.py

@@ -200,13 +200,14 @@ def update_sample_metadata(self, sample: ObjectId | str, metadata: dict[str, Any
     def run_subtask(
         self, task: type[BaseTask], samples: list[ObjectId | str], **kwargs
     ):
-        """Run a task as a subtask within the task. basically fills in task_id and lab_view for you.
-            this command blocks until the subtask is completed.
+        """
+        Run a task as a subtask within the task. basically fills in task_id and lab_view for you.
+        this command blocks until the subtask is completed.
 
         Args:
-        task (Type[BaseTask]): The type/class of the Task to run.
-        samples (List[Union[ObjectId, str]]): List of sample IDs or names.
-        **kwargs: will be passed to the Task method via the parameters entry in the task collection.
+            task (Type[BaseTask]): The type/class of the Task to run.
+            samples (List[Union[ObjectId, str]]): List of sample IDs or names.
+            **kwargs: will be passed to the Task method via the parameters entry in the task collection.
         """
         if not issubclass(task, BaseTask):
             raise TypeError("task must be a subclass of BaseTask!")

alab_management/logger.py

@@ -132,6 +132,9 @@ def get_latest_device_signal(
             Optional[Any]: dictionary with result.
 
             dict example:
+
+            .. code-block::
+
                 {
                     "device_name": device_name,
                     "signal_name": signal_name,

alab_management/resource_manager/resource_requester.py

@@ -59,22 +59,25 @@ class ResourceRequestItem(BaseModel):
 class ResourcesRequest(RootModel):
     """
     This class is used to validate the resource request. Each request should have a format of
-    [
-        {
-            "device":{
-                "identifier": "name" or "type" or "nodevice",
-                "content": string corresponding to identifier
-            },
-            "sample_positions": [
-                {
-                    "prefix": prefix of sample position,
-                    "number": integer number of such positions requested.
-                },
-                ...
-            ]
-        },
-        ...
-    ].
+
+    .. code-block::
+
+      [
+          {
+              "device":{
+                  "identifier": "name" or "type" or "nodevice",
+                  "content": string corresponding to identifier
+              },
+              "sample_positions": [
+                  {
+                      "prefix": prefix of sample position,
+                      "number": integer number of such positions requested.
+                  },
+                  ...
+              ]
+          },
+          ...
+      ].
 
     See Also
     --------

alab_management/task_view/task_enums.py

@@ -47,7 +47,7 @@ class CancelingProgress(Enum):
 
     PENDING: The canceling process has been initiated.
     WORKER_NOTIFIED: The worker has been notified to cancel the request, which means an
-        abort error has been raised in the worker.
+      abort error has been raised in the worker.
     """
 
     PENDING = auto()

docs/source/advance_topics.md

@@ -0,0 +1,10 @@
+# Advance Topics
+
+In this section, we will discuss some of the more advanced topics that can help you better set up the lab.
+
+```{toctree}
+:maxdepth: 1
+:hidden:
+
+test
+```