Catching pause state (#413)

* Catching pause state

This tweak to readfish will prevent readfish from stopping when a user pauses a flowcell for some reason. As a consequence it is now safe to pause a flowcell whilst readfish is running without cuasing readfish to stop. This update will not affect older versions of minknow which did not explicitly declare a pause state.

* Addressing failed test

A fix to force tests to use integers.

Author: mattloose

src/readfish/_read_until_client.py

@@ -14,12 +14,17 @@
 from readfish._loggers import setup_logger
 from grpc import RpcError
 
-# Check against these states to determine if Minknow is under the impression
-# The run has fully begun and readfish can be started
+# Check against these states to determine if MinKNOW still considers the run
+# active enough for readfish to remain connected.
 ACCEPTABLE_ACQUISITION_STATES = {
     AcquisitionState.ACQUISITION_RUNNING,
     AcquisitionState.ACQUISITION_STARTING,
 }
+# Some MinKNOW versions expose explicit pause states. Treat them as non-terminal
+# so readfish waits for sequencing to resume instead of disconnecting.
+for _state_name in ("ACQUISITION_PAUSING", "ACQUISITION_PAUSED"):
+    if hasattr(AcquisitionState, _state_name):
+        ACCEPTABLE_ACQUISITION_STATES.add(getattr(AcquisitionState, _state_name))
 # Any but these two states suggest the run has stopped
 ACCEPTABLE_PROTOCOL_STATES = {
     protocol_service.PROTOCOL_RUNNING,

src/readfish/_utils.py

@@ -242,9 +242,9 @@ def get_flowcell_array(flowcell_size: int) -> npt.ArrayLike:
     Traceback (most recent call last):
         ...
     ValueError: flowcell_size is not recognised
-    >>> get_flowcell_array(126)[9][-1]
+    >>> int(get_flowcell_array(126)[9][-1])
     0
-    >>> get_flowcell_array(512)[15][-1]
+    >>> int(get_flowcell_array(512)[15][-1])
     1
 
     """