Feature/check minknow

src/readfish/__about__.py

@@ -3,3 +3,8 @@
 """
 
 __version__ = "2024.0.0"
+# Warning is the last supported version of MinKNOW for this version of readfish
+# Users running this version will receive the warning shown if they are running this version of readfish.
+__warning__ = [["5.9", f"Readfish {__version__} will not be supported in the next version of MinKNOW. Please update to the latest version of Readfish or do not update MinKNOW if you are concerned about version control."]]
+# Compatability is either the maximum or minimum version of MinKNOW that this version of readfish is compatible with.
+__compatability__ = [["6.0","lte"]]

src/readfish/__compatability__.py

@@ -0,0 +1,11 @@
+"""__compatability__.py
+This file allows us to check versions of MinKNOW against versions of readfish.
+"""
+
+from readfish.__about__ import __version__
+
+# Warning is the last supported version of MinKNOW for this version of readfish
+# Users running this version will receive the warning shown if they are running this version of readfish.
+__warning__ = [["5.9", f"Readfish {__version__} will not be supported in the next version of MinKNOW. Please update to the latest version of Readfish or do not update MinKNOW if you are concerned about version control."]]
+# Compatability is either the maximum or minimum version of MinKNOW that this version of readfish is compatible with.
+__compatability__ = [["6.0","lte"]]

src/readfish/_utils.py

@@ -10,6 +10,7 @@
 from enum import IntEnum
 import re
 import base64
+from packaging.version import parse as parse_version
 from typing import Any, Mapping, Sequence
 import zlib
 
@@ -18,11 +19,14 @@
 from minknow_api.manager import Manager, FlowCellPosition
 from minknow_api import Connection
 
+
 if sys.version_info < (3, 11):
     from exceptiongroup import BaseExceptionGroup
 
 from readfish._channels import FLONGLE_CHANNELS, MINION_CHANNELS
-
+from readfish.__about__ import __version__ as readfish_version
+from readfish.__compatability__ import __compatability__ as compatible_version
+from readfish.__compatability__ import __warning__ as warning_version
 
 MODULE_LOGGER = logging.getLogger(__name__)
 
@@ -449,6 +453,48 @@ def get_device(
             return position
     raise ValueError(f"Could not find device {device!r}")
 
+def get_version(
+        host: str = "127.0.0.1", port: int = None, logger: logging.Logger = None
+) -> str:
+    """Get the version of MinKNOW
+
+    :param host: The host the RPC is listening on, defaults to "127.0.0.1"
+    :param port: The port the RPC is listening on, defaults to None
+    :raises ValueError: If the version of Readfish is incompatible with the version of MinKNOW.
+    :raises Warning: If the version of Readfish may need to be updated soon.
+    :return: The version of MinKNOW
+    """
+    manager = Manager(host=host, port=port)
+    minknow_version = parse_version(manager.core_version)
+    # Check compatability
+    for cv, direction in compatible_version:
+        ver_cv = parse_version(cv)
+        if direction == "gte":
+            if minknow_version <= ver_cv:
+                raise ValueError(
+                    f"Compatability check failed. Readfish version {readfish_version} is not compatible with MinKNOW version {minknow_version}. You need to update readfish."
+                )
+        elif direction == "lte":
+            if minknow_version >= ver_cv:
+                raise ValueError(
+                    f"Compatability check failed. Readfish version {readfish_version} is not compatible with MinKNOW version {minknow_version}. You need to downgrade readfish."
+                )
+    for wv, message in warning_version:
+        warn = False
+        ver_wv = parse_version(wv)
+        if ver_wv.major == minknow_version.major:
+            if ver_wv.minor == minknow_version.minor:
+                if ver_wv.micro == minknow_version.micro:
+                    warn=True
+                else:
+                    warn=True
+            else:
+                warn=True
+        if warn:
+            logger.info(
+                f"Warning: {message}"
+            )
+    return None
 
 if __name__ == "__main__":
     import doctest

src/readfish/entry_points/targets.py

@@ -88,6 +88,7 @@
 from readfish._statistics import ReadfishStatistics
 from readfish._utils import (
     get_device,
+    get_version,
     send_message,
     ChunkTracker,
     Severity,
@@ -485,6 +486,10 @@ def run(
     # Setup logger used in this entry point, this one should be passed through
     logger = logging.getLogger(f"readfish.{args.command}")
 
+    # Check MinKNOW version
+
+    minKNOW_version = get_version(host=args.host, port=args.port, logger=logger)
+
     # Fetch sequencing device
     position = get_device(args.device, host=args.host, port=args.port)
 

src/readfish/plugins/dorado.py

@@ -10,6 +10,7 @@
 from collections import namedtuple
 from pathlib import Path
 from typing import Iterable, TYPE_CHECKING
+from packaging.version import parse as parse_version
 
 import numpy as np
 import numpy.typing as npt
@@ -66,6 +67,18 @@ def __init__(
         self.supported_barcode_kits = None
         self.supported_basecall_models = None
         self.run_information = run_information
+        if self.run_information:
+            self.guppy_version = self.run_information.software_versions.guppy_connected_version
+
+            if parse_version(self.guppy_version) >= parse_version("7.3.9"):
+                logging.info(
+                    f"Connected to caller version {self.guppy_version}."
+                )
+            else:
+                raise RuntimeError(
+                    f"Connected to caller version {self.guppy_version}. This plugin requires a version of Dorado >= 7.3.9."
+                )
+
         if sample_rate:
             self.sample_rate = float(sample_rate)
         else:

src/readfish/plugins/guppy.py

@@ -10,6 +10,7 @@
 from collections import namedtuple
 from pathlib import Path
 from typing import Iterable, TYPE_CHECKING
+from packaging.version import parse as parse_version
 
 import numpy as np
 import numpy.typing as npt
@@ -62,6 +63,18 @@ def __init__(
         self.supported_basecall_models = None
         self.run_information = run_information
 
+        if self.run_information:
+            self.guppy_version = self.run_information.software_versions.guppy_connected_version
+
+            if parse_version(self.guppy_version) < parse_version("7.3.9"):
+                logging.info(
+                    f"Connected to caller version {self.guppy_version}."
+                )
+            else:
+                raise RuntimeError(
+                    f"Connected to caller version {self.guppy_version}. This plugin requires a version of Dorado or Guppy < 7.3.9. Try changing [caller_settings.guppy] to [caller_settings.dorado]."
+                )
+
         # Set our own priority
         self.guppy_params = kwargs
         self.guppy_params["priority"] = PyGuppyClient.high_priority