opentrons 8.6.0a1__py3-none-any.whl → 8.6.0a2__py3-none-any.whl

opentrons/_version.py

@@ -1,14 +1,7 @@
 # file generated by setuptools-scm
 # don't change, don't track in version control
 
-__all__ = [
-    "__version__",
-    "__version_tuple__",
-    "version",
-    "version_tuple",
-    "__commit_id__",
-    "commit_id",
-]
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
 
 TYPE_CHECKING = False
 if TYPE_CHECKING:
@@ -16,19 +9,13 @@ if TYPE_CHECKING:
     from typing import Union
 
     VERSION_TUPLE = Tuple[Union[int, str], ...]
-    COMMIT_ID = Union[str, None]
 else:
     VERSION_TUPLE = object
-    COMMIT_ID = object
 
 version: str
 __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
-commit_id: COMMIT_ID
-__commit_id__: COMMIT_ID
 
-__version__ = version = '8.6.0a1'
-__version_tuple__ = version_tuple = (8, 6, 0, 'a1')
-
-__commit_id__ = commit_id = None
+__version__ = version = '8.6.0a2'
+__version_tuple__ = version_tuple = (8, 6, 0, 'a2')

opentrons/hardware_control/scripts/update_module_fw.py

@@ -0,0 +1,274 @@
+"""Module Firmware update script."""
+import argparse
+import asyncio
+from glob import glob
+import os
+import re
+import subprocess
+import sys
+from typing import Dict, Final, List, Optional
+
+from opentrons.drivers.rpi_drivers import usb
+from opentrons.hardware_control.module_control import MODULE_PORT_REGEX
+from opentrons.hardware_control import modules
+from opentrons.hardware_control.modules.mod_abc import AbstractModule
+from opentrons.hardware_control.modules.update import update_firmware
+from opentrons.hardware_control.types import BoardRevision
+
+
+# Constants for checking if module is back online
+ONLINE_RETRIES = 3
+DELAY_S = 5
+
+
+MODULES: Final[Dict[str, str]] = {
+    "temp-deck": "tempdeck",
+    "mag-deck": "magdeck",
+    "thermocycler": "thermocycler",
+    "heater-shaker": "heatershaker",
+    "absorbance-reader": "absorbancereader",
+    "flex-stacker": "flexstacker",
+}
+
+
+def parse_version(filepath: str) -> str:
+    """Parse the version string from the filename."""
+    _, ext = os.path.splitext(os.path.basename(filepath))
+    ext_pattern = re.escape(ext.lstrip("."))
+    pattern = rf"@(v\d+(?:\.\d+)*)\.{ext_pattern}"
+    match = re.search(pattern, os.path.basename(filepath))
+    return match.group(1) if match else ""
+
+
+def scan_connected_modules() -> List[modules.ModuleAtPort]:
+    """Scan for connected modules and return list of
+    tuples of serial ports and device names
+    """
+    discovered_modules = []
+    devices = glob("/dev/ot_module*")
+    for port in devices:
+        symlink_port = port.split("dev/")[1]
+        module_at_port = get_module_at_port(symlink_port)
+        if module_at_port:
+            discovered_modules.append(module_at_port)
+    return discovered_modules
+
+
+def get_module_at_port(port: str) -> Optional[modules.ModuleAtPort]:
+    """Given a port, returns either a ModuleAtPort
+    if it is a recognized module, or None if not recognized.
+    """
+    match = MODULE_PORT_REGEX.search(port)
+    if match:
+        name = match.group(1).lower()
+        if name not in modules.MODULE_TYPE_BY_NAME:
+            print(f"Unexpected module connected: {name} on {port}")
+            return None
+        return modules.ModuleAtPort(port=f"/dev/{port}", name=name)
+    return None
+
+
+async def build_module(
+    mod: modules.ModuleAtPort, loop: asyncio.AbstractEventLoop
+) -> Optional[AbstractModule]:
+    try:
+        # Get the device path and
+        port = subprocess.check_output(["readlink", "-f", mod.port]).decode().strip()
+        # remove the symlink for the device, so its freed by the robot-server
+        print(f"Removing symlink {mod.port}")
+        subprocess.check_call(["unlink", mod.port])
+        # wwait some time to let the device teardown
+        await asyncio.sleep(2)
+        # create an instance of the module using the device path
+        return await modules.build(
+            port=port,
+            usb_port=mod.usb_port,
+            type=modules.MODULE_TYPE_BY_NAME[mod.name],
+            simulating=False,
+            hw_control_loop=loop,
+        )
+    except Exception:
+        return None
+
+
+async def teardown_module(module: AbstractModule) -> None:
+    """Tearsdown the module so it can be used again by the robot-server.."""
+    name = module.name()
+    serial = module.device_info["serial"]
+    port_name = module.usb_port.name
+    command = f"echo '{port_name}' | tee /sys/bus/usb/drivers/usb"
+    print(f"Removing module: {name} {serial}")
+    try:
+        # stop the poller and disconnect serial
+        await module._poller.stop()  # type: ignore
+        await module._driver.disconnect()  # type: ignore
+        # unbind the device from usb and re-bind to simulate unplug
+        subprocess.run(f"{command}/unbind", shell=True, capture_output=True)
+        await asyncio.sleep(2)
+        subprocess.run(f"{command}/bind", shell=True, capture_output=True)
+    except Exception:
+        pass
+
+
+def enable_udev_rules(enable: bool) -> None:
+    """Enable/Disable creation of opentrons modules by the hardware controller.
+
+    This is done so the module is not automatically picked up by the server
+    while we are updating it.
+    """
+    rule = "95-opentrons-modules.rules"
+    original = f"/etc/udev/rules.d/{rule}"
+    destination = f"/var/lib/{rule}"
+    src = original if not enable else destination
+    dst = destination if not enable else original
+    msg = "Disabl" if not enable else "Enabl"
+    if not os.path.exists(src):
+        sys.exit(f"ERROR: Rule file not found: {src}")
+
+    try:
+        print(f"{msg}ing udev: Moving rule {src} -> {dst}")
+        subprocess.check_call(["mount", "-o", "remount,rw", "/"])
+        subprocess.check_call(["mv", src, dst])
+    except Exception as e:
+        sys.exit(
+            f"ERROR: Could not {msg}e udev rule: {rule}\n{e}",
+        )
+    finally:
+        subprocess.check_call(["mount", "-o", "remount,ro", "/"])
+        subprocess.check_call(["udevadm", "control", "--reload-rules"])
+
+
+def check_dev_exist(port: str) -> bool:
+    """True if the device with the given port exists in /dev."""
+    try:
+        return subprocess.run(["ls", port], capture_output=True).returncode == 0
+    except Exception:
+        return False
+
+
+async def main(args: argparse.Namespace) -> None:  # noqa: C901
+    """Entry point for script."""
+    mod_name = MODULES[args.module]
+    target_version = parse_version(args.file)
+    if not os.path.exists(args.file):
+        sys.exit(f"Invalid filepath: {args.file}")
+    if not target_version:
+        sys.exit(f"Target version could not be parsed from file: {args.file}")
+
+    print("Setting up...")
+    loop = asyncio.get_running_loop()
+    usb_bus = usb.USBBus(BoardRevision.FLEX_B2)  # todo: get this from the robot
+    print(f"Searching for {mod_name} modules in /dev/")
+    mods = scan_connected_modules()
+    mods = usb_bus.match_virtual_ports(mods)  # type: ignore
+    if not mods:
+        print("No modules found")
+        return
+
+    # Disable udev rules so modules aren't re-created by the server when they update
+    teardown_modules: List[AbstractModule] = []
+    enable_udev_rules(False)
+    print("\n------------------------------------------")
+    for mod in mods:
+        if mod_name not in mod.name:
+            continue
+
+        # Create an instance of the opentrons module
+        print(f"Found mod: {mod.name} at {mod.port}")
+        module = await build_module(mod, loop)
+        if module is None:
+            continue
+
+        name = module.name()
+        version = module.device_info["version"]
+        serial = module.device_info["serial"]
+        model = module.device_info["model"]
+        teardown_modules.append(module)
+        print(f"Created module: {module.name()} {model} {serial} {version}")
+
+        # Check that the update file is for this module
+        file_prefix = module.firmware_prefix()
+        if file_prefix not in args.file:
+            print(f"ERROR: Target module does not match file: {mod_name} {args.file}")
+            continue
+
+        # Check if the module is one we care about
+        if args.serial and serial not in args.serial:
+            continue
+
+        # Check if the module needs an update
+        if version == target_version and not args.force:
+            print(f"Module {name} {serial} is up-to-date.")
+            continue
+
+        print(f"Updating {name} {model} {serial}: {version} -> {target_version}")
+        await update_firmware(module, args.file)
+
+        # wait for the device to come online
+        for retry in range(ONLINE_RETRIES):
+            if retry >= ONLINE_RETRIES:
+                print(f"Module {serial} failed to come back online.")
+                break
+
+            print(f"Checking if {name} at {module.port} is online...")
+            await asyncio.sleep(DELAY_S)
+            if not check_dev_exist(module.port):
+                print("Not online")
+                continue
+
+            # re-open serial connection
+            if not await module._driver.is_connected():  # type: ignore
+                await module._driver.connect()  # type: ignore
+
+            # refresh the device info
+            print(f"Device {module.port} is back online, refreshing device info.")
+            device_info = (await module._driver.get_device_info()).to_dict()  # type: ignore
+            success = device_info["version"] == target_version
+            msg = "updated successfully!" if success else "failed to update"
+            print(f"Device {name} {serial} {msg}")
+            break
+
+    print("------------------------------------------\n")
+    print("Tearing down")
+    # Enable udev rules and teardown the module so they can be pick-up by the robot-server
+    enable_udev_rules(True)
+    for module in teardown_modules:
+        await teardown_module(module)
+    print("Done")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Module FW Update.")
+    parser.add_argument(
+        "--module",
+        help="The module target to be updated.",
+        type=str,
+        required=True,
+        choices=MODULES.keys(),
+    )
+    parser.add_argument(
+        "--file",
+        help="""Path to binary file containing the FW executable"""
+        """Must have format `module-name@vx.x.x.bin/hex`, ex, flex-stacker@v0.0.1.bin""",
+        type=str,
+        required=True,
+    )
+    parser.add_argument(
+        "--serial",
+        help="The specific serial numbers of the devices to update.",
+        type=str,
+        nargs="+",
+    )
+    parser.add_argument(
+        "--force",
+        help="Force install the update, even if the versions are the same.",
+        action="store_true",
+        default=False,
+    )
+    args = parser.parse_args()
+    try:
+        asyncio.run(main(args))
+    except Exception as e:
+        print("ERROR: Unhandled Exception: ", e)
+        # Re-enable udev rules
+        enable_udev_rules(True)

opentrons/protocol_engine/state/commands.py

@@ -380,7 +380,13 @@ class CommandStore(HasState[CommandState], HandlesActions):
             prev_entry.command.intent in (CommandIntent.PROTOCOL, None)
             and action.type == ErrorRecoveryType.WAIT_FOR_RECOVERY
         ):
-            self._state.queue_status = QueueStatus.AWAITING_RECOVERY
+            if (
+                self._state.queue_status == QueueStatus.PAUSED
+                or self._state.is_door_blocking
+            ):
+                self._state.queue_status = QueueStatus.AWAITING_RECOVERY_PAUSED
+            else:
+                self._state.queue_status = QueueStatus.AWAITING_RECOVERY
             self._state.recovery_target = _RecoveryTargetInfo(
                 command_id=action.command_id,
                 state_update_if_false_positive=state_update_if_false_positive,

{opentrons-8.6.0a1.dist-info → opentrons-8.6.0a2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: opentrons
-Version: 8.6.0a1
+Version: 8.6.0a2
 Summary: The Opentrons API is a simple framework designed to make writing automated biology lab protocols easy.
 Project-URL: opentrons.com, https://www.opentrons.com
 Project-URL: Source Code On Github, https://github.com/Opentrons/opentrons/tree/edge/api
@@ -24,7 +24,7 @@ Requires-Dist: click<9,>=8.0.0
 Requires-Dist: importlib-metadata>=1.0; python_version < '3.8'
 Requires-Dist: jsonschema<4.18.0,>=3.0.1
 Requires-Dist: numpy<2,>=1.20.0
-Requires-Dist: opentrons-shared-data==8.6.0a1
+Requires-Dist: opentrons-shared-data==8.6.0a2
 Requires-Dist: packaging>=21.0
 Requires-Dist: pydantic-settings<3,>=2
 Requires-Dist: pydantic<3,>=2.0.0
@@ -32,6 +32,6 @@ Requires-Dist: pyserial>=3.5
 Requires-Dist: pyusb==1.2.1
 Requires-Dist: typing-extensions<5,>=4.0.0
 Provides-Extra: flex-hardware
-Requires-Dist: opentrons-hardware[flex]==8.6.0a1; extra == 'flex-hardware'
+Requires-Dist: opentrons-hardware[flex]==8.6.0a2; extra == 'flex-hardware'
 Provides-Extra: ot2-hardware
-Requires-Dist: opentrons-hardware==8.6.0a1; extra == 'ot2-hardware'
+Requires-Dist: opentrons-hardware==8.6.0a2; extra == 'ot2-hardware'

{opentrons-8.6.0a1.dist-info → opentrons-8.6.0a2.dist-info}/RECORD

@@ -1,5 +1,5 @@
 opentrons/__init__.py,sha256=TQ_Ca_zzAM3iLzAysWKkFkQHG8-imihxDPQbLCYrf-E,4533
-opentrons/_version.py,sha256=TKZI6EwgFGSALxTwZXT3sPWvwD0HNFHjfuboucfB5rI,712
+opentrons/_version.py,sha256=GNMqhyBM4WyqEn46p7PGtrzujTlw5TeW__t1rYiBsMc,519
 opentrons/execute.py,sha256=Y88qICDiHWQjU0L4Ou7DI5OXXu7zZcdkUvNUYmZqIfc,29282
 opentrons/legacy_broker.py,sha256=XnuEBBlrHCThc31RFW2UR0tGqctqWZ-CZ9vSC4L9whU,1553
 opentrons/ordered_set.py,sha256=g-SB3qA14yxHu9zjGyc2wC7d2TUCBE6fKZlHAtbPzI8,4082
@@ -206,6 +206,7 @@ opentrons/hardware_control/scripts/ot3gripper,sha256=vK6wdD7MOMBURhpFDSzU_eZUfPc
 opentrons/hardware_control/scripts/ot3repl,sha256=arOMCJCqhT0jrpVaYJeS2oNNMG_jLfZwKT6_YeSL-bU,359
 opentrons/hardware_control/scripts/repl.py,sha256=RojtHjYV6sa6O4SeNEgs5SvnAK0imQK_XqoLQTKlzWU,5982
 opentrons/hardware_control/scripts/tc_control.py,sha256=V6hOzoRXL3xqIUEz8Raldd45aO2JgN5m5Hr08c1G8Ko,2741
+opentrons/hardware_control/scripts/update_module_fw.py,sha256=FqX4y5_Ghs-uY1_KjbQZpVu8be9XR91MJy1owGt3LLc,9795
 opentrons/legacy_commands/__init__.py,sha256=erkaz7hc2iHsTtjpFDWrR1V5n47it3U1qxD2zL9CkuE,63
 opentrons/legacy_commands/commands.py,sha256=lgImZ0Y3gZrMKDVioaOXWqa6mMJCNKDa8p-lQhTghWk,14530
 opentrons/legacy_commands/helpers.py,sha256=Bc7mjK6V7b4h472NCx_qSwD0ojd_DM7mPg18tjo1DIQ,5228
@@ -456,7 +457,7 @@ opentrons/protocol_engine/state/_move_types.py,sha256=STLssWsXMY92F_asAQrixv10A6
 opentrons/protocol_engine/state/_well_math.py,sha256=hppbOs4G6yQ6wgvKQWNhOs2zdYA_MwFW7qKgg2bGyx0,9714
 opentrons/protocol_engine/state/addressable_areas.py,sha256=3tjP7EedkpD5_tjTXa2n0PlQRRf1ttLrh_hOl9k0ThI,28811
 opentrons/protocol_engine/state/command_history.py,sha256=cz3Nllk045OpK6r9m4ByZr2hcCYo4pTy-2uoIZtV5XE,12241
-opentrons/protocol_engine/state/commands.py,sha256=YNPfx5PRyogc-bUzkq7sktwSCmTzssslnzYn3nMYR9g,45367
+opentrons/protocol_engine/state/commands.py,sha256=y5WE2pKmnMalgHFHEiBnBurO2TZ9wVPDMpS8Y9wMyrs,45612
 opentrons/protocol_engine/state/config.py,sha256=7jSGxC6Vqj1eA8fqZ2I3zjlxVXg8pxvcBYMztRIx9Mg,1515
 opentrons/protocol_engine/state/files.py,sha256=w8xxxg8HY0RqKKEGSfHWfrjV54Gb02O3dwtisJ-9j8E,1753
 opentrons/protocol_engine/state/fluid_stack.py,sha256=uwkf0qYk1UX5iU52xmk-e3yLPK8OG-TtMCcBqrkVFpM,5932
@@ -593,8 +594,8 @@ opentrons/util/linal.py,sha256=IlKAP9HkNBBgULeSf4YVwSKHdx9jnCjSr7nvDvlRALg,5753
 opentrons/util/logging_config.py,sha256=7et4YYuQdWdq_e50U-8vFS_QyNBRgdnqPGAQJm8qrIo,9954
 opentrons/util/logging_queue_handler.py,sha256=ZsSJwy-oV8DXwpYiZisQ1PbYwmK2cOslD46AcyJ1E4I,2484
 opentrons/util/performance_helpers.py,sha256=ew7H8XD20iS6-2TJAzbQeyzStZkkE6PzHt_Adx3wbZQ,5172
-opentrons-8.6.0a1.dist-info/METADATA,sha256=6KTuHgy1y5dweiTc8EtwQOvxQuJ_OB93FLPuNR9kU2A,1607
-opentrons-8.6.0a1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-opentrons-8.6.0a1.dist-info/entry_points.txt,sha256=fTa6eGCYkvOtv0ov-KVE8LLGetgb35LQLF9x85OWPVw,106
-opentrons-8.6.0a1.dist-info/licenses/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
-opentrons-8.6.0a1.dist-info/RECORD,,
+opentrons-8.6.0a2.dist-info/METADATA,sha256=cYFFLWaqACc2IODIfrDWwlHmMo3gwbsx_Tda1r2hX9Q,1607
+opentrons-8.6.0a2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+opentrons-8.6.0a2.dist-info/entry_points.txt,sha256=fTa6eGCYkvOtv0ov-KVE8LLGetgb35LQLF9x85OWPVw,106
+opentrons-8.6.0a2.dist-info/licenses/LICENSE,sha256=z8d0m5b2O9McPEK1xHG_dWgUBT6EfBDz6wA0F7xSPTA,11358
+opentrons-8.6.0a2.dist-info/RECORD,,