SYMBOL INDEX (702 symbols across 38 files)

FILE: pyhamilton/__init__.py
  function full_paths_list (line 46) | def full_paths_list(directory_abs_path):
  function recursive_copy (line 51) | def recursive_copy(source_dir, target_dir):
  function autoconfig (line 65) | def autoconfig():
  function create_project (line 99) | def create_project():
  function create_ai_project (line 104) | def create_ai_project():

FILE: pyhamilton/consumables/consumables.py
  class VolumeConsumptionTracker (line 7) | class VolumeConsumptionTracker:
    method __init__ (line 8) | def __init__(self, num_positions):
    method aspirate_volume (line 12) | def aspirate_volume(self, well_index, volume):
  class TrackedContainer (line 15) | class TrackedContainer:
    method __init__ (line 18) | def __init__(self):
    method aspirate_volume (line 21) | def aspirate_volume(self, well_index, volume):
  class TrackedReagentVessel (line 28) | class TrackedReagentVessel(TrackedContainer):
    method __init__ (line 29) | def __init__(self, *args, **kwargs):
    method assign_reagent_map (line 32) | def assign_reagent_map(self, reagent_name: str, positions: list[int]) ...
    method reset_volumes (line 42) | def reset_volumes(self):
    method calculate_required_reagent_volume (line 48) | def calculate_required_reagent_volume(self, reagent_name: str):
    method all_required_reagent_volumes (line 57) | def all_required_reagent_volumes(self):
    method reagent_positions (line 60) | def reagent_positions(self, reagent_name):
  class ReagentTrackedPlate96 (line 65) | class ReagentTrackedPlate96(Plate96, TrackedReagentVessel):
    method __init__ (line 66) | def __init__(self, *args, **kwargs):
    method aspirate_volume (line 73) | def aspirate_volume(self, well_index, volume):
  class ReagentTrackedBulkPlate (line 76) | class ReagentTrackedBulkPlate(BulkReagentPlate, TrackedReagentVessel):
    method __init__ (line 77) | def __init__(self, *args, **kwargs):
    method aspirate_volume (line 84) | def aspirate_volume(self, well_index, volume):
    method assign_reagent_map (line 88) | def assign_reagent_map(self, reagent_name, positions):
    method calculate_required_reagent_volume (line 92) | def calculate_required_reagent_volume(self, reagent_name):
  class ReagentTrackedPlate24 (line 96) | class ReagentTrackedPlate24(Plate24, TrackedReagentVessel):
    method __init__ (line 97) | def __init__(self, *args, **kwargs):
    method aspirate_volume (line 104) | def aspirate_volume(self, well_index, volume):
  class ReagentTrackedReservoir60mL (line 107) | class ReagentTrackedReservoir60mL(Reservoir60mL, TrackedReagentVessel):
    method __init__ (line 108) | def __init__(self, *args, **kwargs):
    method aspirate_volume (line 115) | def aspirate_volume(self, well_index, volume):
    method calculate_required_reagent_volume (line 118) | def calculate_required_reagent_volume(self, reagent_name):
    method height_to_volume (line 123) | def height_to_volume(self, height):
  class ReagentTrackedFalconCarrier24 (line 126) | class ReagentTrackedFalconCarrier24(FalconCarrier24, TrackedReagentVessel):
    method __init__ (line 127) | def __init__(self, *args, **kwargs):
    method aspirate_volume (line 134) | def aspirate_volume(self, well_index, volume):
  class ReagentTrackedEppiCarrier32 (line 137) | class ReagentTrackedEppiCarrier32(EppiCarrier32, TrackedReagentVessel):
    method __init__ (line 138) | def __init__(self, *args, **kwargs):
    method aspirate_volume (line 145) | def aspirate_volume(self, well_index, volume):
  function get_class_name (line 150) | def get_class_name(obj):
  function generate_reagent_summary (line 154) | def generate_reagent_summary(tracked_vessels: list, units_default: str =...
  function generate_tip_use_summary (line 214) | def generate_tip_use_summary(tracked_tips_list, output_file=None):
  function tracked_volume_aspirate (line 302) | def tracked_volume_aspirate(ham_int: HamiltonInterface, plate_poss: list...
  function tracked_volume_aspirate_96 (line 315) | def tracked_volume_aspirate_96(ham_int: HamiltonInterface, plate: Tracke...

FILE: pyhamilton/defaults.py
  class Defaults (line 15) | class Defaults:
  function _read_file (line 29) | def _read_file() -> dict[str, Any]:
  function defaults (line 43) | def defaults(**overrides) -> Defaults:
  function save (line 59) | def save(new_defaults: Defaults | None = None) -> None:
  function reload (line 70) | def reload() -> Defaults:

FILE: pyhamilton/devices/centrifuge_wrappers.py
  function centrifuge_initialize (line 16) | def centrifuge_initialize(ham, label, node_name, simulate, always_init):
  function centrifuge_get_drive_status (line 22) | def centrifuge_get_drive_status(ham, label):
  function centrifuge_set_run (line 29) | def centrifuge_set_run(ham, label, array_speed, array_acceleration,

FILE: pyhamilton/devices/hhs_wrappers.py
  function hhs_begin_monitoring (line 17) | def hhs_begin_monitoring(ham, device_number, tolerance_range, interval, ...
  function hhs_create_star_device (line 23) | def hhs_create_star_device(ham, star_device='ML_STAR', used_node=1):
  function hhs_create_usb_device (line 31) | def hhs_create_usb_device(ham, used_node):
  function hhs_end_monitoring (line 37) | def hhs_end_monitoring(ham, device_number):
  function hhs_get_firmware_version (line 43) | def hhs_get_firmware_version(ham, device_number):
  function hhs_get_serial_num (line 49) | def hhs_get_serial_num(ham, device_number):
  function hhs_get_shaker_param (line 55) | def hhs_get_shaker_param(ham, device_number):
  function hhs_get_shaker_speed (line 62) | def hhs_get_shaker_speed(ham, device_number):
  function hhs_get_temp_param (line 68) | def hhs_get_temp_param(ham, device_number):
  function hhs_get_temp (line 75) | def hhs_get_temp(ham, device_number):
  function hhs_get_temp_state (line 81) | def hhs_get_temp_state(ham, device_number):
  function hhs_set_simulation (line 87) | def hhs_set_simulation(ham, simulate):
  function hhs_send_firmware_cmd (line 96) | def hhs_send_firmware_cmd(ham, device_number, command, parameter):
  function hhs_set_plate_lock (line 104) | def hhs_set_plate_lock(ham, device_number, plate_lock):
  function hhs_set_shaker_param (line 108) | def hhs_set_shaker_param(ham, device_number, shaking_direction, shaking_...
  function hhs_set_temp_param (line 114) | def hhs_set_temp_param(ham, device_number, start_timeout, tolerance_rang...
  function hhs_set_usb_trace (line 119) | def hhs_set_usb_trace(ham, trace):
  function hhs_start_all_shaker (line 125) | def hhs_start_all_shaker(ham, shaking_speed):
  function hhs_start_all_shaker_timed (line 131) | def hhs_start_all_shaker_timed(ham, shaking_speed, shaking_time):
  function hhs_start_shaker (line 136) | def hhs_start_shaker(ham, device_number, shaking_speed):
  function hhs_start_shaker_timed (line 140) | def hhs_start_shaker_timed(ham, device_number, shaking_speed, shaking_ti...
  function hhs_start_temp_ctrl (line 145) | def hhs_start_temp_ctrl(ham, device_number, temperature, wait_for_temp_r...
  function hhs_stop_all_shakers (line 152) | def hhs_stop_all_shakers(ham):
  function hhs_stop_shaker (line 157) | def hhs_stop_shaker(ham, device_number):
  function hhs_stop_temp_ctrl (line 161) | def hhs_stop_temp_ctrl(ham, device_number):
  function hhs_terminate (line 165) | def hhs_terminate(ham):
  function hhs_wait_for_shaker (line 169) | def hhs_wait_for_shaker(ham, device_number):
  function hhs_wait_for_temp_ctrl (line 173) | def hhs_wait_for_temp_ctrl(ham, device_number):
  class HHS (line 177) | class HHS:
    method __init__ (line 179) | def __init__(self, node, sequence, lmgr: LayoutManager):
    method layout_name (line 185) | def layout_name(self):

FILE: pyhamilton/devices/hig_wrappers.py
  function hig_connect (line 20) | def hig_connect(ham, device_id, adapter_device_id, simulation_mode):
  function hig_disconnect (line 27) | def hig_disconnect(ham):
  function hig_home (line 32) | def hig_home(ham):
  function hig_spin (line 38) | def hig_spin(ham, Gs, acceleration_pct, deceleration_pct, time):
  function hig_spin_and_wait (line 45) | def hig_spin_and_wait(ham, Gs, acceleration, deceleration, time):
  function hig_open_shield (line 50) | def hig_open_shield(ham, bucket_index):
  function hig_close_shield (line 55) | def hig_close_shield(ham):
  function hig_is_spinning (line 60) | def hig_is_spinning(ham):
  function hig_home (line 67) | def hig_home(ham):

FILE: pyhamilton/devices/mpe_wrappers.py
  function mpe2_connect_ip (line 25) | def mpe2_connect_ip(ham, instrument_name, port_number, simulation_mode, ...
  function mpe2_connect_com (line 32) | def mpe2_connect_com(ham, com_port, baud_rate, simulation_mode, options ...
  function mpe2_clamp_filter_plate (line 38) | def mpe2_clamp_filter_plate(ham, device_id):
  function mpe2_collection_plate_placed (line 44) | def mpe2_collection_plate_placed(ham, device_id, collection_plate_height...
  function mpe2_collection_plate_removed (line 50) | def mpe2_collection_plate_removed(ham, device_id):
  function mpe2_disconnect (line 56) | def mpe2_disconnect(ham, device_id):
  function mpe2_initialize (line 62) | def mpe2_initialize(ham, device_id):
  function mpe2_initialize_with_params (line 67) | def mpe2_initialize_with_params(ham, device_id, smart, waste_container_i...
  function mpe2_filter_plate_placed (line 72) | def mpe2_filter_plate_placed(ham, device_id, filter_height, nozzle_height):
  function mpe2_filter_plate_removed (line 77) | def mpe2_filter_plate_removed(ham, device_id):
  function mpe2_process_filter_to_collection_plate (line 82) | def mpe2_process_filter_to_collection_plate(ham, device_id, control_poin...
  function mpe2_process_filter_to_waste_container (line 87) | def mpe2_process_filter_to_waste_container(ham, device_id, control_point...
  function mpe2_retrieve_filter_plate (line 92) | def mpe2_retrieve_filter_plate(ham, device_id):
  function mpe2_start_mpe_vacuum (line 97) | def mpe2_start_mpe_vacuum(ham, device_id, waste_container_id='', disable...
  function mpe2_stop_vacuum (line 102) | def mpe2_stop_vacuum(ham, device_id):
  function mpe2_get_vacuum_status (line 107) | def mpe2_get_vacuum_status(ham, device_id):
  function mpe2_get_pressure_readings (line 112) | def mpe2_get_pressure_readings(ham, device_id):
  function mpe2_dispense (line 118) | def mpe2_dispense(ham, device_id, source_id, well_volume, flow_rate_aspi...
  function mpe2_prime (line 124) | def mpe2_prime(ham, device_id, source_id, well_volume, flow_rate, waste_...
  function mpe2_flush (line 130) | def mpe2_flush(ham, device_id, well_volume, flow_rate, waste_container_id):
  function mpe2_evaporate (line 136) | def mpe2_evaporate(ham, device_id, plate_height, needle_offset, well_dep...
  function mpe2_evaporate_with_rate (line 143) | def mpe2_evaporate_with_rate(ham, device_id, plate_height, needle_offset...
  function mpe2_evaporate_end (line 148) | def mpe2_evaporate_end(ham, device_id, timeout):
  function mpe2_get_temperature_range (line 153) | def mpe2_get_temperature_range(ham, device_id):
  function mpe2_get_heater_status (line 158) | def mpe2_get_heater_status(ham, device_id, reset):
  function mpe2_get_heater_range (line 163) | def mpe2_get_heater_range(ham, device_id, reset):

FILE: pyhamilton/devices/odtc_wrappers.py
  function odtc_abort (line 21) | def odtc_abort(ham, device_id, lock_id):
  function odtc_connect (line 27) | def odtc_connect(ham, simulation_mode, local_ip, device_ip, device_port ...
  function odtc_initialize (line 39) | def odtc_initialize(ham, device_id, lock_id = ''):
  function odtc_close_door (line 45) | def odtc_close_door(ham, device_id, lock_id = ''):
  function odtc_download_protocol (line 51) | def odtc_download_protocol(ham, device_id, protocol_file, lock_id = ''):
  function odtc_evaluate_error (line 57) | def odtc_evaluate_error(ham, device_id, lock_id = ''):
  function odtc_execute_protocol (line 63) | def odtc_execute_protocol(ham, device_id, method_name, simulating, prior...
  function odtc_get_status (line 83) | def odtc_get_status(ham, device_id, simulating):
  function odtc_open_door (line 113) | def odtc_open_door(ham, device_id, lock_id = ''):
  function odtc_read_actual_temperature (line 119) | def odtc_read_actual_temperature(ham, device_id, lock_id = ''):
  function odtc_reset (line 129) | def odtc_reset(ham, device_id, simulation_mode, timeout, str_device_id =...
  function odtc_stop_method (line 135) | def odtc_stop_method(ham, device_id, lock_id):
  function odtc_terminate (line 141) | def odtc_terminate(ham, device_id):
  function odtc_wait_for_idle (line 147) | def odtc_wait_for_idle(ham, device_id, simulating, check_interval=5, max...

FILE: pyhamilton/devices/pH_wrappers.py
  function ph_controller_initialize (line 27) | def ph_controller_initialize(ham, port_number, raise_first_exception=Tru...
  function ph_controller_parameters (line 32) | def ph_controller_parameters(ham, module_id, seq_gripper, seq_wash, seq_...
  function ph_controller_pickup (line 49) | def ph_controller_pickup(ham, module_id, seq_module, raise_first_excepti...
  function ph_controller_park (line 53) | def ph_controller_park(ham, module_id, seq_module, raise_first_exception...
  function ph_controller_calibrate (line 58) | def ph_controller_calibrate(ham, module_id, seq_module, seq_solution_1,s...
  function ph_controller_measure_cycle (line 73) | def ph_controller_measure_cycle(ham, module_id, pos, measure_height, pro...
  function ph_controller_wash (line 93) | def ph_controller_wash(ham, module_id, raise_first_exception=True, wait_...
  function ph_controller_dry (line 97) | def ph_controller_dry(ham, module_id, raise_first_exception=True, wait_o...
  function ph_controller_loadconfig (line 101) | def ph_controller_loadconfig(ham, raise_first_exception=True, wait_on_re...
  function ph_controller_saveconfig (line 108) | def ph_controller_saveconfig(ham, bluetooth_port, num_wash_cycles, num_d...
  function ph_initialize (line 120) | def ph_initialize(ham, comport, simulate, asynch=False, raise_first_exce...
  function ph_req_battery_data (line 125) | def ph_req_battery_data(ham, module_id, raise_first_exception=True, wait...
  function ph_measure (line 131) | def ph_measure(ham, module_id, temperature, probePattern, raise_first_ex...
  function ph_measure_dynamic (line 137) | def ph_measure_dynamic(ham, module_id, temperature, precision, timeout, ...
  function ph_request_calibration (line 144) | def ph_request_calibration(ham, module_id, probe_number, raise_first_exc...
  function ph_request_probe_data (line 153) | def ph_request_probe_data(ham, module_id, raise_first_exception=True, wa...
  function ph_request_technical_data (line 161) | def ph_request_technical_data(ham, module_id, hardware_number, raise_fir...
  function ph_calibrate (line 167) | def ph_calibrate(ham, module_id, cal_level, cal_value, cal_temperature, ...
  function ph_calibrate_dynamically (line 174) | def ph_calibrate_dynamically(ham, module_id, variance, timeout, cal_leve...
  function ph_wakeup (line 182) | def ph_wakeup(ham, module_id, raise_first_exception=True, wait_on_respon...
  function ph_sleep (line 186) | def ph_sleep(ham, module_id, raise_first_exception=True, wait_on_respons...
  function ph_washer_initialize (line 190) | def ph_washer_initialize(ham, comport, simulate, raise_first_exception=T...
  function ph_washer_wash (line 195) | def ph_washer_wash(ham, module_id, cycle_num, raise_first_exception=True...
  function ph_washer_terminate (line 199) | def ph_washer_terminate(ham, module_id, raise_first_exception=True, wait...
  function ph_dryer_initialize (line 203) | def ph_dryer_initialize(ham, comport, simulate, raise_first_exception=Tr...
  function ph_dryer_start (line 208) | def ph_dryer_start(ham, module_id, raise_first_exception=True, wait_on_r...
  function ph_dryer_stop (line 212) | def ph_dryer_stop(ham, module_id, raise_first_exception=True, wait_on_re...
  function ph_dryer_terminate (line 216) | def ph_dryer_terminate(ham, module_id, raise_first_exception=True, wait_...

FILE: pyhamilton/devices/tec_wrappers.py
  function initialize_tec (line 10) | def initialize_tec(ham, controller_id, simulating):
  function set_temperature_target_tec (line 15) | def set_temperature_target_tec(ham, target_temp, controller_id, device_id):
  function get_temperature_tec (line 20) | def get_temperature_tec(ham:HamiltonInterface, controller_id, device_id,...
  function start_temperature_control_tec (line 26) | def start_temperature_control_tec(ham, controller_id, device_id):
  function stop_temperature_control_tec (line 31) | def stop_temperature_control_tec(ham, controller_id, device_id):
  function terminate_tec (line 36) | def terminate_tec(ham, stop_all_devices):

FILE: pyhamilton/interface.py
  function invert_columns (line 15) | def invert_columns(pos_str: str, sep: str = ';') -> str:
  class HamiltonCmdTemplate (line 27) | class HamiltonCmdTemplate:
    method unique_id (line 37) | def unique_id():
    method __init__ (line 41) | def __init__(self, cmd_name, params_list):
    method assemble_cmd (line 63) | def assemble_cmd(self, *args, **kwargs):
    method assert_valid_cmd (line 79) | def assert_valid_cmd(self, cmd_dict):
  function labware_pos_str (line 134) | def labware_pos_str(labware, idx):
  function _make_new_hamilton_serv_handler (line 138) | def _make_new_hamilton_serv_handler(resp_indexing_fn):
  class HamiltonServerHandler (line 144) | class HamiltonServerHandler(server.BaseHTTPRequestHandler):
    method set_indexing_fn (line 150) | def set_indexing_fn(cls, fn):
    method send_str (line 155) | def send_str(cmd_str):
    method has_queued_cmds (line 164) | def has_queued_cmds():
    method pop_response (line 168) | def pop_response(idx):
    method _set_headers (line 172) | def _set_headers(self):
    method do_GET (line 177) | def do_GET(self):
    method do_HEAD (line 183) | def do_HEAD(self):
    method do_POST (line 186) | def do_POST(self):
    method log_message (line 197) | def log_message(self, *args, **kwargs):
  function run_hamilton_process (line 201) | def run_hamilton_process():
  class HamiltonResponseStatus (line 231) | class HamiltonResponseStatus(Enum):
  class HamiltonResponse (line 253) | class HamiltonResponse:
    method _compute_status (line 304) | def _compute_status(self):
    method _return_data (line 342) | def _return_data(self, fields):
    method _moduleID (line 351) | def _moduleID(self):
    method _parse_return (line 358) | def _parse_return(self):
    method digest (line 393) | def digest(self, fields=None):
    method raise_first_exception (line 399) | def raise_first_exception(self):
  class DispenseResult (line 433) | class DispenseResult:
  class AspirateResult (line 439) | class AspirateResult:
  class HamiltonServerThread (line 445) | class HamiltonServerThread(Thread):
    method __init__ (line 448) | def __init__(self, address, port):
    method run (line 467) | def run(self):
    method disconnect (line 492) | def disconnect(self):
    method has_exited (line 497) | def has_exited(self):
  class HamiltonInterface (line 501) | class HamiltonInterface:
    method __init__ (line 527) | def __init__(self, address=None, port=None, simulating = False, debug=...
    method _open (line 557) | def _open(self):
    method start (line 578) | def start(self):
    method stop (line 619) | def stop(self):
    method __enter__ (line 676) | def __enter__(self):
    method __exit__ (line 680) | def __exit__(self, exc_type, exc_value, tb):
    method is_open (line 692) | def is_open(self):
    method send_command (line 696) | def send_command(self, template=None, block_until_sent=False, *args, *...
    method wait_on_response (line 738) | def wait_on_response(self, id, timeout=60, raise_first_exception=False...
    method parse_response (line 783) | def parse_response(self, server_response:str, raise_first_exception:bo...
    method _block_until_sq_clear (line 804) | def _block_until_sq_clear(self):
    method set_log_dir (line 810) | def set_log_dir(self, log_dir):
    method log (line 819) | def log(self, msg, msg_type='info'):
    method _dump_log_queue (line 823) | def _dump_log_queue(self):
    method log_and_raise (line 835) | def log_and_raise(self, err):
    method _channel_var (line 840) | def _channel_var(pos_tuples):
    method _compound_pos_str (line 849) | def _compound_pos_str(pos_tuples):
    method _compound_pos_str_96 (line 856) | def _compound_pos_str_96(labware96):
    method _assert_parallel_nones (line 862) | def _assert_parallel_nones(list1, list2):
    method initialize (line 868) | def initialize(self, **more_options):
    method aspirate (line 886) | def aspirate(self, pos_tuples, vols, **more_options) -> AspirateResult:
    method dispense (line 948) | def dispense(self, pos_tuples, vols, **more_options) -> DispenseResult:
    method tip_pick_up (line 1007) | def tip_pick_up(self, pos_tuples, **more_options):
    method tip_eject (line 1030) | def tip_eject(self, pos_tuples=None, **more_options):
    method tip_pick_up_96 (line 1062) | def tip_pick_up_96(self, tip96, **more_options):
    method tip_eject_96 (line 1080) | def tip_eject_96(self, tip96=None, **more_options):
    method aspirate_96 (line 1106) | def aspirate_96(self, plate96, vol, **more_options):
    method tip_pick_up_mph_columns (line 1135) | def tip_pick_up_mph_columns(self, tip_96, num_columns_from_left, **mor...
    method dispense_96 (line 1160) | def dispense_96(self, plate96, vol, **more_options):
    method aspirate_384_quadrant (line 1191) | def aspirate_384_quadrant(self, plate384, quadrant, vol, **more_options):
    method dispense_384_quadrant (line 1216) | def dispense_384_quadrant(self, plate384, quadrant, vol, **more_options):
    method set_labware_property (line 1241) | def set_labware_property(self, labware_id, property_name, property_val...
    method _compound_pos_str_384_quad (line 1262) | def _compound_pos_str_384_quad(plate384, quadrant):
    method move_plate (line 1272) | def move_plate(self, source_plate, target_plate, CmplxGetDict=None, Cm...
    method move_by_seq (line 1335) | def move_by_seq(self, source_plate_seq, target_plate_seq, CmplxGetDict...
    method get_plate_gripper_seq (line 1400) | def get_plate_gripper_seq(self, source_plate_seq, gripHeight, gripWidt...
    method move_plate_gripper_seq (line 1424) | def move_plate_gripper_seq(self, dest_plate_seq, **more_options):
    method place_plate_gripper_seq (line 1435) | def place_plate_gripper_seq(self, dest_plate_seq, tool_sequence, **mor...
    method move_plate_gripper (line 1447) | def move_plate_gripper(self, source_poss, dest_poss, **more_options):
    method move_sequence (line 1459) | def move_sequence(self, sequence, xDisplacement=0, yDisplacement=0, zD...
    method load_carrier (line 1475) | def load_carrier(self, carrier_name, **more_options):
    method unload_carrier (line 1514) | def unload_carrier(self, carrier_name, **more_options):
  class JSONLogger (line 1525) | class JSONLogger:
    method __init__ (line 1526) | def __init__(self):
    method log (line 1530) | def log(self, message):
    method set_log_dir (line 1533) | def set_log_dir(self, log_dir):

FILE: pyhamilton/liquid_class_db.py
  class DispenseMode (line 12) | class DispenseMode(Enum):
    method to_code (line 25) | def to_code(self) -> int:
    method from_code (line 38) | def from_code(code: int) -> 'DispenseMode':
    method from_string (line 54) | def from_string(cls, identifier: str) -> 'DispenseMode':
  function _check_access_dialect (line 63) | def _check_access_dialect() -> None:
  function _build_engine (line 71) | def _build_engine(mdb_path: str):
  function load_liquid_classes (line 80) | def load_liquid_classes():
  function _get_liquid_class_data (line 134) | def _get_liquid_class_data(liquid_class_name: str, columns: Union[str, L...
  function check_liquid_class_exists (line 169) | def check_liquid_class_exists(liquid_class_name: str) -> bool:
  function liquid_class_has_parameter (line 192) | def liquid_class_has_parameter(liquid_class_name: str, parameter: str, v...
  function get_liquid_class_column_details (line 218) | def get_liquid_class_column_details() -> List[Dict[str, Any]]:
  function get_liquid_class_columns (line 232) | def get_liquid_class_columns() -> List[str]:
  function get_liquid_class_columns_with_types (line 241) | def get_liquid_class_columns_with_types() -> Dict[str, str]:
  function print_table_schema (line 250) | def print_table_schema():
  function get_all_table_names (line 277) | def get_all_table_names() -> List[str]:
  function get_liquid_class_dispense_mode (line 290) | def get_liquid_class_dispense_mode(liquid_class_name: str) -> str:
  function get_liquid_class_volume (line 306) | def get_liquid_class_volume(liquid_class_name: str, nominal=False) -> int:
  function get_liquid_class_parameter (line 336) | def get_liquid_class_parameter(liquid_class_name: str, parameter_name: s...
  function create_correction_curve (line 354) | def create_correction_curve(data: Tuple[float, ...]) -> collections.Orde...
  function unpack_doubles_dynamic (line 367) | def unpack_doubles_dynamic(byte_string: bytes) -> tuple:
  function export_liquid_classes_to_csv (line 377) | def export_liquid_classes_to_csv(directory="./liquid_class_data", filena...

FILE: pyhamilton/liquid_classes.py
  class AspirateParameter (line 11) | class AspirateParameter(Enum):
  class DispenseParameter (line 21) | class DispenseParameter(Enum):
  function copy_liquid_class (line 54) | def copy_liquid_class(ham_int, template_liquid_class: str, new_liquid_cl...
  function set_aspirate_parameter (line 62) | def set_aspirate_parameter(ham_int, liquid_class: str, parameter: Aspira...
  function set_dispense_parameter (line 71) | def set_dispense_parameter(ham_int, liquid_class: str, parameter: Dispen...
  function set_tip_type (line 80) | def set_tip_type(ham_int, liquid_class: str, tip_type: int):
  function set_dispense_mode (line 87) | def set_dispense_mode(ham_int, liquid_class: str, dispense_mode: int):
  function set_correction_curve (line 95) | def set_correction_curve(ham_int, liquid_class: str, nominal_array: list...
  function validate_liquid_class_definitions (line 105) | def validate_liquid_class_definitions(definitions: list):
  function create_liquid_class_from_dict (line 160) | def create_liquid_class_from_dict(
  function create_liquid_class_from_json (line 260) | def create_liquid_class_from_json(

FILE: pyhamilton/liquid_handling_wrappers.py
  function labware_pos_str (line 27) | def labware_pos_str(labware, idx):
  function compound_pos_str (line 30) | def compound_pos_str(pos_tuples):
  function compound_pos_str_96 (line 34) | def compound_pos_str_96(labware96):
  function cells_384_to_1536 (line 37) | def cells_384_to_1536(well, idx):
  function cells_96_to_384 (line 40) | def cells_96_to_384(well, idx):
  function wells_384_to_96 (line 43) | def wells_384_to_96(x):
  function get_cells_from_position_384 (line 48) | def get_cells_from_position_384(well):
  function get_cells_from_position_96 (line 51) | def get_cells_from_position_96(well):
  function get_384w_quadrant (line 54) | def get_384w_quadrant(quadrant):
  function compound_pos_str_384_quad (line 57) | def compound_pos_str_384_quad(labware384, quadrant):
  function initialize (line 61) | def initialize(ham, asynch=False):
  function hepa_on (line 68) | def hepa_on(ham, speed=15, asynch=False, **more_options):
  function wash_empty_refill (line 76) | def wash_empty_refill(ham, asynch=False, **more_options):
  function move_plate (line 85) | def move_plate(ham, source_plate, target_plate, CmplxGetDict=None, Cmplx...
  function move_by_seq (line 89) | def move_by_seq(ham, source_plate_seq, target_plate_seq, CmplxGetDict=No...
  function channel_var (line 93) | def channel_var(pos_tuples):
  function tip_pick_up (line 100) | def tip_pick_up(ham_int, pos_tuples, **more_options):
  function tip_eject (line 104) | def tip_eject(ham_int, pos_tuples=None, **more_options):
  function assert_parallel_nones (line 108) | def assert_parallel_nones(list1, list2):
  class TimerHandle (line 114) | class TimerHandle:
    method __init__ (line 115) | def __init__(self, seconds):
    method wait (line 121) | def wait(self, skip=False):
  function start_timer (line 127) | def start_timer(seconds):
  function aspirate (line 134) | def aspirate(ham_int, pos_tuples, vols, **more_options):
  function dispense (line 138) | def dispense(ham_int, pos_tuples, vols, **more_options):
  function tip_pick_up_96 (line 143) | def tip_pick_up_96(ham_int, tip96, **more_options):
  function tip_eject_96 (line 147) | def tip_eject_96(ham_int, tip96=None, **more_options):
  function aspirate_96 (line 151) | def aspirate_96(ham_int, plate96, vol, **more_options):
  function dispense_96 (line 155) | def dispense_96(ham_int, plate96, vol, **more_options):
  function aspirate_384_quadrant (line 159) | def aspirate_384_quadrant(ham_int, plate384, quadrant, vol, **more_optio...
  function dispense_384_quadrant (line 163) | def dispense_384_quadrant(ham_int, plate384, quadrant, vol, **more_optio...
  function copy_liquid_class (line 189) | def copy_liquid_class(ham_int, template_liquid_class, new_liquid_class):
  function set_aspirate_parameter (line 193) | def set_aspirate_parameter(ham_int, LiquidClass, Parameter, Value):
  function set_dispense_parameter (line 198) | def set_dispense_parameter(ham_int, LiquidClass, Parameter, Value):
  function set_tip_type (line 203) | def set_tip_type(ham_int, LiquidClass, TipType):
  function set_correction_curve (line 207) | def set_correction_curve(ham_int, LiquidClass, NominalArray, CorrectedAr...
  function move_sequence (line 211) | def move_sequence(ham_int, sequence, xDisplacement=0, yDisplacement=0, z...
  function tilt_module_initialize (line 215) | def tilt_module_initialize(ham_int, module_name, comport, trace_level, s...
  function tilt_module_move (line 222) | def tilt_module_move(ham_int, module_name, angle):
  function get_plate_gripper_seq (line 226) | def get_plate_gripper_seq(ham, source_plate_seq, gripHeight, gripWidth, ...
  function move_plate_gripper_seq (line 230) | def move_plate_gripper_seq(ham, dest_plate_seq, **more_options):
  function place_plate_gripper_seq (line 234) | def place_plate_gripper_seq(ham, dest_plate_seq, tool_sequence, **more_o...
  function move_plate_gripper (line 238) | def move_plate_gripper(ham, dest_poss, **more_options):
  function move_plate_using_gripper (line 243) | def move_plate_using_gripper(ham_int: HamiltonInterface, source: str, de...
  function tracked_tip_pick_up (line 252) | def tracked_tip_pick_up(ham_int: HamiltonInterface, tips_tracker: Tracke...
  function tracked_tip_eject (line 270) | def tracked_tip_eject(ham_int: HamiltonInterface, tips_tracker: TrackedT...
  function tracked_tip_pick_up_96 (line 281) | def tracked_tip_pick_up_96(ham_int: HamiltonInterface, tips_tracker: Tra...
  function tip_support_pickup_columns (line 293) | def tip_support_pickup_columns(ham_int: HamiltonInterface, tips:TrackedT...
  class StderrLogger (line 301) | class StderrLogger:
    method __init__ (line 302) | def __init__(self, level):
    method write (line 306) | def write(self, message):
  function add_stderr_logging (line 311) | def add_stderr_logging(logger_name=None):
  function normal_logging (line 315) | def normal_logging(ham_int, method_local_dir):
  function run_async (line 334) | def run_async(funcs):
  function run_async_dict (line 347) | def run_async_dict(func):
  function yield_in_chunks (line 357) | def yield_in_chunks(sliceable, n):
  function log_banner (line 365) | def log_banner(banner_text):

FILE: pyhamilton/ngs/loading/deck_annotation.py
  function load_image_pil (line 41) | def load_image_pil(path: str):
  function load_regions_from_json (line 47) | def load_regions_from_json(path: str):
  function save_regions_to_json (line 70) | def save_regions_to_json(path: str, regions_list: list, image_path_str: ...
  function draw_all_elements (line 92) | def draw_all_elements(canvas):
  function get_closest_point_index (line 116) | def get_closest_point_index(mouse_pos, points, thresh=5):
  function on_mouse_down (line 123) | def on_mouse_down(event):
  function on_mouse_right_click (line 150) | def on_mouse_right_click(event):
  function on_mouse_up (line 160) | def on_mouse_up(event):
  function on_mouse_move (line 165) | def on_mouse_move(event):
  function on_key_press (line 170) | def on_key_press(event, root):
  function save_json (line 176) | def save_json():
  function update_treeview (line 186) | def update_treeview():
  function on_treeview_click (line 198) | def on_treeview_click(event):
  function edit_name (line 221) | def edit_name(item_id):
  function set_name (line 237) | def set_name(item_id):
  function edit_color (line 249) | def edit_color(item_id):
  function edit_resource_type (line 257) | def edit_resource_type(item_id):
  function set_resource_type (line 274) | def set_resource_type(item_id):
  function delete_selected_region (line 286) | def delete_selected_region():
  function main (line 296) | def main():

FILE: pyhamilton/ngs/loading/loading_vis.py
  class Region (line 49) | class Region:
    method from_dict (line 57) | def from_dict(cls, name: str, d: Dict) -> "Region":
  class ReagentVessel (line 91) | class ReagentVessel:
    method __init__ (line 92) | def __init__(self, name: str):
    method layout_name (line 95) | def layout_name(self):
    method __init__ (line 721) | def __init__(self, name):
    method layout_name (line 724) | def layout_name(self):
  class LoadingVis (line 101) | class LoadingVis:
    method __init__ (line 111) | def __init__(
    method _shift_regions (line 237) | def _shift_regions(self, offset: Tuple[int, int]) -> None:
    method _crop_to_regions (line 248) | def _crop_to_regions(self, margin: int = 12) -> None:
    method _auto_trim_uniform_borders (line 266) | def _auto_trim_uniform_borders(self, tol: int = 3, max_crop: int = 400...
    method _apply_alias_rules (line 299) | def _apply_alias_rules(self, region_name) -> str:
    method _create_vessels_from_data (line 307) | def _create_vessels_from_data(self) -> List[DeckResource]:
    method _load_reagent_map (line 322) | def _load_reagent_map(self, reagent_data: Union[str, Path, Dict]) -> N...
    method render (line 380) | def render(
    method show (line 512) | def show(
    method save (line 539) | def save(self, img_bgr: np.ndarray, out_path: Union[str, Path]) -> None:
    method missing_for (line 544) | def missing_for(self, vessels: List[DeckResource]) -> List[str]:
    method has_tube_rack_data (line 553) | def has_tube_rack_data(self) -> bool:
    method _cleanup_cv_windows (line 558) | def _cleanup_cv_windows(self, deck_window_name, plate_enabled):
    method show_dialogues (line 573) | def show_dialogues(
    method ShowDialogues (line 705) | def ShowDialogues(self, *args, **kwargs):
  class ReagentVessel (line 720) | class ReagentVessel:
    method __init__ (line 92) | def __init__(self, name: str):
    method layout_name (line 95) | def layout_name(self):
    method __init__ (line 721) | def __init__(self, name):
    method layout_name (line 724) | def layout_name(self):

FILE: pyhamilton/ngs/loading/plate_96_render.py
  function render_plate_96 (line 27) | def render_plate_96(
  function _draw_text_simple (line 197) | def _draw_text_simple(canvas: np.ndarray, text: str, pos: Tuple[int, int...

FILE: pyhamilton/ngs/loading/rendering_helpers.py
  function draw_text_pillow (line 28) | def draw_text_pillow(img_bgr: np.ndarray, text: str, org: Tuple[int, int],
  function _resolve_font_path (line 76) | def _resolve_font_path(pref: Optional[str] = ARIAL_TTF) -> Optional[str]:
  function _measure_text_pillow (line 84) | def _measure_text_pillow(text: str, font_path: Optional[str], px: Union[...
  function _rescale_image (line 108) | def _rescale_image(img: np.ndarray, scale: float) -> np.ndarray:
  function _ascii_label (line 118) | def _ascii_label(s: str) -> str:
  function _label_from_info_dict (line 125) | def _label_from_info_dict(info: Dict, *, unit_default: str, fallback: st...
  function _name_to_color_bgr (line 139) | def _name_to_color_bgr(name: str) -> Tuple[int, int, int]:
  function _norm_key (line 148) | def _norm_key(k: str) -> str:
  function _ensure_bgr (line 151) | def _ensure_bgr(img: np.ndarray) -> np.ndarray:
  function _draw_transparent_rect (line 161) | def _draw_transparent_rect(
  function _draw_transparent_polygon (line 174) | def _draw_transparent_polygon(
  function _rect_xyxy (line 195) | def _rect_xyxy(p1, p2) -> Tuple[int, int, int, int]:
  function _rect_overlap_area (line 201) | def _rect_overlap_area(a, b) -> int:
  function _intersects_any (line 208) | def _intersects_any(r, rects) -> bool:
  function _fan_offsets (line 211) | def _fan_offsets(max_shift: int, step: int):
  function _fmt_volume (line 220) | def _fmt_volume(vol: Any, unit_default: str) -> str:
  function _preferred_side_for_key (line 230) | def _preferred_side_for_key(key_norm: str) -> str:
  function _best_label_box_outside (line 249) | def _best_label_box_outside(
  function _get_polygon_min_area_rect_center_and_bbox (line 420) | def _get_polygon_min_area_rect_center_and_bbox(points: List[Tuple[int, i...
  function _min_distance_to_polygon (line 453) | def _min_distance_to_polygon(rect_xyxy: Tuple[int, int, int, int], poly_...
  function _find_poly_edge_x (line 499) | def _find_poly_edge_x(poly_points: List[Tuple[int, int]], y_min: int, y_...

FILE: pyhamilton/ngs/loading/tube_rack_render.py
  class TubeRackRenderer (line 41) | class TubeRackRenderer:
    method render_tube_rack_screen (line 43) | def render_tube_rack_screen(
    method show_tkinter_modal (line 202) | def show_tkinter_modal(

FILE: pyhamilton/ngs/protocol.py
  class Protocol (line 8) | class Protocol:
    method __init__ (line 10) | def __init__(self):
    method prompt_step_selection (line 24) | def prompt_step_selection(self):
    method reset_tracked_resources (line 334) | def reset_tracked_resources(self):
    method run_selected_steps (line 356) | def run_selected_steps(self, steps: list, simulation: bool = True, win...
    method end (line 377) | def end(self):
    method run_protocol (line 394) | def run_protocol(self, simulating=False, output_file="reagent_summary....
    method show_loading_dialogues (line 410) | def show_loading_dialogues(self, parent=None):

FILE: pyhamilton/ngs/tadm.py
  class USBTraceParser (line 13) | class USBTraceParser:
    method __init__ (line 17) | def __init__(self, debug: bool = False):
    method parse_file (line 20) | def parse_file(self, filename: str | Path):
  class LiquidHandlerCommand (line 63) | class LiquidHandlerCommand:
  class Association (line 77) | class Association:
  class TraceParser (line 85) | class TraceParser:
    method __init__ (line 86) | def __init__(self, debug=False):
    method parse_liquid_handler_trace (line 91) | def parse_liquid_handler_trace(self, content: str):
    method extract_channel_info (line 152) | def extract_channel_info(self, line: str):
    method associate_commands (line 173) | def associate_commands(self) -> List[Association]:
  function extract_clean_command (line 206) | def extract_clean_command(trace_line: str) -> str:
  function format_channel_info (line 230) | def format_channel_info(lh_cmd: LiquidHandlerCommand) -> str:
  function generate_json_report (line 241) | def generate_json_report(associations: List, output_file: str):
  function get_last_usb_data_block (line 307) | def get_last_usb_data_block() -> Optional[dict]:
  function generate_tadm_report_with_json (line 342) | def generate_tadm_report_with_json(html_output="tadm_report.html", json_...
  function generate_html_report (line 385) | def generate_html_report(associations: list, output_file: str):
  function usb_block_plot_base64 (line 485) | def usb_block_plot_base64(usb_block: dict) -> str:
  function find_most_recent_trace_file (line 502) | def find_most_recent_trace_file(directory: Path, pattern: str) -> Option...
  function generate_tadm_report (line 520) | def generate_tadm_report(output = "tadm_report.html"):

FILE: pyhamilton/ngs/tests/bead_cleanup.py
  function estimate_tip_consumption (line 103) | def estimate_tip_consumption(num_samples: int):
  function initialize (line 112) | def initialize(simulation=True):
  function BeadCleanup (line 124) | def BeadCleanup(num_samples, sample_volume, starting_from=0):

FILE: pyhamilton/ngs/tests/hhs.py
  class HHS (line 29) | class HHS:
    method __init__ (line 31) | def __init__(self, node, sequence):
    method layout_name (line 35) | def layout_name(self):
    method node (line 38) | def node(self):
  function initialize_hhs (line 49) | def initialize_hhs(simulation):

FILE: pyhamilton/ngs/tests/magnetic_bead_cleanup.py
  function magnetic_bead_cleanup (line 15) | def magnetic_bead_cleanup():
  class HHS (line 78) | class HHS:
    method __init__ (line 80) | def __init__(self, node, layout_name):
  function initialize_hhs (line 93) | def initialize_hhs(ham_int, simulating):

FILE: pyhamilton/ngs/tests/multi_dispense.py
  function condense_volumes (line 29) | def condense_volumes(lst, max_volume):

FILE: pyhamilton/ngs/tests/thermal_cycler/thermal_cycler_with_transport.py
  function thermal_cycle_with_plate_movement (line 15) | def thermal_cycle_with_plate_movement(ham_int, source_plate_sequence, od...

FILE: pyhamilton/odtc/odtc_protocol.py
  class ThermalCyclerProtocol (line 4) | class ThermalCyclerProtocol:
    method __init__ (line 8) | def __init__(self, creator="stefan", variant=960000, plate_type=0, flu...
    method add_step (line 28) | def add_step(self, plateau_temp, plateau_time, slope=1, overshoot_temp...
    method add_pcr_cycle (line 49) | def add_pcr_cycle(self, denaturation_temp, denaturation_time, annealin...
    method add_final_extension (line 65) | def add_final_extension(self, temp, time):
    method set_pid_parameters (line 69) | def set_pid_parameters(self, pid_number, p_heating, p_cooling, i_heati...
    method set_pre_method (line 79) | def set_pre_method(self, block_temp=25, lid_temp=110):
    method generate_xml (line 85) | def generate_xml(self, filename="protocol.xml"):

FILE: pyhamilton/oemerr.py
  class HamiltonError (line 3) | class HamiltonError(Exception):
  class HamiltonDeckResourceError (line 13) | class HamiltonDeckResourceError(HamiltonError):
  class ResourceUnavailableError (line 19) | class ResourceUnavailableError(HamiltonDeckResourceError):
  class HamiltonInterfaceError (line 29) | class HamiltonInterfaceError(HamiltonError):
  class HamiltonTimeoutError (line 35) | class HamiltonTimeoutError(HamiltonInterfaceError):
  class InvalidErrCodeError (line 41) | class InvalidErrCodeError(HamiltonInterfaceError):
  class HamiltonReturnParseError (line 47) | class HamiltonReturnParseError(HamiltonInterfaceError):
  class HamiltonStepError (line 57) | class HamiltonStepError(HamiltonError):
  class HamiltonSyntaxError (line 63) | class HamiltonSyntaxError(HamiltonStepError):
  class HardwareError (line 69) | class HardwareError(HamiltonStepError):
  class NotExecutedError (line 75) | class NotExecutedError(HamiltonStepError):
  class ClotError (line 81) | class ClotError(HamiltonStepError):
  class BarcodeError (line 87) | class BarcodeError(HamiltonStepError):
  class InsufficientLiquidError (line 93) | class InsufficientLiquidError(HamiltonStepError):
  class TipPresentError (line 99) | class TipPresentError(HamiltonStepError):
  class NoTipError (line 105) | class NoTipError(HamiltonStepError):
  class NoCarrierError (line 111) | class NoCarrierError(HamiltonStepError):
  class ExecutionError (line 117) | class ExecutionError(HamiltonStepError):
  class PressureLLDError (line 123) | class PressureLLDError(HamiltonStepError):
  class CalibrateError (line 129) | class CalibrateError(HamiltonStepError):
  class UnloadError (line 135) | class UnloadError(HamiltonStepError):
  class PressureLLDError (line 141) | class PressureLLDError(HamiltonStepError):
  class ParameterError (line 147) | class ParameterError(HamiltonStepError):
  class CoverOpenError (line 153) | class CoverOpenError(HamiltonStepError):
  class ImproperAspirationOrDispenseError (line 159) | class ImproperAspirationOrDispenseError(HamiltonStepError):
  class WashLiquidError (line 165) | class WashLiquidError(HamiltonStepError):
  class TemperatureError (line 171) | class TemperatureError(HamiltonStepError):
  class TADMOvershotError (line 177) | class TADMOvershotError(HamiltonStepError):
  class LabwareError (line 189) | class LabwareError(HamiltonStepError):
  class LabwareGrippedError (line 195) | class LabwareGrippedError(HamiltonStepError):
  class LabwareLostError (line 201) | class LabwareLostError(HamiltonStepError):
  class IllegalTargetPlatePositionError (line 207) | class IllegalTargetPlatePositionError(HamiltonStepError):
  class IllegalInterventionError (line 213) | class IllegalInterventionError(HamiltonStepError):
  class TADMUndershotError (line 219) | class TADMUndershotError(HamiltonStepError):
  class PositionError (line 231) | class PositionError(HamiltonStepError):
  class UnexpectedcLLDError (line 237) | class UnexpectedcLLDError(HamiltonStepError):
  class AreaAlreadyOccupiedError (line 243) | class AreaAlreadyOccupiedError(HamiltonStepError):
  class ImpossibleToOccupyAreaError (line 249) | class ImpossibleToOccupyAreaError(HamiltonStepError):
  class AntiDropControlError (line 255) | class AntiDropControlError(HamiltonStepError):
  class DecapperError (line 261) | class DecapperError(HamiltonStepError):
  class DecapperHandlingError (line 267) | class DecapperHandlingError(HamiltonStepError):
  class SlaveError (line 273) | class SlaveError(HamiltonStepError):
  class WrongCarrierError (line 279) | class WrongCarrierError(HamiltonStepError):
  class NoCarrierBarcodeError (line 285) | class NoCarrierBarcodeError(HamiltonStepError):
  class LiquidLevelError (line 291) | class LiquidLevelError(HamiltonStepError):
  class NotDetectedError (line 299) | class NotDetectedError(HamiltonStepError):
  class NotAspiratedError (line 305) | class NotAspiratedError(HamiltonStepError):
  class ImproperDispensationError (line 313) | class ImproperDispensationError(HamiltonStepError):
  class NoLabwareError (line 321) | class NoLabwareError(HamiltonStepError):
  class UnexpectedLabwareError (line 331) | class UnexpectedLabwareError(HamiltonStepError):
  class WrongLabwareError (line 337) | class WrongLabwareError(HamiltonStepError):
  class BarcodeMaskError (line 343) | class BarcodeMaskError(HamiltonStepError):
  class BarcodeNotUniqueError (line 349) | class BarcodeNotUniqueError(HamiltonStepError):
  class BarcodeAlreadyUsedError (line 355) | class BarcodeAlreadyUsedError(HamiltonStepError):
  class KitLotExpiredError (line 361) | class KitLotExpiredError(HamiltonStepError):
  class DelimiterError (line 367) | class DelimiterError(HamiltonStepError):

FILE: pyhamilton/pipetting/pipetting.py
  function prewet_tips (line 11) | def prewet_tips(ham_int, tip_type, dispense_mode):
  function condense_volumes (line 14) | def condense_volumes(lst, vol, max_volume):
  function get_fitting_dispense_positions (line 19) | def get_fitting_dispense_positions(asp_vols, disp_vols, disp_pos):
  function build_dispense_batches (line 34) | def build_dispense_batches(aspiration_volumes, all_dispense_positions, a...
  function distribute_positions_to_channel_ops (line 70) | def distribute_positions_to_channel_ops(positions_to_distribute, referen...
  function print_transfers (line 111) | def print_transfers(source_wells, destination_wells, vols):
  function batch_columnwise_positions (line 125) | def batch_columnwise_positions(positions):
  function split_volumes_by_max_volume (line 131) | def split_volumes_by_max_volume(volumes, max_volume):
  function set_parallel_nones (line 148) | def set_parallel_nones(positions, reference):
  function pip_transfer (line 159) | def pip_transfer(ham_int: HamiltonInterface, tips: List[Tuple[DeckResour...
  function pip_pool (line 233) | def pip_pool(ham_int: HamiltonInterface, tips: List[Tuple[DeckResource, ...
  function shear_plate_96 (line 306) | def shear_plate_96(ham_int: HamiltonInterface, tips:List[Tuple[DeckResou...
  function mix_plate (line 325) | def mix_plate(ham_int: HamiltonInterface, tips:List[Tuple[DeckResource, ...
  function multi_dispense (line 346) | def multi_dispense(ham_int: HamiltonInterface, tips:List[Tuple[DeckResou...
  function multi_aspirate (line 415) | def multi_aspirate(ham_int: HamiltonInterface, tips:List[Tuple[DeckResou...
  function mph_tip_pickup_support (line 463) | def mph_tip_pickup_support(ham_int: HamiltonInterface, tips: TrackedTips...
  function transfer_96 (line 474) | def transfer_96(ham_int: HamiltonInterface, tips:List[Tuple[DeckResource...
  function double_aspirate_supernatant_96 (line 501) | def double_aspirate_supernatant_96(ham_int: HamiltonInterface, tips: Tra...
  function ethanol_wash (line 535) | def ethanol_wash(ham_int: HamiltonInterface, tips: TrackedTips, tip_supp...
  function pip_mix (line 558) | def pip_mix(ham_int: HamiltonInterface, tips: TrackedTips, positions_to_...
  function aspirate_all_for_stamp (line 594) | def aspirate_all_for_stamp(ham_int, tips, source_plate, volume, liquid_c...
  function aspirate_all (line 606) | def aspirate_all(ham_int, tips, source_plate, volume, liquid_class,

FILE: pyhamilton/pipetting/trough_manager.py
  function check_volumes_in_troughs (line 4) | def check_volumes_in_troughs(ham_int: HamiltonInterface, aspiration_posi...
  function select_trough (line 19) | def select_trough(ham_int: HamiltonInterface, aspiration_positions, volu...
  function prompt_insufficient_volume (line 26) | def prompt_insufficient_volume(ham_int, troughs, volume):
  function accumulate_residual_volume (line 29) | def accumulate_residual_volume(ham_int, troughs, volumes):
  function manage_multiple_troughs (line 38) | def manage_multiple_troughs(ham_int, aspiration_positions, volume, liqui...

FILE: pyhamilton/resources/deckresource.py
  class ResourceType (line 13) | class ResourceType:
    method __init__ (line 48) | def __init__(self, resource_class, *args):
  class LayoutManager (line 60) | class LayoutManager:
    method get_manager (line 77) | def get_manager(checksum):
    method initial_printable (line 88) | def initial_printable(line, start=0):
    method layline_objid (line 97) | def layline_objid(line):
    method layline_first_field (line 111) | def layline_first_field(line):
    method field_starts_with (line 115) | def field_starts_with(field, prefix):
    method name_from_line (line 122) | def name_from_line(line):
    method line_has_prefixed_name (line 129) | def line_has_prefixed_name(prefix):
    method _read_layfile_lines (line 135) | def _read_layfile_lines(layfile_path):
    method _layfile_checksum (line 153) | def _layfile_checksum(layfile_path):
    method layfiles_equal (line 158) | def layfiles_equal(lay_path_1, lay_path_2):
    method __init__ (line 161) | def __init__(self, layfile_path, install=True):
    method assign_unused_resource (line 171) | def assign_unused_resource(self, restype, order_key=None, reverse=Fals...
    method verify_position_ids (line 218) | def verify_position_ids(self, resource):
    method _find_resource_line (line 279) | def _find_resource_line(self, resource_name):
    method _extract_position_ids_from_line (line 315) | def _extract_position_ids_from_line(line, obj_id):
  class ResourceIterItem (line 340) | class ResourceIterItem:
    method __init__ (line 342) | def __init__(self, resource, index):
  class Tip (line 348) | class Tip(ResourceIterItem):
  class Vessel (line 352) | class Vessel(ResourceIterItem):
    method record_removal (line 357) | def record_removal(self, ml, dest=None):
    method record_addition (line 362) | def record_addition(self, ml, source):
    method current_volume (line 367) | def current_volume(self):
  class DeckResource (line 371) | class DeckResource:
    class align (line 373) | class align:
    class types (line 377) | class types:
    method __init__ (line 380) | def __init__(self, layout_name):
    method _alignment_delta (line 383) | def _alignment_delta(self, int_start, int_end):
    method _assert_idx_in_range (line 386) | def _assert_idx_in_range(self, idx_or_vessel):
    method layout_name (line 394) | def layout_name(self):
    method position_id (line 402) | def position_id(self, idx):
    method alignment_delta (line 423) | def alignment_delta(self, start, end):
    method __iter__ (line 439) | def __iter__(self):
    method assign_label (line 443) | def assign_label(self, label: str):
  class Standard96 (line 450) | class Standard96(DeckResource):
    method well_coords (line 454) | def well_coords(self, idx):
    method _alignment_delta (line 458) | def _alignment_delta(self, start, end):
    method position_id (line 465) | def position_id(self, idx):
  class Tip96 (line 470) | class Tip96(Standard96):
    method __init__ (line 472) | def __init__(self, layout_name):
    method position_id (line 478) | def position_id(self, idx): # tips use 1-indexed int ids descending co...
  function resource_list_with_prefix (line 484) | def resource_list_with_prefix(layout_manager:LayoutManager, prefix:str, ...
  class BulkReagentPlate (line 495) | class BulkReagentPlate(Standard96):
    method __init__ (line 497) | def __init__(self, layout_name):
    method position_id (line 503) | def position_id(self, idx):
  class Waste96 (line 508) | class Waste96(BulkReagentPlate):
    method __init__ (line 510) | def __init__(self, layout_name):
  class Plate96 (line 513) | class Plate96(Standard96):
    method __init__ (line 515) | def __init__(self, layout_name):
  class Plate24 (line 522) | class Plate24(DeckResource):
    method __init__ (line 524) | def __init__(self, layout_name):
    method well_coords (line 530) | def well_coords(self, idx):
    method _alignment_delta (line 534) | def _alignment_delta(self, start, end):
    method position_id (line 540) | def position_id(self, idx):
  class Plate12 (line 545) | class Plate12(DeckResource):
    method __init__ (line 547) | def __init__(self, layout_name):
    method well_coords (line 553) | def well_coords(self, idx):
    method _alignment_delta (line 557) | def _alignment_delta(self, start, end):
    method position_id (line 563) | def position_id(self, idx):
  class Plate6 (line 567) | class Plate6(DeckResource):
    method __init__ (line 569) | def __init__(self, layout_name):
    method well_coords (line 575) | def well_coords(self, idx):
    method _alignment_delta (line 579) | def _alignment_delta(self, start, end):
    method position_id (line 585) | def position_id(self, idx):
  class Plate384 (line 590) | class Plate384(DeckResource):
    method __init__ (line 592) | def __init__(self, layout_name):
    method well_coords (line 598) | def well_coords(self, idx):
    method _alignment_delta (line 602) | def _alignment_delta(self, start, end):
    method position_id (line 608) | def position_id(self, idx):
  class Plate1536 (line 612) | class Plate1536(DeckResource):
    method __init__ (line 614) | def __init__(self, layout_name):
    method well_coords (line 620) | def well_coords(self, idx):
    method _alignment_delta (line 624) | def _alignment_delta(self, start, end):
    method position_id (line 630) | def position_id(self, idx):
  class Reservoir60mL (line 635) | class Reservoir60mL(DeckResource):
    method __init__ (line 637) | def __init__(self, layout_name):
    method well_coords (line 643) | def well_coords(self, idx):
    method _alignment_delta (line 647) | def _alignment_delta(self, start, end):
    method position_id (line 653) | def position_id(self, idx):
  class LVKBalanceVial (line 656) | class LVKBalanceVial(DeckResource):
    method __init__ (line 658) | def __init__(self, layout_name):
    method well_coords (line 664) | def well_coords(self, idx):
    method _alignment_delta (line 668) | def _alignment_delta(self, start, end):
    method position_id (line 674) | def position_id(self, idx):
  class EppiCarrier32 (line 677) | class EppiCarrier32(DeckResource):
    method __init__ (line 679) | def __init__(self, layout_name):
    method well_coords (line 686) | def well_coords(self, idx):
    method _alignment_delta (line 690) | def _alignment_delta(self, start, end):
    method position_id (line 696) | def position_id(self, idx):
  class FalconCarrier24 (line 700) | class FalconCarrier24(DeckResource):
    method __init__ (line 702) | def __init__(self, layout_name):
    method well_coords (line 709) | def well_coords(self, idx):
    method _alignment_delta (line 713) | def _alignment_delta(self, start, end):
    method position_id (line 719) | def position_id(self, idx):
  class Lid (line 722) | class Lid(DeckResource):
    method __init__ (line 724) | def __init__(self, layout_name):
  function layout_item (line 727) | def layout_item(lmgr, item_class, item_name):

FILE: pyhamilton/resources/enums.py
  class TipType (line 5) | class TipType(IntEnum):
    method volume (line 39) | def volume(self) -> int:
    method from_volume (line 74) | def from_volume(cls, volume: int) -> "TipType":
    method has_filter (line 88) | def has_filter(self) -> bool:
    method is_needle (line 101) | def is_needle(self) -> bool:
    method is_384_compatible (line 114) | def is_384_compatible(self) -> bool:

FILE: pyhamilton/resources/managed_resources.py
  function _get_conn (line 31) | def _get_conn():
  function _ensure_table (line 41) | def _ensure_table() -> None:
  class TrackedTips (line 56) | class TrackedTips:
    method __init__ (line 65) | def __init__(self,
    method from_prefix (line 98) | def from_prefix(cls,
    method mark_occupied (line 117) | def mark_occupied(self, index: int) -> None:
    method mark_unoccupied (line 122) | def mark_unoccupied(self, index: int) -> None:
    method is_occupied (line 127) | def is_occupied(self, index: int) -> bool:
    method count_remaining (line 130) | def count_remaining(self) -> int:
    method total_tips (line 133) | def total_tips(self) -> int:
    method fetch_next (line 136) | def fetch_next(self, n: int) -> List[Tuple[DeckResource, int]]:
    method fetch_rack (line 166) | def fetch_rack(self) -> Optional[DeckResource]:
    method fetch_rack_with_min_columns (line 182) | def fetch_rack_with_min_columns(self, min_columns: int) -> Optional[Tu...
    method reset_all (line 228) | def reset_all(self) -> None:
    method replace_tips (line 248) | def replace_tips(self, positions: List[Tuple[DeckResource, int]]) -> N...
    method fill_rack_from_occupancy_map (line 286) | def fill_rack_from_occupancy_map(self, rack: DeckResource, occupancy_m...
    method _hydrate_from_db (line 352) | def _hydrate_from_db(self) -> bool:
    method _update_row (line 375) | def _update_row(self, position_idx: int, occupied: bool) -> None:
    method _flush_entire_state (line 386) | def _flush_entire_state(self) -> None:
  function _get_stacked_conn (line 401) | def _get_stacked_conn():
  function _ensure_stacked_table (line 408) | def _ensure_stacked_table() -> None:
  class StackedResources (line 426) | class StackedResources:
    method __init__ (line 432) | def __init__(self,
    method from_prefix (line 462) | def from_prefix(cls,
    method get_stacked (line 477) | def get_stacked(self) -> List[str]:
    method count (line 481) | def count(self) -> int:
    method fetch_next (line 485) | def fetch_next(self) -> str:
    method put_back (line 499) | def put_back(self) -> str:
    method reset_all (line 521) | def reset_all(self) -> None:
    method _hydrate_from_db (line 548) | def _hydrate_from_db(self) -> None:
    method _update_row (line 565) | def _update_row(self, rname: str, *, available: bool) -> None:
    method _flush_entire_state (line 574) | def _flush_entire_state(self, conn) -> None:
  class TipSupportTracker (line 582) | class TipSupportTracker:
    method __init__ (line 587) | def __init__(self, resource):
    method _update_rack_in_tracker (line 594) | def _update_rack_in_tracker(self, rack, tip_occupancies, tip_tracker, ...
    method remove_rack (line 601) | def remove_rack(self, rack=None):
    method has_available_tips (line 607) | def has_available_tips(self, num_tips: int) -> bool:
    method _rightmost_indices_for_n_columns (line 610) | def _rightmost_indices_for_n_columns(self, n: int):
    method fetch_n_columns (line 620) | def fetch_n_columns(self, ham_int: HamiltonInterface, n: int, tip_trac...
    method tip_support_add_rack (line 650) | def tip_support_add_rack(self, ham_int: HamiltonInterface, tracked_tip...

FILE: pyhamilton/templates/ai_template/preprompt.py
  function complete (line 80) | def complete(prompt):

FILE: pyhamilton/templates/ai_template/robot_method.py
  function assist (line 18) | def assist(prompt, safe = False):

FILE: pyhamilton/templates/ai_template/voice.py
  function voice_to_text (line 11) | def voice_to_text():

FILE: pyhamilton/transport/transport.py
  class GrippedResource (line 13) | class GrippedResource(str, Enum):
    method __str__ (line 21) | def __str__(self) -> str:  # pragma: no‑cover – makes reprs nicer when...
    method parse (line 25) | def parse(cls, s: Union[str, "GrippedResource"]) -> "GrippedResource":
  class GripDirection (line 36) | class GripDirection(IntEnum):
  class GripperParams (line 47) | class GripperParams:
    method _complex_dict (line 66) | def _complex_dict(self, orientation: int) -> Dict[str, float]:
    method as_iswap_call (line 76) | def as_iswap_call(self) -> Tuple[int, Dict[str, float], Dict[str, floa...
  function get_core_gripper_params (line 149) | def get_core_gripper_params(
  function get_gripper_params (line 172) | def get_gripper_params(
  function transport_resource (line 205) | def transport_resource(

FILE: tests/interface_tests.py
  class Test_HamiltonInterface (line 217) | class Test_HamiltonInterface:
    method test_parse_response_status_when_ (line 274) | def test_parse_response_status_when_(
    method test_parse_response_return_data_when_ (line 346) | def test_parse_response_return_data_when_(
    method test_parse_response_parsed_result_when_ (line 390) | def test_parse_response_parsed_result_when_(
    method test_parse_response_raise_exception_when_ (line 440) | def test_parse_response_raise_exception_when_(