Test heater shaker

Makefile

@@ -1,7 +1,7 @@
 SHELL := /bin/bash
 
 MONOREPO_URI := https://github.com/Opentrons/opentrons.git
-OT2_VERSION_TAG := v4.3.0
+OT2_VERSION_TAG := v6.1.0
 OT2_MONOREPO_DIR := ot2monorepoClone
 
 # Parsers output to here
@@ -30,7 +30,7 @@ setup:
 
 venvs/ot2:
 	mkdir -p venvs
-	virtualenv venvs/ot2
+	virtualenv -p=3.8 venvs/ot2
 	source venvs/ot2/bin/activate && \
 	pip install -e otcustomizers && \
 	pip install -r protolib/requirements.txt && \

protoBuilds/1bcd67/normalization.ot2.apiv2.py.json

@@ -1,5 +1,5 @@
 {
-    "content": "import math\nimport json\n\nmetadata = {\n    'protocolName': 'Normalization',\n    'author': 'Nick <[email protected]>',\n    'source': 'Protocol Library',\n    'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n    [dil_json_1, dil_json_2, dil_json_3, p1000_mount, m300_mount, final_vol\n     ] = get_values(  # noqa: F821\n        'dil_json_1', 'dil_json_2', 'dil_json_3', 'p1000_mount', 'm300_mount',\n        'final_vol')\n\n    # labware\n    dw_plate = ctx.load_labware('thermofisherabgene_96_wellplate_2200ul', '8',\n                                'deepwell plate')\n    final_dilution_plates = [\n        ctx.load_labware('nunc_96_wellplate_500ul', slot,\n                         f'final dilution plate {i+1}')\n        for i, slot in enumerate(['4', '5', '6'])]\n    diluent = ctx.load_labware('thermofishernalgene_1_reservoir_300000ul',\n                               '9', 'diluent').wells()[0]\n    tipracks1000 = [\n        ctx.load_labware('opentrons_96_tiprack_1000ul', slot)\n        for slot in ['10']]\n    tipracks300 = [\n        ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n        for slot in ['7']]\n\n    # pipettes\n    if p1000_mount == m300_mount:\n        raise Exception('Pipette mounts cannot match.')\n    p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n                                tip_racks=tipracks1000)\n    p300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n                               tip_racks=tipracks300)\n\n    tip_data = {\n        'single': {\n            'count': 0,\n            'tips': [\n                well for rack in tipracks300[::-1]\n                for col in rack.columns()[::-1]\n                for well in col[::-1]]\n        },\n        'multi': {\n            'count': 0,\n            'tips': [well for rack in tipracks300 for well in rack.rows()[0]]\n        }\n    }\n\n    def pickup_p300(mode='single'):\n        current = 0.1 if mode == 'single' else 0.5\n        ctx._implementation._hw_manager.hardware._attached_instruments[\n            p300._implementation.get_mount()].update_config_item(\n                'pick_up_current', current)\n\n        p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n        tip_data[mode]['count'] += 1\n\n    def extract_well_name(well_obj):\n        return well_obj.display_name.split(' ')[0]\n\n    def custom_transfer(vol, source, dest, pip=p300):\n        num_trans = math.ceil(vol/pip.max_volume)\n        vol_per_trans = vol/num_trans\n        for n in range(num_trans):\n            pip.aspirate(vol_per_trans, source)\n            pip.dispense(vol_per_trans, dest)\n\n    def determine_dil(col):\n        rows = 'ABCDEFGH'\n        col = dw_plate.rows()[0].index(col)\n        dict = [dict1, dict2, dict3][col % 3]\n        wells_to_check = [row + str(col+1) for row in rows]\n        for well in wells_to_check:\n            if dict[well]:\n                return True\n        return False\n\n    # pre-parse `None` to `null`\n    dil_json_1 = dil_json_1.replace('None', 'null')\n    dil_json_2 = dil_json_2.replace('None', 'null')\n    dil_json_3 = dil_json_3.replace('None', 'null')\n\n    # read .json files as dictionaries\n    dict1 = json.loads(dil_json_1)\n    dict2 = json.loads(dil_json_2)\n    dict3 = json.loads(dil_json_3)\n\n    map_dil_wells = {\n        well_set[0]: {\n            well_set[0]: dict1[extract_well_name(well_set[0])],\n            well_set[1]: dict2[extract_well_name(well_set[1])],\n            well_set[2]: dict3[extract_well_name(well_set[2])]\n        }\n        for well_set in [\n            row[i*3:(i+1)*3] for i in range(4) for row in dw_plate.rows()]\n    }\n\n    final_locations = []\n    for key, dict in map_dil_wells.items():\n        final_well = None\n        for well, vol in dict.items():\n            if vol:\n                final_well = well\n        final_locations.append(final_well)\n\n    # pre-add diluent\n    pickup_p300('multi')\n    for col in dw_plate.rows()[0]:\n        if determine_dil(col):\n            for _ in range(4):  # 4x 200ul = 800ul\n                p300.transfer(200, diluent, col, new_tip='never')\n    p300.drop_tip()\n\n    # prompt user to transfer neat sample\n    display_wells = [\n        well for well, vol in dict1.items() if vol]\n    display_vols = [\n        round(vol, 2) for vol in dict1.values() if vol]\n    sample_str = '\\n'.join([\n        f'Transfer {display_vol}uL to well {display_well} of deepwell \\\nplate on slot 8.'\n        for display_well, display_vol in zip(display_wells, display_vols)])\n    ctx.pause(msg=sample_str)\n\n    # perform dilutions\n    for set in map_dil_wells.values():\n        for i, (well, vol) in enumerate(set.items()):\n            if i > 0 and vol:  # neat is manually added\n                if vol <= 200:\n                    pip = p300\n                    pickup_p300('single')\n                else:\n                    pip = p1000\n                    p1000.pick_up_tip()\n                custom_transfer(vol, list(set.keys())[i-1], well, pip)\n                pip.mix(5, 200, well)\n                pip.drop_tip()\n\n    # final transfer\n    final_targets = [\n        well for plate in final_dilution_plates for well in plate.rows()[0]]\n\n    for source, dest in zip(final_locations, final_targets):\n        if source:\n            col = int(source.display_name.split(' ')[0][1:])\n            if col % 3 == 1:\n                pip.mix(5, 200, source)\n            p1000.transfer(final_vol, source, dest)\n",
+    "content": "import math\nimport json\n\nmetadata = {\n    'protocolName': 'Normalization',\n    'author': 'Nick <[email protected]>',\n    'source': 'Protocol Library',\n    'apiLevel': '2.11'\n}\n\n\ndef run(ctx):\n\n    [dil_json_1, dil_json_2, dil_json_3, p1000_mount, m300_mount, final_vol\n     ] = get_values(  # noqa: F821\n        'dil_json_1', 'dil_json_2', 'dil_json_3', 'p1000_mount', 'm300_mount',\n        'final_vol')\n\n    # labware\n    dw_plate = ctx.load_labware('thermofisherabgene_96_wellplate_2200ul', '8',\n                                'deepwell plate')\n    final_dilution_plates = [\n        ctx.load_labware('nunc_96_wellplate_500ul', slot,\n                         f'final dilution plate {i+1}')\n        for i, slot in enumerate(['4', '5', '6'])]\n    diluent = ctx.load_labware('thermofishernalgene_1_reservoir_300000ul',\n                               '9', 'diluent').wells()[0]\n    tipracks1000 = [\n        ctx.load_labware('opentrons_96_tiprack_1000ul', slot)\n        for slot in ['10']]\n    tipracks300 = [\n        ctx.load_labware('opentrons_96_tiprack_300ul', slot)\n        for slot in ['7']]\n\n    # pipettes\n    if p1000_mount == m300_mount:\n        raise Exception('Pipette mounts cannot match.')\n    p1000 = ctx.load_instrument('p1000_single_gen2', p1000_mount,\n                                tip_racks=tipracks1000)\n    p300 = ctx.load_instrument('p300_multi_gen2', m300_mount,\n                               tip_racks=tipracks300)\n\n    tip_data = {\n        'single': {\n            'count': 0,\n            'tips': [\n                well for rack in tipracks300[::-1]\n                for col in rack.columns()[::-1]\n                for well in col[::-1]]\n        },\n        'multi': {\n            'count': 0,\n            'tips': [well for rack in tipracks300 for well in rack.rows()[0]]\n        }\n    }\n\n    def pickup_p300(mode='single'):\n        current = 0.1 if mode == 'single' else 0.5\n        ctx._hw_manager.hardware._attached_instruments[\n            p300._implementation.get_mount()].update_config_item(\n                'pick_up_current', current)\n\n        p300.pick_up_tip(tip_data[mode]['tips'][tip_data[mode]['count']])\n        tip_data[mode]['count'] += 1\n\n    def extract_well_name(well_obj):\n        return well_obj.display_name.split(' ')[0]\n\n    def custom_transfer(vol, source, dest, pip=p300):\n        num_trans = math.ceil(vol/pip.max_volume)\n        vol_per_trans = vol/num_trans\n        for n in range(num_trans):\n            pip.aspirate(vol_per_trans, source)\n            pip.dispense(vol_per_trans, dest)\n\n    def determine_dil(col):\n        rows = 'ABCDEFGH'\n        col = dw_plate.rows()[0].index(col)\n        dict = [dict1, dict2, dict3][col % 3]\n        wells_to_check = [row + str(col+1) for row in rows]\n        for well in wells_to_check:\n            if dict[well]:\n                return True\n        return False\n\n    # pre-parse `None` to `null`\n    dil_json_1 = dil_json_1.replace('None', 'null')\n    dil_json_2 = dil_json_2.replace('None', 'null')\n    dil_json_3 = dil_json_3.replace('None', 'null')\n\n    # read .json files as dictionaries\n    dict1 = json.loads(dil_json_1)\n    dict2 = json.loads(dil_json_2)\n    dict3 = json.loads(dil_json_3)\n\n    map_dil_wells = {\n        well_set[0]: {\n            well_set[0]: dict1[extract_well_name(well_set[0])],\n            well_set[1]: dict2[extract_well_name(well_set[1])],\n            well_set[2]: dict3[extract_well_name(well_set[2])]\n        }\n        for well_set in [\n            row[i*3:(i+1)*3] for i in range(4) for row in dw_plate.rows()]\n    }\n\n    final_locations = []\n    for key, dict in map_dil_wells.items():\n        final_well = None\n        for well, vol in dict.items():\n            if vol:\n                final_well = well\n        final_locations.append(final_well)\n\n    # pre-add diluent\n    pickup_p300('multi')\n    for col in dw_plate.rows()[0]:\n        if determine_dil(col):\n            for _ in range(4):  # 4x 200ul = 800ul\n                p300.transfer(200, diluent, col, new_tip='never')\n    p300.drop_tip()\n\n    # prompt user to transfer neat sample\n    display_wells = [\n        well for well, vol in dict1.items() if vol]\n    display_vols = [\n        round(vol, 2) for vol in dict1.values() if vol]\n    sample_str = '\\n'.join([\n        f'Transfer {display_vol}uL to well {display_well} of deepwell \\\nplate on slot 8.'\n        for display_well, display_vol in zip(display_wells, display_vols)])\n    ctx.pause(msg=sample_str)\n\n    # perform dilutions\n    for set in map_dil_wells.values():\n        for i, (well, vol) in enumerate(set.items()):\n            if i > 0 and vol:  # neat is manually added\n                if vol <= 200:\n                    pip = p300\n                    pickup_p300('single')\n                else:\n                    pip = p1000\n                    p1000.pick_up_tip()\n                custom_transfer(vol, list(set.keys())[i-1], well, pip)\n                pip.mix(5, 200, well)\n                pip.drop_tip()\n\n    # final transfer\n    final_targets = [\n        well for plate in final_dilution_plates for well in plate.rows()[0]]\n\n    for source, dest in zip(final_locations, final_targets):\n        if source:\n            col = int(source.display_name.split(' ')[0][1:])\n            if col % 3 == 1:\n                pip.mix(5, 200, source)\n            p1000.transfer(final_vol, source, dest)\n",
     "custom_labware_defs": [
         {
             "brand": {