Merge branch 'edge' into abr-jira-fixes

.github/workflows/analyses-snapshot-test.yaml

@@ -45,12 +45,13 @@ jobs:
     timeout-minutes: 15
     runs-on: ubuntu-latest
     env:
+      BASE_IMAGE_NAME: opentrons-python-base:3.10
       ANALYSIS_REF: ${{ github.event.inputs.ANALYSIS_REF || github.head_ref || 'edge' }}
       SNAPSHOT_REF: ${{ github.event.inputs.SNAPSHOT_REF || github.head_ref || 'edge' }}
       # If we're running because of workflow_dispatch, use the user input to decide
       # whether to open a PR on failure. Otherwise, there is no user input,
       # so we only open a PR if the PR has the label 'gen-analyses-snapshot-pr'
-      OPEN_PR_ON_FAILURE: ${{ (github.event_name == 'workflow_dispatch' && github.events.inputs.OPEN_PR_ON_FAILURE) || ((github.event_name != 'workflow_dispatch') && (contains(github.event.pull_request.labels.*.name, 'gen-analyses-snapshot-pr'))) }}
+      OPEN_PR_ON_FAILURE: ${{ (github.event_name == 'workflow_dispatch' && github.event.inputs.OPEN_PR_ON_FAILURE) || ((github.event_name != 'workflow_dispatch') && (contains(github.event.pull_request.labels.*.name, 'gen-analyses-snapshot-pr'))) }}
       PR_TARGET_BRANCH: ${{ github.event.pull_request.base.ref || 'not a pr'}}
     steps:
       - name: Checkout Repository
@@ -71,9 +72,24 @@ jobs:
             echo "Analyses snapshots match ${{ env.PR_TARGET_BRANCH }} snapshots."
           fi
 
-      - name: Docker Build
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build base image
+        id: build_base_image
+        uses: docker/build-push-action@v6
+        with:
+          context: analyses-snapshot-testing/citools
+          file: analyses-snapshot-testing/citools/Dockerfile.base
+          push: false
+          load: true
+          tags: ${{ env.BASE_IMAGE_NAME }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+
+      - name: Build analysis image
         working-directory: analyses-snapshot-testing
-        run: make build-opentrons-analysis
+        run: make build-opentrons-analysis BASE_IMAGE_NAME=${{ env.BASE_IMAGE_NAME }} ANALYSIS_REF=${{ env.ANALYSIS_REF }} CACHEBUST=${{ github.run_number }}
 
       - name: Set up Python 3.13
         uses: actions/setup-python@v5
@@ -112,8 +128,8 @@ jobs:
           commit-message: 'fix(analyses-snapshot-testing): heal analyses snapshots'
           title: 'fix(analyses-snapshot-testing): heal ${{ env.ANALYSIS_REF }} snapshots'
           body: 'This PR was requested on the PR https://github.com/${{ github.repository }}/pull/${{ github.event.pull_request.number }}'
-          branch: 'analyses-snapshot-testing/${{ env.ANALYSIS_REF }}-from-${{ env.SNAPSHOT_REF}}'
-          base: ${{ env.SNAPSHOT_REF}}
+          branch: 'analyses-snapshot-testing/${{ env.ANALYSIS_REF }}-from-${{ env.SNAPSHOT_REF }}'
+          base: ${{ env.SNAPSHOT_REF }}
 
       - name: Comment on feature PR
         if: always() && steps.create_pull_request.outcome == 'success' && github.event_name == 'pull_request'
@@ -135,5 +151,5 @@ jobs:
           commit-message: 'fix(analyses-snapshot-testing): heal ${{ env.ANALYSIS_REF }} snapshots'
           title: 'fix(analyses-snapshot-testing): heal ${{ env.ANALYSIS_REF }} snapshots'
           body: 'The ${{ env.ANALYSIS_REF }} overnight analyses snapshot test is failing. This PR was opened to alert us to the failure.'
-          branch: 'analyses-snapshot-testing/${{ env.ANALYSIS_REF }}-from-${{ env.SNAPSHOT_REF}}'
-          base: ${{ env.SNAPSHOT_REF}}
+          branch: 'analyses-snapshot-testing/${{ env.ANALYSIS_REF }}-from-${{ env.SNAPSHOT_REF }}'
+          base: ${{ env.SNAPSHOT_REF }}

Makefile

@@ -152,6 +152,10 @@ push:
 	sleep 1
 	$(MAKE) -C $(UPDATE_SERVER_DIR) push
 
+.PHONY: push-folder
+PUSH_HELPER := abr-testing/abr_testing/tools/make_push.py
+push-folder:
+	$(OT_PYTHON) $(PUSH_HELPER)
 
 .PHONY: push-ot3
 push-ot3:

abr-testing/abr_testing/data_collection/abr_calibration_logs.py

@@ -286,6 +286,7 @@ def run(
     ip_json_file = os.path.join(storage_directory, "IPs.json")
     try:
         ip_file = json.load(open(ip_json_file))
+        robot_dict = ip_file.get("ip_address_list")
     except FileNotFoundError:
         print(f"Add .json file with robot IPs to: {storage_directory}.")
         sys.exit()
@@ -294,7 +295,7 @@ def run(
         ip_or_all = input("IP Address or ALL: ")
         calibration_data = []
         if ip_or_all.upper() == "ALL":
-            ip_address_list = ip_file["ip_address_list"]
+            ip_address_list = list(robot_dict.keys())
             for ip in ip_address_list:
                 saved_file_path, calibration = read_robot_logs.get_calibration_offsets(
                     ip, storage_directory

abr-testing/abr_testing/data_collection/abr_google_drive.py

@@ -48,7 +48,11 @@ def create_data_dictionary(
         file_path = os.path.join(storage_directory, filename)
         if file_path.endswith(".json"):
             with open(file_path) as file:
-                file_results = json.load(file)
+                try:
+                    file_results = json.load(file)
+                except json.decoder.JSONDecodeError:
+                    print(f"Skipped file {file_path} bc no data.")
+                    continue
         else:
             continue
         if not isinstance(file_results, dict):

abr-testing/abr_testing/data_collection/get_run_logs.py

@@ -17,7 +17,7 @@ def get_run_ids_from_robot(ip: str) -> Set[str]:
             f"http://{ip}:31950/runs", headers={"opentrons-version": "3"}
         )
         run_data = response.json()
-        run_list = run_data["data"]
+        run_list = run_data.get("data", "")
     except requests.exceptions.RequestException:
         print(f"Could not connect to robot with IP {ip}")
         run_list = []
@@ -104,10 +104,11 @@ def get_all_run_logs(
     ip_json_file = os.path.join(storage_directory, "IPs.json")
     try:
         ip_file = json.load(open(ip_json_file))
+        robot_dict = ip_file.get("ip_address_list")
     except FileNotFoundError:
         print(f"Add .json file with robot IPs to: {storage_directory}.")
         sys.exit()
-    ip_address_list = ip_file["ip_address_list"]
+    ip_address_list = list(robot_dict.keys())
     runs_from_storage = read_robot_logs.get_run_ids_from_google_drive(google_drive)
     for ip in ip_address_list:
         runs = get_run_ids_from_robot(ip)

abr-testing/abr_testing/protocol_simulation/abr_sim_check.py

@@ -46,7 +46,7 @@ def get_files() -> Tuple[Dict[str, Dict[str, Union[str, Path]]], List[Path]]:
     labware_defs = []
     for root, directories, _ in os.walk(root_dir):
         for directory in directories:
-            if directory == "active_protocols":
+            if directory not in exclude:
                 active_dir = os.path.join(root, directory)
                 for file in os.listdir(
                     active_dir
@@ -100,7 +100,6 @@ def get_files() -> Tuple[Dict[str, Dict[str, Union[str, Path]]], List[Path]]:
     exclude = [
         "__init__.py",
         "helpers.py",
-        "shared_vars_and_funcs.py",
     ]
     print("Simulating Protocols")
     file_dict, labware_defs = get_files()

abr-testing/abr_testing/protocols/active_protocols/10_ZymoBIOMICS_Magbead_DNA_Cells_Flex.py

@@ -17,7 +17,7 @@
     "protocolName": "Flex ZymoBIOMICS Magbead DNA Extraction: Cells",
 }
 
-requirements = {"robotType": "OT-3", "apiLevel": "2.20"}
+requirements = {"robotType": "OT-3", "apiLevel": "2.21"}
 """
 Slot A1: Tips 1000
 Slot A2: Tips 1000
@@ -94,7 +94,6 @@ def run(ctx: protocol_api.ProtocolContext) -> None:
         bind_time_1 = bind_time_2 = wash_time = 0.25
         drybeads = 0.5
         lysis_rep_1 = lysis_rep_2 = bead_reps_2 = 1
-    PK_vol = 20.0
     bead_vol = 25.0
     starting_vol = lysis_vol + sample_vol
     binding_buffer_vol = bind_vol + bead_vol
@@ -137,7 +136,7 @@ def run(ctx: protocol_api.ProtocolContext) -> None:
     """
     lysis_ = res1.wells()[0]
     binding_buffer = res1.wells()[1:4]
-    bind2_res = res1.wells()[4:6]
+    bind2_res = res1.wells()[4:8]
     wash1 = res1.wells()[6:8]
     elution_solution = res1.wells()[-1]
     wash2 = res2.wells()[:6]
@@ -149,16 +148,12 @@ def run(ctx: protocol_api.ProtocolContext) -> None:
     samps = sample_plate.wells()[: (8 * num_cols)]
 
     liquid_vols_and_wells: Dict[str, List[Dict[str, Well | List[Well] | float]]] = {
-        "Lysis": [{"well": lysis_, "volume": lysis_vol}],
-        "PK": [{"well": lysis_, "volume": PK_vol}],
-        "Beads": [{"well": binding_buffer, "volume": bead_vol}],
-        "Binding": [{"well": binding_buffer, "volume": bind_vol}],
-        "Binding 2": [{"well": bind2_res, "volume": bind2_vol}],
-        "Wash 1": [{"well": wash1_vol, "volume": wash1}],
-        "Wash 2": [{"well": wash2_vol, "volume": wash2}],
-        "Wash 3": [{"well": wash3_vol, "volume": wash3}],
-        "Final Elution": [{"well": elution_solution, "volume": elution_vol}],
-        "Samples": [{"well": samps, "volume": 0}],
+        "Lysis and PK": [{"well": lysis_, "volume": 12320.0}],
+        "Beads and Binding": [{"well": binding_buffer, "volume": 11875.0}],
+        "Binding 2": [{"well": bind2_res, "volume": 13500.0}],
+        "Final Elution": [{"well": elution_solution, "volume": 52000}],
+        "Samples": [{"well": samps, "volume": 0.0}],
+        "Reagents": [{"well": res2.wells(), "volume": 9000.0}],
     }
     flattened_list_of_wells = helpers.find_liquid_height_of_loaded_liquids(
         ctx, liquid_vols_and_wells, m1000

abr-testing/abr_testing/protocols/active_protocols/11_Dynabeads_IP_Flex_96well_RIT.py

@@ -16,7 +16,7 @@
 
 requirements = {
     "robotType": "OT-3",
-    "apiLevel": "2.20",
+    "apiLevel": "2.21",
 }
 
 

abr-testing/abr_testing/protocols/active_protocols/12_KAPA HyperPlus Library Prep.py

@@ -21,7 +21,7 @@
     "author": "Your Name <[email protected]>",
 }
 
-requirements = {"robotType": "Flex", "apiLevel": "2.20"}
+requirements = {"robotType": "Flex", "apiLevel": "2.21"}
 
 tt_50 = 0
 tt_200 = 0
@@ -50,6 +50,7 @@ def add_parameters(parameters: ParameterContext) -> None:
         default=False,
     )
     helpers.create_disposable_lid_parameter(parameters)
+    helpers.create_tc_lid_deck_riser_parameter(parameters)
     helpers.create_two_pipette_mount_parameters(parameters)
     parameters.add_int(
         variable_name="num_samples",
@@ -85,6 +86,7 @@ def run(ctx: ProtocolContext) -> None:
     dry_run = ctx.params.dry_run  # type: ignore[attr-defined]
     pipette_1000_mount = ctx.params.pipette_mount_1  # type: ignore[attr-defined]
     pipette_50_mount = ctx.params.pipette_mount_2  # type: ignore[attr-defined]
+    deck_riser = ctx.params.deck_riser  # type: ignore[attr-defined]
     REUSE_ETOH_TIPS = True
     REUSE_RSB_TIPS = (
         True  # Reuse tips for RSB buffer (adding RSB, mixing, and transferring)
@@ -158,7 +160,7 @@ def run(ctx: ProtocolContext) -> None:
     unused_lids: List[Labware] = []
     # Load TC Lids
     if disposable_lid:
-        unused_lids = helpers.load_disposable_lids(ctx, 5, ["C3"])
+        unused_lids = helpers.load_disposable_lids(ctx, 5, ["C3"], deck_riser)
     # Import Global Variables
 
     global tip50

abr-testing/abr_testing/protocols/active_protocols/1_Simple Normalize Long Right.py

@@ -17,7 +17,7 @@
 
 requirements = {
     "robotType": "Flex",
-    "apiLevel": "2.20",
+    "apiLevel": "2.21",
 }
 
 
@@ -121,8 +121,6 @@ def run(protocol: ProtocolContext) -> None:
         style=SINGLE, start="H1", tip_racks=[tiprack_x_1, tiprack_x_2, tiprack_x_3]
     )
     helpers.find_liquid_height_of_all_wells(protocol, p1000, wells)
-    tiprack_x_1.reset()
-
     sample_quant_csv = """
     sample_plate_1, Sample_well,DYE,DILUENT
     sample_plate_1,A1,0,100

abr-testing/abr_testing/protocols/active_protocols/2_BMS_PCR_Protocol.py

@@ -14,21 +14,24 @@
     "protocolName": "PCR Protocol with TC Auto Sealing Lid",
     "author": "Rami Farawi <[email protected]",
 }
-requirements = {"robotType": "OT-3", "apiLevel": "2.20"}
+requirements = {"robotType": "OT-3", "apiLevel": "2.21"}
 
 
 def add_parameters(parameters: ParameterContext) -> None:
     """Parameters."""
     helpers.create_single_pipette_mount_parameter(parameters)
     helpers.create_disposable_lid_parameter(parameters)
     helpers.create_csv_parameter(parameters)
+    helpers.create_tc_lid_deck_riser_parameter(parameters)
 
 
 def run(ctx: ProtocolContext) -> None:
     """Protocol."""
     pipette_mount = ctx.params.pipette_mount  # type: ignore[attr-defined]
     disposable_lid = ctx.params.disposable_lid  # type: ignore[attr-defined]
     parsed_csv = ctx.params.parameters_csv.parse_as_csv()  # type: ignore[attr-defined]
+    deck_riser = ctx.params.deck_riser  # type: ignore[attr-defined]
+
     rxn_vol = 50
     real_mode = True
     # DECK SETUP AND LABWARE
@@ -60,7 +63,7 @@ def run(ctx: ProtocolContext) -> None:
 
     # Opentrons tough pcr auto sealing lids
     if disposable_lid:
-        unused_lids = helpers.load_disposable_lids(ctx, 3, ["C3"])
+        unused_lids = helpers.load_disposable_lids(ctx, 3, ["C3"], deck_riser)
     used_lids: List[Labware] = []
 
     # LOAD PIPETTES
@@ -205,4 +208,6 @@ def run(ctx: ProtocolContext) -> None:
                 ctx.move_labware(lid_on_plate, "C2", use_gripper=True)
             else:
                 ctx.move_labware(lid_on_plate, used_lids[-2], use_gripper=True)
+        p50.drop_tip()
+        p50.configure_nozzle_layout(style=SINGLE, start="A1", tip_racks=tiprack_50)
         helpers.find_liquid_height_of_all_wells(ctx, p50, wells_to_probe_flattened)

abr-testing/abr_testing/protocols/active_protocols/3_OT3 ABR Normalize with Tubes.py

@@ -9,7 +9,7 @@
     "source": "Protocol Library",
 }
 
-requirements = {"robotType": "Flex", "apiLevel": "2.20"}
+requirements = {"robotType": "Flex", "apiLevel": "2.21"}
 
 # SCRIPT SETTINGS
 ABR_TEST = True
@@ -340,5 +340,4 @@ def run(ctx: ProtocolContext) -> None:
         )
 
         current += 1
-    print(wells_with_liquids)
     helpers.find_liquid_height_of_all_wells(ctx, p50, wells_with_liquids)

abr-testing/abr_testing/protocols/active_protocols/5_96ch complex protocol with single tip Pick Up.py

@@ -22,7 +22,7 @@
 
 requirements = {
     "robotType": "OT-3",
-    "apiLevel": "2.20",
+    "apiLevel": "2.21",
 }
 
 
@@ -44,13 +44,15 @@ def add_parameters(parameters: ParameterContext) -> None:
     helpers.create_tip_size_parameter(parameters)
     helpers.create_dot_bottom_parameter(parameters)
     helpers.create_disposable_lid_parameter(parameters)
+    helpers.create_tc_lid_deck_riser_parameter(parameters)
 
 
 def run(ctx: ProtocolContext) -> None:
     """Protocol."""
     b = ctx.params.dot_bottom  # type: ignore[attr-defined]
     TIPRACK_96_NAME = ctx.params.tip_size  # type: ignore[attr-defined]
     disposable_lid = ctx.params.disposable_lid  # type: ignore[attr-defined]
+    deck_riser = ctx.params.deck_riser  # type: ignore[attr-defined]
 
     waste_chute = ctx.load_waste_chute()
 
@@ -61,7 +63,7 @@ def run(ctx: ProtocolContext) -> None:
         helpers.temp_str, "C1"
     )  # type: ignore[assignment]
     if disposable_lid:
-        unused_lids = helpers.load_disposable_lids(ctx, 3, ["A4"])
+        unused_lids = helpers.load_disposable_lids(ctx, 3, ["A4"], deck_riser)
     used_lids: List[Labware] = []
     thermocycler.open_lid()
     h_s.open_labware_latch()

abr-testing/abr_testing/protocols/active_protocols/7_HDQ_DNA_Bacteria_Flex.py

@@ -23,7 +23,7 @@
 
 requirements = {
     "robotType": "OT-3",
-    "apiLevel": "2.20",
+    "apiLevel": "2.21",
 }
 """
 Slot A1: Tips 1000

abr-testing/abr_testing/protocols/active_protocols/9_Magmax_RNA_Cells_Flex.py

@@ -25,7 +25,7 @@
 
 requirements = {
     "robotType": "OT-3",
-    "apiLevel": "2.20",
+    "apiLevel": "2.21",
 }
 """
 Slot A1: Tips 200