Merge branch 'add-abr-protocols' of https://github.com/Opentrons/open…

…trons into add-abr-protocols
Opentrons · Nov 7, 2024 · defc508 · defc508
2 parents 1bdf055 + 3890d70
commit defc508
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diff --git a/.github/workflows/app-test-build-deploy.yaml b/.github/workflows/app-test-build-deploy.yaml
@@ -318,19 +318,28 @@ jobs:
         if: startsWith(matrix.os, 'windows') && contains(needs.determine-build-type.outputs.type, 'release')
         shell: cmd
         env:
-          SM_HOST: ${{ secrets.SM_HOST }}
+          SM_HOST: ${{ secrets.SM_HOST_V2 }}
           SM_CLIENT_CERT_FILE: "D:\\Certificate_pkcs12.p12"
-          SM_CLIENT_CERT_PASSWORD: ${{secrets.SM_CLIENT_CERT_PASSWORD}}
-          SM_API_KEY: ${{secrets.SM_API_KEY}}
+          SM_CLIENT_CERT_PASSWORD: ${{secrets.SM_CLIENT_CERT_PASSWORD_V2}}
+          SM_API_KEY: ${{secrets.SM_API_KEY_V2}}
         run: |
-          curl -X GET  https://one.digicert.com/signingmanager/api-ui/v1/releases/Keylockertools-windows-x64.msi/download -H "x-api-key:${{secrets.SM_API_KEY}}" -o Keylockertools-windows-x64.msi
+          curl -X GET  https://one.digicert.com/signingmanager/api-ui/v1/releases/Keylockertools-windows-x64.msi/download -H "x-api-key:${{secrets.SM_API_KEY_V2}}" -o Keylockertools-windows-x64.msi
           msiexec /i Keylockertools-windows-x64.msi /quiet /qn
           smksp_registrar.exe list
           smctl.exe keypair ls
           C:\Windows\System32\certutil.exe -csp "DigiCert Signing Manager KSP" -key -user
           smksp_cert_sync.exe
           smctl.exe healthcheck --all
 
+      # Do the frontend dist bundle
+      - name: 'bundle ${{matrix.variant}} frontend'
+        env:
+          OT_APP_MIXPANEL_ID: ${{ secrets.OT_APP_MIXPANEL_ID }}
+          OT_APP_INTERCOM_ID: ${{ secrets.OT_APP_INTERCOM_ID }}
+          OPENTRONS_PROJECT: ${{ steps.project.outputs.project }}
+        run: |
+          make -C app dist
+
       # build the desktop app and deploy it
       - name: 'build ${{matrix.variant}} app for ${{ matrix.os }}'
         if: matrix.target == 'desktop'
@@ -339,18 +348,14 @@ jobs:
           OT_APP_MIXPANEL_ID: ${{ secrets.OT_APP_MIXPANEL_ID }}
           OT_APP_INTERCOM_ID: ${{ secrets.OT_APP_INTERCOM_ID }}
           WINDOWS_SIGN: ${{ format('{0}', contains(needs.determine-build-type.outputs.type, 'release')) }}
-          SM_HOST: ${{secrets.SM_HOST}}
-          SM_CLIENT_CERT_FILE: "D:\\Certificate_pkcs12.p12"
-          SM_CLIENT_CERT_PASSWORD: ${{secrets.SM_CLIENT_CERT_PASSWORD}}
-          SM_API_KEY: ${{secrets.SM_API_KEY}}
-          SM_CODE_SIGNING_CERT_SHA1_HASH: ${{secrets.SM_CODE_SIGNING_CERT_SHA1_HASH}}
-          SM_KEYPAIR_ALIAS: ${{secrets.SM_KEYPAIR_ALIAS}}
+          SM_CODE_SIGNING_CERT_SHA1_HASH: ${{secrets.SM_CODE_SIGNING_CERT_SHA1_HASH_V2}}
+          SM_KEYPAIR_ALIAS: ${{secrets.SM_KEYPAIR_ALIAS_V2}}
           WINDOWS_CSC_FILEPATH: "D:\\opentrons_labworks_inc.crt"
-          CSC_LINK: ${{ secrets.OT_APP_CSC_MACOS }}
-          CSC_KEY_PASSWORD: ${{ secrets.OT_APP_CSC_KEY_MACOS }}
-          APPLE_ID: ${{ secrets.OT_APP_APPLE_ID }}
-          APPLE_APP_SPECIFIC_PASSWORD: ${{ secrets.OT_APP_APPLE_ID_PASSWORD }}
-          APPLE_TEAM_ID: ${{ secrets.OT_APP_APPLE_TEAM_ID }}
+          CSC_LINK: ${{ secrets.OT_APP_CSC_MACOS_V2 }}
+          CSC_KEY_PASSWORD: ${{ secrets.OT_APP_CSC_KEY_MACOS_V2 }}
+          APPLE_ID: ${{ secrets.OT_APP_APPLE_ID_V2 }}
+          APPLE_APP_SPECIFIC_PASSWORD: ${{ secrets.OT_APP_APPLE_ID_PASSWORD_V2 }}
+          APPLE_TEAM_ID: ${{ secrets.OT_APP_APPLE_TEAM_ID_V2 }}
           HOST_PYTHON: python
           OPENTRONS_PROJECT: ${{ steps.project.outputs.project }}
           OT_APP_DEPLOY_BUCKET: ${{ steps.project.outputs.bucket }}

diff --git a/.github/workflows/pd-test-build-deploy.yaml b/.github/workflows/pd-test-build-deploy.yaml
@@ -79,49 +79,49 @@ jobs:
           files: ./coverage/lcov.info
           flags: protocol-designer
 
-  e2e-test:
-    name: 'pd e2e tests'
-    needs: ['js-unit-test']
-    timeout-minutes: 30
-    strategy:
-      matrix:
-        os: ['ubuntu-22.04']
-    runs-on: '${{ matrix.os }}'
-    steps:
-      - uses: 'actions/checkout@v3'
-        with:
-          fetch-depth: 0
-      # https://github.com/actions/checkout/issues/290
-      - name: 'Fix actions/checkout odd handling of tags'
-        if: startsWith(github.ref, 'refs/tags')
-        run: |
-          git fetch -f origin ${{ github.ref }}:${{ github.ref }}
-          git checkout ${{ github.ref }}
-      - uses: 'actions/setup-node@v3'
-        with:
-          node-version: '18.19.0'
-      - name: 'install udev for usb-detection'
-        if: startsWith(matrix.os, 'ubuntu')
-        run: |
-          # WORKAROUND: Remove microsoft debian repo due to https://github.com/microsoft/linux-package-repositories/issues/130. Remove line below after it is resolved
-          sudo rm -f /etc/apt/sources.list.d/microsoft-prod.list
-          sudo apt-get update && sudo apt-get install libudev-dev
-      - name: 'cache yarn cache'
-        uses: actions/cache@v3
-        with:
-          path: |
-            ${{ github.workspace }}/.yarn-cache
-            ${{ github.workspace }}/.npm-cache
-          key: js-${{ secrets.GH_CACHE_VERSION }}-${{ runner.os }}-yarn-${{ hashFiles('yarn.lock') }}
-          restore-keys: |
-            js-${{ secrets.GH_CACHE_VERSION }}-${{ runner.os }}-yarn-
-      - name: 'setup-js'
-        run: |
-          npm config set cache ./.npm-cache
-          yarn config set cache-folder ./.yarn-cache
-          make setup-js
-      - name: 'test-e2e'
-        run: make -C protocol-designer test-e2e
+  # e2e-test:
+  #   name: 'pd e2e tests'
+  #   needs: ['js-unit-test']
+  #   timeout-minutes: 30
+  #   strategy:
+  #     matrix:
+  #       os: ['ubuntu-22.04']
+  #   runs-on: '${{ matrix.os }}'
+  #   steps:
+  #     - uses: 'actions/checkout@v3'
+  #       with:
+  #         fetch-depth: 0
+  #     # https://github.com/actions/checkout/issues/290
+  #     - name: 'Fix actions/checkout odd handling of tags'
+  #       if: startsWith(github.ref, 'refs/tags')
+  #       run: |
+  #         git fetch -f origin ${{ github.ref }}:${{ github.ref }}
+  #         git checkout ${{ github.ref }}
+  #     - uses: 'actions/setup-node@v3'
+  #       with:
+  #         node-version: '18.19.0'
+  #     - name: 'install udev for usb-detection'
+  #       if: startsWith(matrix.os, 'ubuntu')
+  #       run: |
+  #         # WORKAROUND: Remove microsoft debian repo due to https://github.com/microsoft/linux-package-repositories/issues/130. Remove line below after it is resolved
+  #         sudo rm -f /etc/apt/sources.list.d/microsoft-prod.list
+  #         sudo apt-get update && sudo apt-get install libudev-dev
+  #     - name: 'cache yarn cache'
+  #       uses: actions/cache@v3
+  #       with:
+  #         path: |
+  #           ${{ github.workspace }}/.yarn-cache
+  #           ${{ github.workspace }}/.npm-cache
+  #         key: js-${{ secrets.GH_CACHE_VERSION }}-${{ runner.os }}-yarn-${{ hashFiles('yarn.lock') }}
+  #         restore-keys: |
+  #           js-${{ secrets.GH_CACHE_VERSION }}-${{ runner.os }}-yarn-
+  #     - name: 'setup-js'
+  #       run: |
+  #         npm config set cache ./.npm-cache
+  #         yarn config set cache-folder ./.yarn-cache
+  #         make setup-js
+  #     - name: 'test-e2e'
+  #       run: make -C protocol-designer test-e2e
   build-pd:
     name: 'build protocol designer artifact'
     needs: ['js-unit-test']

diff --git a/abr-testing/abr_testing/data_collection/abr_calibration_logs.py b/abr-testing/abr_testing/data_collection/abr_calibration_logs.py
@@ -82,7 +82,7 @@ def module_helper(
                 y = one_module["moduleOffset"]["offset"].get("y", "")
                 z = one_module["moduleOffset"]["offset"].get("z", "")
             except KeyError:
-                pass
+                continue
             if mod_serial in module_sheet_serials and modified in module_modify_dates:
                 continue
             module_row = (

diff --git a/abr-testing/abr_testing/data_collection/read_robot_logs.py b/abr-testing/abr_testing/data_collection/read_robot_logs.py
@@ -110,6 +110,7 @@ def identify_labware_ids(
     file_results: Dict[str, Any], labware_name: Optional[str]
 ) -> List[str]:
     """Determine what type of labware is being picked up."""
+    list_of_labware_ids: List[str] = []
     if labware_name:
         labwares = file_results.get("labware", "")
         list_of_labware_ids = []
@@ -341,8 +342,9 @@ def hs_commands(file_results: Dict[str, Any]) -> Dict[str, float]:
             )
     if temp_time is not None and deactivate_time is None:
         # If heater shaker module is not deactivated, protocol completedAt time stamp used.
+        default = commandData[len(commandData) - 1].get("completedAt")
         protocol_end = datetime.strptime(
-            file_results.get("completedAt", ""), "%Y-%m-%dT%H:%M:%S.%f%z"
+            file_results.get("completedAt", default), "%Y-%m-%dT%H:%M:%S.%f%z"
         )
         temp_duration = (protocol_end - temp_time).total_seconds()
         hs_temps[hs_temp] = hs_temps.get(hs_temp, 0.0) + temp_duration
@@ -389,8 +391,9 @@ def temperature_module_commands(file_results: Dict[str, Any]) -> Dict[str, Any]:
                 tm_temps[tm_temp] = tm_temps.get(tm_temp, 0.0) + temp_duration
     if temp_time is not None and deactivate_time is None:
         # If temperature module is not deactivated, protocol completedAt time stamp used.
+        default = commandData[len(commandData) - 1].get("completedAt")
         protocol_end = datetime.strptime(
-            file_results.get("completedAt", ""), "%Y-%m-%dT%H:%M:%S.%f%z"
+            file_results.get("completedAt", default), "%Y-%m-%dT%H:%M:%S.%f%z"
         )
         temp_duration = (protocol_end - temp_time).total_seconds()
         tm_temps[tm_temp] = tm_temps.get(tm_temp, 0.0) + temp_duration
@@ -473,15 +476,17 @@ def thermocycler_commands(file_results: Dict[str, Any]) -> Dict[str, float]:
                 block_temps[block_temp] = block_temps.get(block_temp, 0.0) + block_time
     if block_on_time is not None and block_off_time is None:
         # If thermocycler block not deactivated protocol completedAt time stamp used
+        default = commandData[len(commandData) - 1].get("completedAt")
         protocol_end = datetime.strptime(
-            file_results.get("completedAt", ""), "%Y-%m-%dT%H:%M:%S.%f%z"
+            file_results.get("completedAt", default), "%Y-%m-%dT%H:%M:%S.%f%z"
         )
         temp_duration = (protocol_end - block_on_time).total_seconds()
-        block_temps[block_temp] = block_temps.get(block_temp, 0.0) + temp_duration
+
     if lid_on_time is not None and lid_off_time is None:
         # If thermocycler lid not deactivated protocol completedAt time stamp used
+        default = commandData[len(commandData) - 1].get("completedAt")
         protocol_end = datetime.strptime(
-            file_results.get("completedAt", ""), "%Y-%m-%dT%H:%M:%S.%f%z"
+            file_results.get("completedAt", default), "%Y-%m-%dT%H:%M:%S.%f%z"
         )
         temp_duration = (protocol_end - lid_on_time).total_seconds()
         lid_temps[lid_temp] = block_temps.get(lid_temp, 0.0) + temp_duration

diff --git a/abr-testing/abr_testing/protocol_simulation/abr_sim_check.py b/abr-testing/abr_testing/protocol_simulation/abr_sim_check.py
@@ -5,9 +5,9 @@
 from pathlib import Path
 
 
-def run(file_to_simulate: str) -> None:
+def run(file_to_simulate: Path) -> None:
     """Simulate protocol and raise errors."""
-    protocol_name = Path(file_to_simulate).stem
+    protocol_name = file_to_simulate.stem
     try:
         simulation_metrics.main(file_to_simulate, False)
     except Exception:
@@ -29,6 +29,6 @@ def run(file_to_simulate: str) -> None:
             if file.endswith(".py"):  # If it's a Python file
                 if file in exclude:
                     continue
-                file_path = os.path.join(root, file)
-                print(f"Simulating protocol: {file_path}")
+                file_path = Path(os.path.join(root, file))
+                print(f"Simulating protocol: {file_path.stem}")
                 run(file_path)