Merge branch 'edge' into chore-electron-update-v26

.github/workflows/app-test-build-deploy.yaml

@@ -85,7 +85,7 @@ jobs:
           make setup-js
       - name: 'test frontend packages'
         run: |
-          yarn jest --coverage=true --ci=true --collectCoverageFrom="app/src/**/*.(js|ts|tsx)" app/src components/src shared-data/js
+          make -C app test-cov
       - name: 'Upload coverage report'
         uses: codecov/codecov-action@v3
         with:
@@ -141,8 +141,7 @@ jobs:
           yarn config set cache-folder ${{ github.workspace }}/.yarn-cache
           make setup-js
       - name: 'test native(er) packages'
-        run: |
-          yarn jest --coverage=true --ci=true --collectCoverageFrom="(app-shell|app-shell-odd| discovery-client)/src/**/*.(js|ts|tsx)" app-shell/src app-shell-odd/src discovery-client/src
+        run: make test-js-internal tests="app-shell/src app-shell-odd/src discovery-client/src" cov_opts="--coverage=true --ci=true --collectCoverageFrom='(app-shell|app-shell-odd| discovery-client)/src/**/*.(js|ts|tsx)'"
       - name: 'Upload coverage report'
         uses: 'codecov/codecov-action@v3'
         with:
@@ -315,7 +314,8 @@ jobs:
   deploy-release-app:
     name: 'Deploy built app artifacts to S3'
     runs-on: 'ubuntu-22.04'
-    needs: ['js-unit-test', 'backend-unit-test', 'build-app', 'determine-build-type']
+    needs:
+      ['js-unit-test', 'backend-unit-test', 'build-app', 'determine-build-type']
     if: contains(fromJSON(needs.determine-build-type.outputs.variants), 'release') || contains(fromJSON(needs.determine-build-type.outputs.variants), 'internal-release')
     steps:
       - name: 'download run app builds'
@@ -401,15 +401,15 @@ jobs:
         uses: slackapi/[email protected]
         if: contains(fromJSON(needs.determine-build-type.outputs.variants), 'internal-release')
         with:
-          payload: "{\"branch_or_tag\":\"${{ github.ref_name }}\",\"build_type\":\"${{ needs.determine-build-type.outputs.type }}\", \"gh_linkback\":\"https://github.com/Opentrons/opentrons/tree/${{ github.ref_name }}\", \"windows_build\":\"${{ env._ACCESS_URL }}/${{steps.names.outputs.windows-internal-release}}\", \"mac_build\":\"${{ env._ACCESS_URL }}/${{steps.names.outputs.mac-internal-release}}\", \"linux_build\":\"${{ env._ACCESS_URL }}/${{steps.names.outputs.linux-internal-release}}\"}"
+          payload: '{"branch_or_tag":"${{ github.ref_name }}","build_type":"${{ needs.determine-build-type.outputs.type }}", "gh_linkback":"https://github.com/Opentrons/opentrons/tree/${{ github.ref_name }}", "windows_build":"${{ env._ACCESS_URL }}/${{steps.names.outputs.windows-internal-release}}", "mac_build":"${{ env._ACCESS_URL }}/${{steps.names.outputs.mac-internal-release}}", "linux_build":"${{ env._ACCESS_URL }}/${{steps.names.outputs.linux-internal-release}}"}'
         env:
           SLACK_WEBHOOK_URL: ${{ secrets.OT_APP_OT3_SLACK_NOTIFICATION_WEBHOOK_URL }}
           _ACCESS_URL: https://${{env._APP_DEPLOY_BUCKET_OT3}}/${{env._APP_DEPLOY_FOLDER_OT3}}
       - name: 'slack notify release'
         uses: slackapi/[email protected]
         if: contains(fromJSON(needs.determine-build-type.outputs.variants), 'release')
         with:
-          payload: "{\"branch_or_tag\":\"${{ github.ref_name }}\",\"build_type\":\"${{ needs.determine-build-type.outputs.type }}\", \"gh_linkback\":\"https://github.com/Opentrons/opentrons/tree/${{ github.ref_name }}\", \"windows_build\":\"${{ env._ACCESS_URL }}/${{steps.names.outputs.windows-release}}\", \"mac_build\":\"${{ env._ACCESS_URL }}/${{steps.names.outputs.mac-release}}\", \"linux_build\":\"${{ env._ACCESS_URL }}/${{steps.names.outputs.linux-release}}\"}"
+          payload: '{"branch_or_tag":"${{ github.ref_name }}","build_type":"${{ needs.determine-build-type.outputs.type }}", "gh_linkback":"https://github.com/Opentrons/opentrons/tree/${{ github.ref_name }}", "windows_build":"${{ env._ACCESS_URL }}/${{steps.names.outputs.windows-release}}", "mac_build":"${{ env._ACCESS_URL }}/${{steps.names.outputs.mac-release}}", "linux_build":"${{ env._ACCESS_URL }}/${{steps.names.outputs.linux-release}}"}'
         env:
           SLACK_WEBHOOK_URL: ${{ secrets.OT_APP_ROBOTSTACK_SLACK_NOTIFICATION_WEBHOOK_URL }}
           _ACCESS_URL: https://${{env._APP_DEPLOY_BUCKET_ROBOTSTACK}}/${{env._APP_DEPLOY_FOLDER_ROBOTSTACK}}

.github/workflows/components-test-build-deploy.yaml

@@ -62,8 +62,7 @@ jobs:
           yarn config set cache-folder ./.yarn-cache
           make setup-js
       - name: 'run components unit tests'
-        run: |
-          yarn jest --coverage=true --ci=true --collectCoverageFrom="components/src/**/*.(js|ts|tsx)" components/src
+        run: make -C components test-cov
       - name: 'Upload coverage report'
         uses: codecov/codecov-action@v3
         with:

.github/workflows/ll-test-build-deploy.yaml

@@ -69,8 +69,7 @@ jobs:
           yarn config set cache-folder ./.yarn-cache
           make setup-js
       - name: 'run labware library unit tests'
-        run: |
-          yarn jest --coverage=true --ci=true --collectCoverageFrom="labware-library/src/**/*.(js|ts|tsx)" labware-library/src
+        run: make -C labware-library test-cov
       - name: 'Upload coverage report'
         uses: codecov/codecov-action@v3
         with:

.github/workflows/pd-test-build-deploy.yaml

@@ -71,8 +71,7 @@ jobs:
           yarn config set cache-folder ./.yarn-cache
           make setup-js
       - name: 'run PD unit tests'
-        run: |
-          yarn jest --coverage=true --ci=true --collectCoverageFrom="protocol-designer/src/**/*.(js|ts|tsx)" protocol-designer/src
+        run: make -C protocol-designer test-cov
       - name: 'Upload coverage report'
         uses: codecov/codecov-action@v3
         with:

.github/workflows/react-api-client-test.yaml

@@ -57,8 +57,7 @@ jobs:
           yarn config set cache-folder ./.yarn-cache
           make setup-js
       - name: 'run react-api-client unit tests'
-        run: |
-          yarn jest --coverage=true --ci=true --collectCoverageFrom="react-api-client/src/**/*.(js|ts|tsx)" react-api-client/src
+        run: make -C react-api-client test-cov
       - name: 'Upload coverage report'
         uses: codecov/codecov-action@v3
         with:

.github/workflows/shared-data-test-lint-deploy.yaml

@@ -133,8 +133,7 @@ jobs:
           yarn config set cache-folder ./.yarn-cache
           make setup-js
       - name: 'run shared-data JS unit tests'
-        run: |
-          yarn jest --coverage=true --ci=true --collectCoverageFrom="shared-data/js/**/*.(js|ts|tsx)" shared-data/js
+        run: make -C shared-data test-cov
       - name: 'Upload coverage report'
         uses: codecov/codecov-action@v3
         with:

.github/workflows/step-generation-test.yaml

@@ -58,8 +58,7 @@ jobs:
           yarn config set cache-folder ./.yarn-cache
           make setup-js
       - name: 'run step generation unit tests'
-        run: |
-          yarn jest --coverage=true --ci=true --collectCoverageFrom="step-generation/src/**/*.(js|ts|tsx)" step-generation/src
+        run: make -C step-generation test-cov
       - name: 'Upload coverage report'
         uses: codecov/codecov-action@v3
         with:

Makefile

@@ -5,6 +5,8 @@
 include ./scripts/python.mk
 
 API_DIR := api
+API_CLIENT_DIR := api-client
+APP_DIR := app
 APP_SHELL_DIR := app-shell
 APP_SHELL_ODD_DIR := app-shell-odd
 COMPONENTS_DIR := components
@@ -15,8 +17,10 @@ NOTIFY_SERVER_DIR := notify-server
 PROTOCOL_DESIGNER_DIR := protocol-designer
 SHARED_DATA_DIR := shared-data
 UPDATE_SERVER_DIR := update-server
+REACT_API_CLIENT_DIR := react-api-client
 ROBOT_SERVER_DIR := robot-server
 SERVER_UTILS_DIR := server-utils
+STEP_GENERATION_DIR := step-generation
 SYSTEM_SERVER_DIR := system-server
 HARDWARE_DIR := hardware
 USB_BRIDGE_DIR := usb-bridge
@@ -195,12 +199,7 @@ test-py: test-py-windows
 	$(MAKE) -C $(USB_BRIDGE_DIR) test
 
 .PHONY: test-js
-test-js:
-	yarn jest \
-		--coverage=$(cover) \
-		--watch=$(watch) \
-		--updateSnapshot=$(updateSnapshot) \
-		--ci=$(if $(CI),true,false)
+test-js: test-js-internal
 
 # lints and typechecks
 .PHONY: lint
@@ -261,3 +260,11 @@ circular-dependencies-js:
 	yarn madge $(and $(CI),--no-spinner --no-color) --circular labware-library/src/index.tsx
 	yarn madge $(and $(CI),--no-spinner --no-color) --circular app/src/index.tsx
 	yarn madge $(and $(CI),--no-spinner --no-color) --circular components/src/index.ts
+
+.PHONY: test-js-internal
+test-js-internal:
+	yarn jest $(tests) $(test_opts) $(cov_opts)
+
+.PHONY: test-js-%
+test-js-%: 
+	$(MAKE) test-js-internal tests="$(if $(tests),$(foreach test,$(tests),$*/$(test)),$*)" test_opts="$(test_opts)" cov_opts="$(cov_opts)"

api-client/Makefile

@@ -17,3 +17,7 @@ clean:
 .PHONY: build
 build:
 	rollup --config rollup.config.js
+
+.PHONY: test
+test:
+	$(MAKE) -C .. test-js-api-client

api/docs/v2/new_advanced_running.rst

@@ -77,7 +77,7 @@ Creating the dummy protocol requires you to:
     1. Use the ``metadata`` or ``requirements`` dictionary to specify the API version. (See :ref:`v2-versioning` for details.) Use the same API version as you did in :py:meth:`opentrons.execute.get_protocol_api`.
     2. Define a ``run()`` function.
     3. Load all of your labware in their initial locations.
-    4. Load your smallest capacity pipette and specify its ``tipracks``.
+    4. Load your smallest capacity pipette and specify its ``tip_racks``.
     5. Call ``pick_up_tip()``. Labware Position Check can't run if you don't pick up a tip.
 
 For example, the following dummy protocol will use a P300 Single-Channel GEN2 pipette to enable Labware Position Check for an OT-2 tip rack, NEST reservoir, and NEST flat well plate.
@@ -116,13 +116,13 @@ This automatically generated code uses generic names for the loaded labware. If
     
 .. versionadded:: 2.12
 
-Once you've executed this code in Jupyter Notebook, all subsequent positional calculations for this reservoir in slot D2 will be adjusted 0.1 mm to the right, 0.2 mm to the back, and 0.3 mm up.
+Once you've executed this code in Jupyter Notebook, all subsequent positional calculations for this reservoir in slot 2 will be adjusted 0.1 mm to the right, 0.2 mm to the back, and 0.3 mm up.
 
-Remember, you should only add ``.set_offset()`` commands to protocols run outside of the Opentrons App. And you should follow the behavior of Labware Position Check, i.e., *do not* reuse offset measurements unless they apply to the *same labware* in the *same deck slot* on the *same robot*.
+Remember, you should only add ``set_offset()`` commands to protocols run outside of the Opentrons App. And you should follow the behavior of Labware Position Check, i.e., *do not* reuse offset measurements unless they apply to the *same labware* in the *same deck slot* on the *same robot*.
 
 .. warning::
 
-	Improperly reusing offset data may cause your robot to move to an unexpected position or crash against other labware, which can lead to incorrect protocol execution or damage your equipment. The same applies when running protocols with ``.set_offset()`` commands in the Opentrons App. When in doubt: run Labware Position Check again and update your code!
+	Improperly reusing offset data may cause your robot to move to an unexpected position or crash against labware, which can lead to incorrect protocol execution or damage your equipment. The same applies when running protocols with ``set_offset()`` commands in the Opentrons App. When in doubt: run Labware Position Check again and update your code!
 
 Using Custom Labware
 --------------------
@@ -144,6 +144,7 @@ To disable the robot server, open a Jupyter terminal session by going to **New >
 Command Line
 ------------
 
+.. TODO update with separate links to OT-2 and Flex setup, when new Flex process is in manual or on help site
 The robot's command line is accessible either by going to **New > Terminal** in Jupyter or `via SSH <https://support.opentrons.com/s/article/Connecting-to-your-OT-2-with-SSH>`_.
 
 To execute a protocol from the robot's command line, copy the protocol file to the robot with ``scp`` and then run the protocol with ``opentrons_execute``:

api/docs/v2/new_pipette.rst

@@ -310,34 +310,50 @@ The single- and multi-channel P50 GEN1 pipettes are the exceptions here. If your
 Volume Modes
 ============
 
-The Flex 1-Channel 50 µL and Flex 8-Channel 50 µL pipettes must operate in a low-volume mode to accurately dispense 1 µL of liquid. Set low-volume mode by calling :py:meth:`.InstrumentContext.configure_for_volume` with the amount of liquid you plan to aspirate, in µL::
+The Flex 1-Channel 50 µL and Flex 8-Channel 50 µL pipettes must operate in a low-volume mode to accurately dispense very small volumes of liquid. Set the volume mode by calling :py:meth:`.InstrumentContext.configure_for_volume` with the amount of liquid you plan to aspirate, in µL::
 
     pipette50.configure_for_volume(1)
     pipette50.pick_up_tip()
     pipette50.aspirate(1, plate["A1"])
     
 .. versionadded:: 2.15
 
+Passing different values to ``configure_for_volume()`` changes the minimum and maximum volume of Flex 50 µL pipettes as follows:
+
+.. list-table::
+    :header-rows: 1
+    :widths: 2 3 3
+
+    * - Value
+      - Minimum Volume (µL)
+      - Maximum Volume (µL)
+    * - 1–4.9
+      - 1
+      - 30
+    * - 5–50
+      - 5
+      - 50
+
 .. note::
     The pipette must not contain liquid when you call ``configure_for_volume()``, or the API will raise an error.
 
-    Also, if the pipette is in a well location that may contain liquid, it will move upward to ensure it is not immersed in liquid before changing its mode.
+    Also, if the pipette is in a well location that may contain liquid, it will move upward to ensure it is not immersed in liquid before changing its mode. Calling ``configure_for_volume()`` *before* ``pick_up_tip()`` helps to avoid this situation.
 
-In a protocol that handles many different volumes, it's a good practice to call this function immediately before each :py:meth:`.transfer` or :py:meth:`.aspirate`, specifying the volume that you are about to handle. When operating with a list of volumes, nest ``configure_for_volume()`` inside a ``for`` loop to ensure that the pipette is properly configured for each volume:
+In a protocol that handles many different volumes, it's a good practice to call ``configure_for_volume()`` once for each :py:meth:`.transfer` or :py:meth:`.aspirate`, specifying the volume that you are about to handle. When operating with a list of volumes, nest ``configure_for_volume()`` inside a ``for`` loop to ensure that the pipette is properly configured for each volume:
 
 .. code-block:: python
     
     volumes = [1, 2, 3, 4, 1, 5, 2, 8]
     sources = plate.columns()[0]
     destinations = plate.columns()[1]
     for i in range(8):
-        pipette50.pick_up_tip()
         pipette50.configure_for_volume(volumes[i])
+        pipette50.pick_up_tip()
         pipette50.aspirate(volume=volumes[i], location=sources[i])
         pipette50.dispense(location=destinations[i])
         pipette50.drop_tip()
 
-If you know that all your liquid handling will take place in a specific mode, then you can call ``configure_for_volume()`` just once with a nominal volume. Or if all the volumes correspond to the pipette's default mode, you don't have to call ``configure_for_volume()`` at all.
+If you know that all your liquid handling will take place in a specific mode, then you can call ``configure_for_volume()`` just once with a representative volume. Or if all the volumes correspond to the pipette's default mode, you don't have to call ``configure_for_volume()`` at all.
 
 
 .. _new-plunger-flow-rates:

app-shell-odd/Makefile

@@ -85,3 +85,7 @@ dev: export NODE_ENV := development
 dev:
 	webpack
 	$(electron)
+
+.PHONY: test
+test:
+	$(MAKE) -C .. test-js-app-shell-odd

app-shell/Makefile

@@ -15,6 +15,9 @@ PORT ?= 8090
 # TODO(mc, 2018-08-07): figure out a better way to do this
 ui_dir := ../app
 
+# Path of source package
+SRC_PATH = app-shell
+
 # cross-platform noop command
 noop := cd .
 
@@ -23,6 +26,14 @@ dist_files = $(if $(filter $(1),robot-stack),"dist/**/Opentrons-*","dist/**/Open
 update_files := "dist/@(alpha|beta|latest)*.@(yml|json)"
 publish_dir := dist/publish
 
+# These variables can be overriden when make is invoked to customize the
+# behavior of jest. For instance,
+# make test tests=src/__tests__/http.test.ts would run only the
+# specified test
+tests ?= $(SRC_PATH)/src
+cov_opts ?= --coverage=true --ci=true --collectCoverageFrom='app-shell/src/**/*.(js|ts|tsx)'
+test_opts ?=
+
 # Other SSH args for robot
 ssh_opts ?= $(default_ssh_opts)
 
@@ -173,3 +184,7 @@ dev: export OPENTRONS_PROJECT := $(OPENTRONS_PROJECT)
 dev: clean-dev-autoupdate ./dev-app-update.yml
 	webpack
 	$(electron)
+
+.PHONY: test
+test:
+	$(MAKE) -C .. test-js-app-shell

app-shell/scripts/before-pack.js

@@ -124,7 +124,7 @@ module.exports = function beforeBuild(context) {
         'install',
         `--target=${path.join(PYTHON_DESTINATION, sitePackages)}`,
         path.join(__dirname, '../../shared-data/python'),
-        path.join(__dirname, '../../hardware'),
+        path.join(__dirname, '../../hardware[flex]'),
         path.join(__dirname, '../../api'),
         'pandas==1.4.3',
       ])

app/Makefile

@@ -9,6 +9,9 @@ PATH := $(shell cd .. && yarn bin):$(PATH)
 # dev server port
 PORT ?= 8090
 
+# Path of source package
+SRC_PATH = app
+
 OPENTRONS_PROJECT ?= robot-stack
 
 # dependency directories for dev
@@ -18,6 +21,13 @@ discovery_client_dir := ../discovery-client
 
 # override webpack's default hashing algorithm for node 18: https://github.com/webpack/webpack/issues/14532
 export NODE_OPTIONS := --openssl-legacy-provider
+# These variables can be overriden when make is invoked to customize the
+# behavior of jest. For instance,
+# make test tests=src/pages/Labware/__tests__/hooks.test.tsx would run only the
+# specified test
+tests ?=
+cov_opts ?= --coverage=true --ci=true --collectCoverageFrom='app/src/**/*.(js|ts|tsx)'
+test_opts ?=
 
 # standard targets
 #####################################################################
@@ -80,3 +90,11 @@ dev-shell-odd: export OT_APP_UI__HEIGHT := 600
 dev-shell-odd:
 	wait-on http-get://localhost:$(PORT)
 	$(MAKE) -C $(shell_odd_dir) dev OPENTRONS_PROJECT=$(OPENTRONS_PROJECT)
+
+.PHONY: test
+test:
+	make -C .. test-js-app tests="$(tests)" test_opts="$(test_opts)"
+
+.PHONY: test-cov
+test-cov:
+	make -C .. test-js-app tests=$(tests) test_opts="$(test_opts)" cov_opts="$(cov_opts)"