Merge branch 'edge' into ethanfjones-patch-1

.dockerignore

@@ -0,0 +1,38 @@
+./api-server
+./app
+./labware-library
+./node_modules
+./protocol-designer
+./discovery-client
+./coverage
+./components
+./app-shell
+./update-server
+./step-generation
+
+.pytest_cache
+.flake8
+.idea
+.pypy_cache
+dist
+build
+yarn.lock
+Pipfile.lock
+
+__pycache__
+*.pyc
+*.pyo
+*.pyd
+.Python
+env
+pip-log.txt
+pip-delete-this-directory.txt
+.tox
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+*.log
+.git

.opentrons_config/config.json

@@ -0,0 +1,18 @@
+{
+  "labware_database_file": "/config/opentrons.db",
+  "labware_calibration_offsets_dir_v2": "/config/labware/v2/offsets",
+  "labware_user_definitions_dir_v2": "/config/labware/v2/custom_definitions",
+  "feature_flags_file": "/config/feature_flags.json",
+  "robot_settings_file": "/config/robot_settings.json",
+  "deck_calibration_file": "/config/deck_calibration.json",
+  "log_dir": "/config/logs",
+  "api_log_file": "/config/logs/api.log",
+  "serial_log_file": "/config/logs/serial.log",
+  "wifi_keys_dir": "/config/user_storage/opentrons_data/network_keys",
+  "hardware_controller_lockfile": "/config/hardware.lock",
+  "pipette_config_overrides_dir": "/config/pipettes",
+  "tip_length_calibration_dir": "/config/tip_lengths",
+  "robot_calibration_dir": "/config/robot",
+  "pipette_calibration_dir": "/config/robot/pipettes",
+  "custom_tiprack_dir": "/config/tip_lengths/custom_tiprack_definitions"
+}

.opentrons_config/feature_flags.json

@@ -0,0 +1,17 @@
+{
+  "shortFixedTrash": null,
+  "calibrateToBottom": null,
+  "deckCalibrationDots": null,
+  "useProtocolApi2": null,
+  "disableHomeOnBoot": null,
+  "useOldAspirationFunctions": null,
+  "enableDoorSafetySwitch": null,
+  "enableTipLengthCalibration": null,
+  "enableHttpProtocolSessions": null,
+  "enableFastProtocolUpload": null,
+  "enableProtocolEngine": null,
+  "disableLogAggregation": null,
+  "enableApi1BackCompat": null,
+  "useV1HttpApi": null,
+  "_version": 9
+}

.opentrons_config/pipettes/P20SV202020070101.json

@@ -0,0 +1 @@
+{ "model": "p20_single_v2.0" }

.opentrons_config/pipettes/P3HMV202020041605.json

@@ -0,0 +1 @@
+{ "model": "p20_multi_v2.0" }

CONTRIBUTING.md

@@ -148,6 +148,12 @@ Your computer will need the following tools installed to be able to develop with
   pyenv install 3.7.6
   ```
 
+  **MacOS Big Sur Note:** due to this [known issue](https://github.com/pyenv/pyenv/issues/1737) we recommend using:
+
+  ```shell
+  pyenv install 3.7.10
+  ```
+
 - Node v12 - [nvm][] is optional, but recommended
 
   ```shell

DOCKER.md

@@ -0,0 +1,28 @@
+Docker Guide  
+=======================  
+Included in this repo are the tools to run a containerized Opentrons robot stack in docker.
+
+This includes the `robot-server` connected to the hardware emulation application. The emulation application includes the Smoothie and magnetic, temperature, and thermocycler modules.
+
+## Requirements
+
+- A clone of this repo.
+- An installation [docker](https://docs.docker.com/get-docker/)
+- An installation of [docker-compose](https://docs.docker.com/compose/install/)
+
+## How to use
+
+Start a terminal and change directory to the root of this repo.
+
+1. Build
+   Enter `docker-compose build --force-rm` at the terminal.
+
+2. Run
+   Enter `docker-compose up` at the terminal. _The build and run stages can be combined `docker-compose up --build`._
+
+3. Start the Opentrons application. The docker container will appear as `dev`. Connect and run just as you would on a robot.
+
+## Known Issues
+
+- Pipettes cannot be changed at run time.
+- Pipettes are fixed as `p20_multi_v2.0` on the left mount and `p20_single_v2.0` on the right.

Dockerfile

@@ -0,0 +1,29 @@
+FROM ubuntu as base
+RUN apt-get update && apt-get install -y python3 pip
+
+FROM base as builder
+COPY scripts scripts
+COPY LICENSE LICENSE
+
+COPY shared-data shared-data
+
+COPY api/MANIFEST.in api/MANIFEST.in
+COPY api/setup.py api/setup.py
+COPY api/pypi-readme.rst api/pypi-readme.rst
+COPY api/src/opentrons api/src/opentrons
+
+COPY notify-server/setup.py notify-server/setup.py
+COPY notify-server/README.rst notify-server/README.rst
+COPY notify-server/notify_server notify-server/notify_server
+
+COPY robot-server/setup.py robot-server/setup.py
+COPY robot-server/robot_server robot-server/robot_server
+
+RUN cd shared-data/python && python3 setup.py bdist_wheel -d /dist/
+RUN cd api && python3 setup.py bdist_wheel -d /dist/
+RUN cd notify-server && python3 setup.py bdist_wheel -d /dist/
+RUN cd robot-server && python3 setup.py bdist_wheel -d /dist/
+
+FROM base
+COPY --from=builder /dist /dist
+RUN pip install /dist/*

api/MANIFEST.in

@@ -1,5 +1,4 @@
 include src/opentrons/package.json
 graft src/opentrons/config
 graft src/opentrons/resources
-include src/opentrons/server/openapi.json
 exclude pyproject.toml

api/docs/v2/new_atomic_commands.rst

@@ -213,8 +213,8 @@ The examples in this section should be inserted in the following:
     metadata = {'apiLevel': '|apiLevel|'}
 
     def run(protocol):
-        tiprack = protocol.load_labware('corning_96_wellplate_360ul_flat', 2)
-        plate = protocol.load_labware('opentrons_96_tiprack_300ul', 3)
+        plate = protocol.load_labware('corning_96_wellplate_360ul_flat', 2)
+        tiprack = protocol.load_labware('opentrons_96_tiprack_300ul', 3)
         pipette = protocol.load_instrument('p300_single_gen2', mount='left', tip_racks=[tiprack])
         pipette.pick_up_tip()
         # example code goes here

api/docs/v2/new_examples.rst

@@ -47,6 +47,7 @@ This accomplishes the same thing as the following basic commands:
         p300.aspirate(100, plate['A1'])
         p300.dispense(100, plate['B1'])
         p300.return_tip()
+        p300.drop_tip()
 
 ******************************
 

api/src/opentrons/hardware_control/controller.py

@@ -269,17 +269,16 @@ def disengage_axes(self, axes: List[str]):
         self._smoothie_driver.disengage_axis(''.join(axes))
 
     def set_lights(self, button: Optional[bool], rails: Optional[bool]):
-        if opentrons.config.IS_ROBOT:
-            if button is not None:
-                self.gpio_chardev.set_button_light(blue=button)
-            if rails is not None:
-                self.gpio_chardev.set_rail_lights(rails)
+        if button is not None:
+            self.gpio_chardev.set_button_light(blue=button)
+        if rails is not None:
+            self.gpio_chardev.set_rail_lights(rails)
 
     def get_lights(self) -> Dict[str, bool]:
-        if not opentrons.config.IS_ROBOT:
-            return {}
-        return {'button': self.gpio_chardev.get_button_light()[2],
-                'rails': self.gpio_chardev.get_rail_lights()}
+        return {
+            'button': self.gpio_chardev.get_button_light()[2],
+            'rails': self.gpio_chardev.get_rail_lights()
+        }
 
     def pause(self):
         self._smoothie_driver.pause()

api/src/opentrons/hardware_control/emulation/app.py

@@ -28,7 +28,7 @@ async def run_server(host: str, port: int, handler: ConnectionHandler) -> None:
 
 async def run() -> None:
     """Run the module emulators."""
-    host = "127.0.0.1"
+    host = "0.0.0.0"
 
     await asyncio.gather(
         run_server(host=host,

docker-compose.yml

@@ -0,0 +1,27 @@
+version: '3'
+services:
+  emulator:
+    build: .
+    command: python3 -m opentrons.hardware_control.emulation.app
+    ports:
+      - '9996:9996'
+      - '9997:9997'
+      - '9998:9998'
+      - '9999:9999'
+  robot-server:
+    build: .
+    command: uvicorn "robot_server:app" --host 0.0.0.0 --port 31950 --ws wsproto --reload
+    ports:
+      - '31950:31950'
+    environment:
+      - OT_API_CONFIG_DIR=/config
+      - OT_SMOOTHIE_EMULATOR_URI=socket://emulator:9996
+      - OT_THERMOCYCLER_EMULATOR_URI=socket://emulator:9997
+      - OT_TEMPERATURE_EMULATOR_URI=socket://emulator:9998
+      - OT_MAGNETIC_EMULATOR_URI=socket://emulator:9999
+    links:
+      - 'emulator'
+    depends_on:
+      - 'emulator'
+    volumes:
+      - .opentrons_config:/config:rw

labware-library/cypress/integration/labware-creator/reservoir.spec.js

@@ -83,20 +83,14 @@ context('Reservoirs', () => {
       it('tests number of rows', () => {
         cy.get("input[name='gridRows']").focus().blur()
         cy.contains('Number of rows must be a number').should('exist')
-        cy.get("input[name='gridRows']").type('10').blur()
+        cy.get("input[name='gridRows']").type('1').blur()
         cy.contains('Number of rows must be a number').should('not.exist')
       })
 
-      it('tests are all of your rows evenly spaced', () => {
-        cy.get("input[name='regularRowSpacing'][value='false']").check({
-          force: true,
-        })
-        cy.contains(
-          'Your labware is not compatible with the Labware Creator'
-        ).should('exist')
-        cy.get("input[name='regularRowSpacing'][value='true']").check({
-          force: true,
-        })
+      it('should not ask if all of your rows evenly spaced, since we only have one row', () => {
+        cy.get("input[name='regularRowSpacing'][value='false']").should(
+          'not.exist'
+        )
       })
 
       it('tests number of columns', () => {
@@ -125,7 +119,7 @@ context('Reservoirs', () => {
     it('tests volume', () => {
       cy.get("input[name='wellVolume']").focus().blur()
       cy.contains('Max volume per well must be a number').should('exist')
-      cy.get("input[name='wellVolume']").type('10').blur()
+      cy.get("input[name='wellVolume']").type('250').blur()
       cy.contains('Max volume per well must be a number').should('not.exist')
     })
 
@@ -152,11 +146,11 @@ context('Reservoirs', () => {
         cy.get("input[name='wellYDimension']").should('exist')
         cy.get("input[name='wellXDimension']").focus().blur()
         cy.contains('Well X must be a number').should('exist')
-        cy.get("input[name='wellXDimension']").type('10').blur()
+        cy.get("input[name='wellXDimension']").type('8').blur()
         cy.contains('Well X must be a number').should('not.exist')
         cy.get("input[name='wellYDimension']").focus().blur()
         cy.contains('Well Y must be a number').should('exist')
-        cy.get("input[name='wellYDimension']").type('10').blur()
+        cy.get("input[name='wellYDimension']").type('60').blur()
         cy.contains('Well Y must be a number').should('not.exist')
       })
 
@@ -181,19 +175,15 @@ context('Reservoirs', () => {
         cy.get("img[src*='_v.']").should('exist')
         cy.get("input[name='wellDepth']").focus().blur()
         cy.contains('Depth must be a number').should('exist')
-        cy.get("input[name='wellDepth']").type('10').blur()
+        cy.get("input[name='wellDepth']").type('70').blur()
         cy.contains('Depth must be a number').should('not.exist')
       })
 
       it('tests well spacing', () => {
         cy.get("input[name='gridSpacingX']").focus().blur()
         cy.contains('X Spacing (Xs) must be a number').should('exist')
-        cy.get("input[name='gridSpacingX']").type('10').blur()
+        cy.get("input[name='gridSpacingX']").type('12').blur()
         cy.contains('X Spacing (Xs) must be a number').should('not.exist')
-        cy.get("input[name='gridSpacingY']").focus().blur()
-        cy.contains('Y Spacing (Ys) must be a number').should('exist')
-        cy.get("input[name='gridSpacingY']").type('10').blur()
-        cy.contains('Y Spacing (Ys) must be a number').should('not.exist')
       })
 
       it('tests grid offset', () => {
@@ -203,7 +193,7 @@ context('Reservoirs', () => {
         cy.contains('X Offset (Xo) must be a number').should('not.exist')
         cy.get("input[name='gridOffsetY']").focus().blur()
         cy.contains('Y Offset (Yo) must be a number').should('exist')
-        cy.get("input[name='gridOffsetY']").type('10').blur()
+        cy.get("input[name='gridOffsetY']").type('45').blur()
         cy.contains('Y Offset (Yo) must be a number').should('not.exist')
       })
 
@@ -228,10 +218,10 @@ context('Reservoirs', () => {
         cy.get("input[name='brandId']").type('001')
 
         // File info
-        cy.get("input[placeholder='TestPro 100 Reservoir 10 µL']").should(
+        cy.get("input[placeholder='TestPro 10 Reservoir 250 µL']").should(
           'exist'
         )
-        cy.get("input[placeholder='testpro_100_reservoir_10ul']").should(
+        cy.get("input[placeholder='testpro_10_reservoir_250ul']").should(
           'exist'
         )