Merge branch 'release/1.8'

.github/workflows/tests_stationA_prot1.yml

@@ -0,0 +1,36 @@
+name: Station A prot1 tests
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the pipeline with several tests to check if everything works
+on: [push, pull_request]
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        parameters: [ "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot1_comb1_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot1_comb2_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot1_comb3_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot1_comb4_pars.json"
+                    ]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r ${GITHUB_WORKSPACE}/requirements.txt
+          mkdir ~/.opentrons
+          cp ${GITHUB_WORKSPACE}/custom_defaults/* ~/.opentrons
+      - name: Create test script
+        run: |
+          echo "testing"
+          python ${GITHUB_WORKSPACE}/tests/run_tests.py \
+            -j ${{ matrix.parameters }} \
+            -t ${GITHUB_WORKSPACE}/protocols/S3/stationA_protocol1_buffer_S3.ot2.apiv2.py \
+            -o /tmp/tmp_test.py
+      - name: Simulate script
+        run: |
+          opentrons_simulate -L ${GITHUB_WORKSPACE}/labware /tmp/tmp_test.py

.github/workflows/tests_stationA_prot2.yml

@@ -0,0 +1,39 @@
+name: Station A prot2 tests
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the pipeline with several tests to check if everything works
+on: [push, pull_request]
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        parameters: [ "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot2_comb1_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot2_comb2_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot2_comb3_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot2_comb4_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot2_comb5_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot2_comb6_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot2_comb7_pars.json"
+                    ]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r ${GITHUB_WORKSPACE}/requirements.txt
+          mkdir ~/.opentrons
+          cp ${GITHUB_WORKSPACE}/custom_defaults/* ~/.opentrons
+      - name: Create test script
+        run: |
+          echo "testing"
+          python ${GITHUB_WORKSPACE}/tests/run_tests.py \
+            -j ${{ matrix.parameters }} \
+            -t ${GITHUB_WORKSPACE}/protocols/S3/stationA_protocol2_beads_S3.ot2.apiv2.py \
+            -o /tmp/tmp_test.py
+      - name: Simulate script
+        run: |
+          opentrons_simulate -L ${GITHUB_WORKSPACE}/labware /tmp/tmp_test.py

.github/workflows/tests_stationA_prot3.yml

@@ -0,0 +1,40 @@
+name: Station A prot3 tests
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the pipeline with several tests to check if everything works
+on: [push, pull_request]
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        parameters: [ "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot3_comb1_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot3_comb2_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot3_comb3_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot3_comb4_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot3_comb5_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot3_comb6_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot3_comb7_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationA_prot3_comb8_pars.json"
+                    ]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r ${GITHUB_WORKSPACE}/requirements.txt
+          mkdir ~/.opentrons
+          cp ${GITHUB_WORKSPACE}/custom_defaults/* ~/.opentrons
+      - name: Create test script
+        run: |
+          echo "testing"
+          python ${GITHUB_WORKSPACE}/tests/run_tests.py \
+            -j ${{ matrix.parameters }} \
+            -t ${GITHUB_WORKSPACE}/protocols/S3/stationA_protocol3_lysates_S3.ot2.apiv2.py \
+            -o /tmp/tmp_test.py
+      - name: Simulate script
+        run: |
+          opentrons_simulate -L ${GITHUB_WORKSPACE}/labware /tmp/tmp_test.py

.github/workflows/tests_stationB_prot1.yml

@@ -0,0 +1,38 @@
+name: Station B prot1 tests
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the pipeline with several tests to check if everything works
+on: [push, pull_request]
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        # Removed comb1,3 and 5 due to a bug in the api, tall deep wells fail on simulation
+        parameters: [ "${GITHUB_WORKSPACE}/tests/par_tests/stationB_prot1_comb2_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationB_prot1_comb4_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationB_prot1_comb6_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationB_prot1_comb7_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationB_prot1_comb8_pars.json"
+                    ]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r ${GITHUB_WORKSPACE}/requirements.txt
+          mkdir ~/.opentrons
+          cp ${GITHUB_WORKSPACE}/custom_defaults/* ~/.opentrons
+      - name: Create test script
+        run: |
+          echo "testing"
+          python ${GITHUB_WORKSPACE}/tests/run_tests.py \
+            -j ${{ matrix.parameters }} \
+            -t ${GITHUB_WORKSPACE}/protocols/S3/stationB_protocol1_extraction_S3.ot2.apiv2.py \
+            -o /tmp/tmp_test.py
+      - name: Simulate script
+        run: |
+          opentrons_simulate -L ${GITHUB_WORKSPACE}/labware /tmp/tmp_test.py

.github/workflows/tests_stationC_prot1.yml

@@ -0,0 +1,42 @@
+name: Station C prot1 tests
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the pipeline with several tests to check if everything works
+on: [push, pull_request]
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        parameters: [ "${GITHUB_WORKSPACE}/tests/par_tests/stationC_prot1_comb1_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationC_prot1_comb2_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationC_prot1_comb3_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationC_prot1_comb4_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationC_prot1_comb5_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationC_prot1_comb6_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationC_prot1_comb7_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationC_prot1_comb8_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationC_prot1_comb9_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationC_prot1_comb10_pars.json"
+                    ]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r ${GITHUB_WORKSPACE}/requirements.txt
+          mkdir ~/.opentrons
+          cp ${GITHUB_WORKSPACE}/custom_defaults/* ~/.opentrons
+      - name: Create test script
+        run: |
+          echo "testing"
+          python ${GITHUB_WORKSPACE}/tests/run_tests.py \
+            -j ${{ matrix.parameters }} \
+            -t ${GITHUB_WORKSPACE}/protocols/S3/stationC_protocol1_pcr_S3.ot2.apiv2.py \
+            -o /tmp/tmp_test.py
+      - name: Simulate script
+        run: |
+          #opentrons_simulate -L ${GITHUB_WORKSPACE}/labware /tmp/tmp_test.py

.github/workflows/tests_stationC_prot2.yml

@@ -0,0 +1,35 @@
+name: Station C prot2 tests
+# This workflow is triggered on pushes and PRs to the repository.
+# It runs the pipeline with several tests to check if everything works
+on: [push, pull_request]
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        parameters: [ "${GITHUB_WORKSPACE}/tests/par_tests/stationC_prot2_comb1_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationC_prot2_comb2_pars.json",
+                      "${GITHUB_WORKSPACE}/tests/par_tests/stationC_prot2_comb3_pars.json"
+                    ]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: 3.7
+      - name: Install Dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r ${GITHUB_WORKSPACE}/requirements.txt
+          mkdir ~/.opentrons
+          cp ${GITHUB_WORKSPACE}/custom_defaults/* ~/.opentrons
+      - name: Create test script
+        run: |
+          echo "testing"
+          python ${GITHUB_WORKSPACE}/tests/run_tests.py \
+            -j ${{ matrix.parameters }} \
+            -t ${GITHUB_WORKSPACE}/protocols/S3/stationC_protocol2_pcrmulti_S3.ot2.apiv2.py \
+            -o /tmp/tmp_test.py
+      - name: Simulate script
+        run: |
+          #opentrons_simulate -L ${GITHUB_WORKSPACE}/labware /tmp/tmp_test.py

.gitignore

@@ -2,6 +2,7 @@
 __pycache__/
 *.py[cod]
 *$py.class
+virtualenv
 
 # C extensions
 *.so

CHANGELOG

@@ -1,3 +1,54 @@
+## Version 1.8
+
+New features:
+- Reduced dispense speed when dispensing washes from the top of the wells to avoid spaying in protocol B.
+- Implemented reuse of tips for elutes in protocol B.
+- Added double definition of labware to fuse both reuse tips protocol B options in only one files.
+
+Protocol modifications:
+- Increased supernatant removal to 810 ul to remove all of it in protocol B.
+- Removed reuse of first tip in washes in protocol B.
+- Protocol B labware layout has now two possible configurations, a legacy one for the old version of the protocol without tips reuse and the new optimised one.
+- Protocol C does not mix master mix any longer if not prepared in the machine to avoid creating bubbles.
+
+Bug fixes:
+- Replaced default plate for biorad in protocol C.
+- Fixed tip tracking for the case where we have same p20 both multi-channel and single-channel in protocol C.
+- Fixed bug not transferring samples for exactly 8 samples with multi-channel in protocol C.
+- Fixed bug not changing trash for 48 samples exactly in protocol B.
+- Fixed bug added missing pick up tip for protocol C.
+- Fixed bug mm_tube not decalred in protocol C.
+
+## Version 1.7
+
+New features:
+- Added json sending using request. Requests python module is installed in all robots.
+- Automatic tests added using github actions for all protocols (except C station due to a bug in opentrons_simulate v.3.17.0 )
+- New protocol for using multi p20 pipette in station C for transferring extracts.
+- Now there are two pauses in B station for removing trash tips when > 48 samples. One after mix y another after remove_supernatant.
+- Added tip-reuse option for Station B protocol 1 (extraction).
+- Added labware definition for biotix tip rack 300 ul (needs testing).
+- Added labware definition for biotix tip rack 1000 ul (needs testing).
+- Added labware ecogen deepwell to protocols A (this was missing in last release).
+
+Protocol modification:
+- For MM3 distribution in station C protocol 1 tip is changed every three columns.
+- Once mastermix is mixed in station C protocol 1 tip is changed.
+- Only one p20 rack tips in station C protocol 1 in slot 6.
+
+Bug fixes:
+- Fixed unset variable in dispense_beads protocol 1 station B. 2ab984b
+
+## Version 1.6
+Hotfix:
+- Fix bug in hommogenize function in C protocol, used pip instead of
+p300.
+
+## Version 1.5
+Hotfix:
+- Removed comments where MAGNET_HEIGHT variable that were bothering
+opentronsweb
+
 ## Version 1.4
 Documentation:
 - Added user manual in spanish and english.

configuration_scripts/S3/rename_robots/S3-C3

@@ -0,0 +1,18 @@
+NEW_SERIAL_NUMBER = "S3-C3"
+
+from opentrons import robot
+import os
+
+robot.comment(f"Setting serial number to {NEW_SERIAL_NUMBER}.")
+
+if not robot.is_simulating():
+    with open("/var/serial", "w") as serial_number_file:
+        serial_number_file.write(NEW_SERIAL_NUMBER + "\n")
+    with open("/etc/machine-info", "w") as serial_number_file:
+        serial_number_file.write(f"DEPLOYMENT=production\nPRETTY_HOSTNAME={NEW_SERIAL_NUMBER}\n")
+    with open("/etc/hostname", "w") as serial_number_file:
+        serial_number_file.write(NEW_SERIAL_NUMBER + "\n")
+
+    os.sync()
+
+    robot.comment("Done.")

configuration_scripts/S3/static_ips/S3-C3_static_ip.py

@@ -0,0 +1,33 @@
+STATIC_IP = "169.254.100.100/16"
+
+keyfile_contents = f"""\
+# This file was placed here by Opentrons Support to work around suspected issues with mDNS.
+# Normally, IP addresses are assigned dynamically by the "wired-linklocal" or "wired" connection.
+# This overrides both of those to set a known, static IP address.
+[connection]
+id=support-team-wired-static-ip
+type=ethernet
+autoconnect-priority=20
+interface-name=eth0
+permissions=
+[ethernet]
+cloned-mac-address=permanent
+mac-address-blacklist=
+[ipv4]
+dns-search=
+method=manual
+addresses={STATIC_IP}
+"""
+
+from opentrons import robot
+import os
+
+robot.comment(f"Run this protocol to permanently set the wired IP address of your OT-2 to {STATIC_IP}.")
+
+if not robot.is_simulating():
+	with open("/var/lib/NetworkManager/system-connections/support-team-wired-static-ip", "w") as keyfile:
+		keyfile.write(keyfile_contents)
+	os.sync()
+	robot.comment("Done.")
+
+robot.comment("Restart your OT-2 to apply the changes.")

custom_defaults/deck_calibration.json

@@ -0,0 +1,28 @@
+{
+    "gantry_calibration": [
+        [
+            1.0003,
+            -0.0032,
+            0.0,
+            -0.5771
+        ],
+        [
+            -0.0008,
+            1.0004,
+            0.0,
+            3.5125
+        ],
+        [
+            0.0,
+            0.0,
+            1.0,
+            -24.801
+        ],
+        [
+            0.0,
+            -0.0,
+            0.0,
+            1.0
+        ]
+    ]
+}