Update to MADSci v0.8

.pre-commit-config.yaml

@@ -12,12 +12,12 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.1
+    rev: 0.9.1
     hooks:
       - id: nbstripout
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.14.1
+    rev: v0.15.14
     hooks:
       # Run the linter.
       - id: ruff

Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/ad-sdl/madsci
+FROM ghcr.io/ad-sdl/madsci:v0.8.0
 
 LABEL org.opencontainers.image.source=https://github.com/AD-SDL/ot2_module
 LABEL org.opencontainers.image.description="Drivers and REST API's for the Opentrons OT2 LiquidHandling robots"
@@ -13,10 +13,14 @@ RUN mkdir -p ot2_module
 COPY ./src ot2_module/src
 COPY ./README.md ot2_module/README.md
 COPY ./pyproject.toml ot2_module/pyproject.toml
-COPY ./tests ot2_module/tests
 
+# Install into the madsci venv (system pip would land in /usr/lib site-packages,
+# invisible to the venv interpreter the entrypoint actually runs).
 RUN --mount=type=cache,target=/root/.cache \
-    pip install -e ./ot2_module
+    uv pip install --python ${MADSCI_VENV}/bin/python -e ./ot2_module
+
+# Note: do not switch USER here — the base entrypoint runs userdel/useradd as
+# root to remap UID/GID to the host's, then drops to the madsci user itself.
 
 CMD ["python", "ot2_module/src/ot2_rest_node.py"]
 

definitions/otflex_template.node.yaml

@@ -0,0 +1,11 @@
+node_name: otflex_template
+node_url: null
+node_description: Template for a MADSci Opentrons OT2 node
+node_type: device
+module_name: otflex_module
+module_version: 0.0.2
+capabilities:
+  admin_commands: []
+commands: {}
+is_template: true
+config_defaults: {}

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "ot2_module"
-version = "2.0.0"
+version = "2.0.1"
 description = "Software for automatting an OT2 liquid_handler"
 authors = [
     {name = "Ryan D. Lewis", email="ryan.lewis@anl.gov"},
@@ -9,11 +9,11 @@ authors = [
     {name = "Tobias Ginsburg", email = "tginsburg@anl.gov"},
 ]
 dependencies = [
-    "madsci.node_module~=0.5.0",
-    "madsci.client~=0.5.0",
-    "madsci.common~=0.5.0"
+    "madsci.node_module~=0.8.0",
+    "madsci.client~=0.8.0",
+    "madsci.common~=0.8.0"
 ]
-requires-python = ">=3.9.1"
+requires-python = ">=3.10"
 readme = "README.md"
 license = {text = "MIT"}
 

scripts/delete_all_runs.py

@@ -1,4 +1,5 @@
 """delete all runs"""
+
 from argparse import ArgumentParser
 
 import requests

src/ot2_interface/config.py

@@ -1,4 +1,5 @@
 """Stores dataclasses/args/config for the ot2 drivers"""
+
 import json
 from argparse import ArgumentParser, Namespace
 from pathlib import Path

src/ot2_interface/ot2_driver_http.py

@@ -23,6 +23,7 @@ class RobotStatus(Enum):
     FAILED = "failed"
     PAUSED = "paused"
     OFFLINE = "offline"
+    STOPPED = "stopped"
 
 
 class RunStatus(Enum):

src/ot2_interface/protopiler/config.py

@@ -1,4 +1,5 @@
 """Dataclasses and other configuration used in the protopiler"""
+
 from pathlib import Path
 from typing import List, Literal, Optional, TypeVar, Union
 

src/ot2_interface/protopiler/deconstructor.py

@@ -1,4 +1,5 @@
 """Deconstructor, parses a protocol and turns it into a config"""
+
 import re
 import subprocess
 from argparse import ArgumentParser

src/ot2_interface/protopiler/protopiler.py

@@ -1,4 +1,5 @@
 """Protopiler is designed to compile a config yaml into a working protocol"""
+
 import argparse
 import copy
 from datetime import datetime
@@ -7,6 +8,7 @@
 from typing import Dict, Generator, List, Optional, Tuple, Union
 
 import pandas as pd
+
 from ot2_interface.protopiler.config import (
     Clear_Pipette,
     CommandBase,
@@ -501,7 +503,7 @@ def yaml_to_protocol(
                         "#location#", f'"{location}"'
                     )
                     labware_command = labware_command.replace(
-                        "#nickname#", f'{"module"}'
+                        "#nickname#", f"{'module'}"
                     )
                     labware_command = labware_command.replace(
                         "#labware_name#", f'"{name}"'

src/ot2_interface/protopiler/resource_manager.py

@@ -1,4 +1,5 @@
 """Class to manage/keep track of resources used by a protocol"""
+
 import json
 import re
 from argparse import ArgumentParser

src/ot2_interface/protopiler/test_configs/basic_config.py

@@ -1,4 +1,5 @@
 """basic config module"""
+
 from opentrons import protocol_api
 
 metadata = {