Update to MADSci v0.8

Lifts the module from v0.5 (the previous release on main) through v0.6
to v0.8 in one go for the RAPID 446 grimm rebuild.

The v0.5 -> v0.6 work was carried in the working tree but never landed
upstream; layering v0.8 changes on top here brings everything together.
This branch is preferred over the existing `madsci_0_7` branch, which
had the API rename done but commented out the entire `startup_handler`
resource-creation block (deck / slots / mounts) -- a regression we
explicitly avoided.

v0.5 -> v0.6 (carried forward):
- Resource names now in v0.8 convention: {node_name}.deck,
  {node_name}.deck.nest_{i}, {node_name}.{mount}_mount.
- `slot_count` -> `nest_count` in the deck container attributes.
- `add_to_database=True` dropped from sub-templates (parent's
  `add_to_database=True` handles them).
- `STOPPED` value added to the RobotStatus enum.
- `rate_limit_requests: int = 500` config option added.

v0.6 -> v0.8 (this round):
- pyproject.toml + pdm.lock: pin madsci.{node_module,client,common}~=0.8.0;
  bump requires-python to >=3.10.
- src/ot2_rest_node.py: rename self.node_definition.{node_name,node_id}
  -> self.node_info.* (20 sites: 4 in startup_handler for protocols path
  + deck/slot/mount names, 8 in _create_ot2_templates for created_by=,
  8 in execute() for log messages).
- Dockerfile rewritten on the v0.8 base:
  - Pin to ghcr.io/ad-sdl/madsci:v0.8.0.
  - `uv pip install --python ${MADSCI_VENV}/bin/python -e ./ot2_module`
    so the editable install lands in the venv the runtime actually uses.
  - **No `USER` directive** -- the base entrypoint runs userdel/useradd
    as root to remap UID/GID to the host's, then drops to madsci itself.
    A trailing `USER madsci` breaks the entrypoint with
    "usermod: cannot lock /etc/passwd; try again later."
  - No dialout groups baked in -- OT-2s and Flex are network-only.

Verified end-to-end on grimm with all three OT2-family nodes:
  ot2_spongebob /status -> ready: true, /state ot2_status_code: idle
  ot2_patrick   /status -> ready: true, /state ot2_status_code: idle
  otflex_sandy  /status -> ready: true, /state ot2_status_code: failed
                (Flex's hardware state, not a container-side problem)

45 deck/slot/mount resources auto-created in postgres with the v0.8
`{node_name}.deck.nest_N` naming. ULIDs preserved via registry for
all three nodes.

Author: RPL

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"]
 

pdm.lock

@@ -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"}
 

pyproject.toml

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