Adding support for Biotek Multiflo, MultiFloFX and 405TS; Improving support of EL406

.github/CODEOWNERS

@@ -1,6 +1,13 @@
 # Default owners
 * @PyLabRobot/core-team
 
+# Agilent BioTek washers and dispensers
+/docs/user_guide/agilent/405ts/ @stefanmaak
+/docs/user_guide/agilent/el406/ @stefanmaak
+/docs/user_guide/agilent/multiflo/ @stefanmaak
+/docs/user_guide/agilent/multiflofx/ @stefanmaak
+/pylabrobot/agilent/biotek/lhc/ @stefanmaak
+
 # BMG CLARIOstar
 /docs/user_guide/bmg_labtech/clariostar/ @BioCam
 /pylabrobot/legacy/plate_reading/bmg_labtech/ @BioCam

CHANGELOG.md

@@ -20,11 +20,24 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 - `Resource.rotate`, `rotate_to` and `rotated` take an optional `pivot_coordinate`: a point in the resource's own frame that stays where it is, so a resource can turn about its centre, an edge, or any other point rather than only about its origin. `location` carries by however far the turn moved that point. Raises `NoLocationError` when the resource has no location, since there is nothing to carry. (#1249)
 - `LinkBody` (`pylabrobot.resources.LinkBody`): one rigid member of a manipulator, an ordinary resource whose origin is a corner and which carries its `proximal_joint` and `distal_joint` as coordinates within it. The link is the line between the two joints and `length` is the distance, `None` on a member that ends the chain. A member turns about its proximal joint rather than its origin. (#1249)
 - `MechanicalGripper` (`pylabrobot.resources.MechanicalGripper`): a `LinkBody` that ends the chain, holding what it takes between two fingers. Its far end is a `tool_center_point` rather than a joint, it is sized to its body because `jaw_width` moves the fingers, and the jaws straddle the grip centre. (#1249)
+- Agilent BioTek 405 TS washer (`pylabrobot.agilent.biotek.lhc.Washer405TS`), MultiFlo (`MultiFlo`) and MultiFlo FX (`MultiFloFX`) dispensers, alongside the EL406 in one shared package: one device model, wire protocol and protocol-file format, with per-model differences expressed as configuration. Each model exposes the capability objects its fitted hardware supports (`PlateWasher`, `SyringeDispenser`, `PeristalticDispenser`) and reads the options the instrument has fitted on `setup()`.
+- `.LHC` protocol files can be read, checked and run (`pylabrobot.agilent.biotek.lhc.Protocol`, `read`, `write`), including comparing the instrument settings a file records against the instrument in front of you (`compare_settings`).
+- Serial transport for these instruments alongside FTDI, chosen by the port string.
+- Strip washing, 1536-well washing and peristaltic wash dispense/aspirate operations, and a public `get_status()` reporting the instrument's run state and activity.
+- User guide notebooks for the 405 TS, EL406, MultiFlo and MultiFlo FX (`docs/user_guide/agilent/`).
 
 ### Fixed
 
 - Imported `unittest.mock` in `pylabrobot/centrifuge/centrifuge_tests.py` (pre-existing bug that prevented the test class from running).
 
+### Changed
+
+- Agilent BioTek EL406 moved from `pylabrobot.agilent.biotek.el406.EL406` to `pylabrobot.agilent.biotek.lhc.EL406`. Its operations take the step objects each operation is defined by (`...protocols.steps.steps`) and the parameter groups they are built from (`...steps.step_parts`) rather than long flat keyword lists -- `wash()` went from 39 keyword arguments to nine. Every step is checked against the settings read at `setup()` before anything moves, and plate geometry is resolved from the PyLabRobot `Plate` resource instead of being passed per command.
+
+### Removed
+
+- `pylabrobot.agilent.biotek.el406`, replaced by `pylabrobot.agilent.biotek.lhc`.
+
 ## 0.2.1
 
 ### Added

docs/_static/devices.json

@@ -61,6 +61,22 @@
     "manager": "https://discuss.pylabrobot.org/u/rickwierenga",
     "oem": "https://www.agilent.com/en/product/automated-liquid-handling/automated-microplate-management/microplate-centrifuge"
   },
+  {
+    "id": "biotek-405-ts",
+    "vendor": "Agilent (BioTek)",
+    "name": "405 TS",
+    "kind": "plate washer",
+    "capabilities": [
+      "plate washing"
+    ],
+    "status": "mostly",
+    "api": "pylabrobot.agilent.biotek.lhc.Washer405TS",
+    "api_version": "v1",
+    "code_slug": "agilent/biotek/lhc",
+    "doc_slug": "agilent/405ts/hello-world",
+    "manager": "https://discuss.pylabrobot.org/u/rickwierenga",
+    "oem": "https://www.agilent.com/en/product/microplate-instrumentation/automated-liquid-dispensing-handling/automated-microplate-washers-dispensers/biotek-405-ts-microplate-washer-1623261"
+  },
   {
     "id": "biotek-cytation-1",
     "vendor": "Agilent (BioTek)",
@@ -118,12 +134,46 @@
       "dispensing"
     ],
     "status": "mostly",
-    "api": "pylabrobot.agilent.biotek.el406.EL406",
+    "api": "pylabrobot.agilent.biotek.lhc.EL406",
     "api_version": "v1",
-    "code_slug": "agilent/biotek/el406",
+    "code_slug": "agilent/biotek/lhc",
+    "doc_slug": "agilent/el406/hello-world",
     "manager": "https://discuss.pylabrobot.org/u/rickwierenga",
     "oem": "https://www.agilent.com/en/product/cell-analysis/microplate-automation-detection/microplate-washers-dispensers/biotek-el406-washer-dispenser-1623255"
   },
+  {
+    "id": "biotek-multiflo",
+    "vendor": "Agilent (BioTek)",
+    "name": "MultiFlo",
+    "kind": "bulk dispenser",
+    "capabilities": [
+      "dispensing"
+    ],
+    "status": "mostly",
+    "api": "pylabrobot.agilent.biotek.lhc.MultiFlo",
+    "api_version": "v1",
+    "code_slug": "agilent/biotek/lhc",
+    "doc_slug": "agilent/multiflo/hello-world",
+    "manager": "https://discuss.pylabrobot.org/u/rickwierenga",
+    "oem": "https://www.agilent.com/en/product/microplate-instrumentation/automated-liquid-dispensing-handling/automated-microplate-dispensers/biotek-multiflo-microplate-dispenser-1623263"
+  },
+  {
+    "id": "biotek-multiflo-fx",
+    "vendor": "Agilent (BioTek)",
+    "name": "MultiFlo FX",
+    "kind": "bulk dispenser",
+    "capabilities": [
+      "dispensing",
+      "plate washing"
+    ],
+    "status": "mostly",
+    "api": "pylabrobot.agilent.biotek.lhc.MultiFloFX",
+    "api_version": "v1",
+    "code_slug": "agilent/biotek/lhc",
+    "doc_slug": "agilent/multiflofx/hello-world",
+    "manager": "https://discuss.pylabrobot.org/u/rickwierenga",
+    "oem": "https://www.agilent.com/en/product/microplate-instrumentation/automated-liquid-dispensing-handling/automated-microplate-dispensers/biotek-multiflo-fx-multi-mode-dispenser-1623264"
+  },
   {
     "id": "biotek-synergy-h1",
     "vendor": "Agilent (BioTek)",

docs/api/pylabrobot.agilent.rst

@@ -18,44 +18,153 @@ BenchCel 4R
     PlateNotchSettings
 
 
-BioTek EL406
-------------
+BioTek washers and dispensers
+-----------------------------
 
-.. currentmodule:: pylabrobot.agilent.biotek.el406
+One class per model. Each exposes the capability objects its fitted hardware supports.
+
+.. currentmodule:: pylabrobot.agilent.biotek.lhc
 
 .. autosummary::
   :toctree: _autosummary
   :nosignatures:
   :recursive:
 
     EL406
+    MultiFlo
+    MultiFloFX
+    Washer405TS
+    Protocol
+    read
+    write
 
-.. currentmodule:: pylabrobot.agilent.biotek.el406.plate_washer
+.. currentmodule:: pylabrobot.agilent.biotek.lhc.devices.components
 
 .. autosummary::
   :toctree: _autosummary
   :nosignatures:
   :recursive:
 
     PlateWasher
+    SyringeDispenser
+    PeristalticDispenser
 
-.. currentmodule:: pylabrobot.agilent.biotek.el406.syringe_dispenser
+.. currentmodule:: pylabrobot.agilent.biotek.lhc.devices
 
 .. autosummary::
   :toctree: _autosummary
   :nosignatures:
   :recursive:
 
-    SyringeDispenser
+    InstrumentSettings
+    SettingsComparison
 
-.. currentmodule:: pylabrobot.agilent.biotek.el406.peristaltic_dispenser
+Steps
+~~~~~
+
+One class per operation the instruments perform, holding everything that operation can be given.
+A capability method takes these where it takes a step, and a protocol file stores them.
+
+.. currentmodule:: pylabrobot.agilent.biotek.lhc.protocols.steps.steps
 
 .. autosummary::
   :toctree: _autosummary
   :nosignatures:
   :recursive:
 
-    PeristalticDispenser
+    ManifoldWash
+    ManifoldDispense
+    ManifoldAspirate
+    ManifoldPrime
+    ManifoldAutoClean
+    Wash1536
+    StripWash
+    StripDispense
+    StripAspirate
+    StripPrime
+    SyringeDispense
+    SyringePrime
+    PeriDispense
+    PeriRandomAccessDispense
+    PeriPrime
+    PeriPurge
+    PeriWashDispense
+    PeriWashAspirate
+    ShakeSoak
+
+.. currentmodule:: pylabrobot.agilent.biotek.lhc.protocols.steps
+
+.. autosummary::
+  :toctree: _autosummary
+  :nosignatures:
+  :recursive:
+
+    Step
+    step_from_definition
+
+Step parts
+~~~~~~~~~~
+
+The groups of parameters the steps above are built from: where in the well a step works, which
+stages of a wash run, and the optional behaviours a step can switch on.
+
+.. currentmodule:: pylabrobot.agilent.biotek.lhc.protocols.steps.step_parts.positioning
+
+.. autosummary::
+  :toctree: _autosummary
+  :nosignatures:
+  :recursive:
+
+    Positioning
+
+.. currentmodule:: pylabrobot.agilent.biotek.lhc.protocols.steps.step_parts.groups
+
+.. autosummary::
+  :toctree: _autosummary
+  :nosignatures:
+  :recursive:
+
+    WashStages
+    Sectors
+    PreDispense
+    SecondaryAspirate
+    VacuumDelay
+    Shake
+    Soak
+    Submerge
+    RandomAccess
+    WellVolumeMap
+
+.. currentmodule:: pylabrobot.agilent.biotek.lhc.protocols.steps.step_parts.masks
+
+.. autosummary::
+  :toctree: _autosummary
+  :nosignatures:
+  :recursive:
+
+    WellMask
+
+.. currentmodule:: pylabrobot.agilent.biotek.lhc.protocols.validation
+
+.. autosummary::
+  :toctree: _autosummary
+  :nosignatures:
+  :recursive:
+
+    ValidationReport
+    StepReport
+    Rejection
+
+.. currentmodule:: pylabrobot.agilent.biotek.lhc.error_handling
+
+.. autosummary::
+  :toctree: _autosummary
+  :nosignatures:
+  :recursive:
+
+    BiotekError
+    LinkError
+    RejectedError
 
 
 BioTek Cytation