remove mystery resources and add docs (#287)

docs/api/pylabrobot.resources.rst

@@ -89,18 +89,6 @@ Falcon
     falcon.tubes
 
 
-Greiner
--------
-
-.. autosummary::
-  :toctree: _autosummary
-  :nosignatures:
-  :recursive:
-
-    greiner
-    greiner.plates
-
-
 Hamilton
 --------
 
@@ -115,18 +103,6 @@ Hamilton
     hamilton.STARLetDeck
 
 
-Limbro
-------
-
-.. autosummary::
-  :toctree: _autosummary
-  :nosignatures:
-  :recursive:
-
-    limbro
-    limbro.plates
-
-
 ML Star resources
 -----------------
 

docs/resources/library/agenbio.md

@@ -0,0 +1,10 @@
+# Agenbio
+
+[Company Page](https://agenbio.en.made-in-china.com)
+
+## Plates
+
+| Description | Image | PLR definition |
+|-|-|-|
+| 'AGenBio_4_wellplate_Vb'<br>Part no.: RES-75-4MW<br>[manufacturer website](https://agenbio.en.made-in-china.com/product/ZTqYVMiCkpcF/China-Medical-Consumable-Plastic-Reagent-Reservoir-Disposable-4-Channel-Troughs-Reagent-Reservoir.html?) | ![](img/agenbio/AGenBio_4_wellplate_Vb.webp) | `AGenBio_4_wellplate_Vb` |
+| 'AGenBio_1_wellplate_Fl'<br>Part no.: RES-75-4MW<br>[manufacturer website](https://agenbio.en.made-in-china.com/product/pZWaBIPvZMkm/China-Res-190-F-Lad-Consumables-of-Flat-Reservoir.html) | ![](img/agenbio/AGenBio_1_wellplate_Fl.webp) | `AGenBio_1_wellplate_Fl` |

docs/resources/library/celltreat.md

@@ -1,8 +1,8 @@
 # CellTreat
 
-## Plats
+## Plates
 
 | Description | Image | PLR definition |
 |-|-|-|
 | 'CellTreat_6_DWP_16300ul_Fb'<br>Part no.: 229105<br>[manufacturer website](https://www.celltreat.com/product/229105/) | ![](img/celltreat/CellTreat_6_DWP_16300ul_Fb.jpg) | `CellTreat_6_DWP_16300ul_Fb` |
-| 'CellTreat_96_DWP_350ul_Ub'<br>Part no.: 229591<br>[manufacturer website](https://www.celltreat.com/product/229591/)  | ![](img/celltreat/CellTreat_96_DWP_350ul_Ub.jpg) | `CellTreat_96_DWP_350ul_Ub`  |
+| Same as 229590 (229590 is sold with lids) 'CellTreat_96_wellplate_350ul_Ub'<br>Part no.: 229591<br>[manufacturer website](https://www.celltreat.com/product/229591/)  | ![](img/celltreat/CellTreat_96_wellplate_350ul_Ub.jpg) | `CellTreat_96_wellplate_350ul_Ub`  |

docs/resources/library/corning_costar.md

@@ -10,6 +10,7 @@ As of 2014, Corning had five major business sectors: display technologies, envir
 
 | Description               | Image              | PLR definition |
 |--------------------|--------------------|--------------------|
-| 'Cos_6_MWP_16800ul_Fb'<br>Part no.: 3516<br>[manufacturer website](https://ecatalog.corning.com/life-sciences/b2b/UK/en/Microplates/Assay-Microplates/96-Well-Microplates/Costar%C2%AE-Multiple-Well-Cell-Culture-Plates/p/3516) <br><br>- Material: ? <br>- Cleanliness: 3516: sterilized by gamma irradiation <br>- Nonreversible lids with condensation rings to reduce contamination <br>- Treated for optimal cell attachment <br>- Cell growth area: 9.5 cm² (approx.) <br>- Total volume: 16.8 mL| ![](img/corning_costar/Cos_6_MWP_16800ul_Fb.jpg) | `Cos_6_MWP_16800ul_Fb` |
-| 'Cos_96_DWP_2mL_Vb'<br>Part no.: 3516<br>[manufacturer website](https://ecatalog.corning.com/life-sciences/b2b/UK/en/Microplates/Assay-Microplates/96-Well-Microplates/Costar%C2%AE-Multiple-Well-Cell-Culture-Plates/p/3516) <br><br>- Material: Polypropylene <br>- Resistant to many common organic solvents (e.g., DMSO, ethanol, methanol) <br>- 3960: Sterile and DNase- and RNase-free <br>- Total volume: 2 mL <br>- Features uniform skirt heights for greater robotic gripping surface| ![](img/corning_costar/Cos_96_DWP_2mL_Vb.jpg) | `Cos_96_DWP_2mL_Vb` |
-[ 'Cor_96_wellplate_360ul_Fb' <br>Part no.: 353376<br>[manufacturer website](https://ecatalog.corning.com/life-sciences/b2b/NL/en/Microplates/Assay-Microplates/96-Well-Microplates/Falcon®-96-well-Polystyrene-Microplates/p/353376) <br><br>- Material: TC-treated polystyrene <br> - Cleanliness: sterile <br>- Total volume:  392 uL <br>- Working volume: 25-340 uL | ![](img/corning_costar/Cos_96_wellplate_360ul_Fb.jpg) | `Cor_96_wellplate_360ul_Fb` |
+| 'Cos_6_wellplate_16800ul_Fb'<br>Part no.: 3516<br>[manufacturer website](https://ecatalog.corning.com/life-sciences/b2b/UK/en/Microplates/Assay-Microplates/96-Well-Microplates/Costar%C2%AE-Multiple-Well-Cell-Culture-Plates/p/3516) <br><br>- Material: ? <br>- Cleanliness: 3516: sterilized by gamma irradiation <br>- Nonreversible lids with condensation rings to reduce contamination <br>- Treated for optimal cell attachment <br>- Cell growth area: 9.5 cm² (approx.) <br>- Total volume: 16.8 mL| ![](img/corning_costar/Cos_6_wellplate_16800ul_Fb.jpg) | `Cos_6_wellplate_16800ul_Fb` |
+| 'Cos_96_wellplate_2mL_Vb'<br>Part no.: 3516<br>[manufacturer website](https://ecatalog.corning.com/life-sciences/b2b/UK/en/Microplates/Assay-Microplates/96-Well-Microplates/Costar%C2%AE-Multiple-Well-Cell-Culture-Plates/p/3516) <br><br>- Material: Polypropylene <br>- Resistant to many common organic solvents (e.g., DMSO, ethanol, methanol) <br>- 3960: Sterile and DNase- and RNase-free <br>- Total volume: 2 mL <br>- Features uniform skirt heights for greater robotic gripping surface| ![](img/corning_costar/Cos_96_wellplate_2mL_Vb.jpg) | `Cos_96_wellplate_2mL_Vb` |
+'Cor_96_wellplate_360ul_Fb' <br>Part no.: 353376<br>[manufacturer website](https://ecatalog.corning.com/life-sciences/b2b/NL/en/Microplates/Assay-Microplates/96-Well-Microplates/Falcon®-96-well-Polystyrene-Microplates/p/353376) <br><br>- Material: TC-treated polystyrene <br> - Cleanliness: sterile <br>- Total volume:  392 uL <br>- Working volume: 25-340 uL | ![](img/corning_costar/Cor_96_wellplate_360ul_Fb.jpg) | `Cor_96_wellplate_360ul_Fb` |
+'Cor_6_wellplate_Fl' <br>Part no.: 3471<br>[manufacturer website](https://ecatalog.corning.com/life-sciences/b2c/US/en/Microplates/Assay-Microplates/96-Well-Microplates/Costar®-Multiple-Well-Cell-Culture-Plates/p/3471) | ![](img/corning_costar/Cor_6_wellplate_Fl.jpg) | `Cor_6_wellplate_Fl` |

docs/resources/library/eppendorf.md

@@ -13,3 +13,9 @@ Company page: [Eppendorf Wikipedia](https://en.wikipedia.org/wiki/Eppendorf_(com
 | Description               | Image              | PLR definition |
 |--------------------|--------------------|--------------------|
 | 'Eppendorf_96_wellplate_250ul_Vb'<br>Part no.: 0030133374<br>[manufacturer website](https://www.eppendorf.com/gb-en/Products/Laboratory-Consumables/Plates/Eppendorf-twintec-PCR-Plates-p-0030133374) <br><br> - Material: polycarbonate (frame), polypropylene (wells)<br> - part of the twin.tec(R) product line<br> - WARNING: not ANSI/SLAS 1-2004 footprint dimenions (123x81 mm^2!) ==> requires `PlateAdapter`<br> - 'Can be divided into 4 segments of 24 wells each to prevent waste and save money'. | ![](img/eppendorf/Eppendorf_96_wellplate_250ul_Vb_COMPLETE.png) ![](img/eppendorf/Eppendorf_96_wellplate_250ul_Vb_DIVIDED.png) | `Eppendorf_96_wellplate_250ul_Vb` |
+
+## Tubes
+
+| Description               | Image              | PLR definition |
+|--------------------|--------------------|--------------------|
+| "Common eppendorf tube" 'Eppendorf_DNA_LoBind_1_5ml_Vb'<br>Part no.: 0030133374<br>[manufacturer website](https://www.fishersci.com/shop/products/dna-lobind-microcentrifuge-tubes/13698791) | ![](img/eppendorf/Eppendorf_DNA_LoBind_1_5ml_Vb.webp) | `Eppendorf_DNA_LoBind_1_5ml_Vb` |

docs/resources/library/falcon.md

@@ -1,5 +1,13 @@
 # Falcon
 
+# Plates
+
+| Description               | Image              | PLR definition |
+|--------------------|--------------------|--------------------|
+| Falcon_96_wellplate_Fl [manufacturer website](https://www.fishersci.com/shop/products/falcon-96-well-cell-culture-treated-flat-bottom-microplate/087722C) | ![](img/falcon/Falcon_96_wellplate_Fl.webp) | `Falcon_96_wellplate_Fl`
+| Falcon_96_wellplate_Rb [manufacturer website](https://ecatalog.corning.com/life-sciences/b2c/US/en/Microplates/Assay-Microplates/96-Well-Microplates/Falcon®-96-well-Polystyrene-Microplates/p/353077) | ![](img/falcon/Falcon_96_wellplate_Rb.jpg) | `Falcon_96_wellplate_Rb`
+| Falcon_96_wellplate_Fl_Black [manufacturer website](https://www.fishersci.com/shop/products/falcon-96-well-imaging-plate-lid/08772225) | ![](img/falcon/Falcon_96_wellplate_Fl_Black.jpg) | `Falcon_96_wellplate_Fl_Black`
+
 ## Tubes
 
 | Description               | Image              | PLR definition |

docs/resources/library/porvair.md

@@ -4,6 +4,12 @@ Company history: [Porvair Filtration Group](https://www.porvairfiltration.com/ab
 
 > Porvair Filtration Group, a wholly owned subsidiary of Porvair plc, is a specialist filtration and environmental technology group involved in developing, designing and manufacturing filtration and separation solutions to industry sectors such as the aviation, molten metal, energy, water treatment and life sciences markets. Porvair plc is a publically owned company with four principal subsidiaries: Porvair Filtration Group Ltd., Porvair Sciences Ltd., Selee Corporation and Seal Analytical Ltd.
 
+## Plates
+
+| Description               | Image              | PLR definition |
+|--------------------|--------------------|--------------------|
+| 'Porvair_24_wellplate_Vb'<br>Part no.: 390108<br>[manufacturer website](https://www.microplates.com/product/78-ml-reservoir-plate-2-rows-of-12-v-bottom/) | ![](img/porvair/Porvair_24_wellplate_Vb.jpg) | `Porvair_24_wellplate_Vb` |
+
 ## Reservoirs
 
 | Description               | Image              | PLR definition |

docs/resources/library/revvity.md

@@ -8,4 +8,4 @@ Company wikipedia: [Revvity, Inc. (formerly PerkinElmer, Inc.)](https://en.wikip
 
 | Description               | Image              | PLR definition |
 |--------------------|--------------------|--------------------|
-| 'Revvity_ProxiPlate_384Plus'<br>Part no.: 6008280<br>[manufacturer website](https://www.perkinelmer.com/uk/Product/proxiplate-384-plus-50w-6008280) | ![](img/revvity/revvity_ProxiPlate-384-Plus-White-384-shallow-well-Microplate.jpg) | `Revvity_ProxiPlate_384Plus`
+| 'Revvity_384_wellplate_28ul_Ub'<br>Part no.: 6008280<br>[manufacturer website](https://www.revvity.com/product/proxiplate-384-plus-50w-6008280) | ![](img/revvity/Revvity_384_wellplate_28ul_Ub.jpg) | `Revvity_384_wellplate_28ul_Ub`

docs/resources/library/vwr.md

@@ -0,0 +1,9 @@
+# VWR
+
+Company page: [Wikipedia](https://en.wikipedia.org/wiki/VWR_International)
+
+## Troughs
+
+| Description               | Image              | PLR definition |
+|--------------------|--------------------|--------------------|
+| 'VWRReagentReservoirs25mL'<br>Part no.: 89094<br>[manufacturer website](https://us.vwr.com/store/product/4694822/vwr-disposable-pipetting-reservoirs)<br>Polystyrene Reservoirs | ![](img/vwr/VWRReagentReservoirs25mL.jpg.avif) | `VWRReagentReservoirs25mL` |

pylabrobot/resources/__init__.py

@@ -58,9 +58,7 @@
 from .corning_axygen import *
 from .eppendorf import *
 from .falcon import *
-from .greiner import *
 from .hamilton import *
-from .limbro import *
 from .ml_star import *
 from .opentrons import *
 from .porvair import *

pylabrobot/resources/alpaqua/magnetic_racks.py

@@ -1,4 +1,3 @@
-"""Alpaqua magnetic racks"""
 # currently implemented as PlateAdapter to enable simple and fast assignment
 # of plates to them, with self-correcting location placement
 

pylabrobot/resources/celltreat/plates.py

@@ -18,19 +18,38 @@
 def CellTreat_96_wellplate_350ul_Ub(name: str, lid: Optional[Lid] = None) -> Plate:
   """
   CellTreat cat. no.: 229591
+
+  Same as 229590 (229590 is sold with lids)
+
   - Material: Polystyrene
   - Tissue culture treated: No
   """
   # WELL_UBOTTOM_HEIGHT = 2.81 # absolute height of cylindrical segment, measured
   # WELL_DIAMETER = 6.69 # measured
 
+  WELL_RADIUS = 3.175
+
   well_kwargs = {
     "size_x": 6.35,
     "size_y": 6.35,
     "size_z": 10.04,
     "bottom_type": WellBottomType.U,
+    "compute_volume_from_height": lambda liquid_height: compute_volume_from_height_cylinder(
+      liquid_height, WELL_RADIUS
+    ),
+    "compute_height_from_volume": lambda liquid_volume: compute_height_from_volume_cylinder(
+      liquid_volume, WELL_RADIUS
+    ),
+    "material_z_thickness": 1.55,
+    "cross_section_type": CrossSectionType.CIRCLE,
+    "max_volume": 300,
   }
 
+  # in 229590, which should be the same.
+  # dx=10.7,  # measured
+  # dy=8.75,  # measured
+  # dz=2.6,  # calibrated manually
+
   return Plate(
     name=name,
     size_x=127.76,
@@ -124,45 +143,7 @@ def CellTreat_6_wellplate_16300ul_Fb_Lid(name: str) -> Lid:
 
 
 def CellTreat_96_wellplate_U(name: str, lid: Optional[Lid] = None) -> Plate:
-  """
-  CellTreat cat. no.: 229590
-  - Material: Polystyrene
-  - Tissue culture treated: No
-  """
-  WELL_RADIUS = 3.175
-
-  well_kwargs = {
-    "size_x": 6.35,
-    "size_y": 6.35,
-    "size_z": 10.04,
-    "bottom_type": WellBottomType.U,
-    "compute_volume_from_height": lambda liquid_height: compute_volume_from_height_cylinder(
-      liquid_height, WELL_RADIUS
-    ),
-    "compute_height_from_volume": lambda liquid_volume: compute_height_from_volume_cylinder(
-      liquid_volume, WELL_RADIUS
-    ),
-    "material_z_thickness": 1.55,
-    "cross_section_type": CrossSectionType.CIRCLE,
-    "max_volume": 300,
-  }
-
-  return Plate(
-    name=name,
-    size_x=127.76,
-    size_y=85.11,
-    size_z=14.30,  # without lid
-    lid=lid,
-    model=CellTreat_96_wellplate_U.__name__,
-    ordered_items=create_ordered_items_2d(
-      Well,
-      num_items_x=12,
-      num_items_y=8,
-      dx=10.7,  # measured
-      dy=8.75,  # measured
-      dz=2.6,  # calibrated manually
-      item_dx=9,
-      item_dy=9,
-      **well_kwargs,
-    ),
+  raise NotImplementedError(
+    "This plate is the same as CellTreat_96_wellplate_350ul_Ub. This "
+    "function will be removed in the future."
   )

pylabrobot/resources/corning_axygen/plates.py

@@ -1,5 +1,3 @@
-"""Corning Axygen plates"""
-
 from pylabrobot.resources.plate import Lid, Plate
 from pylabrobot.resources.well import (
   Well,