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rickwierengarickwierenga
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deprecate _L and _P in resource definitions (#288)
1 parent 9a9bb39 commit 15dce32

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24 files changed

+292
-164
lines changed

24 files changed

+292
-164
lines changed

‎CHANGELOG.md

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -59,14 +59,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
5959
- `Thermo_TS_96_wellplate_1200ul_Rb` (https://github.com/PyLabRobot/pylabrobot/pull/215)
6060
- `Thermo_AB_96_wellplate_300ul_Vb_EnduraPlate` (https://github.com/PyLabRobot/pylabrobot/pull/215)
6161
- `adapter_hole_size_z` and `plate_z_offset` parameters to `PlateAdapter` (https://github.com/PyLabRobot/pylabrobot/pull/215)
62-
- `wide_high_volume_tip_with_filter` and `HTF_L_WIDE` (https://github.com/PyLabRobot/pylabrobot/pull/222)
62+
- `wide_high_volume_tip_with_filter` and `HTF_WIDE` (https://github.com/PyLabRobot/pylabrobot/pull/222)
6363
- Serialize code cells and closures (https://github.com/PyLabRobot/pylabrobot/pull/220)
6464
- `Container.get_anchor()` now supports `"cavity_bottom"` as an argument for `z` (https://github.com/PyLabRobot/pylabrobot/pull/205/)
6565
- `pylabrobot.resources.utils.query` for basic querying (https://github.com/PyLabRobot/pylabrobot/commit/4a07f6a32a9a33d0370eb9c29015567c98aea002)
6666
- `HamiltonLiquidHandler.allow_firmware_planning` to allow STAR/Vantage to plan complex liquid handling operations automatically (may break hardware agnosticity unexpectedly) (https://github.com/PyLabRobot/pylabrobot/pull/224)
6767
- `size_z` and `nesting_z_height` for `Cor_96_wellplate_360ul_Fb_Lid` (https://github.com/PyLabRobot/pylabrobot/pull/226)
6868
- `NestedTipRack` (https://github.com/PyLabRobot/pylabrobot/pull/228)
69-
- `HTF_L_ULTRAWIDE`, `ultrawide_high_volume_tip_with_filter` (https://github.com/PyLabRobot/pylabrobot/pull/229/)
69+
- `HTF_ULTRAWIDE`, `ultrawide_high_volume_tip_with_filter` (https://github.com/PyLabRobot/pylabrobot/pull/229/)
7070
- `get_absolute_size_x`, `get_absolute_size_y`, `get_absolute_size_z` for `Resource` (https://github.com/PyLabRobot/pylabrobot/pull/235)
7171
- `Cytation5Backend` for plate reading on BioTek Cytation 5 (https://github.com/PyLabRobot/pylabrobot/pull/238)
7272
- imaging (https://github.com/PyLabRobot/pylabrobot/pull/277)
@@ -93,6 +93,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
9393
- `ThermoScientific_96_DWP_1200ul_Rd` in favor of `Thermo_TS_96_wellplate_1200ul_Rb` (https://github.com/PyLabRobot/pylabrobot/pull/215)
9494
- `Azenta4titudeFrameStar_96_wellplate_skirted` in favor of `Azenta4titudeFrameStar_96_wellplate_200ul_Vb` (https://github.com/PyLabRobot/pylabrobot/pull/205/)
9595
- `Cos_96_DWP_2mL_Vb` in favor of `Cos_96_wellplate_2mL_Vb (https://github.com/PyLabRobot/pylabrobot/pull/205/)`
96+
- Resource definitions with `_L` and `_P`, it is easy enough to use the stem and `.rotated(z=90)` for `_P` (https://github.com/PyLabRobot/pylabrobot/pull/288)
9697

9798
### Fixed
9899

‎docs/user_guide/basic.ipynb

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -115,7 +115,7 @@
115115
"- {class}`~pylabrobot.resources.ml_star.tip_carriers.TIP_CAR_480_A00` tip carrier\n",
116116
"- {class}`~pylabrobot.resources.ml_star.plate_carriers.PLT_CAR_L5AC_A00` plate carrier\n",
117117
"- {class}`~pylabrobot.resources.corning_costar.plates.Cor_96_wellplate_360ul_Fb` wells\n",
118-
"- {class}`~pylabrobot.resources.ml_star.tip_racks.HTF_L` tips"
118+
"- {class}`~pylabrobot.resources.ml_star.tip_racks.HTF` tips"
119119
]
120120
},
121121
{
@@ -128,7 +128,7 @@
128128
" TIP_CAR_480_A00,\n",
129129
" PLT_CAR_L5AC_A00,\n",
130130
" Cor_96_wellplate_360ul_Fb,\n",
131-
" HTF_L,\n",
131+
" HTF,\n",
132132
")"
133133
]
134134
},
@@ -146,7 +146,7 @@
146146
"outputs": [],
147147
"source": [
148148
"tip_car = TIP_CAR_480_A00(name=\"tip carrier\")\n",
149-
"tip_car[0] = HTF_L(name=\"tips_01\")"
149+
"tip_car[0] = HTF(name=\"tips_01\")"
150150
]
151151
},
152152
{

‎docs/user_guide/moving-channels-around.ipynb

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -38,14 +38,14 @@
3838
"outputs": [],
3939
"source": [
4040
"from pylabrobot.liquid_handling import LiquidHandler, STAR\n",
41-
"from pylabrobot.resources import STARDeck, TIP_CAR_480_A00, HTF_L\n",
41+
"from pylabrobot.resources import STARDeck, TIP_CAR_480_A00, HTF\n",
4242
"\n",
4343
"lh = LiquidHandler(backend=STAR(), deck=STARDeck())\n",
4444
"await lh.setup()\n",
4545
"\n",
4646
"# assign a tip rack\n",
4747
"tip_carrier = TIP_CAR_480_A00(name=\"tip_carrier\")\n",
48-
"tip_carrier[0] = tip_rack = HTF_L(name=\"tip_rack\")\n",
48+
"tip_carrier[0] = tip_rack = HTF(name=\"tip_rack\")\n",
4949
"lh.deck.assign_child_resource(tip_carrier, rails=0)"
5050
]
5151
},

‎docs/user_guide/using-the-visualizer.ipynb

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -143,7 +143,7 @@
143143
" TIP_CAR_480_A00,\n",
144144
" PLT_CAR_L5AC_A00,\n",
145145
" Cor_96_wellplate_360ul_Fb,\n",
146-
" HTF_L\n",
146+
" HTF\n",
147147
")"
148148
]
149149
},
@@ -155,11 +155,11 @@
155155
"outputs": [],
156156
"source": [
157157
"tip_car = TIP_CAR_480_A00(name='tip carrier')\n",
158-
"tip_car[0] = tip_rack1 = HTF_L(name='tips_01', with_tips=False)\n",
159-
"tip_car[1] = tip_rack2 = HTF_L(name='tips_02', with_tips=False)\n",
160-
"tip_car[2] = tip_rack3 = HTF_L(name='tips_03', with_tips=False)\n",
161-
"tip_car[3] = tip_rack4 = HTF_L(name='tips_04', with_tips=False)\n",
162-
"tip_car[4] = tip_rack5 = HTF_L(name='tips_05', with_tips=False)"
158+
"tip_car[0] = tip_rack1 = HTF(name='tips_01', with_tips=False)\n",
159+
"tip_car[1] = tip_rack2 = HTF(name='tips_02', with_tips=False)\n",
160+
"tip_car[2] = tip_rack3 = HTF(name='tips_03', with_tips=False)\n",
161+
"tip_car[3] = tip_rack4 = HTF(name='tips_04', with_tips=False)\n",
162+
"tip_car[4] = tip_rack5 = HTF(name='tips_05', with_tips=False)"
163163
]
164164
},
165165
{

‎docs/user_guide/using-trackers.ipynb

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@
3131
"from pylabrobot.liquid_handling.backends.chatterbox_backend import ChatterboxBackend\n",
3232
"from pylabrobot.resources import (\n",
3333
" TIP_CAR_480_A00,\n",
34-
" HTF_L,\n",
34+
" HTF,\n",
3535
" PLT_CAR_L5AC_A00,\n",
3636
" Cor_96_wellplate_360ul_Fbate_360ul_Fb,\n",
3737
" set_tip_tracking,\n",
@@ -105,7 +105,7 @@
105105
"metadata": {},
106106
"outputs": [],
107107
"source": [
108-
"tip_carrier[0] = tip_rack = HTF_L(name=\"tip rack\")"
108+
"tip_carrier[0] = tip_rack = HTF(name=\"tip rack\")"
109109
]
110110
},
111111
{
@@ -142,7 +142,7 @@
142142
"metadata": {},
143143
"outputs": [],
144144
"source": [
145-
"tip_carrier[1] = empty_tip_rack = HTF_L(name=\"empty tip rack\", with_tips=False)"
145+
"tip_carrier[1] = empty_tip_rack = HTF(name=\"empty tip rack\", with_tips=False)"
146146
]
147147
},
148148
{
@@ -996,4 +996,4 @@
996996
},
997997
"nbformat": 4,
998998
"nbformat_minor": 2
999-
}
999+
}

‎pylabrobot/gui/gui.py

Lines changed: 26 additions & 26 deletions
Original file line numberDiff line numberDiff line change
@@ -50,58 +50,58 @@ def list_resources():
5050
return jsonify(
5151
plates=[
5252
"Cos_1536_10ul",
53-
"Cos_1536_10ul_L",
53+
"Cos_1536_10ul",
5454
"Cos_1536_10ul_P",
5555
"Cos_384_DW",
56-
"Cos_384_DW_L",
56+
"Cos_384_DW",
5757
"Cos_384_DW_P",
5858
"Cos_384_PCR",
59-
"Cos_384_PCR_L",
59+
"Cos_384_PCR",
6060
"Cos_384_PCR_P",
6161
"Cos_384_Sq",
62-
"Cos_384_Sq_L",
62+
"Cos_384_Sq",
6363
"Cos_384_Sq_P",
6464
"Cos_384_Sq_Rd",
65-
"Cos_384_Sq_Rd_L",
65+
"Cos_384_Sq_Rd",
6666
"Cos_384_Sq_Rd_P",
6767
"Cos_96_DW_1mL",
68-
"Cos_96_DW_1mL_L",
68+
"Cos_96_DW_1mL",
6969
"Cos_96_DW_1mL_P",
7070
"Cos_96_DW_2mL",
71-
"Cos_96_DW_2mL_L",
71+
"Cos_96_DW_2mL",
7272
"Cos_96_DW_2mL_P",
7373
"Cos_96_DW_500ul",
74-
"Cos_96_DW_500ul_L",
74+
"Cos_96_DW_500ul",
7575
"Cos_96_DW_500ul_P",
7676
"Cor_96_wellplate_360ul_Fb",
77-
"Cor_96_wellplate_360ul_Fb_L",
77+
"Cor_96_wellplate_360ul_Fb",
7878
"Cor_96_wellplate_360ul_Fb_P",
7979
"Cos_96_FL",
8080
"Cos_96_Filter",
81-
"Cos_96_Filter_L",
81+
"Cos_96_Filter",
8282
"Cos_96_Filter_P",
83-
"Cos_96_Fl_L",
83+
"Cos_96_Fl",
8484
"Cos_96_Fl_P",
8585
"Cos_96_HalfArea",
86-
"Cos_96_HalfArea_L",
86+
"Cos_96_HalfArea",
8787
"Cos_96_HalfArea_P",
8888
"Cos_96_PCR",
89-
"Cos_96_PCR_L",
89+
"Cos_96_PCR",
9090
"Cos_96_PCR_P",
9191
"Cos_96_ProtCryst",
92-
"Cos_96_ProtCryst_L",
92+
"Cos_96_ProtCryst",
9393
"Cos_96_ProtCryst_P",
9494
"Cos_96_Rd",
95-
"Cos_96_Rd_L",
95+
"Cos_96_Rd",
9696
"Cos_96_Rd_P",
9797
"Cos_96_SpecOps",
98-
"Cos_96_SpecOps_L",
98+
"Cos_96_SpecOps",
9999
"Cos_96_SpecOps_P",
100100
"Cos_96_UV",
101-
"Cos_96_UV_L",
101+
"Cos_96_UV",
102102
"Cos_96_UV_P",
103103
"Cos_96_Vb",
104-
"Cos_96_Vb_L",
104+
"Cos_96_Vb",
105105
"Cos_96_Vb_P",
106106
],
107107
plate_carriers=[
@@ -197,21 +197,21 @@ def list_resources():
197197
"TIP_CAR_NTR_A00",
198198
],
199199
tip_racks=[
200-
"FourmlTF_L",
200+
"FourmlTF",
201201
"FourmlTF_P",
202-
"FivemlT_L",
202+
"FivemlT",
203203
"FivemlT_P",
204-
"HTF_L",
204+
"HTF",
205205
"HTF_P",
206-
"HT_L",
206+
"HT",
207207
"HT_P",
208-
"LTF_L",
208+
"LTF",
209209
"LTF_P",
210-
"LT_L",
210+
"LT",
211211
"LT_P",
212-
"STF_L",
212+
"STF",
213213
"STF_P",
214-
"ST_L",
214+
"ST",
215215
"ST_P",
216216
],
217217
)

‎pylabrobot/liquid_handling/backends/chatterbox_tests.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
66
)
77
from pylabrobot.resources import (
88
Cor_96_wellplate_360ul_Fb,
9-
HTF_L,
9+
HTF,
1010
Coordinate,
1111
)
1212
from pylabrobot.resources.hamilton import STARLetDeck
@@ -19,7 +19,7 @@ def setUp(self) -> None:
1919
self.deck = STARLetDeck()
2020
self.backend = LiquidHandlerChatterboxBackend(num_channels=8)
2121
self.lh = LiquidHandler(self.backend, deck=self.deck)
22-
self.tip_rack = HTF_L(name="tip_rack")
22+
self.tip_rack = HTF(name="tip_rack")
2323
self.deck.assign_child_resource(self.tip_rack, rails=3)
2424
self.plate = Cor_96_wellplate_360ul_Fb(name="plate")
2525
self.deck.assign_child_resource(self.plate, rails=9)

‎pylabrobot/liquid_handling/backends/hamilton/STAR_tests.py

Lines changed: 6 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -17,13 +17,13 @@
1717
TIP_CAR_480_A00,
1818
TIP_CAR_288_C00,
1919
PLT_CAR_L5AC_A00,
20-
HT_P,
21-
HTF_L,
20+
HT,
21+
HTF,
2222
Cor_96_wellplate_360ul_Fb,
2323
no_volume_tracking,
2424
)
2525
from pylabrobot.resources.hamilton import STARLetDeck
26-
from pylabrobot.resources.ml_star import STF_L
26+
from pylabrobot.resources.ml_star import STF
2727

2828
from tests.usb import MockDev, MockEndpoint
2929

@@ -221,8 +221,8 @@ async def asyncSetUp(self):
221221
self.lh = LiquidHandler(self.mockSTAR, deck=self.deck)
222222

223223
self.tip_car = TIP_CAR_480_A00(name="tip carrier")
224-
self.tip_car[1] = self.tip_rack = STF_L(name="tip_rack_01")
225-
self.tip_car[2] = self.tip_rack2 = HTF_L(name="tip_rack_02")
224+
self.tip_car[1] = self.tip_rack = STF(name="tip_rack_01")
225+
self.tip_car[2] = self.tip_rack2 = HTF(name="tip_rack_02")
226226
self.deck.assign_child_resource(self.tip_car, rails=1)
227227

228228
self.plt_car = PLT_CAR_L5AC_A00(name="plate carrier")
@@ -900,12 +900,10 @@ async def test_discard_tips(self):
900900
)
901901

902902
async def test_portrait_tip_rack_handling(self):
903-
# Test with an alternative setup.
904-
905903
deck = STARLetDeck()
906904
lh = LiquidHandler(self.mockSTAR, deck=deck)
907905
tip_car = TIP_CAR_288_C00(name="tip carrier")
908-
tip_car[0] = tr = HT_P(name="tips_01")
906+
tip_car[0] = tr = HT(name="tips_01").rotated(z=90)
909907
assert tr.rotation.z == 90
910908
assert tr.location == Coordinate(82.6, 0, 0)
911909
deck.assign_child_resource(tip_car, rails=2)

‎pylabrobot/liquid_handling/backends/hamilton/vantage_tests.py

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -6,8 +6,8 @@
66
Coordinate,
77
TIP_CAR_480_A00,
88
PLT_CAR_L5AC_A00,
9-
HT_L,
10-
LT_L,
9+
HT,
10+
LT,
1111
Cor_96_wellplate_360ul_Fb,
1212
)
1313
from pylabrobot.resources.hamilton import VantageDeck
@@ -244,8 +244,8 @@ async def asyncSetUp(self):
244244
self.lh = LiquidHandler(self.mockVantage, deck=self.deck)
245245

246246
self.tip_car = TIP_CAR_480_A00(name="tip carrier")
247-
self.tip_car[0] = self.tip_rack = HT_L(name="tip_rack_01")
248-
self.tip_car[1] = self.small_tip_rack = LT_L(name="tip_rack_02")
247+
self.tip_car[0] = self.tip_rack = HT(name="tip_rack_01")
248+
self.tip_car[1] = self.small_tip_rack = LT(name="tip_rack_02")
249249
self.deck.assign_child_resource(self.tip_car, rails=18)
250250

251251
self.plt_car = PLT_CAR_L5AC_A00(name="plate carrier")

‎pylabrobot/liquid_handling/backends/http_tests.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@
99
from pylabrobot.resources import (
1010
PLT_CAR_L5AC_A00,
1111
TIP_CAR_480_A00,
12-
HTF_L,
12+
HTF,
1313
Cor_96_wellplate_360ul_Fb,
1414
no_tip_tracking,
1515
no_volume_tracking,
@@ -74,7 +74,7 @@ async def asyncSetUp(self) -> None: # type: ignore
7474

7575
self.deck = STARLetDeck()
7676
self.tip_carrier = TIP_CAR_480_A00(name="tip_carrier")
77-
self.tip_carrier[0] = self.tip_rack = HTF_L(name="tiprack")
77+
self.tip_carrier[0] = self.tip_rack = HTF(name="tiprack")
7878
self.plate_carrier = PLT_CAR_L5AC_A00(name="plate_carrier")
7979
self.plate_carrier[0] = self.plate = Cor_96_wellplate_360ul_Fb(name="plate")
8080
self.deck.assign_child_resource(self.tip_carrier, rails=3)

‎pylabrobot/liquid_handling/backends/serializing_backend_tests.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@
99
TIP_CAR_480_A00,
1010
PLT_CAR_L5AC_A00,
1111
Cor_96_wellplate_360ul_Fb,
12-
STF_L,
12+
STF,
1313
Coordinate,
1414
no_tip_tracking,
1515
no_volume_tracking,
@@ -27,7 +27,7 @@ async def asyncSetUp(self) -> None:
2727
await self.lh.setup()
2828

2929
self.tip_car = TIP_CAR_480_A00(name="tip carrier")
30-
self.tip_car[0] = self.tip_rack = STF_L(name="tip_rack_01")
30+
self.tip_car[0] = self.tip_rack = STF(name="tip_rack_01")
3131
self.deck.assign_child_resource(self.tip_car, rails=1)
3232

3333
self.plt_car = PLT_CAR_L5AC_A00(name="plate carrier")

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