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docs(api): Remove deprecated behavior from api docs #7828

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merged 4 commits into from
May 27, 2021
Merged

docs(api): Remove deprecated behavior from api docs #7828

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db29f20
Change instances of wells to well
ethanfjones-zz May 24, 2021
d92a18e
Fixup: Remove deprecated behavior, change back other examples to corr…
May 27, 2021
05a4513
Merge branch 'edge' into ethanfjones-patch-1
Laura-Danielle May 27, 2021
e98f97d
Fix stray return_tip() from merge mistake.
SyntaxColoring May 27, 2021
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14 changes: 7 additions & 7 deletions api/docs/v2/new_examples.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -44,8 +44,8 @@ This accomplishes the same thing as the following basic commands:
p300 = protocol.load_instrument('p300_single', 'right', tip_racks=[tiprack_1])

p300.pick_up_tip()
p300.aspirate(100, plate.wells('A1'))
p300.dispense(100, plate.wells('B1'))
p300.aspirate(100, plate.well('A1'))
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Technically, this is deprecated behavior. I'm wondering if we should just remove this completely from the docs to discourage users from using this.

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Gotcha so wells can only be used with distribute/transfer?

I only tested this with the aspirate and assumed the others were just a typo.

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@SyntaxColoring SyntaxColoring May 24, 2021 •
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The deprecated behavior is that the well name is passed as an argument to the .wells() function, instead of as an index into the list that it returns.

In other words, instead of this:

plate.wells('B1')

It should be one of these:

plate.wells()[1]  # I *think* index 1 is B1?
# or
plate.wells_by_name()['B1']
# Edit to add: or this one too
plate['B1']

Note that this method takes args for backward-compatibility, but use of args is deprecated and will be removed in future versions. Args can be either strings or integers, but must all be the same type (e.g.: self.wells(1, 4, 8) or self.wells(‘A1’, ‘B2’), but self.wells(‘A1’, 4) is invalid.

(from https://docs.opentrons.com/v2/new_protocol_api.html?highlight=wells#opentrons.protocol_api.labware.Labware.wells)

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I agree with Laura that our example code shouldn't be using the deprecated plate.wells(well_name) form.

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Sorry I'm not getting notifications on my github comments for some reason.

The equivalent of plate.well('B1') is now -> plate['B1']. If a user wants to have a list of wells, they should simply use python indexing; i.e. plate.wells()[0:7] which would give the first column of a 96 well labware.

@ethanfjones, I'm not sure I follow Gotcha so wells can only be used with distribute/transfer?. You can only use a single well when using the "atomic" commands such as aspirate or dispense. You can use a single well or a list of wells for advanced commands such as distribute or transfer.

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@Laura-Danielle and Mr. Syntax, thanks for the response.

Your explanation makes sense to me!

p300.dispense(100, plate.well('B1'))
p300.return_tip()

******************************
Expand Down Expand Up @@ -74,7 +74,7 @@ Loops in Python allow your protocol to perform many actions, or act upon many we

# range() starts at 0 and stops before 8, creating a range of 0-7
for i in range(8):
p300.distribute(200, reservoir.wells()[i], plate.rows()[i])
p300.distribute(200, reservoir.well()[i], plate.rows()[i])
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This should still be .wells().


******************************

Expand All @@ -99,7 +99,7 @@ The OT-2 pipettes can do some things that a human cannot do with a pipette, like

p300.pick_up_tip()

for well in reservoir.wells()[:4]:
for well in reservoir.well()[:4]:
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Same here.

p300.aspirate(35, well)
p300.air_gap(10)

Expand Down Expand Up @@ -128,13 +128,13 @@ This example first spreads a diluent to all wells of a plate. It then dilutes 8
tiprack_2 = protocol.load_labware('opentrons_96_tiprack_300ul', 3)
reservoir = protocol.load_labware('usascientific_12_reservoir_22ml', 4)
p300 = protocol.load_instrument('p300_single', 'right', tip_racks=[tiprack_1, tiprack_2])
p300.distribute(50, reservoir['A12'], plate.wells()) # dilutent
p300.distribute(50, reservoir['A12'], plate.well()) # dilutent
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Same for this example as well.


# loop through each row
for i in range(8):

# save the source well and destination column to variables
source = reservoir.wells()[i]
source = reservoir.well()[i]
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Also here

row = plate.rows()[i]

# transfer 30uL of source to first well in column
Expand Down Expand Up @@ -183,4 +183,4 @@ This example deposits various volumes of liquids into the same plate of wells an
89, 90, 91, 92, 93, 94, 95, 96
]

p300.distribute(water_volumes, reservoir['A12'], plate.wells())
p300.distribute(water_volumes, reservoir['A12'], plate.well())